@article {pmid38041127, year = {2023}, author = {Diaz, GR and Gaire, TN and Ferm, P and Case, L and Caixeta, LS and Goldsmith, TJ and Armstrong, J and Noyes, NR}, title = {Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {61}, pmid = {38041127}, issn = {2524-4671}, support = {Grantee No. GNT-20212290//Fulbright Scholarship/ ; Contract No. 085-2020-FONDECYT//Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica from Peru/ ; MnDRIVE Graduate Student Professional Development award//MnDRIVE Global Food Ventures Program/ ; }, abstract = {BACKGROUND: Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.<br><br>RESULTS: Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48&#xa0;h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.<br><br>CONCLUSIONS: Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.}, }
@article {pmid38033561, year = {2023}, author = {Protasov, E and Nonoh, JO and Kästle Silva, JM and Mies, US and Hervé, V and Dietrich, C and Lang, K and Mikulski, L and Platt, K and Poehlein, A and Köhler-Ramm, T and Miambi, E and Boga, HI and Feldewert, C and Ngugi, DK and Plarre, R and Sillam-Dussès, D and Šobotník, J and Daniel, R and Brune, A}, title = {Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1281628}, pmid = {38033561}, issn = {1664-302X}, abstract = {Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.}, }
@article {pmid38029671, year = {2023}, author = {Sun, F and Wang, Y and Wang, Y and Sun, C and Cheng, H and Wu, M}, title = {Insights into the spatial distributions of bacteria, archaea, ammonia-oxidizing bacteria and archaea communities in sediments of Daya Bay, northern South China Sea.}, journal = {Marine pollution bulletin}, volume = {198}, number = {}, pages = {115850}, doi = {10.1016/j.marpolbul.2023.115850}, pmid = {38029671}, issn = {1879-3363}, abstract = {Microbe plays an important role in the biogeochemical cycles of the coastal waters. However, comprehensive information about the microbe in the gulf waters is lacking. This study employed high-throughput sequencing and quantitative PCR (qPCR) to investigate the distribution patterns of bacterial, archaeal, ammonia-oxidizing bacterial (AOB), and archaeal (AOA) communities in Daya Bay. Community compositions and principal coordinates analysis (PCoA) exhibited significant spatial characteristics in the diversity and distributions of bacteria, archaea, AOB, and AOA. Notably, various microbial taxa (bacterial, archaeal, AOB, and AOA) exhibited significant differences in different regions, playing crucial roles in nitrogen, sulfur metabolism, and organic carbon mineralization. Canonical correlation analysis (CCA) or redundancy analysis (RDA) indicated that environmental parameters such as temperature, salinity, nitrate, total nitrogen, silicate, and phosphate strongly influenced the distributions of bacterial, archaeal, AOB, and AOA. This study deepens the understanding of the composition and ecological function of prokaryotes in the bay.}, }
@article {pmid38029211, year = {2023}, author = {Huber, M and Vogel, N and Borst, A and Pfeiffer, F and Karamycheva, S and Wolf, YI and Koonin, EV and Soppa, J}, title = {Unidirectional gene pairs in archaea and bacteria require overlaps or very short intergenic distances for translational coupling via termination-reinitiation and often encode subunits of heteromeric complexes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1291523}, doi = {10.3389/fmicb.2023.1291523}, pmid = {38029211}, issn = {1664-302X}, abstract = {Genomes of bacteria and archaea contain a much larger fraction of unidirectional (serial) gene pairs than convergent or divergent gene pairs. Many of the unidirectional gene pairs have short overlaps of -4 nt and -1 nt. As shown previously, translation of the genes in overlapping unidirectional gene pairs is tightly coupled. Two alternative models for the fate of the post-termination ribosome predict either that overlaps or very short intergenic distances are essential for translational coupling or that the undissociated post-termination ribosome can scan through long intergenic regions, up to hundreds of nucleotides. We aimed to experimentally resolve the contradiction between the two models by analyzing three native gene pairs from the model archaeon Haloferax volcanii and three native pairs from Escherichia coli. A two reporter gene system was used to quantify the reinitiation frequency, and several stop codons in the upstream gene were introduced to increase the intergenic distances. For all six gene pairs from two species, an extremely strong dependence of the reinitiation efficiency on the intergenic distance was unequivocally demonstrated, such that even short intergenic distances of about 20 nt almost completely abolished translational coupling. Bioinformatic analysis of the intergenic distances in all unidirectional gene pairs in the genomes of H. volcanii and E. coli and in 1,695 prokaryotic species representative of 49 phyla showed that intergenic distances of -4 nt or -1 nt (= short gene overlaps of 4 nt or 1 nt) were by far most common in all these groups of archaea and bacteria. A small set of genes in E. coli, but not in H. volcanii, had intergenic distances of around +10 nt. Our experimental and bioinformatic analyses clearly show that translational coupling requires short gene overlaps, whereas scanning of intergenic regions by the post-termination ribosome occurs rarely, if at all. Short overlaps are enriched among genes that encode subunits of heteromeric complexes, and co-translational complex formation requiring precise subunit stoichiometry likely confers an evolutionary advantage that drove the formation and conservation of overlapping gene pairs during evolution.}, }
@article {pmid38012208, year = {2023}, author = {Mara, P and Geller-McGrath, D and Edgcomb, V and Beaudoin, D and Morono, Y and Teske, A}, title = {Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7768}, pmid = {38012208}, issn = {2041-1723}, support = {OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; JP19H00730//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H00154//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Archaea/genetics ; Metagenome/genetics ; Geologic Sediments/chemistry ; Phylogeny ; Bacteria/genetics ; *Crenarchaeota ; RNA, Ribosomal, 16S ; }, abstract = {Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere.}, }
@article {pmid38007550, year = {2023}, author = {Yang, Y and Liu, H and Zhang, Y and Fang, X and Zhong, X and Lv, J}, title = {Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20722}, pmid = {38007550}, issn = {2045-2322}, support = {2452021124//Talent Special Fund Grant from Northwest A&amp;F university/ ; S202210712582//Innovation and entrepreneurship training program for College Students from Northwest A&amp;F university/ ; A314021402-202218//Foundation of the State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/ ; 42077135//National natural science foundation of China/ ; }, mesh = {Animals ; Swine ; *Archaea ; Ammonia ; Soil ; Urea ; Nitrogen ; Dissolved Organic Matter ; Oxidation-Reduction ; Soil Microbiology ; Phylogeny ; Bacteria/genetics ; *Betaproteobacteria ; Nitrification ; }, abstract = {The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3[-]-N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4[+]-N, thus accelerating the growth of AOB to strengthen nitrification in soil.}, }
@article {pmid38007076, year = {2023}, author = {Zhang, Z and Bo, L and Wang, S and Li, C and Zhang, X and Xue, B and Yang, X and He, X and Shen, Z and Qiu, Z and Zhao, C and Wang, J}, title = {Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117739}, doi = {10.1016/j.envres.2023.117739}, pmid = {38007076}, issn = {1096-0953}, abstract = {In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.}, }
@article {pmid38004804, year = {2023}, author = {Borrel, G and Fadhlaoui, K and Ben Hania, W and Gaci, N and Pehau-Arnaudet, G and Chaudhary, PP and Vandekerckove, P and Ballet, N and Alric, M and O'Toole, PW and Fardeau, ML and Ollivier, B and Brugère, JF}, title = {Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004804}, issn = {2076-2607}, support = {NA/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {The methanogenic strain Mx-05[T] was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05[T] were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05[T] required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05[T] grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L[-1] NaCl (optimum 0.12 mol.L[-1] NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05[T] as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05[T] (JCM 31474T).}, }
@article {pmid37996939, year = {2023}, author = {Tao, S and Veen, GFC and Zhang, N and Yu, T and Qu, L}, title = {Tree and shrub richness modifies subtropical tree productivity by regulating the diversity and community composition of soil bacteria and archaea.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {261}, pmid = {37996939}, issn = {2049-2618}, abstract = {BACKGROUND: Declines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So far, the role of fungal communities in driving tree diversity-productivity relationships has been well assessed in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been less investigated in this context. Here, we investigated how tree and shrub richness affects stand-level tree productivity by regulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2, or 4 species) and shrub richness (0, 2, 4, 8 species) were modified.<br><br>RESULTS: Our findings indicated a noteworthy decline in soil bacterial &#x3b1;-diversity as tree species richness increased from monoculture to 2- and 4- tree species mixtures, but a significant increase in archaeal &#x3b1;-diversity. Additionally, we observed that the impact of shrub species richness on microbial &#x3b1;-diversity was largely dependent on the level of tree species richness. The increase in tree species richness greatly reduced the variability in bacterial community composition and the complexity of co-occurrence network, but this effect was marginal for archaea. Both tree and shrub species richness increased the stand-level tree productivity by regulating the diversity and composition of bacterial community and archaeal diversity, with the effects being mediated via increases in soil C:N ratios.<br><br>CONCLUSIONS: Our findings provide insight into the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight the necessity for a better understanding of prokaryotic communities in forest soils. Video Abstract.}, }
@article {pmid37989750, year = {2023}, author = {Gomes-Filho, JV and Breuer, R and Morales-Filloy, HG and Pozhydaieva, N and Borst, A and Paczia, N and Soppa, J and Höfer, K and Jäschke, A and Randau, L}, title = {Identification of NAD-RNA species and ADPR-RNA decapping in Archaea.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7597}, pmid = {37989750}, issn = {2041-1723}, support = {882789//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*RNA ; *NAD/metabolism ; Adenosine Diphosphate Ribose/metabolism ; Archaea/metabolism ; Chromatography, Liquid ; Tandem Mass Spectrometry ; }, abstract = {NAD is a coenzyme central to metabolism that also serves as a 5'-terminal cap for bacterial and eukaryotic transcripts. Thermal degradation of NAD can generate nicotinamide and ADP-ribose (ADPR). Here, we use LC-MS/MS and NAD captureSeq to detect and identify NAD-RNAs in the thermophilic model archaeon Sulfolobus acidocaldarius and in the halophilic mesophile Haloferax volcanii. None of the four Nudix proteins of S. acidocaldarius catalyze NAD-RNA decapping in vitro, but one of the proteins (Saci_NudT5) promotes ADPR-RNA decapping. NAD-RNAs are converted into ADPR-RNAs, which we detect in S. acidocaldarius total RNA. Deletion of the gene encoding the 5'-3' exonuclease Saci-aCPSF2 leads to a 4.5-fold increase in NAD-RNA levels. We propose that the incorporation of NAD into RNA acts as a degradation marker for Saci-aCPSF2. In contrast, ADPR-RNA is processed by Saci_NudT5 into 5'-p-RNAs, providing another layer of regulation for RNA turnover in archaeal cells.}, }
@article {pmid37987001, year = {2023}, author = {Sarkar, S and Kazarina, A and Hansen, PM and Ward, K and Hargreaves, C and Reese, N and Ran, Q and Kessler, W and de Souza, LFT and Loecke, TD and Sarto, MVM and Rice, CW and Zeglin, LH and Sikes, BA and Lee, STM}, title = {Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.08.566028}, pmid = {37987001}, abstract = {BACKGROUND: Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N 2 O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N 2 O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies.<br><br>RESULTS: We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB.<br><br>CONCLUSIONS: The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.}, }
@article {pmid37973213, year = {2023}, author = {Wolff, P and Lechner, A and Droogmans, L and Grosjean, H and Westhof, E}, title = {Corrigendum: Identification of U[p]47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium.}, journal = {RNA (New York, N.Y.)}, volume = {29}, number = {12}, pages = {1973}, doi = {10.1261/rna.079812.123}, pmid = {37973213}, issn = {1469-9001}, }
@article {pmid37961710, year = {2023}, author = {Zhang, IH and Borer, B and Zhao, R and Wilbert, S and Newman, DK and Babbin, AR}, title = {Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.10.30.564641}, pmid = {37961710}, abstract = {UNLABELLED: Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.<br><br>IMPORTANCE: Archaea from the DPANN superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the 3 global marine oxygen deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.}, }
@article {pmid37955638, year = {2023}, author = {Krawczyk, A and Gosiewski, T and Zapała, B and Kowalska-Duplaga, K and Salamon, D}, title = {Alterations in intestinal Archaea composition in pediatric patients with Crohn's disease based on next-generation sequencing - a pilot study.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2276806}, doi = {10.1080/19490976.2023.2276806}, pmid = {37955638}, issn = {1949-0984}, mesh = {Humans ; Child ; Archaea/genetics ; Pilot Projects ; *Crohn Disease/genetics ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Intestinal dysbiosis can lead to the induction of systemic immune-mediated inflammatory diseases, such as Crohn's disease Although archaea are part of the commensal microbiota, they are still one of the least studied microorganisms. The aim of our study was the standardization of the optimal conditions and primers for sequencing of the gut archaeome using Next Generation Sequencing, and evaluation of the differences between the composition of archaea in patients and healthy volunteers, as well as analysis of the changes that occur in the archaeome of patients depending on disease activity. Newly diagnosed patients were characterized by similar archeal profiles at every taxonomic level as in healthy individuals (the dominance of Methanobacteria at the class level, and Methanobrevibacter at the genus level). In turn, in patients previously diagnosed with Crohn's disease (both in active and remission phase), an increased prevalence of Thermoplasmata, Thermoprotei, Halobacteria (at the class level), and Halococcus, Methanospaera or Picrophilus (at the genus level) were observed. Furthermore, we have found a significant correlation between the patient's parameters and the individual class or species of Archaea. Our study confirms changes in archaeal composition in pediatric patients with Crohn's disease, however, only in long-standing disease. At the beginning of the disease, the archeal profile is similar to that of healthy people. However, in the chronic form of the disease, significant differences in the composition of archaeome begin to appear. It seems that some archaea may be a good indicator of the chronicity and activity of Crohn's disease.}, }
@article {pmid37954235, year = {2023}, author = {Zhang, T and He, W and Liang, Q and Zheng, F and Xiao, X and Zeng, Z and Zhou, J and Yao, W and Chen, H and Zhu, Y and Zhao, J and Zheng, Y and Zhang, C}, title = {Lipidomic diversity and proxy implications of archaea from cold seep sediments of the South China Sea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1241958}, pmid = {37954235}, issn = {1664-302X}, abstract = {Cold seeps on the continental margins are characterized by intense microbial activities that consume a large portion of methane by anaerobic methanotrophic archaea (ANME) through anaerobic oxidation of methane (AOM). Although ANMEs are known to contain unique ether lipids that may have an important function in marine carbon cycling, their full lipidomic profiles and functional distribution in particular cold-seep settings are still poorly characterized. Here, we combined the 16S rRNA gene sequencing and lipidomic approaches to analyze archaeal communities and their lipids in cold seep sediments with distinct methane supplies from the South China Sea. The archaeal community was dominated by ANME-1 in the moderate seepage area with strong methane emission. Low seepage area presented higher archaeal diversity covering Lokiarchaeia, Bathyarchaeia, and Thermoplasmata. A total of 55 core lipids (CLs) and intact polar lipids (IPLs) of archaea were identified, which included glycerol dialkyl glycerol tetraethers (GDGTs), hydroxy-GDGTs (OH-GDGTs), archaeol (AR), hydroxyarchaeol (OH-AR), and dihydroxyarchaeol (2OH-AR). Diverse polar headgroups constituted the archaeal IPLs. High concentrations of dissolved inorganic carbon (DIC) with depleted δ[13]CDIC and high methane index (MI) values based on both CLs (MICL) and IPLs (MIIPL) indicate that ANMEs were active in the moderate seepage area. The ANME-2 and ANME-3 clades were characterized by enhanced glycosidic and phosphoric diether lipids production, indicating their potential role in coupling carbon and phosphurus cycling in cold seep ecosystems. ANME-1, though representing a smaller proportion of total archaea than ANME-2 and ANME-3 in the low seepage area, showed a positive correlation with MIIPL, indicating a different mechanism contributing to the IPL-GDGT pool. This also suggests that MIIPL could be a sensitive index to trace AOM activities performed by ANME-1. Overall, our study expands the understanding of the archaeal lipid composition in the cold seep and improves the application of MI using intact polar lipids that potentially link to extent ANME activities.}, }
@article {pmid37949149, year = {2023}, author = {Manesh, MJH and Willard, DJ and Lewis, AM and Kelly, RM}, title = {Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us?.}, journal = {Bioresource technology}, volume = {391}, number = {Pt B}, pages = {129988}, doi = {10.1016/j.biortech.2023.129988}, pmid = {37949149}, issn = {1873-2976}, abstract = {Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.}, }
@article {pmid37938729, year = {2022}, author = {Wang, L and Wang, Y and Huang, X and Ma, R and Li, J and Wang, F and Jiao, N and Zhang, R}, title = {Potential metabolic and genetic interaction among viruses, methanogen and methanotrophic archaea, and their syntrophic partners.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {50}, pmid = {37938729}, issn = {2730-6151}, support = {91951209//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42006097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2020M671942//China Postdoctoral Science Foundation/ ; }, abstract = {The metabolism of methane in anoxic ecosystems is mainly mediated by methanogens and methane-oxidizing archaea (MMA), key players in global carbon cycling. Viruses are vital in regulating their host fate and ecological function. However, our knowledge about the distribution and diversity of MMA viruses and their interactions with hosts is rather limited. Here, by searching metagenomes containing mcrA (the gene coding for the α-subunit of methyl-coenzyme M reductase) from a wide variety of environments, 140 viral operational taxonomic units (vOTUs) that potentially infect methanogens or methane-oxidizing archaea were retrieved. Four MMA vOTUs (three infecting the order Methanobacteriales and one infecting the order Methanococcales) were predicted to cross-domain infect sulfate-reducing bacteria. By facilitating assimilatory sulfur reduction, MMA viruses may increase the fitness of their hosts in sulfate-depleted anoxic ecosystems and benefit from synthesis of the sulfur-containing amino acid cysteine. Moreover, cell-cell aggregation promoted by MMA viruses may be beneficial for both the viruses and their hosts by improving infectivity and environmental stress resistance, respectively. Our results suggest a potential role of viruses in the ecological and environmental adaptation of methanogens and methane-oxidizing archaea.}, }
@article {pmid37918493, year = {2023}, author = {Lv, PL and Jia, C and Guo, X and Zhao, HP and Chen, R}, title = {Microbial stratification protects denitrifying anaerobic methane oxidation archaea and bacteria from external oxygen shock in membrane biofilm reactor.}, journal = {Bioresource technology}, volume = {391}, number = {Pt A}, pages = {129966}, doi = {10.1016/j.biortech.2023.129966}, pmid = {37918493}, issn = {1873-2976}, abstract = {Different gradients of dissolved oxygen (DO) regulate the microbial community and nitrogen removal pathways of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) coupled process in a batch biofilm reactor. Under completely anaerobic condition, approximately 72 mg NO3[-]-N/L was removed at a daily rate of 6.55 mg N/L, whereas a peak accumulation of 95 mg NO3[-]-N/L was observed during DO reached 0.5 mg/L. There is a decrease in the abundance of Candidatus Methylomirabilis (24.1%), Candidatus Methanoperedens (23.3%), and Candidatus Kuenenia (22.6%) to below 5% when DO levels reached 0.2 mg/L. Moreover, key genes associated with the reverse methanogenesis (mcrA) and anaerobic ammonium oxidase (hzo) decreased. These findings indicate that during oxygen shock, methanotrophs and denitrifiers replace Anammox bacteria on the outer sphere of the biofilm, whereas DAMO bacteria and archaea are protected from external oxygen shock due to the microbial stratification of biofilm.}, }
@article {pmid37938653, year = {2022}, author = {Vigneron, A and Cruaud, P and Lovejoy, C and Vincent, WF}, title = {Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {4}, pmid = {37938653}, issn = {2730-6151}, abstract = {DPANN archaea account for half of the archaeal diversity of the biosphere, but with few cultivated representatives, their metabolic potential and environmental functions are poorly understood. The extreme geochemical and environmental conditions in meromictic ice-capped Lake A, in the Canadian High Arctic, provided an isolated, stratified model ecosystem to resolve the distribution and metabolism of uncultured aquatic DPANN archaea living across extreme redox and salinity gradients, from freshwater oxygenated conditions, to saline, anoxic, sulfidic waters. We recovered 28 metagenome-assembled genomes (MAGs) of DPANN archaea that provided genetic insights into their ecological function. Thiosulfate oxidation potential was detected in aerobic Woesearchaeota, whereas diverse metabolic functions were identified in anaerobic DPANN archaea, including degradation and fermentation of cellular compounds, and sulfide and polysulfide reduction. We also found evidence for "vampiristic" metabolism in several MAGs, with genes coding for pore-forming toxins, peptidoglycan degradation, and RNA scavenging. The vampiristic MAGs co-occurred with other DPANNs having complementary metabolic capacities, leading to the possibility that DPANN form interspecific consortia that recycle microbial carbon, nutrients and complex molecules through a DPANN archaeal shunt, adding hidden novel complexity to anaerobic microbial food webs.}, }
@article {pmid37938279, year = {2021}, author = {Thomas, CM and Taib, N and Gribaldo, S and Borrel, G}, title = {Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {47}, pmid = {37938279}, issn = {2730-6151}, support = {ANR-19-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Other than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood-Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.}, }
@article {pmid37938645, year = {2021}, author = {Huang, L and Chakrabarti, S and Cooper, J and Perez, A and John, SM and Daroub, SH and Martens-Habbena, W}, title = {Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {19}, pmid = {37938645}, issn = {2730-6151}, abstract = {Nitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O-N per µg NOx-N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.}, }
@article {pmid37938628, year = {2021}, author = {Shafiee, RT and Diver, PJ and Snow, JT and Zhang, Q and Rickaby, REM}, title = {Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {1}, pmid = {37938628}, issn = {2730-6151}, abstract = {Ammonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.}, }
@article {pmid37917544, year = {2023}, author = {Cheng, M and Li, XX and Tan, S and Ma, X and Hu, Y and Hou, J and Cui, HL}, title = {Salinigranum marinum sp. nov. and Halohasta salina sp. nov., halophilic archaea isolated from sediment of a marine saltern and inland saline soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {11}, pages = {}, doi = {10.1099/ijsem.0.006143}, pmid = {37917544}, issn = {1466-5034}, abstract = {Two halophilic archaeal strains, ZS-10[T] and GSL13[T], were isolated from the Zhoushan marine saltern in Zhejiang, and an inland saline soil from the Tarim Basin, Xinjiang, PR China, respectively. The cells of strain ZS-10[T] were pleomorphic while those of strain GSL13[T] were rod-shaped. Both of them stained Gram-negative and formed red-pigmented colonies on agar plates and their cells lysed in distilled water. The optimum growth of strain ZS-10[T] was observed at 40 °C, 3.4 M NaCl, 0.03 M MgCl2 and pH 7.5, while that of strain GSL13[T] was at 37 °C, 3.1 M NaCl, 0.5 M MgCl2 and pH 7.5. Phylogenetic and phylogenomic analyses indicated that these two strains were related to Salinigranum and Halohasta, respectively. Strains ZS-10[T] and GSL13[T] could be differentiated from the current members of Salinigranum and Halohasta based on the comparison of diverse phenotypic characteristics. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values among strain ZS-10[T] and current species of Salinigranum were 75.8-78.6 %, 80.6-81.9 % and 24.3-26.1 %, respectively. These values between strain GSL13[T] and current species of Halohasta were 78.4-80.8 %, 79.8-82.8% and 22.7-25.7 %, respectively, clearly below the threshold values for species demarcation. The polar lipids of strain ZS-10[T] were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulphated mannosyl glucosyl diether (S-DGD-1), while those of strain GSL13[T] were phosphatidic acid, PG, PGP-Me, phosphatidylglycerol sulphate and S-DGD-1. The polar lipid profile of strain GSL13[T] was identical to those of Halohasta, whereas strain ZS-10[T] did not contain the minor glycolipids detected in the current Salinigranum species. The phenotypic, phylogenetic and genome-based results suggested that strains ZS-10[T] (=CGMCC 1.12868[T]=JCM 30241[T]) and GSL13[T] (=CGMCC 1.15214[T]=JCM 30841[T]) represent two novel species, for which the names Salinigranum marinum sp. nov. and Halohasta salina sp. nov. are proposed.}, }
@article {pmid37917005, year = {2023}, author = {Prakash, O and Dodsworth, JA and Dong, X and Ferry, JG and L'Haridon, S and Imachi, H and Kamagata, Y and Rhee, SK and Sagar, I and Shcherbakova, V and Wagner, D and Whitman, WB}, title = {Corrigendum: Proposed minimal standards for description of methanogenic archaea.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {11}, pages = {}, doi = {10.1099/ijsem.0.006127}, pmid = {37917005}, issn = {1466-5034}, }
@article {pmid37907951, year = {2023}, author = {Romero, P and Belanche, A and Jiménez, E and Hueso, R and Ramos-Morales, E and Salwen, JK and Kebreab, E and Yáñez-Ruiz, DR}, title = {Rumen microbial degradation of bromoform from red seaweed (Asparagopsis taxiformis) and the impact on rumen fermentation and methanogenic archaea.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {133}, pmid = {37907951}, issn = {1674-9782}, support = {RYC2019-027764-I//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, abstract = {BACKGROUND: The red macroalgae Asparagopsis is an effective methanogenesis inhibitor due to the presence of halogenated methane (CH4) analogues, primarily bromoform (CHBr3). This study aimed to investigate the degradation process of CHBr3 from A. taxiformis in the rumen and whether this process is diet-dependent. An in vitro batch culture system was used according to a 2 × 2 factorial design, assessing two A. taxiformis inclusion rates [0 (CTL) and 2% DM diet (AT)] and two diets [high-concentrate (HC) and high-forage diet (HF)]. Incubations lasted for 72 h and samples of headspace and fermentation liquid were taken at 0, 0.5, 1, 3, 6, 8, 12, 16, 24, 48 and 72 h to assess the pattern of degradation of CHBr3 into dibromomethane (CH2Br2) and fermentation parameters. Additionally, an in vitro experiment with pure cultures of seven methanogens strains (Methanobrevibacter smithii, Methanobrevibacter ruminantium, Methanosphaera stadtmanae, Methanosarcina barkeri, Methanobrevibacter millerae, Methanothermobacter wolfei and Methanobacterium mobile) was conducted to test the effects of increasing concentrations of CHBr3 (0.4, 2, 10 and 50 µmol/L).<br><br>RESULTS: The addition of AT significantly decreased CH4 production (P&#x2009;=&#x2009;0.002) and the acetate:propionate ratio (P&#x2009;=&#x2009;0.003) during a 72-h incubation. The concentrations of CHBr3 showed a rapid decrease with nearly 90% degraded within the first 3&#xa0;h of incubation. On the contrary, CH2Br2 concentration quickly increased during the first 6&#xa0;h and then gradually decreased towards the end of the incubation. Neither CHBr3 degradation nor CH2Br2 synthesis were affected by the type of diet used as substrate, suggesting that the fermentation rate is not a driving factor involved in CHBr3 degradation. The in vitro culture of methanogens showed a dose-response effect of CHBr3 by inhibiting the growth of M. smithii, M. ruminantium, M. stadtmanae, M. barkeri, M. millerae, M. wolfei, and M. mobile.<br><br>CONCLUSIONS: The present work demonstrated that CHBr3 from A. taxiformis is quickly degraded to CH2Br2 in the rumen and that the fermentation rate promoted by different diets is not a driving factor involved in CHBr3 degradation.}, }
@article {pmid37895260, year = {2023}, author = {Ullah, N and Yang, N and Guan, Z and Xiang, K and Wang, Y and Diaby, M and Chen, C and Gao, B and Song, C}, title = {Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea.}, journal = {Genes}, volume = {14}, number = {10}, pages = {}, pmid = {37895260}, issn = {2073-4425}, support = {31671313//The National Natural Science Foundation of China/ ; 32271508//The National Natural Science Foundation of China/ ; xxxxxx//High-end Talent Support Program of Yangzhou University to Chengyi Song/ ; }, mesh = {*Archaea/genetics ; Phylogeny ; Bacteria/genetics ; *CRISPR-Associated Proteins ; }, abstract = {Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis, and an array/repeat analysis. In our analysis, we identified and mined a total of 93 Cas14-homology proteins that ranged in size from 344 aa to 843 aa. The majority of the Cas14-homology proteins discovered in this analysis were found within the Firmicutes group, which contained 37 species, representing 42% of all the Cas14-homology proteins identified. In archaea, the DPANN group had the highest number of species containing Cas14-homology proteins, a total of three species. The phylogenetic analysis results demonstrate the division of Cas14-homology proteins into three clades: Cas14-A, Cas14-B, and Cas14-U. Extensive similarity was observed at the C-terminal end (CTD) through a domain comparison of the three clades, suggesting a potentially shared mechanism of action due to the presence of cutting domains in that region. Additionally, a sequence similarity analysis of all the identified Cas14 sequences indicated a low level of similarity (18%) between the protein variants. The analysis of repeats/arrays in the extended nucleotide sequences of the identified Cas14-homology proteins highlighted that 44 out of the total mined proteins possessed CRISPR-associated repeats, with 20 of them being specific to Cas14. Our study contributes to the increased understanding of Cas14 proteins across prokaryotic genomes. These homologous proteins have the potential for future applications in the mining and engineering of Cas14 proteins.}, }
@article {pmid37890267, year = {2023}, author = {Notaro, A and Zaretsky, M and Molinaro, A and De Castro, C and Eichler, J}, title = {N-glycosylation in Archaea: Unusual sugars and unique modifications.}, journal = {Carbohydrate research}, volume = {534}, number = {}, pages = {108963}, doi = {10.1016/j.carres.2023.108963}, pmid = {37890267}, issn = {1873-426X}, abstract = {Archaea are microorganisms that comprise a distinct branch of the universal tree of life and which are best known as extremophiles, residing in a variety of environments characterized by harsh physical conditions. One seemingly universal trait of Archaea is the ability to perform N-glycosylation. At the same time, archaeal N-linked glycans present variety in terms of both composition and architecture not seen in the parallel eukaryal or bacterial processes. In this mini-review, many of the unique and unusual sugars found in archaeal N-linked glycans as identified by nuclear magnetic resonance spectroscopy are described.}, }
@article {pmid37876779, year = {2023}, author = {Yang, J and Chen, R and Peng, Y and Chai, J and Li, Y and Deng, F}, title = {The role of gut archaea in the pig gut microbiome: a mini-review.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1284603}, pmid = {37876779}, issn = {1664-302X}, abstract = {The gastrointestinal microbiota of swine harbors an essential but often overlooked component: the gut archaea. These enigmatic microorganisms play pivotal roles in swine growth, health, and yield quality. Recent insights indicate that the diversity of gut archaea is influenced by various factors including breed, age, and diet. Such factors orchestrate the metabolic interactions within the porcine gastrointestinal environment. Through symbiotic relationships with bacteria, these archaea modulate the host's energy metabolism and digestive processes. Contemporary research elucidates a strong association between the abundance of these archaea and economically significant traits in swine. This review elucidates the multifaceted roles of gut archaea in swine and underscores the imperative for strategic interventions to modulate their population and functionality. By exploring the probiotic potential of gut archaea, we envisage novel avenues to enhance swine growth, health, and product excellence. By spotlighting this crucial, yet under-investigated, facet of the swine gut microbiome, we aim to galvanize further scientific exploration into harnessing their myriad benefits.}, }
@article {pmid37840747, year = {2023}, author = {Liu, H and Jing, H and Wang, F}, title = {Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1268790}, pmid = {37840747}, issn = {1664-302X}, abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH4+ concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.}, }
@article {pmid37819981, year = {2023}, author = {Cerna-Vargas, JP and Gumerov, VM and Krell, T and Zhulin, IB}, title = {Amine-recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {42}, pages = {e2305837120}, doi = {10.1073/pnas.2305837120}, pmid = {37819981}, issn = {1091-6490}, support = {R35GM131760//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; PID2020-112612GB-I00//MEC | Agencia Estatal de Investigaci&#xf3;n (AEI)/ ; }, abstract = {Bacteria possess various receptors that sense different signals and transmit information to enable an optimal adaptation to the environment. A major limitation in microbiology is the lack of information on the signal molecules that activate receptors. Signals recognized by sensor domains are poorly reflected in overall sequence identity, and therefore, the identification of signals from the amino acid sequence of the sensor alone presents a challenge. Biogenic amines are of great physiological importance for microorganisms and humans. They serve as substrates for aerobic and anaerobic growth and play a role of neurotransmitters and osmoprotectants. Here, we report the identification of a sequence motif that is specific for amine-sensing sensor domains that belong to the Cache superfamily of the most abundant extracellular sensors in prokaryotes. We identified approximately 13,000 sensor histidine kinases, chemoreceptors, receptors involved in second messenger homeostasis and Ser/Thr phosphatases from 8,000 bacterial and archaeal species that contain the amine-recognizing motif. The screening of compound libraries and microcalorimetric titrations of selected sensor domains confirmed their ability to specifically bind biogenic amines. Mutants in the amine-binding motif or domains that contain a single mismatch in the binding motif had either no or a largely reduced affinity for amines. We demonstrate that the amine-recognizing domain originated from the universal amino acid-sensing Cache domain, thus providing insight into receptor evolution. Our approach enables precise "wet"-lab experiments to define the function of regulatory systems and therefore holds a strong promise to enable the identification of signals stimulating numerous receptors.}, }
@article {pmid37815851, year = {2023}, author = {Laird, MG and Adlung, N and Koivisto, JJ and Scheller, S}, title = {Thiol-Disulfide Exchange Kinetics and Redox Potential of the Coenzyme M and Coenzyme B Heterodisulfide, an Electron Acceptor Coupled to Energy Conservation in Methanogenic Archaea.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {}, number = {}, pages = {e202300595}, doi = {10.1002/cbic.202300595}, pmid = {37815851}, issn = {1439-7633}, abstract = {Methanogenic and methanotrophic archaea play important roles in the global carbon cycle by interconverting CO2 and methane. To conserve energy from these metabolic pathways that happen close to the thermodynamic equilibrium, specific electron carriers have evolved to balance the redox potentials between key steps. Reduced ferredoxins required to activate CO2 are provided by energetical coupling to the reduction of the high-potential heterodisulfide (HDS) of coenzyme M (2-mercaptoethanesulfonate) and coenzyme B (7-mercaptoheptanoylthreonine phosphate). While the standard redox potential of this important HDS has been determined previously to be -143 mV (Tietze et al. 2003 DOI:10.1002/cbic.200390053), we have measured thiol disulfide exchange kinetics and reassessed this value by equilibrating thiol-disulfide mixtures of coenzyme M, coenzyme B and mercaptoethanol. We determined the redox potential of the HDS of coenzyme M and coenzyme B to be -16.4 ± 1.7 mV relative to the reference thiol mercaptoethanol (E0' = -264 mV). The resulting E0' values are -281 mV for the HDS, -271 mV for the homodisulfide of coenzyme M, and -270 mV for the homodisulfide of coenzyme B. We discuss the importance of these updated values for the physiology of methanogenic and methanotrophic archaea and their implications in terms of energy conservation.}, }
@article {pmid37805516, year = {2023}, author = {Hu, X and Huang, Y and Gu, G and Hu, H and Yan, H and Zhang, H and Zhang, R and Zhang, D and Wang, K}, title = {Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {75}, pmid = {37805516}, issn = {2524-6372}, support = {41977192//National Natural Science Foundation of China/ ; 2021J060//Natural Science Foundation of Ningbo/ ; SJLY2022001//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; }, abstract = {BACKGROUND: Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.<br><br>RESULTS: The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.<br><br>CONCLUSIONS: Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.}, }
@article {pmid37793447, year = {2023}, author = {Salas, E and Gorfer, M and Bandian, D and Eichorst, SA and Schmidt, H and Horak, J and Rittmann, SKR and Schleper, C and Reischl, B and Pribasnig, T and Jansa, J and Kaiser, C and Wanek, W}, title = {Reevaluation and novel insights into amino sugar and neutral sugar necromass biomarkers in archaea, bacteria, fungi, and plants.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167463}, doi = {10.1016/j.scitotenv.2023.167463}, pmid = {37793447}, issn = {1879-1026}, abstract = {Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall residues are mostly found in their polysaccharide forms of fungal chitin and bacterial peptidoglycan. Microbial necromass biomarkers, particularly amino sugars (AS) such as glucosamine (GlcN) and muramic acid (MurA) have been used to trace fungal and bacterial residues in soils, and to distinguish carbon (C) found in microbial residues from non-microbial organic C. Neutral sugars (NS), particularly the hexose/pentose ratio, have also been proposed as tracers of plant polysaccharides in soils. In our study, we extended the range of biomarkers to include AS and NS compounds in the biomass of 120 species belonging to archaea, bacteria, fungi, or plants. GlcN was the most common AS found in all taxa, contributing 42-91% to total AS content, while glucose was the most common NS found, contributing 56-79% to total NS. We identified talosaminuronic acid, found in archaeal pseudopeptidoglycan, as a new potential biomarker specific for Euryarchaeota. We compared the variability of these compounds between the different taxonomic groups using multivariate approaches, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA) and statistically evaluated their biomarker potential via indicator species analysis. Both NMDS and PLS-DA showcased the variability in the AS and NS contents between the different taxonomic groups, highlighting their potential as necromass residue biomarkers and allowing their extension from separating bacterial and fungal necromass to separating microbes from plants. Finally, we estimated new conversion factors where fungal GlcN is converted to fungal C by multiplying by 10 and MurA is converted to bacterial C by multiplying by 54. Conversion factors for talosaminuronic acid and galactosamine are also proposed to allow estimation of archaeal or all-microbial necromass residue C, respectively.}, }
@article {pmid37771611, year = {2023}, author = {}, title = {Correction to: Putative nucleotide-based second messengers in archaea.}, journal = {microLife}, volume = {4}, number = {}, pages = {uqad039}, doi = {10.1093/femsml/uqad039}, pmid = {37771611}, issn = {2633-6693}, abstract = {[This corrects the article DOI: 10.1093/femsml/uqad027.].}, }
@article {pmid37759261, year = {2023}, author = {Kowalewicz-Kulbat, M and Krawczyk, KT and Szulc-Kielbik, I and Rykowski, S and Denel-Bobrowska, M and Olejniczak, AB and Locht, C and Klink, M}, title = {Cytotoxic effects of halophilic archaea metabolites on ovarian cancer cell lines.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {197}, pmid = {37759261}, issn = {1475-2859}, mesh = {Humans ; Female ; *Ovarian Neoplasms/drug therapy ; Cisplatin ; Cell Line, Tumor ; *Antineoplastic Agents/pharmacology ; HeLa Cells ; }, abstract = {BACKGROUND: Ovarian cancer is one of the most frequent and deadly gynaecological cancers, often resistant to platinum-based chemotherapy, the current standard of care. Halophilic microorganisms have been shown to produce a large variety of metabolites, some of which show toxicity to various cancer cell lines. However, none have yet been shown to be active against ovarian cancer cells. Here, we examined the effects of metabolites secreted by the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae on various cancer cell lines, including ovarian cancer cell lines.<br><br>RESULTS: [1]H NMR analyses of Hrd. rudnickae and Nnm. salaciae culture supernatants contain a complex mixture of metabolites that differ between species, and even between two different strains of the same species, such as Hrd. rudnickae strains 64[T] and 66. By using the MTT and the xCELLigence RTCA assays, we found that the secreted metabolites of all three halophilic strains expressed cytotoxicity to the ovarian cancer cell lines, especially A2780, as well as its cisplatin-resistant derivative A2780cis, in a dose-dependent manner. The other tested cell lines A549, HepG2, SK-OV-3 and HeLa were only minimally, or not at all affected by the archaeal metabolites, and this was only seen with the MTT assay.<br><br>CONCLUSIONS: The halophilic archaea Hrd. rudnickae and Nnm. salaciae, isolated from a Polish salt mine and Lake Medee in the Mediterranean Sea, respectively, secrete metabolites that are active against ovarian cancer cells, including those that are resistant to cisplatin. This opens potential new possibilities for the treatment of these frequent and deadly gynaecological cancers.}, }
@article {pmid37754561, year = {2023}, author = {Liu, WW and Pan, P and Zhou, NY}, title = {The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0176623}, doi = {10.1128/spectrum.01766-23}, pmid = {37754561}, issn = {2165-0497}, abstract = {Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.}, }
@article {pmid37749252, year = {2023}, author = {Medvedeva, S and Borrel, G and Krupovic, M and Gribaldo, S}, title = {A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37749252}, issn = {2058-5276}, support = {ANR-20-CE20-009-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-20-CE20-009-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-20-CE20-009-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-20-CE20-009-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.}, }
@article {pmid37747940, year = {2023}, author = {Murali, R and Yu, H and Speth, DR and Wu, F and Metcalfe, KS and Crémière, A and Laso-Pèrez, R and Malmstrom, RR and Goudeau, D and Woyke, T and Hatzenpichler, R and Chadwick, GL and Connon, SA and Orphan, VJ}, title = {Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea.}, journal = {PLoS biology}, volume = {21}, number = {9}, pages = {e3002292}, doi = {10.1371/journal.pbio.3002292}, pmid = {37747940}, issn = {1545-7885}, abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic (ANME) archaea in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.}, }
@article {pmid37728966, year = {2023}, author = {Tan, S and Cheng, M and Li, XX and Hu, Y and Ma, X and Hou, J and Cui, HL}, title = {Natronosalvus halobius gen. nov., sp. nov., Natronosalvus caseinilyticus sp. nov., Natronosalvus vescus sp. nov., Natronosalvus rutilus sp. nov. and Natronosalvus amylolyticus sp. nov., halophilic archaea isolated from salt lakes and soda lakes.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.006036}, pmid = {37728966}, issn = {1466-5034}, mesh = {Animals ; Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; *Halobacteriales ; *Euryarchaeota ; Amino Acids ; *Cyprinidae ; }, abstract = {Five halophilic archaeal strains (AGai3-5[T], KZCA101[T], CGA3[T], WLHS1[T] and WLHSJ1[T]) were isolated from salt lakes and soda lakes in PR China. These strains had low 16S rRNA gene similarities (91.3-96.0 %) to closely related species of the family Natrialbaceae and may represent a new genus of the family. Phylogenetic and phylogenomic analyses revealed that these strains formed a distinct clade, separate from the nearby genera Natronobiforma and Saliphagus. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity (AAI) values among these five strains and the current members of the family Natrialbaceae were 72-90, 20-42 and 62-91 %, respectively, clearly below the threshold values for species demarcation. According to the critical value of AAI (≤76 %) proposed to differentiate genera within the family Natrialbaceae, it was further indicated that these strains represented a novel genus within the family. These strains could be distinguished from the related genera according to differential phenotypic characteristics. The major lipids of these strains were phosphatidic acid (PA), phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, mannosyl glucosyl diether (DGD-PA), sulphated DGD-1 (S-DGD-PA) and sulphated galactosyl mannosyl glucosyl diether. The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains AGai3-5[T] (=CGMCC 1.16078[T]=JCM 33549[T]), KZCA101[T] (=CGMCC 1.17431[T]=JCM 35074[T]), CGA3[T] (=CGMCC 1.17463[T]=JCM 34318[T]), WLHS1[T] (=CGMCC 1.13780[T]=JCM 33562[T]) and WLHSJ1[T] (=CGMCC 1.13784[T]=JCM 33563[T]) represent five novel species of a new genus within the family Natrialbaceae, named Natronosalvus halobius gen. nov., sp. nov., Natronosalvus caseinilyticus sp. nov., Natronosalvus vescus sp. nov., Natronosalvus rutilus sp. nov. and Natronosalvus amylolyticus sp. nov., respectively.}, }
@article {pmid37727289, year = {2023}, author = {Volmer, JG and McRae, H and Morrison, M}, title = {The evolving role of methanogenic archaea in mammalian microbiomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1268451}, pmid = {37727289}, issn = {1664-302X}, abstract = {Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.}, }
@article {pmid37715368, year = {2023}, author = {Soza-Bolaños, AI and Domínguez-Pérez, RA and Ayala-Herrera, JL and Pérez-Serrano, RM and Soto-Barreras, U and Espinosa-Cristóbal, LF and Rivera-Albarrán, CA and Zaldívar-Lelo de Larrea, G}, title = {Presence of methanogenic archaea in necrotic root canals of patients with or without type 2 diabetes mellitus.}, journal = {Australian endodontic journal : the journal of the Australian Society of Endodontology Inc}, volume = {}, number = {}, pages = {}, doi = {10.1111/aej.12797}, pmid = {37715368}, issn = {1747-4477}, abstract = {Theoretically, a necrotic root canal fulfils all requirements as a niche for methanogens to inhabit. However, their presence in it and its implication in apical periodontitis (AP) is controversial. Therefore, to contribute to ending the controversy, this study aimed to detect and compare methanogens' presence in two distinct niches with supposedly different microenvironments; both were necrotic root canals associated with AP but one from patients with type 2 diabetes mellitus (T2DM) while the other from non-diabetic patients. A clinical examination was performed on 65 T2DM patients and 73 non-diabetic controls. Samples from necrotic root canals were obtained, and methanogens were identified. The presence of methanogens was three times higher (27.6%) in the T2DM group than in non-diabetic patients (8.2%). In addition, methanogens' presence was associated with a higher prevalence of periapical symptoms.}, }
@article {pmid37714340, year = {2023}, author = {Wang, W and Lei, J and Li, M and Zhang, X and Xiang, X and Wang, H and Lu, X and Ma, L and Liu, X and Tuovinen, OH}, title = {Archaea are better adapted to antimony stress than their bacterial counterparts in Xikuangshan groundwater.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166999}, doi = {10.1016/j.scitotenv.2023.166999}, pmid = {37714340}, issn = {1879-1026}, abstract = {Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological differences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb gradient and subjected to 16S rRNA gene amplicon sequencing and bioinformatic analysis. The results demonstrated that bacterial communities were more susceptibly affected by elevated Sb concentration than their archaeal counterparts, and the positive stimulation of Sb concentration on bacterial diversity coincided with the intermediate disturbance hypothesis. Overall, the balance of environmental variables (Sb, pH, and EC), competitive interactions, and stochastic events jointly regulated bacterial and archaeal communities. Linear fitting analysis revealed that Sb significantly drove the deterministic process (heterogeneous selection) of bacterial communities, whereas stochastic process (dispersal limitation) contributed more to archaeal community assembly. In contract, the assembly of Sb-resistant bacteria and archaea was dominated by the stochastic process (undominated), which implied the important role of diversification and drift instead of selection. Compared with Sb-resistant microorganisms, bacterial and archaeal communities showed lower niche width, which may result from the constraints of Sb concentration and competitive interaction. Moreover, Sb-resistant archaea had a higher niche than that of Sb-resistant bacteria via investing on flexible metabolic pathways such as organic metabolism, ammonia oxidation; and carbon fixation to enhance their competitiveness. Our results offered new insights into the ecological adaptation mechanisms of bacteria and archaea in Sb-contaminated groundwater.}, }
@article {pmid37707605, year = {2023}, author = {Deore, KS and Dhakephalkar, PK and Dagar, SS}, title = {Phylogenetically and physiologically diverse methanogenic archaea inhabit the Indian hot spring environments.}, journal = {Archives of microbiology}, volume = {205}, number = {10}, pages = {332}, pmid = {37707605}, issn = {1432-072X}, support = {Ref. No. 23/06/2013(i)EU-V//University Grants Commission/ ; YSS/2015/000718//Science and Engineering Research Board/ ; }, mesh = {Humans ; Archaea/genetics ; *Hot Springs ; *Euryarchaeota ; Culture Media ; India ; }, abstract = {Mesophilic and thermophilic methanogens belonging to the hydrogenotrophic, methylotrophic, and acetotrophic groups were isolated from Indian hot spring environments using BY and BCYT growth media. Following initial Hinf I-based PCR-RFLP screening, 70 methanogens were sequenced to ascertain their identity. These methanogens were phylogenetically and physiologically diverse and represented different taxa distributed across three physiological groups, i.e., hydrogenotrophs (53), methylotrophs (14) and acetotrophs (3). Overall, methanogens representing three families, five genera, and ten species, including two putative novel species, were recognized. The highest number and diversity of methanogens was observed at 40 ℃, dominated by Methanobacterium (10; 3 species), Methanosarcina (9; 3 species), Methanothermobacter (7; 2 species), Methanomethylovorans (5; 1 species) and Methanoculleus (3; 1 species). Both putative novel methanogen species were isolated at 40 ℃ and belonged to the genera Methanosarcina and Methanobacterium. At 55 ℃, limited diversity was observed, and resulted in the isolation of only two genera of methanogens, i.e., Methanothermobacter (28; 2 species) and Methanosarcina (4; 1 species). At 70 ℃, only members of the genus Methanothermobacter (5; 2 species) were isolated, whereas no methanogen could be cultured at 85 ℃. Ours is the first study that documents the extensive range of cultivable methanogenic archaea inhabiting hot springs across various geothermal provinces of India.}, }
@article {pmid37702790, year = {2023}, author = {Zou, D and Chen, J and Zhang, C and Kao, SJ and Liu, H and Li, M}, title = {Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37702790}, issn = {1432-0614}, support = {32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 2022M722175//Postdoctoral Research Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Innovation Program/ ; }, abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.}, }
@article {pmid37700049, year = {2023}, author = {Spang, A}, title = {Uncovering the hidden world of nanosized archaea.}, journal = {Nature reviews. Microbiology}, volume = {21}, number = {10}, pages = {638}, pmid = {37700049}, issn = {1740-1534}, }
@article {pmid37698885, year = {2023}, author = {Oudova-Rivera, B and Crombie, AT and Murrell, JC and Lehtovirta-Morley, LE}, title = {Alcohols as inhibitors of ammonia oxidising archaea and bacteria.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnad093}, pmid = {37698885}, issn = {1574-6968}, abstract = {Ammonia oxidisers are key players in the global nitrogen cycle, and are responsible for the oxidation of ammonia to nitrite, which is further oxidised to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidisers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidising archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidising archaeon 'Candidatus Nitrosocosmicus franklandus' C13 and the ammonia oxidising bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidisers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidisers, with half-maximal inhibitory concentrations (IC50) of 0.19 mM and 0.31 mM, respectively. The inhibition was AMO-specific in 'Ca. N. franklandus' C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by 'Ca. N. franklandus' C13 at a higher threshold concentration than other chain-length alcohols, with 80 mM ethanol being required for complete inhibition of ammonia oxidation.}, }
@article {pmid37668803, year = {2023}, author = {Vipindas, PV and Jabir, T and Venkatachalam, S and Yang, EJ and Jain, A and Krishnan, KP}, title = {Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean.}, journal = {Extremophiles : life under extreme conditions}, volume = {27}, number = {3}, pages = {24}, pmid = {37668803}, issn = {1433-4909}, mesh = {*Archaea/genetics ; Phylogeny ; *Euryarchaeota ; Water ; }, abstract = {Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.}, }
@article {pmid37652180, year = {2023}, author = {Di Giulio, M}, title = {The absence of the evolutionary state of the Prokaryote would imply a polyphyletic origin of proteins and that LUCA, the ancestor of bacteria and that of archaea were progenotes.}, journal = {Bio Systems}, volume = {}, number = {}, pages = {105014}, doi = {10.1016/j.biosystems.2023.105014}, pmid = {37652180}, issn = {1872-8324}, abstract = {I analysed the similarity gradient observed in protein families - of phylogenetically deep fundamental traits - of bacteria and archaea, ranging from cases such as the core of the DNA replication apparatus where there is no sequence similarity between the proteins involved, to cases in which, as in the translation initiation factors, only some proteins involved would be homologs, to cases such as for aminoacyl-tRNA synthetases in which most of the proteins involved would be homologs. This pattern of similarity between bacteria and archaea would seem to be a very clear indication of a transitional evolutionary stage that preceded both the Last Bacterial Common Ancestor and the Last Archaeal Common Ancestor, i.e. progenotic stages. Indeed, this similarity pattern would seem to exemplify an ongoing transition as all the evolutionary phases would be represented in it. Instead, in the cellular stage it is expected that these evolutionary phases should have already been overcome, i.e. completed, and therefore no longer detectable. In fact, if we had really been in the presence of the prokaryotic stage then we should not have observed this similarity pattern in proteins involved in defining the ancestral characters of bacteria and archaea, as the completion of the different cellular structures should have required a very low number of proteins to be late evolved in lineages leading to bacteria and archaea. Indeed, the already reached state of the Prokaryote would have determined complete cellular structures therefore a total absence of proteins to evolve independently in the two main phyletic lineages and able to complete the evolution of a particular character already evidently in a definitive state, which, on the other hand, does not appear to have been the case. All this would have prevented the formation of this pattern of similarity which instead would appear to be real. In conclusion, the existence of this pattern of similarity observed in the families of homologous proteins of bacteria and archaea would imply the absence of the evolutionary stage of the Prokaryote and consequently a progenotic status to be assigned to the LUCA. Indeed, the LUCA stage would have been a stage of evolutionary transition because it is belatedly marked by the presence of all the different evolutionary phases, evidently more easily interpretable within the definition of progenote than that of genote precisely because they are inherent in an evolutionary transition and not to an evolution that has already been achieved. Finally, I discuss the importance of these arguments for the polyphyletic origin of proteins.}, }
@article {pmid37630563, year = {2023}, author = {Xie, L and Yu, S and Lu, X and Liu, S and Tang, Y and Lu, H}, title = {Different Responses of Bacteria and Archaea to Environmental Variables in Brines of the Mahai Potash Mine, Qinghai-Tibet Plateau.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630563}, issn = {2076-2607}, support = {DD20221703//China Geological Survey/ ; }, abstract = {Salt mines feature both autochthonous and allochthonous microbial communities introduced by industrialization. It is important to generate the information on the diversity of the microbial communities present in the salt mines and how they are shaped by the environment representing ecological diversification. Brine from Mahai potash mine (Qianghai, China), an extreme hypersaline environment, is used to produce potash salts for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. In this study, using high-throughput 16S rRNA gene amplicon sequencing and estimation of physicochemical variables, we examined brine samples collected from locations with the gradient of industrial activity intensity and discrete hydrochemical compositions in the Mahai potash mine. Our findings revealed a highly diverse bacterial community, mainly composed of Pseudomonadota in the hypersaline brines from the industrial area, whereas in the natural brine collected from the upstream Mahai salt lake, most of the 16S rRNA gene reads were assigned to Bacteroidota. Halobacteria and halophilic methanogens dominated archaeal populations. Furthermore, we discovered that in the Mahai potash mining area, bacterial communities tended to respond to anthropogenic influences. In contrast, archaeal diversity and compositions were primarily shaped by the chemical properties of the hypersaline brines. Conspicuously, distinct methanogenic communities were discovered in sets of samples with varying ionic compositions, indicating their strong sensitivity to the brine hydrochemical alterations. Our findings provide the first taxonomic snapshot of microbial communities from the Mahai potash mine and reveal the different responses of bacteria and archaea to environmental variations in this high-altitude aquatic ecosystem.}, }
@article {pmid37629622, year = {2023}, author = {Garcia-Bonete, MJ and Rajan, A and Suriano, F and Layunta, E}, title = {The Underrated Gut Microbiota Helminths, Bacteriophages, Fungi, and Archaea.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/life13081765}, pmid = {37629622}, issn = {2075-1729}, abstract = {The microbiota inhabits the gastrointestinal tract, providing essential capacities to the host. The microbiota is a crucial factor in intestinal health and regulates intestinal physiology. However, microbiota disturbances, named dysbiosis, can disrupt intestinal homeostasis, leading to the development of diseases. Classically, the microbiota has been referred to as bacteria, though other organisms form this complex group, including viruses, archaea, and eukaryotes such as fungi and protozoa. This review aims to clarify the role of helminths, bacteriophages, fungi, and archaea in intestinal homeostasis and diseases, their interaction with bacteria, and their use as therapeutic targets in intestinal maladies.}, }
@article {pmid37564293, year = {2023}, author = {Naitam, MG and Ramakrishnan, B and Grover, M and Kaushik, R}, title = {Rhizosphere-dwelling halophilic archaea: a potential candidate for alleviating salinity-associated stress in agriculture.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1212349}, pmid = {37564293}, issn = {1664-302X}, abstract = {Salinity is a serious environmental factor that impedes crop growth and drastically reduces yield. This study aimed to investigate the potential of halophilic archaea isolated from the Rann of Kutch to alleviate the negative impact of salinity on crop growth and yield. The halophilic archaea, which demonstrated high tolerance to salinity levels up to 4.5 M, were evaluated for their ability to promote plant growth in both salt-tolerant and salt-susceptible wheat cultivars. Our assessment focused on their capacity to solubilize essential nutrients, including phosphorus (14-61 mg L[-1]), potassium (37-78 mg L[-1]), and zinc (8-17 mg L[-1]), as well as their production of the phytohormone IAA (17.30 to 49.3 μg ml[-1]). To conduct the experiments, five wheat cultivars (two salt-tolerant and three salt-susceptible) were grown in triplicates using soft MS agar tubes (50 ml) and pots containing 10 kg of soil with an electrical conductivity (EC) of 8 dSm[-1]. Data were collected at specific time points: 21 days after sowing (DAS) for the MS agar experiment, 45 DAS for the pot experiment, and at the time of harvest. In the presence of haloarchaea, the inoculated treatments exhibited significant increases in total protein (46%), sugar (27%), and chlorophyll (31%) levels compared to the un-inoculated control. Furthermore, the inoculation led to an elevated accumulation of osmolyte proline (31.51%) and total carbohydrates (27.85%) while substantially reducing the activity of antioxidant enzymes such as SOD, catalase, and peroxidase by 57-76%, respectively. Notably, the inoculated treatments also showed improved plant vegetative growth parameters compared to the un-inoculated treatments. Interestingly, the positive effects of the halophilic archaea were more pronounced in the susceptible wheat cultivars than in the tolerant cultivars. These findings highlight the growth-promoting abilities of the halophilic archaeon Halolamina pelagica CDK2 and its potential to mitigate the detrimental effects of salinity. Consequently, further evaluation of this halophilic archaeon under field conditions is warranted to explore its potential use in the development of microbial inoculants.}, }
@article {pmid37549709, year = {2023}, author = {Ren, B and Wang, W and Shen, L and Yang, W and Yang, Y and Jin, J and Geng, C}, title = {Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China.}, journal = {The Science of the total environment}, volume = {902}, number = {}, pages = {166089}, doi = {10.1016/j.scitotenv.2023.166089}, pmid = {37549709}, issn = {1879-1026}, abstract = {Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg[-1] N ha[-1]) was 23.35 % higher than that at the intermediate rate (100-150 kg[-1] N ha[-1]) and 20.77 % higher than that at the low rate (< 100 kg[-1] N ha[-1]). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4[+] content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.}, }
@article {pmid37516446, year = {2023}, author = {Manfredini, A and Malusà, E and Pinzari, F and Canfora, L}, title = {Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad169}, pmid = {37516446}, issn = {1365-2672}, abstract = {AIMS: One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community's viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as RNA-based analyses.<br><br>METHODS AND RESULTS: We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and qPCR. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties.<br><br>CONCLUSIONS: The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N cycle in paddy soil.}, }
@article {pmid37504286, year = {2023}, author = {Marín-Paredes, R and Bolívar-Torres, HH and Coronel-Gaytán, A and Martínez-Romero, E and Servín-Garcidueñas, LE}, title = {A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota.}, journal = {Current issues in molecular biology}, volume = {45}, number = {7}, pages = {5849-5864}, pmid = {37504286}, issn = {1467-3045}, support = {IA210617 IA208019//PAPIIT-UNAM/ ; }, abstract = {Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.}, }
@article {pmid37500801, year = {2023}, author = {Esser, SP and Rahlff, J and Zhao, W and Predl, M and Plewka, J and Sures, K and Wimmer, F and Lee, J and Adam, PS and McGonigle, J and Turzynski, V and Banas, I and Schwank, K and Krupovic, M and Bornemann, TLV and Figueroa-Gonzalez, PA and Jarett, J and Rattei, T and Amano, Y and Blaby, IK and Cheng, JF and Brazelton, WJ and Beisel, CL and Woyke, T and Zhang, Y and Probst, AJ}, title = {A predicted CRISPR-mediated symbiosis between uncultivated archaea.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37500801}, issn = {2058-5276}, support = {PR1603/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RA3432/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BE6703/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1553211//National Science Foundation (NSF)/ ; }, abstract = {CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.}, }
@article {pmid37495052, year = {2023}, author = {Cai, Y and Li, H and Qu, G and Hu, Y and Zou, H and Zhao, S and Cheng, M and Chu, X and Ren, N}, title = {Responses of applied voltages on the archaea microbial distribution in sludge digestion.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {139639}, doi = {10.1016/j.chemosphere.2023.139639}, pmid = {37495052}, issn = {1879-1298}, abstract = {As the development of urban population led to the increase of domestic water consumption, consequently the generation of surplus sludge (SS) produced increasingly during sewage treatment processes. In order to enhance the SS resource utilization efficiency, an electricity-assisted anaerobic digestion (EAAD) system was employed to examine the alterations in the digestion broth and the characteristics of gas production. Additionally, the response of applied voltages on the distribution of archaeal community near various electrodes within the sludge was explored. The results revealed that the application of high voltages exceeding 3.0 V hindered the CH4 production but stimulated the CO2 generation. Subsequently, both CH4 and CO2 production were impeded by the applied voltages. Furthermore, the increased voltages significantly decreased the abundance of Methanomicrobia, Methanosaeta, and Methanosarcina, which were crucial determinants of CH4 content in biogas. Notably, the excessively high voltages intensities caused the AD process to halt and even inactivate the microbial flora. Interestingly, the distribution characteristics of archaeal community were influenced not only by the voltages intensity but also exhibited variations between the anode and cathode regions. Moreover, as the applied voltage intensified, the discrepancy of responses between the cathode and anode regions became more pronounced, offering novel theoretical and technical foundations for the advancement of electricity-assisted with AD technology.}, }
@article {pmid37491319, year = {2023}, author = {Williams, AM and Jolley, E and Santiago-Martínez, MG and Chan, CX and Gutell, R and Ferry, JG and Bevilacqua, PC}, title = {In vivo structure probing of RNA in Archaea: Novel insights into the ribosome structure of Methanosarcina acetivorans.}, journal = {RNA (New York, N.Y.)}, volume = {}, number = {}, pages = {}, doi = {10.1261/rna.079687.123}, pmid = {37491319}, issn = {1469-9001}, abstract = {Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. With archaeal species being diverse and having many similarities to both bacteria and eukaryotes, the archaea domain has the potential to be an evolutionary bridge. In this study, we introduce a method for probing RNA structure in vivo in the archaea domain of life. We investigated the structure of ribosomal RNA (rRNA) from Methanosarcina acetivorans, a well-studied anaerobic archaeal species, grown with either methanol or acetate. After probing the RNA in vivo with dimethyl sulfate (DMS), Structure-seq2 libraries were generated, sequenced, and analyzed. We mapped the reactivity of DMS onto the secondary structure of the ribosome, which we determined independently with comparative analysis, and confirmed the accuracy of DMS probing in M. acetivorans Accessibility of the rRNA to DMS in the two carbon sources was found to be quite similar, although some differences were found. Overall, this study establishes the Structure-seq2 pipeline in the archaea domain of life and informs about ribosomal structure within M. acetivorans.}, }
@article {pmid37474649, year = {2023}, author = {Kim, YB and Whon, TW and Kim, JY and Kim, J and Kim, Y and Lee, SH and Park, SE and Kim, EJ and Son, HS and Roh, SW}, title = {In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11746}, pmid = {37474649}, issn = {2045-2322}, mesh = {Humans ; Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Urogenital System ; *Microbiota/genetics ; *Euryarchaeota/genetics ; *Crenarchaeota ; Phylogeny ; }, abstract = {The urogenital microbiota is the potential principal factor in the pathophysiology of urinary tract infection and the protection of urinary tract health. Little is known about the urogenital archaeome although several reports have indicated that the archaeomes of various regions of the human body are associated with health. Accordingly, we aimed to determine the presence and diversity of archaeomes in the human urogenital tract. To explore the urogenital archaeome, voided urine specimens from 373 asymptomatic Korean individuals were used. No difference was observed in body mass index, age, or gender, according to presence of archaea. Analysis of archaeal 16S rRNA gene amplicons of archaea positive samples consisted of simple community structures, including diverse archaea, such as the phyla Methanobacteriota, Thermoproteota, and Halobacteriota. Asymptomatic individuals showed high participant-dependent intervariability in their urogenital archaeomes. The mean relative archaeal abundance was estimated to be 0.89%, and fluorescence in situ hybridisation micrographs provided evidence of archaeal cells in the human urogenital tract. In addition, the urogenital archaeome shared partial taxonomic compositional characteristics with those of the other body sites. In this study, Methanobacteriota, Thermoproteota, and Halobacteriota were suggested as inhabitants of the human urogenital tract, and a distinct human urogenital archaeome was characterised. These findings expand our knowledge of archaea-host associations in the human urogenital tract and may lead to novel insights into the role of archaea in urinary tract health.}, }
@article {pmid37468677, year = {2023}, author = {Banas, I and Esser, SP and Turzynski, V and Soares, A and Novikova, P and May, P and Moraru, C and Hasenberg, M and Rahlff, J and Wilmes, P and Klingl, A and Probst, AJ}, title = {Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37468677}, issn = {1751-7370}, support = {PR1603/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 863664//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.}, }
@article {pmid37464403, year = {2023}, author = {Bargiela, R and Korzhenkov, AA and McIntosh, OA and Toshchakov, SV and Yakimov, MM and Golyshin, PN and Golyshina, OV}, title = {Evolutionary patterns of archaea predominant in acidic environment.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {61}, pmid = {37464403}, issn = {2524-6372}, support = {N 810280//European Regional Development Fund/ ; N 810280//European Regional Development Fund/ ; N 810280//European Regional Development Fund/ ; RPG-2020-190//Leverhulme Trust/ ; RPG-2020-190//Leverhulme Trust/ ; RPG-2020-190//Leverhulme Trust/ ; }, abstract = {BACKGROUND: Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called "alphabet-plasmas", and collectively dubbed "E-plasma", were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.<br><br>RESULTS: Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the "E-plasma" in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of "E-plasma", which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.<br><br>CONCLUSIONS: This study has analysed the metagenome-assembled genome of "E-plasma", which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.}, }
@article {pmid37461084, year = {2023}, author = {Feehan, B and Ran, Q and Dorman, V and Rumback, K and Pogranichniy, S and Ward, K and Goodband, R and Niederwerder, MC and Lee, STM}, title = {Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {35}, pmid = {37461084}, issn = {2524-4671}, support = {NIH U54 HD 090216//Kansas Intellectual and Developmental Disabilities Research Center/ ; P30 GM122731-03//Molecular Regulation of Cell Development and Differentiation - COBRE/ ; NIH S10OD021743//NIH S10 High-End Instrumentation Grant/ ; UL1TR002366//Frontiers CTSA/ ; }, abstract = {BACKGROUND: Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination.<br><br>RESULTS: We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.}, }
@article {pmid37452095, year = {2023}, author = {Wright, CL and Lehtovirta-Morley, LE}, title = {Nitrification and beyond: metabolic versatility of ammonia oxidising archaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37452095}, issn = {1751-7370}, support = {UNITY 852993//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; UNITY 852993//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; DH150187//Royal Society/ ; }, abstract = {Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.}, }
@article {pmid37446705, year = {2023}, author = {Padilla-Vaca, F and de la Mora, J and García-Contreras, R and Ramírez-Prado, JH and Alva-Murillo, N and Fonseca-Yepez, S and Serna-Gutiérrez, I and Moreno-Galván, CL and Montufar-Rodríguez, JM and Vicente-Gómez, M and Rangel-Serrano, &#xc1; and Vargas-Maya, NI and Franco, B}, title = {Two-Component System Sensor Kinases from Asgardian Archaea May Be Witnesses to Eukaryotic Cell Evolution.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {13}, pages = {}, pmid = {37446705}, issn = {1420-3049}, abstract = {The signal transduction paradigm in bacteria involves two-component systems (TCSs). Asgardarchaeota are archaea that may have originated the current eukaryotic lifeforms. Most research on these archaea has focused on eukaryotic-like features, such as genes involved in phagocytosis, cytoskeleton structure, and vesicle trafficking. However, little attention has been given to specific prokaryotic features. Here, the sequence and predicted structural features of TCS sensor kinases analyzed from two metagenome assemblies and a genomic assembly from cultured Asgardian archaea are presented. The homology of the sensor kinases suggests the grouping of Lokiarchaeum closer to bacterial homologs. In contrast, one group from a Lokiarchaeum and a meta-genome assembly from Candidatus Heimdallarchaeum suggest the presence of a set of kinases separated from the typical bacterial TCS sensor kinases. AtoS and ArcB homologs were found in meta-genome assemblies along with defined domains for other well-characterized sensor kinases, suggesting the close link between these organisms and bacteria that may have resulted in the metabolic link to the establishment of symbiosis. Several kinases are predicted to be cytoplasmic; some contain several PAS domains. The data shown here suggest that TCS kinases in Asgardian bacteria are witnesses to the transition from bacteria to eukaryotic organisms.}, }
@article {pmid37429213, year = {2023}, author = {Sun, J and Zhang, A and Zhang, Z and Liu, Y and Zhou, H and Cheng, H and Chen, Z and Li, H and Zhang, R and Wang, Y}, title = {Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments.}, journal = {Marine environmental research}, volume = {190}, number = {}, pages = {106082}, doi = {10.1016/j.marenvres.2023.106082}, pmid = {37429213}, issn = {1879-0291}, abstract = {Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.}, }
@article {pmid37404173, year = {2023}, author = {Kiledal, EA and Shaw, M and Polson, SW and Maresca, JA}, title = {Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0511222}, doi = {10.1128/spectrum.05112-22}, pmid = {37404173}, issn = {2165-0497}, abstract = {Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. IMPORTANCE Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.}, }
@article {pmid37400737, year = {2023}, author = {Li, XX and Tan, S and Cheng, M and Hu, Y and Ma, X and Hou, J and Cui, HL}, title = {Salinilacihabitans rarus gen. nov., sp. nov., Natrononativus amylolyticus gen. nov., sp. nov., Natronobeatus ordinarius gen. nov., sp. nov., and Halovivax gelatinilyticus sp. nov., halophilic archaea, isolated from a salt lake and soda lakes.}, journal = {Extremophiles : life under extreme conditions}, volume = {27}, number = {2}, pages = {15}, pmid = {37400737}, issn = {1433-4909}, support = {32070003//National Natural Science Foundation of China/ ; }, mesh = {Phylogeny ; Lakes ; RNA, Ribosomal, 16S/genetics ; DNA, Archaeal/genetics ; Sequence Analysis, DNA ; Nucleic Acid Hybridization ; *Halobacteriaceae ; China ; Glycolipids ; *Euryarchaeota/genetics ; }, abstract = {Four halophilic archaea strains, AD-4[T], CGA30[T], CGA73[T], and WLHSJ27[T], were isolated from a salt lake and two soda lakes located in different regions of China. The 16S rRNA and rpoB' gene sequence similarities among strains AD-4[T], CGA30[T], CGA73[T], WLHSJ27[T], and the current species of the family Natrialbaceae were 90.9-97.5% and 83.1-91.8%, respectively. The phylogenetic and phylogenomic analyses revealed that these four strains separated from existing genera in the family Natrialbaceae and formed distant branches. The ANI, isDDH, and AAI values among these four strains and the current members of the family Natrialbaceae were 72-79%, 20-25%, and 63-73%, respectively, much lower than the threshold values for species demarcation. Strains AD-4[T], CGA73[T], and WLHSJ27[T] may represent three novel genera of the family Natrialbaceae according to the cutoff value of AAI (≤ 76%) proposed to differentiate genera within the family Natrialbaceae. These four strains could be distinguished from the related genera according to differential phenotypic characteristics. The major phospholipids of these four strains were identical while their glycolipid profiles were diverse. DGD-1 is a major glycolipid found in strain AD-4[T], trace glycolipids, DGD-1, and S-DGD-1, and (or) S-TGD-1 was found in the other three strains. The major respiratory quinones detected in the four strains were menaquinone MK-8 and MK-8(H2). This polyphasic classification indicated that strains AD-4[T], CGA73[T], and WLHSJ27[T] represent three novel species of three new genera with the family Natrialbaceae, and strain CGA30[T] represents a novel species of Halovivax.}, }
@article {pmid37399976, year = {2023}, author = {Li, B and Liang, J and Phillips, MA and Michael, AJ}, title = {Neofunctionalization of S-adenosylmethionine decarboxylase into pyruvoyl-dependent L-ornithine and L-arginine decarboxylases is widespread in bacteria and archaea.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {105005}, doi = {10.1016/j.jbc.2023.105005}, pmid = {37399976}, issn = {1083-351X}, abstract = {S-Adenosylmethionine decarboxylase (AdoMetDC/SpeD) is a key polyamine biosynthetic enzyme required for conversion of putrescine to spermidine. Autocatalytic self-processing of the AdoMetDC/SpeD proenzyme generates a pyruvoyl cofactor from an internal serine. Recently, we discovered that diverse bacteriophages encode AdoMetDC/SpeD homologs that lack AdoMetDC activity and instead decarboxylate L-ornithine or L-arginine. We reasoned that neofunctionalized AdoMetDC/SpeD homologs were unlikely to have emerged in bacteriophages and were probably acquired from ancestral bacterial hosts. To test this hypothesis, we sought to identify candidate AdoMetDC/SpeD homologs encoding L-ornithine and L-arginine decarboxylases in bacteria and archaea. We searched for the anomalous presence of AdoMetDC/SpeD homologs in the absence of its obligatory partner enzyme spermidine synthase, or the presence of two AdoMetDC/SpeD homologs encoded in the same genome. Biochemical characterization of candidate neofunctionalized genes confirmed lack of AdoMetDC activity, and functional presence of L-ornithine or L-arginine decarboxylase activity in proteins from phyla Actinomycetota, Armatimonadota, Planctomycetota, Melainabacteria, Perigrinibacteria, Atribacteria, Chloroflexota, Sumerlaeota, Omnitrophota, Lentisphaerota and Euryarchaeota, the bacterial candidate phyla radiation and DPANN archaea, and the δ-Proteobacteria class. Phylogenetic analysis indicated that L-arginine decarboxylases emerged at least three times from AdoMetDC/SpeD, whereas L-ornithine decarboxylases arose only once, potentially from the AdoMetDC/SpeD-derived L-arginine decarboxylases, revealing unsuspected polyamine metabolic plasticity. Horizontal transfer of the neofunctionalized genes appears to be the more prevalent mode of dissemination. We identified fusion proteins of bona fide AdoMetDC/SpeD with homologous L-ornithine decarboxylases that possess two, unprecedented internal protein-derived pyruvoyl cofactors. These fusion proteins suggest a plausible model for the evolution of the eukaryotic AdoMetDC.}, }
@article {pmid37387308, year = {2023}, author = {Johnsen, U and Ortjohann, M and Reinhardt, A and Turner, JM and Stratton, C and Weber, KR and Sanchez, KM and Maupin-Furlow, J and Davies, C and Schönheit, P}, title = {Discovery of a novel transcriptional regulator of sugar catabolism in archaea.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.15114}, pmid = {37387308}, issn = {1365-2958}, support = {R01 GM057498/NH/NIH HHS/United States ; }, abstract = {The haloarchaeon Haloferax volcanii degrades D-glucose via the semiphosphorylative Entner-Doudoroff pathway and D-fructose via a modified Embden-Meyerhof pathway. Here, we report the identification of GfcR, a novel type of transcriptional regulator that functions as an activator of both D-glucose and D-fructose catabolism. We find that in the presence of D-glucose, GfcR activates gluconate dehydratase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase and also acts as activator of the phosphotransferase system and of fructose-1,6-bisphosphate aldolase, which are involved in uptake and degradation of D-fructose. In addition, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase are activated by GfcR in the presence of D-fructose and also during growth on D-galactose and glycerol. Electrophoretic mobility shift assays indicate that GfcR binds directly to promoters of regulated genes. Specific intermediates of the degradation pathways of the three hexoses and of glycerol were identified as inducer molecules of GfcR. GfcR is composed of a phosphoribosyltransferase (PRT) domain with an N-terminal helix-turn-helix motif and thus shows homology to PurR of Gram-positive bacteria that is involved in the transcriptional regulation of nucleotide biosynthesis. We propose that GfcR of H. volcanii evolved from a PRT-like enzyme to attain a function as a transcriptional regulator of central sugar catabolic pathways in archaea.}, }
@article {pmid37379385, year = {2023}, author = {Wang, J and Qu, YN and Evans, PN and Guo, Q and Zhou, F and Nie, M and Jin, Q and Zhang, Y and Zhai, X and Zhou, M and Yu, Z and Fu, QL and Xie, YG and Hedlund, BP and Li, WJ and Hua, ZS and Wang, Z and Wang, Y}, title = {Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs.}, journal = {Science advances}, volume = {9}, number = {26}, pages = {eadg6004}, pmid = {37379385}, issn = {2375-2548}, mesh = {*Archaea/genetics/metabolism ; Ecosystem ; *Hot Springs ; Methane/metabolism ; Temperature ; Phylogeny ; }, abstract = {Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on [13]C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.}, }
@article {pmid37367666, year = {2023}, author = {Mapelli-Brahm, P and Gómez-Villegas, P and Gonda, ML and León-Vaz, A and León, R and Mildenberger, J and Rebours, C and Saravia, V and Vero, S and Vila, E and Meléndez-Martínez, AJ}, title = {Microalgae, Seaweeds and Aquatic Bacteria, Archaea, and Yeasts: Sources of Carotenoids with Potential Antioxidant and Anti-Inflammatory Health-Promoting Actions in the Sustainability Era.}, journal = {Marine drugs}, volume = {21}, number = {6}, pages = {}, doi = {10.3390/md21060340}, pmid = {37367666}, issn = {1660-3397}, abstract = {Carotenoids are a large group of health-promoting compounds used in many industrial sectors, such as foods, feeds, pharmaceuticals, cosmetics, nutraceuticals, and colorants. Considering the global population growth and environmental challenges, it is essential to find new sustainable sources of carotenoids beyond those obtained from agriculture. This review focuses on the potential use of marine archaea, bacteria, algae, and yeast as biological factories of carotenoids. A wide variety of carotenoids, including novel ones, were identified in these organisms. The role of carotenoids in marine organisms and their potential health-promoting actions have also been discussed. Marine organisms have a great capacity to synthesize a wide variety of carotenoids, which can be obtained in a renewable manner without depleting natural resources. Thus, it is concluded that they represent a key sustainable source of carotenoids that could help Europe achieve its Green Deal and Recovery Plan. Additionally, the lack of standards, clinical studies, and toxicity analysis reduces the use of marine organisms as sources of traditional and novel carotenoids. Therefore, further research on the processing of marine organisms, the biosynthetic pathways, extraction procedures, and examination of their content is needed to increase carotenoid productivity, document their safety, and decrease costs for their industrial implementation.}, }
@article {pmid37349893, year = {2023}, author = {Carré, L and Gonzalez, D and Girard, &#xc9; and Franzetti, B}, title = {Effects of chaotropic salts on global proteome stability in halophilic archaea: Implications for life signatures on Mars.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16451}, pmid = {37349893}, issn = {1462-2920}, support = {ANR-15-IDEX-02//French National Research Agency/ ; //Interdisciplinary Research Institute of Grenoble (IRIG, CEA)/ ; }, abstract = {Halophilic archaea thriving in hypersaline environments, such as salt lakes, offer models for putative life in extraterrestrial brines such as those found on Mars. However, little is known about the effect of the chaotropic salts that could be found in such brines, such as MgCl2 , CaCl2 and (per)chlorate salts, on complex biological samples like cell lysates which could be expected to be more representative of biomarkers left behind putative extraterrestrial life forms. We used intrinsic fluorescence to study the salt dependence of proteomes extracted from five halophilic strains: Haloarcula marismortui, Halobacterium salinarum, Haloferax mediterranei, Halorubrum sodomense and Haloferax volcanii. These strains were isolated from Earth environments with different salt compositions. Among the five strains that were analysed, H. mediterranei stood out as a results of its high dependency on NaCl for its proteome stabilization. Interestingly, the results showed contrasting denaturation responses of the proteomes to chaotropic salts. In particular, the proteomes of strains that are most dependent or tolerant on MgCl2 for growth exhibited higher tolerance towards chaotropic salts that are abundant in terrestrial and Martian brines. These experiments bridge together global protein properties and environmental adaptation and help guide the search for protein-like biomarkers in extraterrestrial briny environments.}, }
@article {pmid37341134, year = {2023}, author = {Iacono, R and De Lise, F and Moracci, M and Cobucci-Ponzano, B and Strazzulli, A}, title = {Glycoside hydrolases from (hyper)thermophilic archaea: structure, function, and applications.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20220196}, pmid = {37341134}, issn = {1744-1358}, abstract = {(Hyper)thermophilic archaeal glycosidases are enzymes that catalyze the hydrolysis of glycosidic bonds to break down complex sugars and polysaccharides at high temperatures. These enzymes have an unique structure that allows them to remain stable and functional in extreme environments such as hot springs and hydrothermal vents. This review provides an overview of the current knowledge and milestones on the structures and functions of (hyper)thermophilic archaeal glycosidases and their potential applications in various fields. In particular, this review focuses on the structural characteristics of these enzymes and how these features relate to their catalytic activity by discussing different types of (hyper)thermophilic archaeal glycosidases, including β-glucosidases, chitinase, cellulases and α-amylases, describing their molecular structures, active sites, and mechanisms of action, including their role in the hydrolysis of carbohydrates. By providing a comprehensive overview of (hyper)thermophilic archaeal glycosidases, this review aims to stimulate further research into these fascinating enzymes.}, }
@article {pmid37334237, year = {2021}, author = {Jarrell, KF and Albers, SV and Machado, JNS}, title = {A comprehensive history of motility and Archaellation in Archaea.}, journal = {FEMS microbes}, volume = {2}, number = {}, pages = {xtab002}, pmid = {37334237}, issn = {2633-6685}, abstract = {Each of the three Domains of life, Eukarya, Bacteria and Archaea, have swimming structures that were all originally called flagella, despite the fact that none were evolutionarily related to either of the other two. Surprisingly, this was true even in the two prokaryotic Domains of Bacteria and Archaea. Beginning in the 1980s, evidence gradually accumulated that convincingly demonstrated that the motility organelle in Archaea was unrelated to that found in Bacteria, but surprisingly shared significant similarities to type IV pili. This information culminated in the proposal, in 2012, that the 'archaeal flagellum' be assigned a new name, the archaellum. In this review, we provide a historical overview on archaella and motility research in Archaea, beginning with the first simple observations of motile extreme halophilic archaea a century ago up to state-of-the-art cryo-tomography of the archaellum motor complex and filament observed today. In addition to structural and biochemical data which revealed the archaellum to be a type IV pilus-like structure repurposed as a rotating nanomachine (Beeby et al. 2020), we also review the initial discoveries and subsequent advances using a wide variety of approaches to reveal: complex regulatory events that lead to the assembly of the archaellum filaments (archaellation); the roles of the various archaellum proteins; key post-translational modifications of the archaellum structural subunits; evolutionary relationships; functions of archaella other than motility and the biotechnological potential of this fascinating structure. The progress made in understanding the structure and assembly of the archaellum is highlighted by comparing early models to what is known today.}, }
@article {pmid37332501, year = {2022}, author = {Pessi, IS and Rutanen, A and Hultman, J}, title = {Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution.}, journal = {FEMS microbes}, volume = {3}, number = {}, pages = {xtac019}, pmid = {37332501}, issn = {2633-6685}, abstract = {Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus 'UBA10452', an uncultured lineage of putative AOA in the order Nitrososphaerales ('terrestrial group I.1b'), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographic, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographic/habitat clusters.}, }
@article {pmid37323904, year = {2023}, author = {Elcheninov, AG and Ugolkov, YA and Elizarov, IM and Klyukina, AA and Kublanov, IV and Sorokin, DY}, title = {Cellulose metabolism in halo(natrono)archaea: a comparative genomics study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1112247}, pmid = {37323904}, issn = {1664-302X}, abstract = {Extremely halophilic archaea are one of the principal microbial community components in hypersaline environments. The majority of cultivated haloarchaea are aerobic heterotrophs using peptides or simple sugars as carbon and energy sources. At the same time, a number of novel metabolic capacities of these extremophiles were discovered recently among which is a capability of growing on insoluble polysaccharides such as cellulose and chitin. Still, polysaccharidolytic strains are in minority among cultivated haloarchaea and their capacities of hydrolyzing recalcitrant polysaccharides are hardly investigated. This includes the mechanisms and enzymes involved in cellulose degradation, which are well studied for bacterial species, while almost unexplored in archaea and haloarchaea in particular. To fill this gap, a comparative genomic analysis of 155 cultivated representatives of halo(natrono)archaea, including seven cellulotrophic strains belonging to the genera Natronobiforma, Natronolimnobius, Natrarchaeobius, Halosimplex, Halomicrobium and Halococcoides was performed. The analysis revealed a number of cellulases, encoded in the genomes of cellulotrophic strains but also in several haloarchaea, for which the capacity to grow on cellulose was not shown. Surprisingly, the cellulases genes, especially of GH5, GH9 and GH12 families, were significantly overrepresented in the cellulotrophic haloarchaea genomes in comparison with other cellulotrophic archaea and even cellulotrophic bacteria. Besides cellulases, the genes for GH10 and GH51 families were also abundant in the genomes of cellulotrophic haloarchaea. These results allowed to propose the genomic patterns, determining the capability of haloarchaea to grow on cellulose. The patterns helped to predict cellulotrophic capacity for several halo(natrono)archaea, and for three of them it was experimentally confirmed. Further genomic search revealed that glucose and cellooligosaccharides import occurred by means of porters and ABC (ATP-binding cassette) transporters. Intracellular glucose oxidation occurred through glycolysis or the semi-phosphorylative Entner-Dudoroff pathway which occurrence was strain-specific. Comparative analysis of CAZymes toolbox and available cultivation-based information allowed proposing two possible strategies used by haloarchaea capable of growing on cellulose: so-called specialists are more effective in degradation of cellulose while generalists are more flexible in nutrient spectra. Besides CAZymes profiles the groups differed in genome sizes, as well as in variability of mechanisms of import and central metabolism of sugars.}, }
@article {pmid37322123, year = {2023}, author = {Taglialegna, A}, title = {A plasmid to modify Archaea.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37322123}, issn = {1740-1534}, }
@article {pmid37317245, year = {2023}, author = {Thompson, TP and Busetti, A and Gilmore, BF}, title = {Quorum Sensing in Halorubrum saccharovorum Facilitates Cross-Domain Signaling between Archaea and Bacteria.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/microorganisms11051271}, pmid = {37317245}, issn = {2076-2607}, abstract = {Quorum Sensing (QS) is a well-studied intercellular communication mechanism in bacteria, regulating collective behaviors such as biofilm formation, virulence, and antibiotic resistance. However, cell-cell signaling in haloarchaea remains largely unexplored. The coexistence of bacteria and archaea in various environments, coupled with the known cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms and the presence of cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms, suggests a possibility for haloarchaea to possess analogous cell-cell signaling or QS systems. Recently, N-acylhomoserine lactone (AHL)-like compounds were identified in haloarchaea; yet, their precise role-for example, persister cell formation-remains ambiguous. This study investigated the capacity of crude supernatant extract from the haloarchaeon Halorubrum saccharovorum CSM52 to stimulate bacterial AHL-dependent QS phenotypes using bioreporter strains. Our findings reveal that these crude extracts induced several AHL-dependent bioreporters and modulated pyocyanin and pyoverdine production in Pseudomonas aeruginosa. Importantly, our study suggests cross-domain communication between archaea and bacterial pathogens, providing evidence for archaea potentially influencing bacterial virulence. Using Thin Layer Chromatography overlay assays, lactonolysis, and colorimetric quantification, the bioactive compound was inferred to be a chemically modified AHL-like compound or a diketopiperazine-like molecule, potentially involved in biofilm formation in H. saccharovorum CSM52. This study offers new insights into putative QS mechanisms in haloarchaea and their potential role in interspecies communication and coordination, thereby enriching our understanding of microbial interactions in diverse environments.}, }
@article {pmid37317170, year = {2023}, author = {Payá, G and Bautista, V and Camacho, M and Esclapez, J and Bonete, MJ}, title = {Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/microorganisms11051196}, pmid = {37317170}, issn = {2076-2607}, abstract = {The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action.}, }
@article {pmid37308591, year = {2023}, author = {Tong, Y and Wu, X and Liu, Y and Chen, H and Zhou, Y and Jiang, L and Li, M and Zhao, S and Zhang, Y}, title = {Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37308591}, issn = {2058-5276}, abstract = {Many bacteriophages evade bacterial immune recognition by substituting adenine with 2,6-diaminopurine (Z) in their genomes. The Z-genome biosynthetic pathway involves PurZ that belongs to the PurA (adenylosuccinate synthetase) family and bears particular similarity to archaeal PurA. However, how the transition of PurA to PurZ occurred during evolution is not clear; recapturing this process may shed light on the origin of Z-containing phages. Here we describe the computer-guided identification and biochemical characterization of a naturally existing PurZ variant, PurZ0, which uses guanosine triphosphate as the phosphate donor rather than the ATP used by PurZ. The atomic resolution structure of PurZ0 reveals a guanine nucleotide binding pocket highly analogous to that of archaeal PurA. Phylogenetic analyses suggest PurZ0 as an intermediate during the evolution of archaeal PurA to phage PurZ. Maintaining the balance of different purines necessitates further evolvement of guanosine triphosphate-using PurZ0 to ATP-using PurZ in adaptation to Z-genome life.}, }
@article {pmid37305433, year = {2023}, author = {van der Does, C and Braun, F and Ren, H and Albers, SV}, title = {Putative nucleotide-based second messengers in archaea.}, journal = {microLife}, volume = {4}, number = {}, pages = {uqad027}, pmid = {37305433}, issn = {2633-6693}, abstract = {Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.}, }
@article {pmid37293225, year = {2023}, author = {Jia, Z and Lipus, D and Burckhardt, O and Bussert, R and Sondermann, M and Bartholomäus, A and Wagner, D and Kallmeyer, J}, title = {Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO2 terrestrial subsurface environments.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1105259}, pmid = {37293225}, issn = {1664-302X}, abstract = {INTRODUCTION: Long-term stability of underground CO2 storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO2 makes the Eger Rift in the Czech Republic a natural analogue to underground CO2 storage. The Eger Rift is a seismically active region and H2 is produced abiotically during earthquakes, providing energy to indigenous microbial communities.<br><br>METHODS: To investigate the response of a microbial ecosystem to high levels of CO2 and H2, we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H2/CO2 headspace to simulate a seismically active period with elevated H2.<br><br>RESULTS AND DISCUSSION: Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50-60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H2 and CO2, specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO2 driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO2 and H2-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO2 concentrations, similar to those found in CCS sites.}, }
@article {pmid37277532, year = {2023}, author = {Catchpole, RJ and Barbe, V and Magdelenat, G and Marguet, E and Terns, M and Oberto, J and Forterre, P and Da Cunha, V}, title = {A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37277532}, issn = {2058-5276}, abstract = {Conjugative plasmids are self-transmissible mobile genetic elements that transfer DNA between host cells via type IV secretion systems (T4SS). While T4SS-mediated conjugation has been well-studied in bacteria, information is sparse in Archaea and known representatives exist only in the Sulfolobales order of Crenarchaeota. Here we present the first self-transmissible plasmid identified in a Euryarchaeon, Thermococcus sp. 33-3. The 103 kbp plasmid, pT33-3, is seen in CRISPR spacers throughout the Thermococcales order. We demonstrate that pT33-3 is a bona fide conjugative plasmid that requires cell-to-cell contact and is dependent on canonical, plasmid-encoded T4SS-like genes. Under laboratory conditions, pT33-3 transfers to various Thermococcales and transconjugants propagate at 100 °C. Using pT33-3, we developed a genetic toolkit that allows modification of phylogenetically diverse Archaeal genomes. We demonstrate pT33-3-mediated plasmid mobilization and subsequent targeted genome modification in previously untransformable Thermococcales species, and extend this process to interphylum transfer to a Crenarchaeon.}, }
@article {pmid37264141, year = {2023}, author = {Zehnle, H and Laso-Pérez, R and Lipp, J and Riedel, D and Benito Merino, D and Teske, A and Wegener, G}, title = {Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37264141}, issn = {2058-5276}, abstract = {Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.}, }
@article {pmid37256053, year = {2023}, author = {Hou, G and Wazir, ZG and Liu, J and Wang, G and Rong, F and Xu, Y and Li, M and Liu, K and Liu, A and Liu, H and Wang, F}, title = {Effects of sulfadiazine and Cu on soil potential nitrification and ammonia-oxidizing archaea and bacteria communities across different soils.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1153199}, pmid = {37256053}, issn = {1664-302X}, abstract = {INTRODUCTION: Sulfadiazine (SDZ) and copper (Cu) are frequently detected in agricultural soils, but little is known on their single or combined impact on ammonia oxidizing microbial community and function across different soils.<br><br>METHODS: In this study, a microcosm was conducted to distinguish the microbial ecotoxicity of SDZ and Cu across different soils by analyzing soil potential nitrification rate (PNR) and the amoA gene sequences.<br><br>RESULTS: The results showed that the single spiking of SDZ caused a consistent decrease of soil PNR among three tested soils, but no consistent synergistic inhibition of SDZ and Cu was observed across these soils. Moreover, across three tested soils, the distinct responses to the single or joint exposure of SDZ and Cu were found in amoA gene abundance, and diversity as well as the identified genus taxa of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Meanwhile, only the specific genus taxa of AOA or AOB consistently corresponded to the variation of soil PNR across different treated soils. The further principal component analysis (PCA) exhibited that the variable influence of SDZ and Cu on ammonia oxidizing microbial community and function was greatly dependent on soil type.<br><br>DISCUSSION: Therefore, in addition to ecological functionality and the specific prokaryotic taxa, soil microbial ecotoxicity of SDZ and Cu also was dependent on edaphic factors derived from soil types. This study proposes an integrative assessment of soil properties and multiple microbial targets to soil contamination management.}, }
@article {pmid37252776, year = {2023}, author = {Wang, BB and Bao, CX and Sun, YP and Hou, J and Cui, HL}, title = {Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., two extremely halophilic archaea isolated from sediment of a salt lake and saline soil of an inland saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005922}, pmid = {37252776}, issn = {1466-5034}, abstract = {Two novel halophilic archaeal strains, Gai3-17[T] and XZYJT26[T], were isolated from the sediment of Gaize salt lake and the saline soil of Mangkang ancient solar saltern in Tibet, PR China, respectively. Strains Gai3-17[T] and XZYJT26[T] were related to each other (96.5 and 89.7% similarity, respectively) and showed 97.5-95.4 and 91.5-87.7% similarities to the current members of Halobacterium based on 16S rRNA and rpoB' genes. The phylogenomic analysis indicated that strains Gai3-17[T] and XZYJT26[T] formed two distinct clades and clustered with the Halobacterium species. The two strains can be differentiated from the type strains of the six species with validly published names based on several phenotypic characteristics. The phospholipids of the two strains were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. One major glycolipid, sulphated galactosyl mannosyl glucosyl diether, was detected in strain Gai3-17[T], while four glycolipids, mannosyl glucosyl diether, sulphated mannosyl glucosyl diether, disulphated mannosyl glucosyl diether and sulphated galactosyl mannosyl glucosyl diether were observed in strain XZYJT26[T]. The average nucleotide identity, digital DNA-DNA hybridization and amino acid identity values among the two strains and the members of Halobacterium were no more than 81, 25 and 77 %, respectively. These overall genome-related indices were below the threshold values for species boundary, indicating that strains Gai3-17[T] and XZYJT26[T] represent two novel species of Halobacterium. Thus, two novel species, Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., are proposed to accommodate strains Gai3-17[T] (=CGMCC 1.16101[T]=JCM 33551[T]) and XZYJT26[T] (=CGMCC 1.16682[T]=JCM 33556[T]), respectively.}, }
@article {pmid37237946, year = {2023}, author = {Ávila-Román, J and Gómez-Villegas, P and de Carvalho, CCCR and Vigara, J and Motilva, V and León, R and Talero, E}, title = {Up-Regulation of the Nrf2/HO-1 Antioxidant Pathway in Macrophages by an Extract from a New Halophilic Archaea Isolated in Odiel Saltworks.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {37237946}, issn = {2076-3921}, abstract = {The production of reactive oxygen species (ROS) plays an important role in the progression of many inflammatory diseases. The search for antioxidants with the ability for scavenging free radicals from the body cells that reduce oxidative damage is essential to prevent and treat these pathologies. Haloarchaea are extremely halophilic microorganisms that inhabit hypersaline environments, such as saltworks or salt lakes, where they have to tolerate high salinity, and elevated ultraviolet (UV) and infrared radiations. To cope with these extreme conditions, haloarchaea have developed singular mechanisms to maintain an osmotic balance with the medium, and are endowed with unique compounds, not found in other species, with bioactive properties that have not been fully explored. This study aims to assess the potential of haloarchaea as a new source of natural antioxidant and anti-inflammatory agents. A carotenoid-producing haloarchaea was isolated from Odiel Saltworks (OS) and identified on the basis of its 16S rRNA coding gene sequence as a new strain belonging to the genus Haloarcula. The Haloarcula sp. OS acetone extract (HAE) obtained from the biomass contained bacterioruberin and mainly C18 fatty acids, and showed potent antioxidant capacity using ABTS assay. This study further demonstrates, for the first time, that pretreatment with HAE of lipopolysaccharide (LPS)-stimulated macrophages results in a reduction in ROS production, a decrease in the pro-inflammatory cytokines TNF-α and IL-6 levels, and up-regulation of the factor Nrf2 and its target gene heme oxygenase-1 (HO-1), supporting the potential of the HAE as a therapeutic agent in the treatment of oxidative stress-related inflammatory diseases.}, }
@article {pmid37223257, year = {2021}, author = {Liu, J and Soler, N and Gorlas, A and Cvirkaite-Krupovic, V and Krupovic, M and Forterre, P}, title = {Extracellular membrane vesicles and nanotubes in Archaea.}, journal = {microLife}, volume = {2}, number = {}, pages = {uqab007}, pmid = {37223257}, issn = {2633-6693}, abstract = {Membrane-bound extracellular vesicles (EVs) are secreted by cells from all three domains of life and their implication in various biological processes is increasingly recognized. In this review, we summarize the current knowledge on archaeal EVs and nanotubes, and emphasize their biological significance. In archaea, the EVs and nanotubes have been largely studied in representative species from the phyla Crenarchaeota and Euryarchaeota. The archaeal EVs have been linked to several physiological processes such as detoxification, biomineralization and transport of biological molecules, including chromosomal, viral or plasmid DNA, thereby taking part in genome evolution and adaptation through horizontal gene transfer. The biological significance of archaeal nanotubes is yet to be demonstrated, although they could participate in EV biogenesis or exchange of cellular contents. We also discuss the biological mechanisms leading to EV/nanotube biogenesis in Archaea. It has been recently demonstrated that, similar to eukaryotes, EV budding in crenarchaea depends on the ESCRT machinery, whereas the mechanism of EV budding in euryarchaeal lineages, which lack the ESCRT-III homologues, remains unknown.}, }
@article {pmid37204206, year = {2023}, author = {Ma, X and Hu, Y and Li, XX and Tan, S and Cheng, M and Hou, J and Cui, HL}, title = {Halomicroarcula laminariae sp. nov. and Halomicroarcula marina sp. nov., extremely halophilic archaea isolated from salted brown alga Laminaria and coastal saline-alkali lands.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005889}, pmid = {37204206}, issn = {1466-5034}, mesh = {*Laminaria ; *Halobacteriaceae ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Glycolipids/chemistry ; Fatty Acids/chemistry ; Base Composition ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Sodium Chloride ; *Halobacteriales ; *Haloarcula ; Comparative Genomic Hybridization ; China ; DNA, Archaeal/genetics ; }, abstract = {Four extremely halophilic archaeal strains, LYG-108[T], LYG-24, DT1[T] and YSSS71, were isolated from salted Laminaria produced in Lianyungang and saline soil from the coastal beach at Jiangsu, PR China. The four strains were found to be related to the current species of Halomicroarcula (showing 88.1-98.5% and 89.3-93.6% similarities, respectively) as revealed by phylogenetic analysis based on 16S rRNA and rpoB' genes. These phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes (average nucleotide identity, DNA-DNA hybridization and average amino acid identity) among these four strains and the Halomicroarcula species were 77-84 %, 23-30 % and 71-83 %, respectively, clearly below the threshold values for species demarcation. Additionally, the phylogenomic and comparative genomic analyses revealed that Halomicroarcula salina YGH18[T] is related to the current species of Haloarcula rather than those of Halomicroarcula, Haloarcula salaria Namwong et al. 2011 is a later heterotypic synonym of Haloarcula argentinensis Ihara et al. 1997, and Haloarcula quadrata Oren et al. 1999 is a later heterotypic synonym of Haloarcula marismortui Oren et al. 1990. The major polar lipids of strains LYG-108[T], LYG-24, DT1[T] and YSSS71 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate, sulphated mannosyl glucosyl diether and additional glycosyl-cardiolipins. All these results showed that strains LYG-108[T] (=CGMCC 1.13607[T]=JCM 32950[T]) and LYG-24 (=CGMCC 1.13605=JCM 32949) represent a new species of the genus Halomicroarcula, for which the name Halomicroarcula laminariae sp. nov. is proposed; strains DT1[T] (=CGMCC 1.18928[T]=JCM 35414[T]) and YSSS71 (=CGMCC 1.18783=JCM 34915) also represent a new species of the genus Halomicroarcula, for which the name Halomicroarcula marina sp. nov. is proposed.}, }
@article {pmid37202434, year = {2023}, author = {Wang, Z and Li, Y and Zheng, W and Ji, Y and Duan, M and Ma, L}, title = {Ammonia oxidizing archaea and bacteria respond to different manure application rates during organic vegetable cultivation in Northwest China.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8064}, pmid = {37202434}, issn = {2045-2322}, abstract = {Ammonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used the amoA gene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, the amoA copy number of AOB treated with 900 kgN ha[-1] was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P < 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified into Nitrosomonas and Nitrosospira, and AOA into Nitrosopumilus and Nitrososphaera. Nitrosomonas and Nitrosopumilus were predominant in treatments that received manure nitrogen at ≥ 900 kg ha[-1] (52.7-56.5%) and when manure was added (72.7-99.8%), respectively, whereas Nitrosospira and Nitrososphaera occupied more than a half percentage in those that received ≤ 600 kg ha[-1] (58.4-84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs' community structures than greater difference manure rate. The bacterial amoA gene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs' variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management.}, }
@article {pmid37198640, year = {2023}, author = {Dondjou, DT and Diedhiou, AG and Mbodj, D and Mofini, MT and Pignoly, S and Ndiaye, C and Diedhiou, I and Assigbetse, K and Manneh, B and Laplaze, L and Kane, A}, title = {Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {42}, pmid = {37198640}, issn = {2524-6372}, abstract = {BACKGROUND: Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta.<br><br>RESULTS: We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages.<br><br>CONCLUSIONS: Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.}, }
@article {pmid37196775, year = {2023}, author = {Aparici, D and Esclapez, J and Bautista, V and Bonete, MJ and Ca Macho, M}, title = {Archaea: current and potential biotechnological applications.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {104080}, doi = {10.1016/j.resmic.2023.104080}, pmid = {37196775}, issn = {1769-7123}, abstract = {Archaea are microorganisms with great ability to colonize some of the most inhospitable environments in nature, managing to survive in places with extreme characteristics for most microorganisms. Its proteins and enzymes are stable and can act under extreme conditions in which other proteins and enzymes would degrade. These attributes make them ideal candidates for use in a wide range of biotechnological applications. This review describes the most important applications, both current and potential, that archaea present in Biotechnology, classifying them according to the sector to which the application is directed. It also analyzes the advantages and disadvantages of its use.}, }
@article {pmid37194083, year = {2023}, author = {Romero, R and Gervasi, MT and DiGiulio, DB and Jung, E and Suksai, M and Miranda, J and Theis, KR and Gotsch, F and Relman, DA}, title = {Are bacteria, fungi, and archaea present in the midtrimester amniotic fluid?.}, journal = {Journal of perinatal medicine}, volume = {}, number = {}, pages = {}, pmid = {37194083}, issn = {1619-3997}, abstract = {OBJECTIVES: This study was conducted to determine whether bacteria, fungi, or archaea are detected in the amniotic fluid of patients who underwent midtrimester amniocentesis for clinical indications.<br><br>METHODS: Amniotic fluid samples from 692 pregnancies were tested by using a combination of culture and end-point polymerase chain reaction (PCR) techniques. Intra-amniotic inflammation was defined as an interleukin-6 concentration >2,935 pg/mL.<br><br>RESULTS: Microorganisms were detected in 0.3% (2/692) of cases based on cultivation, 1.73% (12/692) based on broad-range end-point PCR, and 2% (14/692) based on the combination of both methods. However, most (13/14) of these cases did not have evidence of intra-amniotic inflammation and delivered at term. Therefore, a positive culture or end-point PCR in most patients appears to have no apparent clinical significance.<br><br>CONCLUSIONS: Amniotic fluid in the midtrimester of pregnancy generally does not contain bacteria, fungi, or archaea. Interpretation of amniotic fluid culture and molecular microbiologic results is aided by the assessment of the inflammatory state of the amniotic cavity. The presence of microorganisms, as determined by culture or a microbial signal in the absence of intra-amniotic inflammation, appears to be a benign condition.}, }
@article {pmid37192814, year = {2023}, author = {Grünberger, F and Jüttner, M and Knüppel, R and Ferreira-Cerca, S and Grohmann, D}, title = {Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in Archaea.}, journal = {RNA (New York, N.Y.)}, volume = {}, number = {}, pages = {}, doi = {10.1261/rna.079636.123}, pmid = {37192814}, issn = {1469-9001}, abstract = {Ribosomal RNA (rRNA) maturation in archaea is a complex multi-step process that requires well-defined endo- and exoribonuclease activities to generate fully mature linear rRNAs. However, technical challenges prevented detailed mapping of rRNA processing steps and a systematic analysis of rRNA maturation pathways across the tree of life. In this study, we employed long-read (PCR)-cDNA and direct RNA nanopore-based sequencing to study rRNA maturation in three archaeal model organisms, namely the Euryarchaea Haloferax volcanii and Pyrococcus furiosus and the Crenarchaeon Sulfolobus acidocaldarius. Compared to standard short-read protocols, nanopore sequencing facilitates simultaneous readout of 5'- and 3'-positions, which is required for the classification of rRNA processing intermediates. More specifically, we i) accurately detect and describe rRNA maturation stages by analysis of terminal read positions of cDNA reads and thereupon ii) explore the stage-dependent installation of the KsgA-mediated dimethylations in Haloferax volcanii using basecalling and signal characteristics of direct RNA reads. Due to the single-molecule sequencing capacity of nanopore sequencing, we could detect hitherto unknown intermediates with high confidence, revealing details about the maturation of archaea-specific circular rRNA intermediates. Taken together, our study delineates common principles and unique features of rRNA processing in euryarchaeal and crenarchaeal representatives, thereby significantly expanding our understanding of rRNA maturation pathways in archaea.}, }
@article {pmid37171866, year = {2023}, author = {Pallen, MJ and Rodriguez-R, LM and Alikhan, NF}, title = {Corrigendum: Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005885}, pmid = {37171866}, issn = {1466-5034}, }
@article {pmid37154724, year = {2023}, author = {Demey, LM and Gumerov, VM and Xing, J and Zhulin, IB and DiRita, VJ}, title = {Transmembrane Transcription Regulators Are Widespread in Bacteria and Archaea.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0026623}, doi = {10.1128/spectrum.00266-23}, pmid = {37154724}, issn = {2165-0497}, abstract = {To adapt and proliferate, bacteria must sense and respond to the ever-changing environment. Transmembrane transcription regulators (TTRs) are a family of one-component transcription regulators that respond to extracellular information and influence gene expression from the cytoplasmic membrane. How TTRs function to modulate expression of their target genes while localized to the cytoplasmic membrane remains poorly understood. In part, this is due to a lack of knowledge regarding the prevalence of TTRs among prokaryotes. Here, we show that TTRs are highly diverse and prevalent throughout bacteria and archaea. Our work demonstrates that TTRs are more common than previously appreciated and are enriched within specific bacterial and archaeal phyla and that many TTRs have unique transmembrane region properties that can facilitate association with detergent-resistant membranes. IMPORTANCE One-component signal transduction systems are the major class of signal transduction systems among bacteria and are commonly cytoplasmic. TTRs are a group of unique one-component signal transduction systems that influence transcription from the cytoplasmic membrane. TTRs have been implicated in a wide array of biological pathways critical for both pathogens and human commensal organisms but were considered to be rare. Here, we demonstrate that TTRs are in fact highly diverse and broadly distributed in bacteria and archaea. Our findings suggest that transcription factors can access the chromosome and influence transcription from the membrane in both archaea and bacteria. This study challenges thus the commonly held notion that signal transduction systems require a cytoplasmic transcription factor and highlights the importance of the cytoplasmic membrane in directly influencing signal transduction.}, }
@article {pmid37117330, year = {2023}, author = {Hodgskiss, LH and Melcher, M and Kerou, M and Chen, W and Ponce-Toledo, RI and Savvides, SN and Wienkoop, S and Hartl, M and Schleper, C}, title = {Correction to: Unexpected complexity of the ammonia monooxygenase in archaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-023-01403-2}, pmid = {37117330}, issn = {1751-7370}, }
@article {pmid37100405, year = {2023}, author = {Jaffe, AL and Castelle, CJ and Banfield, JF}, title = {Habitat Transition in the Evolution of Bacteria and Archaea.}, journal = {Annual review of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-micro-041320-032304}, pmid = {37100405}, issn = {1545-3251}, abstract = {Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid37098974, year = {2023}, author = {Chen, X and Molenda, O and Brown, CT and Toth, CRA and Guo, S and Luo, F and Howe, J and Nesbø, CL and He, C and Montabana, EA and Cate, JHD and Banfield, JF and Edwards, EA}, title = {"Candidatus Nealsonbacteria" Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0002523}, doi = {10.1128/aem.00025-23}, pmid = {37098974}, issn = {1098-5336}, abstract = {The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade "Candidatus Nealsonbacteria." Because of its persistence over many years, we hypothesized that "Ca. Nealsonbacteria" DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of "Ca. Nealsonbacteria" DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate "Ca. Nealsonbacteria" in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that "Ca. Nealsonbacteria" DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other "Ca. Nealsonbacteria" found in anoxic environments. IMPORTANCE An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny "Candidatus Nealsonbacteria" cells attached to a large Methanothrix cell, revealing a novel episymbiosis.}, }
@article {pmid37097839, year = {2023}, author = {Prakash, O and Dodsworth, JA and Dong, X and Ferry, JG and L'Haridon, S and Imachi, H and Kamagata, Y and Rhee, SK and Sagar, I and Shcherbakova, V and Wagner, D and Whitman, WB}, title = {Proposed minimal standards for description of methanogenic archaea.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {4}, pages = {}, doi = {10.1099/ijsem.0.005500}, pmid = {37097839}, issn = {1466-5034}, abstract = {Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.}, }
@article {pmid37093039, year = {2023}, author = {Dithugoe, CD and Bezuidt, OKI and Cavan, EL and Froneman, WP and Thomalla, SJ and Makhalanyane, TP}, title = {Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0042022}, doi = {10.1128/msphere.00420-22}, pmid = {37093039}, issn = {2379-5042}, abstract = {The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO2, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.}, }
@article {pmid37083735, year = {2023}, author = {Roux, S and Camargo, AP and Coutinho, FH and Dabdoub, SM and Dutilh, BE and Nayfach, S and Tritt, A}, title = {iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria.}, journal = {PLoS biology}, volume = {21}, number = {4}, pages = {e3002083}, doi = {10.1371/journal.pbio.3002083}, pmid = {37083735}, issn = {1545-7885}, abstract = {The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available to predict the host(s) of uncultivated viruses based on their genome sequences, but thus far individual approaches are limited either in precision or in recall, i.e., for a number of viruses they yield erroneous predictions or no prediction at all. Here, we describe iPHoP, a two-step framework that integrates multiple methods to reliably predict host taxonomy at the genus rank for a broad range of viruses infecting bacteria and archaea, while retaining a low false discovery rate. Based on a large dataset of metagenome-derived virus genomes from the IMG/VR database, we illustrate how iPHoP can provide extensive host prediction and guide further characterization of uncultivated viruses.}, }
@article {pmid37082172, year = {2023}, author = {Zhang, Z and Fusco, S}, title = {Editorial: New insights into the genetic mechanisms of thermophilic archaea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1185784}, pmid = {37082172}, issn = {1664-302X}, }
@article {pmid37073347, year = {2021}, author = {Zhang, CJ and Chen, YL and Sun, YH and Pan, J and Cai, MW and Li, M}, title = {Diversity, metabolism and cultivation of archaea in mangrove ecosystems.}, journal = {Marine life science &amp; technology}, volume = {3}, number = {2}, pages = {252-262}, pmid = {37073347}, issn = {2662-1746}, abstract = {Mangroves comprise a globally significant intertidal ecosystem that contains a high diversity of microorganisms, including fungi, bacteria and archaea. Archaea is a major domain of life that plays important roles in biogeochemical cycles in these ecosystems. In this review, the potential roles of archaea in mangroves are briefly highlighted. Then, the diversity and metabolism of archaeal community of mangrove ecosystems across the world are summarized and Bathyarchaeota, Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Lokiarchaeota are confirmed as the most abundant and ubiquitous archaeal groups. The metabolic potential of these archaeal groups indicates their important ecological function in carbon, nitrogen and sulfur cycling. Finally, some cultivation strategies that could be applied to uncultivated archaeal lineages from mangrove wetlands are suggested, including refinements to traditional cultivation methods based on genomic and transcriptomic information, and numerous innovative cultivation techniques such as single-cell isolation and high-throughput culturing (HTC). These cultivation strategies provide more opportunities to obtain previously uncultured archaea.}, }
@article {pmid37072332, year = {2023}, author = {Nikonov, OS and Nikonova, EY and Tarabarova, AG and Mikhaylina, AO and Kravchenko, OV and Nevskaya, NA and Nikonov, SV}, title = {Recognition of γ-Subunit by β-Subunit in Translation Initiation Factor 2. Stabilization of the GTP-Bound State of I/F 2 in Archaea and Eukaryotes.}, journal = {Biochemistry. Biokhimiia}, volume = {88}, number = {2}, pages = {221-230}, doi = {10.1134/S0006297923020062}, pmid = {37072332}, issn = {1608-3040}, abstract = {Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) functions as a heterotrimeric complex. It consists of three subunits (α, β, γ). α- and β-subunits are bound to γ-subunit by hydrogen bonds and van der Waals interactions, but do not contact each other. Although main functions of the factor are performed by the γ-subunit, reliable formation of αγ and βγ complexes is necessary for its proper functioning. In this work, we introduced mutations in the recognition part of the βγ interface and showed that hydrophobic effect plays a crucial role in the recognition of subunits both in eukaryotes and archaea. Shape and properties of the groove on the surface of γ-subunit facilitates transition of the disordered recognition part of the β-subunit into an α-helix containing approximately the same number of residues in archaea and eukaryotes. In addition, based on the newly obtained data, it was concluded that in archaea and eukaryotes, transition of the γ-subunit to the active state leads to additional contact between the region of switch 1 and C-terminal part of the β-subunit, which stabilizes helical conformation of the switch.}, }
@article {pmid37073339, year = {2021}, author = {Hu, H and Natarajan, VP and Wang, F}, title = {Towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods.}, journal = {Marine life science &amp; technology}, volume = {3}, number = {2}, pages = {231-242}, pmid = {37073339}, issn = {2662-1746}, abstract = {UNLABELLED: The archaea that can be readily cultivated in the laboratory are only a small fraction of the total diversity that exists in nature. Although molecular ecology methods, such as metagenomic sequencing, can provide valuable information independent of cell cultivation, it is only through cultivation-based experiments that they may be fully characterized, both for their physiological and ecological properties. Here, we report our efforts towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods. Initially, cells were retrieved from the sediment samples through a cell extraction procedure and the sediment-free mixed cells were then divided into different size-range fractions by successive filtration through 0.8 µm, 0.6 µm and 0.2 µm membranes. Archaeal 16S rRNA gene analyses indicated noticeable retention of different archaeal groups in different fractions. For each fraction, supplementation with a variety of defined substrates (e.g., methane, sulfate, and lignin) and stepwise dilutions led to highly active enrichment cultures of several archaeal groups with Bathyarchaeota most prominently enriched. Finally, using a roll-bottle technique, three co-cultures consisting of Bathyarchaeota (subgroup-8) and a bacterial species affiliated with either Pseudomonas or Glutamicibacter were obtained. Our results demonstrate that a combination of cell extraction, size fractionation, and roll-bottle isolation methods could be a useful protocol for the successful enrichment and isolation of numerous slow-growing archaeal groups from marine sediments.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-021-00092-0.}, }
@article {pmid37073340, year = {2021}, author = {Cui, HL and Dyall-Smith, ML}, title = {Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments.}, journal = {Marine life science &amp; technology}, volume = {3}, number = {2}, pages = {243-251}, pmid = {37073340}, issn = {2662-1746}, abstract = {UNLABELLED: As a group, the halophilic archaea (class Halobacteria) are the most salt-requiring and salt-resistant microorganisms within the domain Archaea. Halophilic archaea flourish in thalassohaline and athalassohaline environments and require over 100-150 g/L NaCl for growth and structural stability. Natural hypersaline environments vary in salt concentration, chemical composition and pH, and occur in climates ranging from tropical to polar and even under-sea. Accordingly, their resident haloarchaeal species vary enormously, as do their individual population compositions and community structures. These diverse halophilic archaeal strains are precious resources for theoretical and applied research but assessing their taxonomic and metabolic novelty and diversity in natural environments has been technically difficult up until recently. Environmental DNA-based high-throughput sequencing technology has now matured sufficiently to allow inexpensive recovery of massive amounts of sequence data, revealing the distribution and community composition of halophilic archaea in different hypersaline environments. While cultivation of haloarchaea is slow and tedious, and only recovers a fraction of the natural diversity, it is the conventional means of describing new species, and provides strains for detailed study. As of the end of May 2020, the class Halobacteria contains 71 genera and 275 species, 49.8% of which were first isolated from the marine salt environment and 50.2% from the inland salt environment, indicating that both thalassohaline and athalassohaline environments contain diverse halophilic archaea. However, there remain taxa that have not yet been isolated in pure culture, such as the nanohaloarchaea, which are widespread in the salt environment and may be one of the hot spots in the field of halophilic archaea research in the future. In this review, we focus on the cultivation strategies that have been used to isolate extremely halophilic archaea and point out some of the pitfalls and challenges.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-020-00087-3.}, }
@article {pmid37066253, year = {2023}, author = {Cerna-Vargas, JP and Gumerov, VM and Krell, T and Zhulin, IB}, title = {Amine recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.04.06.535858}, pmid = {37066253}, abstract = {Bacteria contain many different receptor families that sense different signals permitting an optimal adaptation to the environment. A major limitation in microbiology is the lack of information on the signal molecules that activate receptors. Due to a significant sequence divergence, the signal recognized by sensor domains is only poorly reflected in overall sequence identity. Biogenic amines are of central physiological relevance for microorganisms and serve for example as substrates for aerobic and anaerobic growth, neurotransmitters or osmoprotectants. Based on protein structural information and sequence analysis, we report here the identification of a sequence motif that is specific for amine-sensing dCache sensor domains (dCache_1AM). These domains were identified in more than 13,000 proteins from 8,000 bacterial and archaeal species. dCache_1AM containing receptors were identified in all major receptor families including sensor kinases, chemoreceptors, receptors involved in second messenger homeostasis and Ser/Thr phosphatases. The screening of compound libraries and microcalorimetric titrations of selected dCache_1AM domains confirmed their capacity to specifically bind amines. Mutants in the amine binding motif or domains that contain a single mismatch in the binding motif, had either no or a largely reduced affinity for amines, illustrating the specificity of this motif. We demonstrate that the dCache_1AM domain has evolved from the universal amino acid sensing domain, providing novel insight into receptor evolution. Our approach enables precise "wet"-lab experiments to define the function of regulatory systems and thus holds a strong promise to address an important bottleneck in microbiology: the identification of signals that stimulate numerous receptors.}, }
@article {pmid37066119, year = {2023}, author = {Lach, J and Strapagiel, D and Matera-Witkiewicz, A and Stączek, P}, title = {Draft genomes of halophilic Archaea strains isolated from brines of the Carpathian Foreland, Poland.}, journal = {Journal of genomics}, volume = {11}, number = {}, pages = {20-25}, pmid = {37066119}, issn = {1839-9940}, abstract = {Halophilic Archaea are a unique group of microorganisms living in saline environments. They constitute a complex group whose biodiversity has not been thoroughly studied. Here, we report three draft genomes of halophilic Archaea isolated from brines, representing the genera of Halorubrum, Halopenitus, and Haloarcula. Two of these strains, Boch-26 and POP-27, were identified as members of the genera Halorubrum and Halopenitus, respectively. However, they could not be assigned to any known species because of the excessive difference in genome sequences between these strains and any other described genomes. In contrast, the third strain, Boch-26, was identified as Haloarcula hispanica. Genome lengths of these isolates ranged from 2.7 Mbp to 3.0 Mbp, and GC content was in the 63.77%-68.77% range. Moreover, functional analysis revealed biosynthetic gene clusters (BGCs) related to terpenes production in all analysed genomes and one BGC for RRE (RiPP recognition element)-dependent RiPP (post-translationally modified peptides) biosynthesis. Moreover, the obtained results enhanced the knowledge about the salt mines microbiota biodiversity as a poorly explored environment so far.}, }
@article {pmid37060102, year = {2023}, author = {Liang, H and Song, ZM and Zhong, Z and Zhang, D and Yang, W and Zhou, L and Older, EA and Li, J and Wang, H and Zeng, Z and Li, YX}, title = {Genomic and metabolic analyses reveal antagonistic lanthipeptides in archaea.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {74}, pmid = {37060102}, issn = {2049-2618}, abstract = {BACKGROUND: Microbes produce diverse secondary metabolites (SMs) such as signaling molecules and antimicrobials that mediate microbe-microbe interaction. Archaea, the third domain of life, are a large and diverse group of microbes that not only exist in extreme environments but are abundantly distributed throughout nature. However, our understanding of archaeal SMs lags far behind our knowledge of those in bacteria and eukarya.<br><br>RESULTS: Guided by genomic and metabolic analysis of archaeal SMs, we discovered two new lanthipeptides with distinct ring topologies from a halophilic archaeon of class Haloarchaea. Of these two lanthipeptides, archalan &#x3b1; exhibited anti-archaeal activities against halophilic archaea, potentially mediating the archaeal antagonistic interactions in the halophilic niche. To our best knowledge, archalan &#x3b1; represents the first lantibiotic and the first anti-archaeal SM from the archaea domain.<br><br>CONCLUSIONS: Our study investigates the biosynthetic potential of lanthipeptides in archaea, linking lanthipeptides to antagonistic interaction via genomic and metabolic analyses and bioassay. The discovery of these archaeal lanthipeptides is expected to stimulate the experimental study of poorly characterized archaeal chemical biology and highlight the potential of archaea as a new source of bioactive SMs. Video Abstract.}, }
@article {pmid37014908, year = {2023}, author = {Cumsille, A and Durán, RE and Rodríguez-Delherbe, A and Saona-Urmeneta, V and Cámara, B and Seeger, M and Araya, M and Jara, N and Buil-Aranda, C}, title = {GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.}, journal = {PLoS computational biology}, volume = {19}, number = {4}, pages = {e1010998}, pmid = {37014908}, issn = {1553-7358}, abstract = {The increase in microbial sequenced genomes from pure cultures and metagenomic samples reflects the current attainability of whole-genome and shotgun sequencing methods. However, software for genome visualization still lacks automation, integration of different analyses, and customizable options for non-experienced users. In this study, we introduce GenoVi, a Python command-line tool able to create custom circular genome representations for the analysis and visualization of microbial genomes and sequence elements. It is designed to work with complete or draft genomes, featuring customizable options including 25 different built-in color palettes (including 5 color-blind safe palettes), text formatting options, and automatic scaling for complete genomes or sequence elements with more than one replicon/sequence. Using a Genbank format file as the input file or multiple files within a directory, GenoVi (i) visualizes genomic features from the GenBank annotation file, (ii) integrates a Cluster of Orthologs Group (COG) categories analysis using DeepNOG, (iii) automatically scales the visualization of each replicon of complete genomes or multiple sequence elements, (iv) and generates COG histograms, COG frequency heatmaps and output tables including general stats of each replicon or contig processed. GenoVi's potential was assessed by analyzing single and multiple genomes of Bacteria and Archaea. Paraburkholderia genomes were analyzed to obtain a fast classification of replicons in large multipartite genomes. GenoVi works as an easy-to-use command-line tool and provides customizable options to automatically generate genomic maps for scientific publications, educational resources, and outreach activities. GenoVi is freely available and can be downloaded from https://github.com/robotoD/GenoVi.}, }
@article {pmid37005419, year = {2023}, author = {Tang, SK and Zhi, XY and Zhang, Y and Makarova, KS and Liu, BB and Zheng, GS and Zhang, ZP and Zheng, HJ and Wolf, YI and Zhao, YR and Jiang, SH and Chen, XM and Li, EY and Zhang, T and Chen, PR and Feng, YZ and Xiang, MX and Lin, ZQ and Shi, JH and Chang, C and Zhang, X and Li, R and Lou, K and Wang, Y and Chang, L and Yin, M and Yang, LL and Gao, HY and Zhang, ZK and Tao, TS and Guan, TW and He, FC and Lu, YH and Cui, HL and Koonin, EV and Zhao, GP and Xu, P}, title = {Cellular differentiation into hyphae and spores in halophilic archaea.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1827}, pmid = {37005419}, issn = {2041-1723}, mesh = {Hyphae/genetics ; Proteomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Streptomyces/genetics ; *Halobacteriaceae/genetics ; Spores ; Cell Differentiation ; Sequence Analysis, DNA ; China ; }, abstract = {Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.}, }
@article {pmid37000350, year = {2023}, author = {Hu, Y and Ma, X and Li, XX and Tan, S and Cheng, M and Hou, J and Cui, HL}, title = {Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine.}, journal = {Extremophiles : life under extreme conditions}, volume = {27}, number = {1}, pages = {9}, pmid = {37000350}, issn = {1433-4909}, abstract = {Four extremely halophilic archaeal strains (ZJ2[T], BND6[T], DT87[T], and YPL30[T]) were isolated from marine environments and a salt mine in China. The 16S rRNA and rpoB' gene sequence similarities among strains ZJ2[T], BND6[T], DT87[T], YPL30[T] and the current species of Natrinema were 93.2-99.3% and 89.2-95.8%, respectively. Both phylogenetic and phylogenomic analyses revealed that strains ZJ2[T], BND6[T], DT87[T], and YPL30[T] cluster with the Natrinema members. The overall genome-related indexes (ANI, isDDH, and AAI) among these four strains and the current species of genus Natrinema were 70-88%, 22-43% and 75-89%, respectively, clearly below the threshold values for species boundary. Strains ZJ2[T], BND6[T], DT87[T], and YPL30[T] could be distinguished from the related species according to differential phenotypic characteristics. The major polar lipids of the four strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), and disulfated mannosyl glucosyl diether (S2-DGD). The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains ZJ2[T] (= CGMCC 1.18786[ T] = JCM 34918[ T]), BND6[T] (= CGMCC 1.18777[ T] = JCM 34909[ T]), DT87[T] (= CGMCC 1.18921[ T] = JCM 35420[ T]), and YPL30[T] (= CGMCC 1.15337[ T] = JCM 31113[ T]) represent four novel species of the genus Natrinema, for which the names, Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., and Natrinema zhouii sp. nov., are proposed.}, }
@article {pmid37000227, year = {2023}, author = {Iguchi, A and Takemura, Y and Danshita, T and Kurihara, T and Aoki, M and Hori, S and Shigematsu, T and Syutsubo, K}, title = {Isolation and physiological properties of methanogenic archaea that degrade tetramethylammonium hydroxide.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37000227}, issn = {1432-0614}, abstract = {Tetramethylammonium hydroxide (TMAH) is a known toxic chemical used in the photolithography process of semiconductor photoelectronic processes. Significant amounts of wastewater containing TMAH are discharged from electronic industries. It is therefore attractive to apply anaerobic treatment to industrial wastewater containing TMAH. In this study, a novel TMAH-degrading methanogenic archaeon was isolated from the granular sludge of a psychrophilic upflow anaerobic sludge blanket (UASB) reactor treating synthetic wastewater containing TMAH. Although the isolate (strain NY-STAYD) was phylogenetically related to Methanomethylovorans uponensis, it was the only isolated Methanomethylovorans strain capable of TMAH degradation. Strain NY-STAYD was capable of degrading methylamine compounds, similar to the previously isolated Methanomethylovorans spp. While the strain was able to grow at temperatures ranging from 15 to 37°C, the cell yield was higher at lower temperatures. The distribution of archaeal cells affiliated with the genus Methanomethylovorans in the original granular sludge was investigated by fluorescence in situ hybridization (FISH) using specific oligonucleotide probe targeting 16S rRNA. The results demonstrated that the TMAH-degrading cells associated with the genus Methanomethylovorans were not intermingled with other microorganisms but rather isolated on the granule's surface as a lone dominant archaeon. KEY POINTS: • A TMAH-degrading methanogenic Methanomethylovorans strain was isolated • This strain was the only known Methanomethylovorans isolate that can degrade TMAH • The highest cell yield of the isolate was obtained at psychrophilic conditions.}, }
@article {pmid36999249, year = {2023}, author = {D'Alò, F and Zucconi, L and Onofri, S and Canini, F and Cannone, N and Malfasi, F and Morais, DK and Starke, R}, title = {Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13152}, pmid = {36999249}, issn = {1758-2229}, abstract = {We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.}, }
@article {pmid36985233, year = {2023}, author = {Cisek, AA and Bąk, I and Cukrowska, B}, title = {Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985233}, issn = {2076-2607}, abstract = {Methanogenic archaea are an important component of the human and animal intestinal microbiota, and yet their presence is rarely reported in publications describing the subject. One of the methods of quantifying the prevalence of methanogens is quantitative real-time PCR (qPCR) of the methanogen-specific mcrA gene, and one of the possible reasons for detection failure is usually a methodology bias. Here, we refined the existing protocol by changing one of the primers and improving the conditions of the qPCR reaction. As a result, at the expense of a slightly lower yet acceptable PCR efficiency, the new assay was characterized by increased specificity and sensitivity and a wider linear detection range of 7 orders of magnitude. The lowest copy number of mcrA quantified at a frequency of 100% was 21 copies per reaction. The other validation parameters tested, such as reproducibility and linearity, also gave satisfactory results. Overall, we were able to minimize the negative impacts of primer dimerization and other cross-reactions on qPCR and increase the number of not only detectable but also quantifiable stool samples-or in this case, chicken droppings.}, }
@article {pmid36985129, year = {2023}, author = {Slobodkin, AI and Ratnikova, NM and Slobodkina, GB and Klyukina, AA and Chernyh, NA and Merkel, AY}, title = {Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030555}, pmid = {36985129}, issn = {2076-2607}, abstract = {The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood-Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.}, }
@article {pmid36949474, year = {2023}, author = {Regueira-Iglesias, A and Vázquez-González, L and Balsa-Castro, C and Vila-Blanco, N and Blanco-Pintos, T and Tamames, J and Carreira, MJ and Tomás, I}, title = {In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {58}, pmid = {36949474}, issn = {2049-2618}, mesh = {Humans ; *Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; DNA Primers/genetics ; Bacteria/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; }, abstract = {BACKGROUND: Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain.<br><br>RESULTS: A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) &#x2265;75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively.<br><br>CONCLUSIONS: Given the three amplicon length categories (100-300, 301-600, and >600 base&#xa0;pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.}, }
@article {pmid36949220, year = {2023}, author = {Lynes, MM and Krukenberg, V and Jay, ZJ and Kohtz, AJ and Gobrogge, CA and Spietz, RL and Hatzenpichler, R}, title = {Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {22}, pmid = {36949220}, issn = {2730-6151}, abstract = {Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.}, }
@article {pmid36927099, year = {2023}, author = {Chen, J and Li, Y and Zhong, C and Xu, Z and Lu, G and Jing, H and Liu, H}, title = {Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0117922}, doi = {10.1128/msystems.01179-22}, pmid = {36927099}, issn = {2379-5077}, abstract = {Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.}, }
@article {pmid36920214, year = {2023}, author = {Adlung, N and Scheller, S}, title = {Application of the Fluorescence-Activating and Absorption-Shifting Tag (FAST) for Flow Cytometry in Methanogenic Archaea.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0178622}, doi = {10.1128/aem.01786-22}, pmid = {36920214}, issn = {1098-5336}, abstract = {Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans have been biochemically characterized and can be genetically engineered by using a variety of existing molecular tools. The anaerobic lifestyle and autofluorescence of methanogens, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives), which require oxygen for chromophore maturation. Recently, the use of a novel oxygen-independent fluorescent activation and absorption-shifting tag (FAST) was demonstrated with M. maripaludis. Similarly, we now describe the use of the tandem activation and absorption-shifting tag protein 2 (tdFAST2), which fluoresces when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. Expression of tdFAST2 in M. acetivorans and M. maripaludis is noncytotoxic and tdFAST2:HBR-3,5DOM fluorescence is clearly distinguishable from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be distinguished, thereby allowing for the possibility of high-throughput investigations of the characteristic dynamics within single and mixed cultures. IMPORTANCE Methane-producing archaea play an essential role in the global carbon cycle and demonstrate great potential for various biotechnological applications, e.g., biofuel production, carbon dioxide capture, and electrochemical systems. Oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins for studying methanogens. By using tdFAST2:HBR-3,5DOM fluorescence, which functions under anaerobic conditions and is distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of the mixed culture dynamics of methanogens via flow cytometry were made possible. This will further help accelerate the sustainable exploitation of methanogens.}, }
@article {pmid36912626, year = {2023}, author = {Li, D and Ren, Z and Zhou, Y and Jiang, L and Zheng, M and Liu, G}, title = {Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0004723}, doi = {10.1128/aem.00047-23}, pmid = {36912626}, issn = {1098-5336}, abstract = {Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.}, }
@article {pmid36893867, year = {2023}, author = {Cheng, H and Yang, Y and He, Y and Zhan, X and Liu, Y and Hu, Z and Huang, H and Yao, X and Yang, W and Jin, J and Ren, B and Liu, J and Hu, Q and Jin, Y and Shen, L}, title = {Spatio-temporal variations of activity of nitrate-driven anaerobic oxidation of methane and community structure of Candidatus Methanoperedens-like archaea in sediment of Wuxijiang river.}, journal = {Chemosphere}, volume = {324}, number = {}, pages = {138295}, doi = {10.1016/j.chemosphere.2023.138295}, pmid = {36893867}, issn = {1879-1298}, abstract = {Nitrate-driven anaerobic oxidation of methane (AOM), catalyzing by Candidatus Methanoperedens-like archaea, is a new addition in the global CH4 cycle. This AOM process acts as a novel pathway for CH4 emission reduction in freshwater aquatic ecosystems; however, its quantitative importance and regulatory factors in riverine ecosystems are nearly unknown. Here, we examined the spatio-temporal changes of the communities of Methanoperedens-like archaea and nitrate-driven AOM activity in sediment of Wuxijiang River, a mountainous river in China. These archaeal community composition varied significantly among reaches (upper, middle, and lower reaches) and between seasons (winter and summer), but their mcrA gene diversity showed no significant spatial or temporal variations. The copy numbers of Methanoperedens-like archaeal mcrA genes were 1.32 × 10[5]-2.47 × 10[7] copies g[-1] (dry weight), and the activity of nitrate-driven AOM was 0.25-1.73 nmol CH4 g[-1] (dry weight) d[-1], which could potentially reduce 10.3% of CH4 emissions from rivers. Significant spatio-temporal variations of mcrA gene abundance and nitrate-driven AOM activity were found. Both the gene abundance and activity increased significantly from upper to lower reaches in both seasons, and were significantly higher in sediment collected in summer than in winter. In addition, the variations of Methanoperedens-like archaeal communities and nitrate-driven AOM activity were largely impacted by the sediment temperature, NH4[+] and organic carbon contents. Taken together, both time and space scales need to be considered for better evaluating the quantitative importance of nitrate-driven AOM in reducing CH4 emissions from riverine ecosystems.}, }
@article {pmid36888658, year = {2023}, author = {Wan, XS and Hou, L and Kao, SJ and Zhang, Y and Sheng, HX and Shen, H and Tong, S and Qin, W and Ward, BB}, title = {Pathways of N2O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {11}, pages = {e2220697120}, doi = {10.1073/pnas.2220697120}, pmid = {36888658}, issn = {1091-6490}, abstract = {The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N2O), to the atmosphere. Most of that N2O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N2O production and their kinetics, however, are not completely understood. Here, we use [15]N and [18]O isotopes to determine the kinetics of N2O production and trace the source of nitrogen (N) and oxygen (O) atoms in N2O produced by a model marine AOA species, Nitrosopumilus maritimus. We find that during ammonia oxidation, the apparent half saturation constants of nitrite and N2O production are comparable, suggesting that both processes are enzymatically controlled and tightly coupled at low ammonia concentrations. The constituent atoms in N2O are derived from ammonia, nitrite, O2, and H2O via multiple pathways. Ammonia is the primary source of N atoms in N2O, but its contribution varies with ammonia to nitrite ratio. The ratio of [45]N2O to [46]N2O (i.e., single or double labeled N) varies with substrate ratio, leading to widely varying isotopic signatures in the N2O pool. O2 is the primary source for O atoms. In addition to the previously demonstrated hybrid formation pathway, we found a substantial contribution by hydroxylamine oxidation, while nitrite reduction is an insignificant source of N2O. Our study highlights the power of dual [15]N-[18]O isotope labeling to disentangle N2O production pathways in microbes, with implications for interpretation of pathways and regulation of marine N2O sources.}, }
@article {pmid36880756, year = {2023}, author = {Taubner, RS and Baumann, LMF and Steiner, M and Pfeifer, K and Reischl, B and Korynt, K and Bauersachs, T and Mähnert, B and Clifford, EL and Peckmann, J and Schuster, B and Birgel, D and Rittmann, SKR}, title = {Lipidomics and Comparative Metabolite Excretion Analysis of Methanogenic Archaea Reveal Organism-Specific Adaptations to Varying Temperatures and Substrate Concentrations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0115922}, doi = {10.1128/msystems.01159-22}, pmid = {36880756}, issn = {2379-5077}, abstract = {Methanogenic archaea possess diverse metabolic characteristics and are an ecologically and biotechnologically important group of anaerobic microorganisms. Although the scientific and biotechnological value of methanogens is evident with regard to their methane-producing physiology, little is known about their amino acid excretion, and virtually nothing is known about the lipidome at different substrate concentrations and temperatures on a quantitative comparative basis. Here, we present the lipidome and a comprehensive quantitative analysis of proteinogenic amino acid excretion as well as methane, water, and biomass production of the three autotrophic, hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanothermococcus okinawensis, and Methanocaldococcus villosus under varying temperatures and nutrient supplies. The patterns and rates of production of excreted amino acids and the lipidome are unique for each tested methanogen and can be modulated by varying the incubation temperature and substrate concentration, respectively. Furthermore, the temperature had a significant influence on the lipidomes of the different archaea. The water production rate was much higher, as anticipated from the rate of methane production for all studied methanogens. Our results demonstrate the need for quantitative comparative physiological studies connecting intracellular and extracellular constraints of organisms to holistically investigate microbial responses to environmental conditions. IMPORTANCE Biological methane production by methanogenic archaea has been well studied for biotechnological purposes. This study reveals that methanogenic archaea actively modulate their lipid inventory and proteinogenic amino acid excretion pattern in response to environmental changes and the possible utilization of methanogenic archaea as microbial cell factories for the targeted production of lipids and amino acids.}, }
@article {pmid36874274, year = {2023}, author = {Mei, R and Kaneko, M and Imachi, H and Nobu, MK}, title = {The origin and evolution of methanogenesis and Archaea are intertwined.}, journal = {PNAS nexus}, volume = {2}, number = {2}, pages = {pgad023}, pmid = {36874274}, issn = {2752-6542}, abstract = {Methanogenesis has been widely accepted as an ancient metabolism, but the precise evolutionary trajectory remains hotly debated. Disparate theories exist regarding its emergence time, ancestral form, and relationship with homologous metabolisms. Here, we report the phylogenies of anabolism-involved proteins responsible for cofactor biosynthesis, providing new evidence for the antiquity of methanogenesis. Revisiting the phylogenies of key catabolism-involved proteins further suggests that the last Archaea common ancestor (LACA) was capable of versatile H2-, CO2-, and methanol-utilizing methanogenesis. Based on phylogenetic analyses of the methyl/alkyl-S-CoM reductase family, we propose that, in contrast to current paradigms, substrate-specific functions emerged through parallel evolution traced back to a nonspecific ancestor, which likely originated from protein-free reactions as predicted from autocatalytic experiments using cofactor F430. After LACA, inheritance/loss/innovation centered around methanogenic lithoautotrophy coincided with ancient lifestyle divergence, which is clearly reflected by genomically predicted physiologies of extant archaea. Thus, methanogenesis is not only a hallmark metabolism of Archaea, but the key to resolve the enigmatic lifestyle that ancestral archaea took and the transition that led to physiologies prominent today.}, }
@article {pmid36842598, year = {2023}, author = {Zheng, P and Zhang, Q and Zou, J and Han, Q and Han, J and Wang, Q and Yao, L and Yu, G and Liang, Y}, title = {A new strategy for the enrichment of ammonia-oxidizing archaea in wastewater treatment systems: The positive role of quorum-sensing signaling molecules.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {162385}, doi = {10.1016/j.scitotenv.2023.162385}, pmid = {36842598}, issn = {1879-1026}, abstract = {Ammonia-oxidizing archaea (AOA) play an important role in natural nitrogen cycle, but are difficult to be enriched in wastewater treatment systems. In this experiment, under ambient temperature and high dissolved oxygen, different types of acyl-homoserine lactones (C6-HSL, C8-HSL, C10-HSL, C14-HSL and 3-oxo-C14-HSL) were added to five wastewater nitrification systems to achieve AOA enrichment. Results showed that AOA couldn't be detected in the blank group without the addition of signaling molecules, while the AOA could be detected in all the reactors with the addition. The enrichment effect of AOA was not obvious with added 100 or 200 nmol/L signaling molecules, while the enrichment effect was both obvious with added C8-HSL of 400 nmol/L and C10-HSL of 800 nmol/L. And relative abundance of AOA increased from undetected in the control group to 1.10 % and 0.96 %, respectively. The exogenous signaling molecules may provide new view for AOA enrichment in wastewater treatment systems.}, }
@article {pmid36835573, year = {2023}, author = {Ngcobo, PE and Nkosi, BVZ and Chen, W and Nelson, DR and Syed, K}, title = {Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835573}, issn = {1422-0067}, abstract = {Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study's results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.}, }
@article {pmid36817958, year = {2023}, author = {Kisly, I and Tamm, T}, title = {Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {1249-1261}, pmid = {36817958}, issn = {2001-0370}, abstract = {In three domains of life, proteins are synthesized by large ribonucleoprotein particles called ribosomes. All ribosomes are composed of ribosomal RNAs (rRNA) and numerous ribosomal proteins (r-protein). The three-dimensional shape of ribosomes is mainly defined by a tertiary structure of rRNAs. In addition, rRNAs have a major role in decoding the information carried by messenger RNAs and catalyzing the peptide bond formation. R-proteins are essential for shaping the network of interactions that contribute to a various aspects of the protein synthesis machinery, including assembly of ribosomes and interaction of ribosomal subunits. Structural studies have revealed that many key components of ribosomes are conserved in all life domains. Besides the core structure, ribosomes contain domain-specific structural features that include additional r-proteins and extensions of rRNA and r-proteins. This review focuses specifically on those r-proteins that are found only in archaeal and eukaryotic ribosomes. The role of these archaea/eukaryote specific r-proteins in stabilizing the ribosome structure is discussed. Several examples illustrate their functions in the formation of the internal network of ribosomal subunits and interactions between the ribosomal subunits. In addition, the significance of these r-proteins in ribosome biogenesis and protein synthesis is highlighted.}, }
@article {pmid36815558, year = {2023}, author = {Dodsworth, JA and Prakash, O}, title = {International Committee on Systematics of Prokaryotes: subcommittee on the taxonomy of methanogenic archaea. Minutes of the closed, online meetings held 24 September 2020 and 8 October 2020.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {2}, pages = {}, doi = {10.1099/ijsem.0.005775}, pmid = {36815558}, issn = {1466-5034}, }
@article {pmid36814573, year = {2023}, author = {Cheng, X and Xiang, X and Yun, Y and Wang, W and Wang, H and Bodelier, PLE}, title = {Archaea and their interactions with bacteria in a karst ecosystem.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1068595}, pmid = {36814573}, issn = {1664-302X}, abstract = {Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 [+] availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca[2+], and NO2 [-]. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.}, }
@article {pmid36808147, year = {2023}, author = {Gios, E and Mosley, OE and Weaver, L and Close, M and Daughney, C and Handley, KM}, title = {Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {13}, pmid = {36808147}, issn = {2730-6151}, abstract = {Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.}, }
@article {pmid36804975, year = {2023}, author = {Zhang, Q and Chen, M and Leng, Y and Wang, X and Fu, Y and Wang, D and Zhao, X and Gao, W and Li, N and Chen, X and Fan, C and Li, Q}, title = {Organic substitution stimulates ammonia oxidation-driven N2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {162183}, doi = {10.1016/j.scitotenv.2023.162183}, pmid = {36804975}, issn = {1879-1026}, abstract = {Partial organic substitution (POS) is pivotal in enhancing soil productivity and changing nitrous oxide (N2O) emissions by profoundly altering soil nitrogen (N) cycling, where ammonia oxidation is a fundamental core process. However, the regulatory mechanisms of N2O production by ammonia oxidizers at the microbial community level under POS regimes remain unclear. This study explored soil ammonia oxidation and related N2O production, further building an understanding of the correlations between ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) activity and community structure in tropical arable soils under four-year field management regimes (CK, without fertilizer N; N, with only inorganic N; M1N1, with 1/2 organic N + 1/2 inorganic N; M1N2, with 1/3 organic N + 2/3 inorganic N). AOA contributed more to potential ammonia oxidation (PAO) than AOB across all treatments. In comparison with CK, N treatment had no obvious effects on PAO and lowered related N2O emissions by decreasing soil pH and downregulating the abundance of AOA- and AOB-amoA. POS regimes significantly enhanced PAO and N2O emissions relative to N treatment by promoting the abundances and contributions of AOA and AOB. The stimulated AOA-dominated N2O production under M1N1 was correlated with promoted development of Nitrososphaera. By contrast, the increased AOB-dominated N2O production under M1N2 was linked to the enhanced development of Nitrosospira multiformis. Our study suggests organic substitutions with different proportions of inorganic and organic N distinctively regulate the development of specific species of ammonia oxidizers to increase associated N2O emissions. Accordingly, appropriate options should be adopted to reduce environmental risks under POS regimes in tropical croplands.}, }
@article {pmid36796795, year = {2023}, author = {Diao, M and Balkema, C and Muñoz, MS and Huisman, J and Muyzer, G}, title = {Succession of bacteria and archaea involved in the nitrogen cycle of a seasonally stratified lake.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnad013}, pmid = {36796795}, issn = {1574-6968}, abstract = {Human-driven changes affect nutrient inputs, oxygen solubility and the hydrodynamics of lakes, which affect biogeochemical cycles mediated by microbial communities. However, information on the succession of microbes involved in nitrogen cycling in seasonally stratified lakes is still incomplete. Here, we investigated the succession of nitrogen-transforming microorganisms in Lake Vechten over 19 months, combining 16S rRNA gene amplicon sequencing and quantification of functional genes. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) and anammox bacteria were abundant in the sediment during winter, accompanied by nitrate in the water column. Nitrogen-fixing bacteria and denitrifying bacteria emerged in the water column in spring when nitrate was gradually depleted. Denitrifying bacteria containing nirS genes were exclusively present in the anoxic hypolimnion. During summer stratification, abundances of AOA, AOB and anammox bacteria decreased sharply in the sediment, and ammonium accumulated in hypolimnion. After lake mixing during fall turnover, abundances of AOA, AOB and anammox bacteria increased and ammonium was oxidized to nitrate. Hence, nitrogen-transforming microorganisms in Lake Vechten displayed a pronounced seasonal succession, which was strongly determined by the seasonal stratification pattern. These results imply that changes in stratification and vertical mixing induced by global warming are likely to alter the nitrogen cycle of seasonally stratified lakes.}, }
@article {pmid36794928, year = {2023}, author = {Akpudo, YM and Bezuidt, OK and Makhalanyane, TP}, title = {Metagenome-Assembled Genomes of Four Southern Ocean Archaea Harbor Multiple Genes Linked to Polyethylene Terephthalate and Polyhydroxybutyrate Plastic Degradation.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0109822}, doi = {10.1128/mra.01098-22}, pmid = {36794928}, issn = {2576-098X}, abstract = {Here, we present four archaeal metagenome-assembled genomes (MAGs) (three Thaumarchaeota MAGs and one Thermoplasmatota MAG) from a polar upwelling zone in the Southern Ocean. These archaea harbor putative genes encoding enzymes such as polyethylene terephthalate (PET) hydrolases (PETases) and polyhydroxybutyrate (PHB) depolymerases, which are associated with microbial degradation of PET and PHB plastics.}, }
@article {pmid36792581, year = {2023}, author = {Filée, J and Becker, HF and Mellottee, L and Eddine, RZ and Li, Z and Yin, W and Lambry, JC and Liebl, U and Myllykallio, H}, title = {Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {838}, pmid = {36792581}, issn = {2041-1723}, abstract = {Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.}, }
@article {pmid36782524, year = {2023}, author = {Beltran, L and Cvirkaite-Krupovic, V and Roberts, J and Wang, F and Kreutzberger, MA and Costa, T and Levental, I and Conticello, V and Egelman, EH and Krupovic, M}, title = {Domesticated conjugation machinery promotes DNA exchange in hyperthermophilic archaea.}, journal = {Biophysical journal}, volume = {122}, number = {3S1}, pages = {11a}, doi = {10.1016/j.bpj.2022.11.291}, pmid = {36782524}, issn = {1542-0086}, }
@article {pmid36759127, year = {2023}, author = {Wolff, P and Lechner, A and Droogmans, L and Grosjean, H and Westhof, E}, title = {Identification of Up47 in three thermophilic archaea, one mesophilic archaeon and one hyperthermophilic bacterium.}, journal = {RNA (New York, N.Y.)}, volume = {}, number = {}, pages = {}, doi = {10.1261/rna.079546.122}, pmid = {36759127}, issn = {1469-9001}, abstract = {Analysis of tRNA modifications profile in several Archaea allowed to observe a novel modified uridine in the V-loop of several tRNAs from two species: Pyrococcus furiosus and Sulfolobus acidocaldarius (Wolff et al. 2020). Recently, Ohira et al. (Ohira et al. 2022) characterized 2'-phosphouridine (Up) at position 47 in tRNAs of thermophilic Sulfurisphaera tokodaii, as well as in several other archaea and thermophilic bacteria. From the presence of the gene arkI corresponding to the RNA kinase responsible for Up47 formation, they also concluded that Up47 should be present in tRNAs of other thermophilic Archaea. Re-analysis of our earlier data confirms that the unidentified residue in tRNAs of both P. furiosus and S. acidocaldarius is indeed 2'phosphouridine followed by m5C48. Moreover, we find this modification in several tRNAs of other Archaea and of the hyperthermophilic bacterium Aquifex aeolicus.}, }
@article {pmid36752722, year = {2023}, author = {Cooper, CR and Lewis, AM and Notey, JS and Mukherjee, A and Willard, DJ and Blum, PH and Kelly, RM}, title = {Interplay between Transcriptional Regulators and VapBC Toxin-Antitoxin Loci During Thermal Stress Response in Extremely Thermoacidophilic Archaea.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16350}, pmid = {36752722}, issn = {1462-2920}, abstract = {Thermoacidophilic archaea lack sigma factors and the large inventory of heat shock proteins (HSP) widespread in bacterial genomes, suggesting other strategies for handling thermal stress are involved. Heat shock transcriptomes for the thermoacidophilic archaeon Saccharolobus (f. Sulfolobus) solfataricus 98/2 revealed genes that were highly responsive to thermal stress, including transcriptional regulators YtrASs (Ssol_2420) and FadRSs (Ssol_0314), as well as Type II Toxin-Antitoxin (TA) loci VapBC6 (Ssol_2337, Ssol_2338) and VapBC22 (Ssol_0819, Ssol_0818). The role, if any, of Type II TA loci during stress response in microorganisms, such as Escherichia coli, is controversial. But, when genes encoding YtrASs , FadRSs , VapC22, VapB6, and VapC6 were systematically mutated in Sa. solfataricus 98/2, significant up-regulation of the other genes within this set was observed, implicating an interconnected regulatory network during thermal stress response. VapBC6 and VapBC22 have close homologs in other Sulfolobales, as well as in other archaea (e.g., Pyrococcus furiosus and Archaeoglobus fulgidus), and their corresponding genes were also heat shock responsive. The interplay between VapBC TA loci and heat shock regulators in Sa. solfataricus 98/2 not only indicates a cellular mechanism for heat shock response that differs from bacteria but one that could have common features within the thermophilic archaea. This article is protected by copyright. All rights reserved.}, }
@article {pmid36752534, year = {2023}, author = {Borg Dahl, M and Kreyling, J and Petters, S and Wang, H and Mortensen, MS and Maccario, L and Sørensen, SJ and Urich, T and Weigel, R}, title = {Warmer winters result in reshaping of the European beech forest soil microbiome (bacteria, archaea and fungi) - with potential implications for ecosystem functioning.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16347}, pmid = {36752534}, issn = {1462-2920}, abstract = {In temperate regions climate warming alters temperature and precipitation regimes. During winter, a decline in insulating snow cover changes the soil environment, where especially frost exposure can have severe implications for soil microorganisms and subsequently for soil nutrient dynamics. Here we investigated winter climate change responses in European beech forests soil microbiome. Nine study sites with each three treatments (snow exclusion, insolation, and ambient) were investigated. Long-term adaptation to average climate was explored by comparing across sites. Triplicated treatment plots were used to evaluate short-term (one single winter) responses. Community profiles of bacteria, archaea and fungi were created using amplicon sequencing. Correlation between the microbiome, vegetation and soil physicochemical properties were found. We identify core members of the forest-microbiome, and link them to key processes e.g. mycorrhizal symbiont and specialized beech wood degraders (fungi) and nitrogen cycling (bacteria, archaea). For bacteria, the shift of the microbiome composition due to short-term soil temperature manipulations in winter was similar to the community differences observed between long-term relatively cold to warm conditions. The results suggest a strong link between the changes in the microbiomes and changes in environmental processes, e.g. nitrogen dynamics, driven by variation in winter climate. This article is protected by copyright. All rights reserved.}, }
@article {pmid36729913, year = {2023}, author = {Denise, R and Babor, J and Gerlt, JA and de Crécy-Lagard, V}, title = {Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.}, journal = {Microbial genomics}, volume = {9}, number = {2}, pages = {}, doi = {10.1099/mgen.0.000926}, pmid = {36729913}, issn = {2057-5858}, }
@article {pmid36724220, year = {2023}, author = {Ngugi, DK and Salcher, MM and Andrei, AS and Ghai, R and Klotz, F and Chiriac, MC and Ionescu, D and Büsing, P and Grossart, HP and Xing, P and Priscu, JC and Alymkulov, S and Pester, M}, title = {Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.}, journal = {Science advances}, volume = {9}, number = {5}, pages = {eadc9392}, doi = {10.1126/sciadv.adc9392}, pmid = {36724220}, issn = {2375-2548}, abstract = {Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.}, }
@article {pmid36721520, year = {2022}, author = {Beddal, A and Boutaiba, S and Laassami, A and Hamaidi, F and Enache, M}, title = {Characterization by polyphasic approach of some indigenous halophilic archaea of Djelfa's rock salt "Hadjr el Meelh", Algeria.}, journal = {Iranian journal of microbiology}, volume = {14}, number = {4}, pages = {535-544}, pmid = {36721520}, issn = {2008-3289}, abstract = {BACKGROUND AND OBJECTIVES: Hadjr El Melh of Djelfa is an example of hypersaline ecosystems, which can harbor a wide variety of microorganisms under hostile physicochemical conditions. Given the importance of the study of halophilic microorganisms present there in terms of fundamental and applied microbiology, the purpose of this study was to characterize some halophilic archaea isolated from the brines of this environment.<br><br>MATERIALS AND METHODS: Eight water samples were chosen randomly and collected for physicochemical and microbiological analyses. Isolation of halophilic archaea was carried out by membrane filter technique. Ten strains were identified by polyphasic approach and tested for enzymes production.<br><br>RESULTS: Water samples of Djelfa's rock salt were slightly acidic to neutral in pH (6.55-7.36) with salinity ranging from 258.68 g/l to 493.91 g/l. Phenotypic, biochemical, taxonomic and phylogenetic characteristics indicated that all strains were classified within the family of Halobacteiaceae. Based on the comparison of DNA sequences encoded 16S rRNA, it was determined that seven strains were affiliated to the genus Haloarcula, two strains were related to the genus Halobacterium and one strain within the genus Haloferax. Production of different enzymes such as protease, amylase, esterase, lipase, lecithinase, gelatinase and cellulase on solid medium indicated that one strain (S2-2) produced amylase, esterase, lecithinase and protease. However, no strains showed cellulolytic or lipolytic activity. Gelatinase was found in all tested strains.<br><br>CONCLUSION: This report constitutes the first preliminary study of culturable halophilic archaea recovered from the brines of Djelfa's rock salt with a promising enzymatic potential in various fields of biotechnology.}, }
@article {pmid36721060, year = {2023}, author = {Hodgskiss, LH and Melcher, M and Kerou, M and Chen, W and Ponce-Toledo, RI and Savvides, SN and Wienkoop, S and Hartl, M and Schleper, C}, title = {Unexpected complexity of the ammonia monooxygenase in archaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36721060}, issn = {1751-7370}, abstract = {Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.}, }
@article {pmid36720870, year = {2023}, author = {Daugeron, MC and Missoury, S and Da Cunha, V and Lazar, N and Collinet, B and van Tilbeurgh, H and Basta, T}, title = {A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {526}, doi = {10.1038/s41467-023-36210-y}, pmid = {36720870}, issn = {2041-1723}, abstract = {In Archaea and Eukaryotes, the synthesis of a universal tRNA modification, N[6]-threonyl-carbamoyl adenosine (t[6]A), is catalyzed by the KEOPS complex composed of Kae1, Bud32, Cgi121, and Pcc1. A fifth subunit, Gon7, is found only in Fungi and Metazoa. Here, we identify and characterize a fifth KEOPS subunit in Archaea. This protein, dubbed Pcc2, is a paralog of Pcc1 and is widely conserved in Archaea. Pcc1 and Pcc2 form a heterodimer in solution, and show modest sequence conservation but very high structural similarity. The five-subunit archaeal KEOPS does not form dimers but retains robust tRNA binding and t[6]A synthetic activity. Pcc2 can substitute for Pcc1 but the resulting KEOPS complex is inactive, suggesting a distinct function for the two paralogs. Comparative sequence and structure analyses point to a possible evolutionary link between archaeal Pcc2 and eukaryotic Gon7. Our work indicates that Pcc2 regulates the oligomeric state of the KEOPS complex, a feature that seems to be conserved from Archaea to Eukaryotes.}, }
@article {pmid36715325, year = {2023}, author = {Yang, Y and Liu, J and Fu, X and Zhou, F and Zhang, S and Zhang, X and Huang, Q and Krupovic, M and She, Q and Ni, J and Shen, Y}, title = {A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad006}, pmid = {36715325}, issn = {1362-4962}, abstract = {Cell cycle regulation is of paramount importance for all forms of life. Here, we report that a conserved and essential cell cycle-specific transcription factor (designated as aCcr1) and its viral homologs control cell division in Sulfolobales. We show that the transcription level of accr1 reaches peak during active cell division (D-phase) subsequent to the expression of CdvA, an archaea-specific cell division protein. Cells over-expressing the 58-aa-long RHH (ribbon-helix-helix) family cellular transcription factor as well as the homologs encoded by large spindle-shaped viruses Acidianus two-tailed virus (ATV) and Sulfolobus monocaudavirus 3 (SMV3) display significant growth retardation and cell division failure, manifesting as enlarged cells with multiple chromosomes. aCcr1 over-expression results in downregulation of 17 genes (>4-fold), including cdvA. A conserved motif, aCcr1-box, located between the TATA-binding box and the translation initiation site of 13 out of the 17 highly repressed genes, is critical for aCcr1 binding. The aCcr1-box is present in the promoters and 5' UTRs of cdvA genes across Sulfolobales, suggesting that aCcr1-mediated cdvA repression is an evolutionarily conserved mechanism by which archaeal cells dictate cytokinesis progression, whereas their viruses take advantage of this mechanism to manipulate the host cell cycle.}, }
@article {pmid36709544, year = {2023}, author = {Umegawa, Y and Kawatake, S and Murata, M and Matsuoka, S}, title = {Combined effect of the head groups and alkyl chains of archaea lipids when interacting with bacteriorhodopsin.}, journal = {Biophysical chemistry}, volume = {294}, number = {}, pages = {106959}, doi = {10.1016/j.bpc.2023.106959}, pmid = {36709544}, issn = {1873-4200}, abstract = {Bacteriorhodopsin (bR), a transmembrane protein with seven α-helices, is highly expressed in the purple membrane (PM) of archaea such as Halobacterium salinarum. It is well known that bR forms two-dimensional crystals with acidic lipids such as phosphatidylglycerol phosphate methyl ester (PGP-Me)-a major component of PM lipids bearing unique chemical structures-methyl-branched alkyl chains, ether linkages, and divalent anionic head groups with two phosphodiester groups. Therefore, we aimed to determine which functional groups of PGP-Me are essential for the boundary lipids of bR and how these functionalities interact with bR. To this end, we compared various well-known phospholipids (PLs) that carry one of the structural features of PGP-Me, and evaluated the affinity of PLs to bR using the centerband-only analysis of rotor-unsynchronized spin echo (COARSE) method in solid-state NMR measurements and thermal shift assays. The results clearly showed that the branched methyl groups of alkyl chains and double negative charges in the head groups are important for PL interactions with bR. We then examined the effect of phospholipids on the monomer-trimer exchange of bR using circular dichroism (CD) spectra. The results indicated that the divalent negative charge in a head group stabilizes the trimer structure, while the branched methyl chains significantly enhance the PLs' affinity for bR, thus dispersing bR trimers in the PM even at high concentrations. Finally, we investigated the effects of PL on the proton-pumping activity of bR based on the decay rate constant of the M intermediate of a bR photocycle. The findings showed that bR activities decreased to 20% in 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA), and in 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) bilayers as compared to that in PM. Meanwhile, 1,2-Diphytanoyl-sn-glycero-3-phosphate (DPhPA) bilayers bearing both negative charges and branched methyl groups preserved over 80% of the activity. These results strongly suggest that the head groups and alkyl chains of phospholipids are essential for boundary lipids and greatly influence the biological function of bR.}, }
@article {pmid36697601, year = {2021}, author = {Sumi, T and Harada, K}, title = {Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea.}, journal = {Communications chemistry}, volume = {4}, number = {1}, pages = {149}, pmid = {36697601}, issn = {2399-3669}, abstract = {The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood-Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.}, }
@article {pmid36694212, year = {2023}, author = {Jaffe, AL and Bardot, C and Le Jeune, AH and Liu, J and Colombet, J and Perrière, F and Billard, H and Castelle, CJ and Lehours, AC and Banfield, JF}, title = {Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {14}, pmid = {36694212}, issn = {2049-2618}, abstract = {BACKGROUND: Permanently stratified lakes contain diverse microbial communities that vary with depth and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined.<br><br>RESULTS: Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that the oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. On the whole, though, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments.<br><br>CONCLUSIONS: Overall, our analyses suggest that environmental gradients in Lac Pavin select for capacities of CPR bacteria and phages to a lesser extent than for other bacteria and archaea. This may be due to the fact that selection in the former groups is indirect and depends primarily on host characteristics. Video Abstract.}, }
@article {pmid36690779, year = {2023}, author = {Yu, Y and Wang, P and Cao, HY and Teng, ZJ and Zhu, Y and Wang, M and McMinn, A and Chen, Y and Xiang, H and Zhang, YZ and Chen, XL and Zhang, YQ}, title = {Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36690779}, issn = {1751-7370}, abstract = {D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.}, }
@article {pmid36687602, year = {2022}, author = {Corona Ramírez, A and Cailleau, G and Fatton, M and Dorador, C and Junier, P}, title = {Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {826117}, pmid = {36687602}, issn = {1664-302X}, abstract = {The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.}, }
@article {pmid36683362, year = {2022}, author = {Tandon, K and Ricci, F and Costa, J and Medina, M and Kühl, M and Blackall, LL and Verbruggen, H}, title = {Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, doi = {10.1093/gigascience/giac127}, pmid = {36683362}, issn = {2047-217X}, abstract = {At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.}, }
@article {pmid36674956, year = {2023}, author = {Baehren, C and Pembaur, A and Weil, PP and Wewers, N and Schult, F and Wirth, S and Postberg, J and Aydin, M}, title = {The Overlooked Microbiome-Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {2}, pages = {}, doi = {10.3390/ijms24021426}, pmid = {36674956}, issn = {1422-0067}, abstract = {In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the relevance of archaea in human health and diseases. Contemporary broad availability and spread of next generation sequencing techniques now enable a stronger focus on such microorganisms, whose cultivation is difficult. However, due to the enormous evolutionary distances between bacteria, archaea and eukaryotes, the implementation of sequencing strategies for smaller laboratory scales needs to be refined to achieve as a holistic view on the microbiome as possible. Here, we present a technical approach that enables simultaneous analyses of archaeal, bacterial and eukaryotic microbial communities to study their roles in development and courses of respiratory disorders. We thus applied combinatorial 16S-/18S-rDNA sequencing strategies for sequencing-library preparation. Considering the lower total microbiota density of airway surfaces, when compared with gut microbiota, we optimized the DNA purification workflow from nasopharyngeal swab specimens. As a result, we provide a protocol that allows the efficient combination of bacterial, archaeal, and eukaryotic libraries for nanopore-sequencing using Oxford Nanopore Technologies MinION devices and subsequent phylogenetic analyses. In a pilot study, this workflow allowed the identification of some environmental archaea, which were not correlated with airway microbial communities before. Moreover, we assessed the protocol's broader applicability using a set of human stool samples. We conclude that the proposed protocol provides a versatile and adaptable tool for combinatorial studies on bacterial, archaeal, and eukaryotic microbiomes on a small laboratory scale.}, }
@article {pmid36671499, year = {2023}, author = {De Lise, F and Iacono, R and Moracci, M and Strazzulli, A and Cobucci-Ponzano, B}, title = {Archaea as a Model System for Molecular Biology and Biotechnology.}, journal = {Biomolecules}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/biom13010114}, pmid = {36671499}, issn = {2218-273X}, abstract = {Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.}, }
@article {pmid36660825, year = {2023}, author = {Nissley, AJ and Penev, PI and Watson, ZL and Banfield, JF and Cate, JHD}, title = {Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkac1273}, pmid = {36660825}, issn = {1362-4962}, support = {T32 066698/GF/NIH HHS/United States ; }, abstract = {The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3'-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.}, }
@article {pmid36659324, year = {2017}, author = {Feng, Y and Dolfing, J and Guo, Z and Zhang, J and Zhang, G and Li, S and Lin, X}, title = {Chronosequencing methanogenic archaea in ancient Longji rice Terraces in China.}, journal = {Science bulletin}, volume = {62}, number = {12}, pages = {879-887}, doi = {10.1016/j.scib.2017.05.024}, pmid = {36659324}, issn = {2095-9281}, abstract = {Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty (CE 1361-1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial- and decadal-scale influences of known historical events, including social turbulences (The Taiping Rebellion, CE 1850-1865), palaeoclimate changes (the Little Ice Age) and recorded natural disasters (earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.}, }
@article {pmid36658397, year = {2023}, author = {Laso-Pérez, R and Wu, F and Crémière, A and Speth, DR and Magyar, JS and Zhao, K and Krupovic, M and Orphan, VJ}, title = {Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {36658397}, issn = {2058-5276}, abstract = {'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.}, }
@article {pmid36639538, year = {2023}, author = {Zhang, CJ and Liu, YR and Cha, G and Liu, Y and Zhou, XQ and Lu, Z and Pan, J and Cai, M and Li, M}, title = {Potential for mercury methylation by Asgard archaea in mangrove sediments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36639538}, issn = {1751-7370}, abstract = {Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The conversion of MeHg from mercury (Hg) is mediated by a variety of anaerobic microorganisms carrying hgcAB genes. Mangrove sediments are potential hotspots of microbial Hg methylation; however, the microorganisms responsible for Hg methylation are poorly understood. Here, we conducted metagenomic and metatranscriptomic analyses to investigate the diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems. The highest hgcA abundance and expression occurred in surface sediments in Shenzhen, where the highest MeHg concentration was also observed. We reconstructed 157 metagenome-assembled genomes (MAGs) carrying hgcA and identified several putative novel Hg-methylators, including one Asgard archaea (Lokiarchaeota). Further analysis of MAGs revealed that Deltaproteobacteria, Euryarchaeota, Bacteroidetes, Chloroflexi, and Lokiarchaeota were the most abundant and active Hg-methylating groups, implying their crucial role in MeHg production. By screening publicly available MAGs, 104 additional Asgard MAGs carrying hgcA genes were identified from a wide range of coast, marine, permafrost, and lake sediments. Protein homology modelling predicts that Lokiarchaeota HgcAB proteins contained the highly conserved amino acid sequences and folding structures required for Hg methylation. Phylogenetic tree revealed that hgcA genes from Asgard clustered with fused hgcAB genes, indicating a transitional stage of Asgard hgcA genes. Our findings thus suggest that Asgard archaea are potential novel Hg-methylating microorganisms and play an important role in hgcA evolution.}, }
@article {pmid36622233, year = {2023}, author = {Jia, Y and Lahm, M and Chen, Q and Powers, L and Gonsior, M and Chen, F}, title = {The Predominance of Ammonia-Oxidizing Archaea in an Oceanic Microbial Community Amended with Cyanobacterial Lysate.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0240522}, doi = {10.1128/spectrum.02405-22}, pmid = {36622233}, issn = {2165-0497}, abstract = {When the oligotrophic microbial community was amended with Synechococcus-derived dissolved organic matter (SDOM) and incubated under the dark condition, archaea relative abundance was initially very low but made up more than 60% of the prokaryotic community on day 60, and remained dominant for at least 9 months. The archaeal sequences were dominated by Candidatus Nitrosopumilus, the Group I.1a Thaumarchaeota. The increase of Thaumarchaeota in the dark incubation corresponded to the period of delayed ammonium oxidation upon an initially steady increase in ammonia, supporting the remarkable competency of Thaumarchaeota in energy utilization and fixation of inorganic carbon in the ocean. IMPORTANCE Thaumarchaeota, which are ammonia-oxidizing archaea (AOA), are mainly chemolithoautotrophs that can fix inorganic carbon to produce organic matter in the dark. Their distinctive physiological traits and high abundance in the water column indicate the significant ecological roles they play in the open ocean. In our study, we found predominant Thaumarchaeota in the microbial community amended with cyanobacteria-derived lysate under the dark condition. Furthermore, Thaumarchaeota remained dominant in the microbial community even after 1 year of incubation. Through the ammonification process, dissolved organic matter (DOM) from cyanobacterial lysate was converted to ammonium which was used as an energy source for Thaumarchaeota to fix inorganic carbon into biomass. Our study further advocates the important roles of Thaumarchaeota in the ocean's biogeochemical cycle.}, }
@article {pmid36584837, year = {2022}, author = {Yang, WT and Shen, LD and Bai, YN}, title = {Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems.}, journal = {Environmental research}, volume = {}, number = {}, pages = {115174}, doi = {10.1016/j.envres.2022.115174}, pmid = {36584837}, issn = {1096-0953}, abstract = {Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH4). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH4 emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH4 emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH4 sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH4 mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.}, }
@article {pmid36573238, year = {2022}, author = {Moll, J and Hoppe, B}, title = {Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14567}, pmid = {36573238}, issn = {2167-8359}, abstract = {Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.}, }
@article {pmid36567186, year = {2022}, author = {Zhang, X and Zhang, C and Liu, Y and Zhang, R and Li, M}, title = {Non-negligible roles of archaea in coastal carbon biogeochemical cycling.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2022.11.008}, pmid = {36567186}, issn = {1878-4380}, abstract = {Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO2 fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.}, }
@article {pmid36552364, year = {2022}, author = {Li, Q and Wang, N and Han, W and Zhang, B and Zang, J and Qin, Y and Wang, L and Liu, J and Zhang, T}, title = {Soil Geochemical Properties Influencing the Diversity of Bacteria and Archaea in Soils of the Kitezh Lake Area, Antarctica.}, journal = {Biology}, volume = {11}, number = {12}, pages = {}, doi = {10.3390/biology11121855}, pmid = {36552364}, issn = {2079-7737}, abstract = {It is believed that polar regions are influenced by global warming more significantly, and because polar regions are less affected by human activities, they have certain reference values for future predictions. This study aimed to investigate the effects of climate warming on soil microbial communities in lake areas, taking Kitezh Lake, Antarctica as the research area. Below-peak soil, intertidal soil, and sediment were taken at the sampling sites, and we hypothesized that the diversity and composition of the bacterial and archaeal communities were different among the three sampling sites. Through 16S rDNA sequencing and analysis, bacteria and archaea with high abundance were obtained. Based on canonical correspondence analysis and redundancy analysis, pH and phosphate had a great influence on the bacterial community whereas pH and nitrite had a great influence on the archaeal community. Weighted gene coexpression network analysis was used to find the hub bacteria and archaea related to geochemical factors. The results showed that in addition to pH, phosphate, and nitrite, moisture content, ammonium, nitrate, and total carbon content also play important roles in microbial diversity and structure at different sites by changing the abundance of some key microbiota.}, }
@article {pmid36544005, year = {2022}, author = {Löwe, J}, title = {Mysterious Asgard archaea microbes reveal their inner secrets.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {36544005}, issn = {1476-4687}, }
@article {pmid36543797, year = {2022}, author = {Zhao, W and Zhong, B and Zheng, L and Tan, P and Wang, Y and Leng, H and de Souza, N and Liu, Z and Hong, L and Xiao, X}, title = {Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7861}, pmid = {36543797}, issn = {2041-1723}, abstract = {Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.}, }
@article {pmid36541769, year = {2022}, author = {Bai, T and Pu, X and Guo, X and Liu, J and Zhao, L and Zhang, X and Zhang, S and Cheng, L}, title = {Effects of Dietary Nonfibrous Carbohydrate/Neutral Detergent Fiber Ratio on Methanogenic Archaea and Cellulose-Degrading Bacteria in the Rumen of Karakul Sheep: a 16S rRNA Gene Sequencing Study.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0129122}, doi = {10.1128/aem.01291-22}, pmid = {36541769}, issn = {1098-5336}, abstract = {The study was conducted to investigate the effects of dietary nonfibrous carbohydrate (NFC)/neutral detergent fiber (NDF) ratio on methanogenic archaea and cellulose-degrading bacteria in Karakul sheep by 16S rRNA gene sequencing. Twelve Karakul sheep were randomly divided into four groups, each group with three replicates, and they were fed with four dietary NFC/NDF ratios at 0.54, 0.96, 1.37, and 1.90 as groups 1, 2, 3, and 4, respectively. The experiment lasted for four periods: I (1 to 18 days), II (19 to 36 days), III (37 to 54 days), and IV (55 to 72 days); during each period, rumen contents were collected before morning feeding to investigate on methanogenic archaea and cellulose-degrading bacteria. The results showed that with an increase in dietary NFC/NDF ratio, the number of rumen archaea operational taxonomic units and the diversity of archaea decrease. The most dominant methanogens did not change with dietary NFC/NDF ratio and prolongation of experimental periods. Methanobrevibacter was the most dominant genus. At the species level, the relative abundance of Methanobrevibacter ruminantium first increased and then decreased when the NFC/NDF ratio increased. When the dietary NFC/NDF ratio was 0.96, the structure of archaea was largely changed, and the relative abundance of Fibrobacter sp. strain UWCM, Ruminococcus flavefaciens, and Ruminococcus albus were the highest. When the dietary NFC/NDF ratio was 1.37, the relative abundance of Butyrivibrio fibrisolvens was higher than for other groups. Based on all the data, we concluded that a dietary NFC/NDF ratio of ca. 0.96 to 1.37 was a suitable ratio to support optimal sheep production. IMPORTANCE CH4 produced by ruminants aggravates the greenhouse effect and cause wastage of feed energy, and CH4 emissions are related to methanogens. According to the current literature, there is a symbiotic relationship between methanogens and cellulolytic bacteria, so reducing methane will inevitably affect the degradation of fiber materials. This experiment used 16S rRNA gene high-throughput sequencing technology to explore the balance relationship between methanogens and cellulolytic bacteria for the first time through a long-term feeding period. The findings provide fundamental data, supporting for the diet structures with potential to reduce CH4 emission.}, }
@article {pmid36529166, year = {2022}, author = {Jiang, Z and Tang, S and Liao, Y and Li, S and Wang, S and Zhu, X and Ji, G}, title = {Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {137585}, doi = {10.1016/j.chemosphere.2022.137585}, pmid = {36529166}, issn = {1879-1298}, abstract = {Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N2O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N2O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N2O through lab-scale subsurface CWs. The N2O emission flux of CW at 8 °C was 1.23 mg m[-2]·h[-1], significantly lower than that at 25 °C (1.92 mg m[-2]·h[-1]). The contribution of ammonia oxidation to N2O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N2O production from AOA increased from 1.91 ng N·g[-1] at 25 °C to 4.11 ng N·g[-1] soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N2O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N2O at low temperature.}, }
@article {pmid36519377, year = {2022}, author = {Kucukyildirim, S and Ozdemirel, HO and Lynch, M}, title = {Similar mutation rates but different mutation spectra in moderate and extremely halophilic archaea.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkac303}, pmid = {36519377}, issn = {2160-1836}, abstract = {Archaea are a major part of Earth`s microbiota and extremely diverse. Yet, we know very little about the process of mutation that drives such diversification. To expand beyond previous work with the moderate halophilic archaeal species Haloferax volcanii, we performed a mutation-accumulation experiment followed by whole-genome sequencing in the extremely halophilic archaeon Halobacterium salinarum. Although H. volcanii and H. salinarum have different salt requirements, both species have highly polyploid genomes and similar GC content. We accumulated mutations for an average of 1250-generations in 67 mutation accumulation lines of H. salinarum, and revealed 84 single-base substitutions and 10 insertion-deletion mutations. The estimated base-substitution mutation rate of 3.99 × 10-10 per site per generation or 1.0 × 10-3 per genome per generation in H. salinarum is similar to that reported for H. volcanii (1.2 × 10-3 per genome per generation), but the genome-wide insertion-deletion rate and spectrum of mutations are somewhat dissimilar in these archaeal species. The spectra of spontaneous mutations were AT biased in both archaea, but they differed in significant ways that may be related to differences in the fidelity of DNA replication/repair mechanisms or a simple result of the different salt concentrations.}, }
@article {pmid36512566, year = {2022}, author = {, }, title = {Expression of Concern: A Versatile Medium for Cultivating Methanogenic Archaea.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0278740}, pmid = {36512566}, issn = {1932-6203}, }
@article {pmid36499474, year = {2022}, author = {Ginsbach, LF and Gonzalez, JM}, title = {Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures.}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, pmid = {36499474}, issn = {1422-0067}, mesh = {*Archaea/metabolism ; Phylogeny ; *Methane/metabolism ; Temperature ; Hot Temperature ; }, abstract = {Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.}, }
@article {pmid36461738, year = {2022}, author = {Ponlachantra, K and Suginta, W and Robinson, RC and Kitaoku, Y}, title = {AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2200119}, doi = {10.1002/bies.202200119}, pmid = {36461738}, issn = {1521-1878}, abstract = {The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.}, }
@article {pmid36445127, year = {2022}, author = {Woo, Y and Cruz, MC and Wuertz, S}, title = {Selective Enrichment of Nitrososphaera viennensis-Like Ammonia-Oxidizing Archaea over Ammonia-Oxidizing Bacteria from Drinking Water Biofilms.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0184522}, doi = {10.1128/spectrum.01845-22}, pmid = {36445127}, issn = {2165-0497}, abstract = {Ammonia-oxidizing archaea (AOA) can oxidize ammonia to nitrite for energy gain. They have been detected in chloraminated drinking water distribution systems (DWDS) along with the more common ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, no members of the AOA have been isolated or enriched from drinking water environments. To begin the investigation of the role of AOA in chloraminated DWDS, we developed a selective approach using biofilm samples from a full-scale operational network as inoculum. A Nitrososphaera viennensis-like AOA taxon was enriched from a mixed community that also included Nitrosomonas-like AOB while gradually scaling up the culture volume. Dimethylthiourea (DMTU) and pyruvate at 100 μM were added to promote the growth of AOA while inhibiting AOB. This resulted in the eventual washout of AOB, while NOB were absent after 2 or 3 rounds of amendment with 24 μM sodium azide. The relative abundance of AOA in the enrichment increased from 0.2% to 39.5% after adding DMTU and pyruvate, and further to 51.6% after filtration through a 0.45-μm pore size membrane, within a period of approximately 6 months. IMPORTANCE Chloramination has been known to increase the risk of nitrification episodes in DWDS due to the presence of ammonia-oxidizing microorganisms. Among them, AOB are more frequently detected than AOA. All publicly available cultures of AOA have been isolated from soil, marine or surface water environments, meaning they are allochthonous to DWDS. Hence, monochloramine exposure studies involving these strains may not accurately reflect their role in DWDS. The described method allows for the rapid enrichment of autochthonous AOA from drinking water nitrifying communities. The high relative abundance of AOA in the resulting enrichment culture reduces any confounding effects of co-existing heterotrophic bacteria when investigating the response of AOA to varied levels of monochloramine in drinking water.}, }
@article {pmid36444822, year = {2022}, author = {Hagagy, N and Abdel-Mawgoud, M and Akhtar, N and Selim, S and AbdElgawad, H}, title = {The new isolated Archaea strain improved grain yield, metabolism and quality of wheat plants under Co stress conditions.}, journal = {Journal of plant physiology}, volume = {280}, number = {}, pages = {153876}, doi = {10.1016/j.jplph.2022.153876}, pmid = {36444822}, issn = {1618-1328}, abstract = {Heavy metal (e.g. cobalt) pollution causes a serious of environmental and agricultural problems. On the other hand, plant growth-promoting microorganisms enhance plant growth and mitigate heavy metal stress. Herein, we isolated and identified the unclassified species strain NARS9, belong to Haloferax,. Cobalt (Co, 200 mg/kg soil) stress mitigating impact of the identified on wheat grains yield, primary and secondary metabolism and grain quality was investigated. Co alone significantly induced Co accumulation in wheat grain (260%), and consequently reduced wheat yield (130%) and quality. Haloferax NARS9 alone significantly enhanced grain chemicals composition (i.e., total sugars (89%) and organic acids (e.g., oxalic and isobutyric acids), essential amino acids (e.g., threonine, lysine, and histidine) and unsaturated fatty acids (e.g. eicosenoic, erucic and tetracosenoic acids). Interestingly, Co stress induced wheat grain yield, reduction were significantly mitigated by Haloferax NARS9 treatment by 26% compared to Co stress alone. Under Co stress, Haloferax NARS9 significantly increased sugar metabolism including sucrose and starch levels and their metabolic enzymes (i.e. invertases, sucrose synthase, starch synthase). This in turn increased organic acid (e.g. oxalic (70%) and malic acids (60%)) and amino acids. levels and biosynthetic enzymes, e.g. glutamine synthetase and threonine synthase. Increased sugars levels by Haloferax NARS9 under Co treatment also provided a route for the biosynthesis of saturated fatty acids, particularly palmitic and stearic acids. Furthermore, Haloferax NARS9 treatment supported the wheat nutritive value through increasing minerals (Ca, Fe, Mn, Zn) and antioxidants i.e., polyphenol, flavonoids, ASC and GSH and total polyamines by 50%, 110%, 400%, 30%, and 90% respectively). These in parallel with the increase in the activity of (phenylalanine ammonia-lyase (110%) in phenolic metabolism). Overall, this study demonstrates the potentiality of Haloferax NARS9 in harnessing carbon and nitrogen metabolism differentially in wheat plants to cope with Co toxicity. Our results also suggested that the use of Haloferax NARS9 in agricultural fields can improve growth and nutritional value of wheat grains.}, }
@article {pmid36434094, year = {2022}, author = {Sato, T and Utashima, SH and Yoshii, Y and Hirata, K and Kanda, S and Onoda, Y and Jin, JQ and Xiao, S and Minami, R and Fukushima, H and Noguchi, A and Manabe, Y and Fukase, K and Atomi, H}, title = {A non-carboxylating pentose bisphosphate pathway in halophilic archaea.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1290}, pmid = {36434094}, issn = {2399-3642}, mesh = {*Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; *Ribose/metabolism ; Pentoses/metabolism ; Archaea/genetics/metabolism ; Guanosine/metabolism ; Phosphates ; }, abstract = {Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.}, }
@article {pmid36414709, year = {2022}, author = {Lee, S and Sieradzki, ET and Nicol, GW and Hazard, C}, title = {Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36414709}, issn = {1751-7370}, abstract = {Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived [13]C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of [13]C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of [13]C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in [13]C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.}, }
@article {pmid36413802, year = {2022}, author = {Matse, DT and Jeyakumar, P and Bishop, P and Anderson, CWN}, title = {Copper induces nitrification by ammonia-oxidizing bacteria and archaea in pastoral soils.}, journal = {Journal of environmental quality}, volume = {}, number = {}, pages = {}, doi = {10.1002/jeq2.20440}, pmid = {36413802}, issn = {1537-2537}, abstract = {Copper (Cu) is the main co-factor in the functioning of the ammonia monooxygenase (AMO) enzyme, which is responsible for the first step of ammonia oxidation. We report a greenhouse-based pot experiment that examines the response of ammonia-oxidizing bacteria and archaea (AOB and AOA) to different bioavailable Cu concentrations in three pastoral soils (Recent, Pallic, and Pumice soils) planted with ryegrass (Lolium perenne L.). Five treatments were used: control (no urine and Cu), urine only at 300 mg N kg[-1] soil (Cu0), urine + 1 mg Cu kg[-1] soil (Cu1), urine + 10 mg Cu kg[-1] soil (Cu10), and urine + 100 mg Cu kg[-1] soil (Cu100). Pots were destructively sampled at Day 0, 1, 7, 15, and 25 after urine application. The AOB/AOA amoA gene abundance was analyzed by real-time quantitative polymerase chain reaction at Days 1 and 15. The AOB amoA gene abundance increased 10.0- and 22.6-fold in the Recent soil and 2.1- and 2.5-fold in the Pallic soil for the Cu10 compared with Cu0 on Days 1 and 15, respectively. In contrast, the Cu100 was associated with a reduction in AOB amoA gene abundance in the Recent and Pallic soils but not in the Pumice soil. This may be due to the influence of soil cation exchange capacity differences on the bioavailable Cu. Bioavailable Cu in the Recent and Pallic soils influenced nitrification and AOB amoA gene abundance, as evidenced by the strong positive correlation between bioavailable Cu, nitrification, and AOB amoA. However, bioavailable Cu did not influence the nitrification and AOA amoA gene abundance increase.}, }
@article {pmid36406397, year = {2022}, author = {Yuan, H and Zhang, W and Yin, H and Zhang, R and Wang, J}, title = {Taxonomic dependency of beta diversity for bacteria, archaea, and fungi in a semi-arid lake.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {998496}, pmid = {36406397}, issn = {1664-302X}, abstract = {Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of Proteobacteria, Chloroflexi, Euryarchaeota, and Rozellomycota increased toward deep water, while Acidobacteria, Parvarchaeota, and Chytridiomycota decreased. For bacteria and archaea, there were significant (p < 0.05) decreasing water-depth patterns for LCBD and LCBDRepl (i.e., species replacement), while increasing patterns for total beta diversity and turnover, implying that total beta diversity and LCBD were dominated by species turnover or LCBDRepl. Further, bacteria showed a strong correlation with archaea regarding LCBD, total beta diversity and turnover. Such parallel patterns among bacteria and archaea were underpinned by similar ecological processes like environmental selection. Total beta diversity and turnover were largely affected by sediment total nitrogen, while LCBD and LCBDRepl were mainly constrained by water NO2 [-]-N and NO3 [-]-N. For fungal community variation, no significant patterns were observed, which may be due to different drivers like water nitrogen or phosphorus. Taken together, our findings provide compelling evidences for disentangling the underlying mechanisms of community variation in multiple aquatic microbial taxonomic groups.}, }
@article {pmid36402873, year = {2022}, author = {Hu, L and Dong, Z and Wang, Z and Xiao, L and Zhu, B}, title = {The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N2O emission in alkaline and neutral purple soils.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19928}, pmid = {36402873}, issn = {2045-2322}, mesh = {*Archaea/genetics ; Nitrification ; Soil/chemistry ; Ammonia ; Soil Microbiology ; Bacteria/genetics ; Oxidation-Reduction ; *Betaproteobacteria/genetics ; }, abstract = {Nitrification is believed to be one of the primary processes of N2O emission in the agroecological system, which is controlled by soil microbes and mainly regulated by soil pH, oxygen content and NH4[+] availability. Previous studies have proved that the relative contributions of ammonia oxidizing bacteria (AOB) and archaea (AOA) to N2O production were varied with soil pH, however, there is still no consensus on the regulating mechanism of nitrification-derived N2O production by soil pH. In this study, 1-octyne (a selective inhibitor of AOB) and acetylene (an inhibitor of AOB and AOA) were used in a microcosm incubation experiment to differentiate the relative contribution of AOA and AOB to N2O emissions in a neutral (pH = 6.75) and an alkaline (pH = 8.35) soils. We found that the amendment of ammonium (NH4[+]) observably stimulated the production of both AOA and AOB-related N2O and increased the ammonia monooxygenase (AMO) gene abundances of AOA and AOB in the two test soils. Among which, AOB dominated the process of ammonia oxidation in the alkaline soil, contributing 70.8% of N2O production derived from nitrification. By contrast, the contribution of AOA and AOB accounted for about one-third of nitrification-related N2O in acidic soil, respectively. The results indicated that pH was a key factor to change abundance and activity of AOA and AOB, which led to the differentiation of derivation of N2O production in purple soils. We speculate that both NH4[+] content and soil pH mediated specialization of ammonia-oxidizing microorganisms together; and both specialization results and N2O yield led to the different N2O emission characteristics in purple soils. These results may help inform the development of N2O reduction strategies in the future.}, }
@article {pmid36400771, year = {2022}, author = {Schoelmerich, MC and Ouboter, HT and Sachdeva, R and Penev, PI and Amano, Y and West-Roberts, J and Welte, CU and Banfield, JF}, title = {A widespread group of large plasmids in methanotrophic Methanoperedens archaea.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7085}, pmid = {36400771}, issn = {2041-1723}, mesh = {*Archaea/metabolism ; Anaerobiosis ; *Methane/metabolism ; Oxidation-Reduction ; Plasmids/genetics ; }, abstract = {Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane, yet their extrachromosomal genetic elements are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments. By manual curation we show that two of the plasmids are large (155,605 bp and 191,912 bp), circular, and may replicate bidirectionally. The plasmids occur in the same copy number as the main chromosome, and plasmid genes are actively transcribed. One of the plasmids encodes three tRNAs, ribosomal protein uL16 and elongation factor eEF2; these genes appear to be missing in the host Methanoperedens genome, suggesting an obligate interdependence between plasmid and host. Our work opens the way for the development of genetic vectors to shed light on the physiology and biochemistry of Methanoperedens, and potentially genetically edit them to enhance growth and accelerate methane oxidation rates.}, }
@article {pmid36385454, year = {2022}, author = {Zhou, Y and Zhou, L and Yan, S and Chen, L and Krupovic, M and Wang, Y}, title = {Diverse viruses of marine archaea discovered using metagenomics.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16287}, pmid = {36385454}, issn = {1462-2920}, abstract = {During the past decade, metagenomics became a method of choice for the discovery of novel viruses. However, host assignment for uncultured viruses remains challenging, especially for archaeal viruses, which are grossly undersampled compared to viruses of bacteria and eukaryotes. Here, we assessed the utility of CRISPR spacer targeting, tRNA gene matching and homology searches for viral signature proteins, such as major capsid proteins, for the assignment of archaeal hosts and validated these approaches on metaviromes from Yangshan Harbor (YSH). We report 35 new genomes of viruses which could be confidently assigned to hosts representing diverse lineages of marine archaea. We show that the archaeal YSH virome is highly diverse, with some viruses enriching the previously described virus groups, such as magroviruses of Marine Group II Archaea (Poseidoniales), and others representing novel groups of marine archaeal viruses. Metagenomic recruitment of Tara Oceans datasets on the YSH viral genomes demonstrated the presence of YSH Poseidoniales and Nitrososphaeria viruses in the global oceans, but also revealed the endemic YSH-specific viral lineages. Furthermore, our results highlight the relationship between the soil and marine thaumarchaeal viruses. We propose three new families within the class Caudoviricetes for the classification of the five complete viral genomes predicted to replicate in marine Poseidoniales and Nitrososphaeria, two ecologically important and widespread archaeal groups. This study illustrates the utility of viral metagenomics in exploring the archaeal virome and provides new insights into the diversity, distribution and evolution of marine archaeal viruses.}, }
@article {pmid36383678, year = {2022}, author = {Ghaly, TM and Tetu, SG and Penesyan, A and Qi, Q and Rajabal, V and Gillings, MR}, title = {Discovery of integrons in Archaea: Platforms for cross-domain gene transfer.}, journal = {Science advances}, volume = {8}, number = {46}, pages = {eabq6376}, pmid = {36383678}, issn = {2375-2548}, abstract = {Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.}, }
@article {pmid36372432, year = {2022}, author = {Kuroda, K and Kubota, K and Kagemasa, S and Nakai, R and Hirakata, Y and Yamamoto, K and Nobu, MK and Narihiro, T}, title = {Novel Cross-domain Symbiosis between Candidatus Patescibacteria and Hydrogenotrophic Methanogenic Archaea Methanospirillum Discovered in a Methanogenic Ecosystem.}, journal = {Microbes and environments}, volume = {37}, number = {4}, pages = {}, doi = {10.1264/jsme2.ME22063}, pmid = {36372432}, issn = {1347-4405}, mesh = {*Archaea/genetics ; Methanospirillum/genetics ; Symbiosis ; Ecosystem ; In Situ Hybridization, Fluorescence ; Phylogeny ; *Euryarchaeota ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To identify novel cross-domain symbiosis between Candidatus Patescibacteria and Archaea, we performed fluorescence in situ hybridization (FISH) on enrichment cultures derived from methanogenic bioreactor sludge with the newly designed 32-520-1066 probe targeting the family-level uncultured clade 32-520/UBA5633 lineage in the class Ca. Paceibacteria. All FISH-detectable 32-520/UBA5633 cells were attached to Methanospirillum, indicating high host specificity. Transmission electron microscopy observations revealed 32-520/UBA5633-like cells that were specifically adherent to the plug structure of Methanospirillum-like rod-shaped cells. The metagenome-assembled genomes of 32-520/UBA5633 encoded unique gene clusters comprising pilin signal peptides and type IV pilins. These results provide novel insights into unseen symbiosis between Ca. Patescibacteria and Archaea.}, }
@article {pmid36367391, year = {2022}, author = {Boyd, ES and Spietz, RL and Kour, M and Colman, DR}, title = {A naturalist perspective of microbiology: Examples from methanogenic archaea.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16285}, pmid = {36367391}, issn = {1462-2920}, abstract = {Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.}, }
@article {pmid36358054, year = {2022}, author = {Gu, S and Wang, R and Xing, H and Yu, M and Shen, S and Zhao, L and Sun, J and Li, Y}, title = {Effects of different low temperature conditions on anaerobic digestion efficiency of pig manure and composition of archaea community.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {86}, number = {5}, pages = {1181-1192}, doi = {10.2166/wst.2022.267}, pmid = {36358054}, issn = {0273-1223}, mesh = {Swine ; Animals ; *Manure ; *Archaea/metabolism ; Anaerobiosis ; Temperature ; Fatty Acids, Volatile/metabolism ; Bioreactors ; Methane/metabolism ; }, abstract = {To explore the effect of low temperature on the anaerobic digestion of pig manure, the anaerobic digestion experiment was carried out under the conditions of inoculum concentration of 30% and TS of 8%. Five low-temperature gradients of 4, 8, 12, 16 and 20 °C were set to study the activities of gas production, pH, solluted chemical oxygen demand (SCOD), volatile fatty acids (VFAs), coenzymes F420 and archaea community composition in the digestion process. The results were demonstrated: as the temperature decreased, the more unstable the gas production became, the less gas production produced, and the later the gas peak occurred. There were no significant peaks at either 4 °C or 8 °C, and the SCOD was unstable over time. From 12 °C, the SCOD increased over time, and the higher the temperature, the faster the growth trend. The pH was always greater than 7.6. 8, 12, 16, 20 °C had different degrees of VFAs accumulation at the late digestion stage. The higher the temperature, the greater the amount of volatile acid accumulation. When the VFAs of each reactor reached the maximum, the proportion of acetic acid also reached the highest. The digestion system of the five treatment groups was dominated by hydrogen-nutrient methanogenic pathway. The results could provide a further reference for the mechanism of anaerobic digestion of pig manure at low temperatures.}, }
@article {pmid36350548, year = {2023}, author = {Hepowit, NL and Maupin-Furlow, JA}, title = {Application of Archaea in Deubiquitinase-Like Enzyme Discovery and Activity Assay.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2591}, number = {}, pages = {151-169}, pmid = {36350548}, issn = {1940-6029}, support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; }, mesh = {*Ubiquitins/metabolism ; *Archaea/metabolism ; Ubiquitin/metabolism ; Eukaryotic Cells/metabolism ; Deubiquitinating Enzymes ; }, abstract = {Archaea can be used as microbial platforms to discover new types of deubiquitinase-like (DUB-like) enzymes and to produce ubiquitin/ubiquitin-like (Ub/Ubl) protein conjugates as substrates for DUB/DUB-like activity assays. Here we outline how to use archaea to synthesize, purify, and assay the activity of DUB-like enzymes with unusual properties, including catalytic activity in hypersaline conditions, organic solvents, and high temperatures. We also outline the application of archaea in forming Ub/Ubl isopeptide linkages that include the covalent attachments of diverse archaeal and eukaryotic Ub/Ubls to target proteins. Archaea form these Ub/Ubl-linked protein conjugates in vivo, and the resulting products are found to serve as useful DUB substrates for in vitro assays.}, }
@article {pmid36332026, year = {2022}, author = {Adam, PS and Kolyfetis, GE and Bornemann, TLV and Vorgias, CE and Probst, AJ}, title = {Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling.}, journal = {Science advances}, volume = {8}, number = {44}, pages = {eabm9651}, pmid = {36332026}, issn = {2375-2548}, abstract = {Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO2-reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called "methanogenesis markers" but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.}, }
@article {pmid36332013, year = {2022}, author = {Verma, A and Åberg-Zingmark, E and Sparrman, T and Mushtaq, AU and Rogne, P and Grundström, C and Berntsson, R and Sauer, UH and Backman, L and Nam, K and Sauer-Eriksson, E and Wolf-Watz, M}, title = {Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.}, journal = {Science advances}, volume = {8}, number = {44}, pages = {eabm4089}, pmid = {36332013}, issn = {2375-2548}, mesh = {Humans ; *Archaea/genetics ; *Adenylate Kinase/chemistry ; Catalysis ; Catalytic Domain ; }, abstract = {Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while [19]F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.}, }
@article {pmid36316034, year = {2023}, author = {Peiter, N and Rother, M}, title = {In vivo probing of SECIS-dependent selenocysteine translation in Archaea.}, journal = {Life science alliance}, volume = {6}, number = {1}, pages = {}, pmid = {36316034}, issn = {2575-1077}, mesh = {*Selenocysteine/genetics ; Archaea/genetics ; *Selenium ; 3' Untranslated Regions ; Base Sequence ; Selenoproteins/genetics ; }, abstract = {Cotranslational insertion of selenocysteine (Sec) proceeds by recoding UGA to a sense codon. This recoding is governed by the Sec insertion sequence (SECIS) element, an RNA structure on the mRNA, but size, location, structure determinants, and mechanism differ for Bacteria, Eukarya, and Archaea. For Archaea, the structure-function relation of the SECIS is poorly understood, as only rather laborious experimental approaches are established. Furthermore, these methods do not allow for quantitative probing of Sec insertion. In order to overcome these limitations, we engineered bacterial β-lactamase into an archaeal selenoprotein, thereby establishing a reporter system, which correlates enzyme activity to Sec insertion. Using this system, in vivo Sec insertion depending on the availability of selenium and the presence of a SECIS element was assessed in Methanococcus maripaludis Furthermore, a minimal SECIS element required for Sec insertion in M. maripaludis was defined and a conserved structural motif shown to be essential for function. Besides developing a convenient tool for selenium research, converting a bacterial enzyme into an archaeal selenoprotein provides proof of concept that novel selenoproteins can be engineered in Archaea.}, }
@article {pmid36314867, year = {2022}, author = {Cha, G and Liu, Y and Yang, Q and Bai, L and Cheng, L and Fan, W}, title = {Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0157422}, pmid = {36314867}, issn = {1098-5336}, mesh = {*Archaea ; Phylogeny ; Ligands ; *Genomics ; Ecosystem ; }, abstract = {Diverse archaea, including many unknown species and phylogenetically deeply rooted taxa, survive in extreme environments. They play crucial roles in the global carbon cycle and element fluxes in many terrestrial, marine, saline, host-associated, hot-spring, and oilfield environments. There is little knowledge of the diversity of chemoreceptors that are presumably involved in their habitat adaptation. Thus, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. The results show that chemoreceptors are significantly richer in archaea of mild environments than in those of extreme environments, that specific ligand-binding domains of the chemoreceptors are strongly associated with specific habitats, and that the number of chemoreceptors correlates with genome size. The results indicate that the successful adaptation of archaea to specific habitats has been associated with the acquisition and maintenance of chemoreceptors, which may be crucial for their survival in these environments. IMPORTANCE Archaea are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but general principles regarding how an archaeal species organizes its chemoreceptor diversity and habitat adaptation are poorly understood. Here, we have explored this diversity through phylogenetic and comparative genomic analyses of complete archaeal genomes. Signaling sensing and adaptation processes are tightly related to the ligand-binding domain, and it is clear that evolution and natural selection in specialized niches under constant conditions have selected for smaller genome sizes. Taken together, our results extend the understanding of archaeal adaptations to different environments and emphasize the importance of ecological constraints in shaping their evolution.}, }
@article {pmid36301308, year = {2022}, author = {Khan, F and Kaza, S}, title = {Crystal structure of an L-type lectin domain from archaea.}, journal = {Proteins}, volume = {}, number = {}, pages = {}, doi = {10.1002/prot.26440}, pmid = {36301308}, issn = {1097-0134}, abstract = {The crystal structures of an L-type lectin domain from Methanocaldococcus jannaschii in apo and mannose-bound forms have been determined. A thorough investigation of L-type lectin domains from several organisms provides insight into the differences in these domains from different kingdoms of life. While the overall fold of the L-type lectin domain is conserved, differences in the lengths of the carbohydrate-binding loops and significant variations in the Mn[2+] -binding site compared to the Ca[2+] -binding site are observed. Furthermore, the sequence and phylogenetic analyses suggest that the archaeal L-type lectin domain is evolutionarily closer to the plant legume lectins than to its bacterial or animal counterparts. This is the first report of the biochemical, structural, sequence, and phylogenetic analyses of an L-type lectin domain from archaea and serves to enhance our understanding of the species-specific differences and evolution of L-type lectin domains.}, }
@article {pmid36280648, year = {2022}, author = {Baati, H and Siala, M and Azri, C and Ammar, E and Trigui, M}, title = {Hydrolytic enzyme screening and carotenoid production evaluation of halophilic archaea isolated from highly heavy metal-enriched solar saltern sediments.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {53}, number = {4}, pages = {1893-1906}, pmid = {36280648}, issn = {1678-4405}, mesh = {RNA, Ribosomal, 16S/genetics ; *Carotenoids ; Antioxidants ; Archaea/genetics ; *Metals, Heavy ; }, abstract = {This paper aimed to screen the enzymatic activities and evaluate the carotenoid production level of twenty-two halophilic archaea isolated from Sfax solar saltern sediments. The molecular identification performed by sequencing the 16S rRNA genes showed that all strains have a high similarity degree (99.7-100%) with Halobacterium salinarum NRC-1. The strains were screened for the presence of eight hydrolase activities using agar plate-based assays. The most detected enzyme was gelatinase (77.27% of total strains), followed by protease (63.63%) and amylase activities (50%). The carotenoid production yields of the strains ranged between 2.027 and 14.880 mg/l. The UV-Visible spectroscopy of pigments revealed that it was a bacterioruberin type. When evaluated and compared to the standard β-carotene, the antioxidant capacities of these pigments showed a scavenging activity of more than 75% at a concentration of 5 μg/ml for three strains (AS16, AS17, and AS18). Then a sequence of one-step optimization processes was performed, using the one-factor-at-a-time approach, to define the optimum conditions for growth and carotenoid production of the highest carotenoid producing strain (AS17). Different environmental factors and nutritional conditions were tested. Variations in these factors were found to deeply influence growth and carotenoid production. A maximum carotenoid production (16.490 mg/l), higher than that of the control (14.880 mg/l), was observed at 37 °C, pH 7, 250 g/l of salinity, with 80% air phase in the flask at 110 rpm, in presence of light and in culture media containing (g/l) 10, yeast extract; 7.5, casamino acid; 20, MgSO4; 4, KCl; and 3, trisodium citrate.}, }
@article {pmid36270146, year = {2022}, author = {Yan, G and Sun, X and Dong, Y and Gao, W and Gao, P and Li, B and Yan, W and Zhang, H and Soleimani, M and Yan, B and Häggblom, MM and Sun, W}, title = {Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning.}, journal = {Water research}, volume = {226}, number = {}, pages = {119247}, doi = {10.1016/j.watres.2022.119247}, pmid = {36270146}, issn = {1879-2448}, mesh = {Humans ; *Archaea/genetics/metabolism ; *Metagenome ; Vanadates/metabolism ; Vanadium/metabolism ; Ecosystem ; Anaerobiosis ; Bacteria/genetics/metabolism ; Methane/metabolism ; Methanosarcina/genetics ; Oxidation-Reduction ; Isotopes ; DNA/metabolism ; }, abstract = {Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F420H2 dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.}, }
@article {pmid36266535, year = {2022}, author = {Shao, N and Fan, Y and Chou, CW and Yavari, S and Williams, RV and Amster, IJ and Brown, SM and Drake, IJ and Duin, EC and Whitman, WB and Liu, Y}, title = {Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1113}, pmid = {36266535}, issn = {2399-3642}, mesh = {*Archaea/genetics/metabolism ; *Mesna/metabolism ; Oxidoreductases/metabolism ; Methane/metabolism ; }, abstract = {Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.}, }
@article {pmid36266339, year = {2022}, author = {Hocher, A and Borrel, G and Fadhlaoui, K and Brugère, JF and Gribaldo, S and Warnecke, T}, title = {Growth temperature and chromatinization in archaea.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1932-1942}, pmid = {36266339}, issn = {2058-5276}, support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; MC-A658-5TY40/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Archaea/genetics ; Temperature ; *Proteomics ; Chromatin/genetics ; }, abstract = {DNA in cells is associated with proteins that constrain its structure and affect DNA-templated processes including transcription and replication. HU and histones are the main constituents of chromatin in bacteria and eukaryotes, respectively, with few exceptions. Archaea, in contrast, have diverse repertoires of nucleoid-associated proteins (NAPs). To analyse the evolutionary and ecological drivers of this diversity, we combined a phylogenomic survey of known and predicted NAPs with quantitative proteomic data. We identify the Diaforarchaea as a hotbed of NAP gain and loss, and experimentally validate candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis. Proteomic analysis across a diverse sample of 19 archaea revealed that NAP investment varies from <0.03% to >5% of total protein. This variation is predicted by growth temperature. We propose that high levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures, with implications for the origin of chromatin in both archaea and eukaryotes.}, }
@article {pmid36256551, year = {2022}, author = {Xin, YJ and Bao, CX and Tan, S and Hou, J and Cui, HL}, title = {Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov., two extremely halophilic archaea isolated from Gobi saline soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {10}, pages = {}, doi = {10.1099/ijsem.0.005543}, pmid = {36256551}, issn = {1466-5034}, mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Soil ; DNA, Archaeal/genetics ; Base Composition ; Sequence Analysis, DNA ; Fatty Acids/chemistry ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; *Halobacteriaceae ; Glycolipids/chemistry ; Sulfates ; Phosphatidylglycerols/analysis ; Nucleotides ; Amino Acids ; Phosphatidic Acids/analysis ; Esters ; }, abstract = {Two extremely halophilic archaeal strains, PSR5[T] and PSR8[T], were isolated from a saline soil sample collected from the Tarim Basin, Xinjiang, PR China. Both strains had two copies of the 16S rRNA genes rrn1 and rrn2, showing 2.6 and 3.9% divergence, respectively. The rrn1 gene of PSR5[T] showed 98.4 and 95.3% similarity to the rrn1 and rrn2 genes of strain PSR8[T]; the rrn2 gene of PSR5[T] displayed 97.4 and 96.7% similarity to those of strain PSR8[T], respectively. Phylogenetic analyses based on the 16S rRNA and rpoB' genes revealed that strains PSR5[T] and PSR8[T] formed a single cluster, and then tightly clustered with the current four Haladaptatus species (93.5-97.1% similarities for the 16S rRNA gene and 89.3-90.9% similarities for the rpoB' gene, respectively). Several phenotypic characteristics differentiate strains PSR5[T] and PSR8[T] from current Haladaptatus members. The polar lipids of the two strains are phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester phosphatidylglycerol sulphate and three glycolipids. One of the glycolipids is sulphated mannosyl glucosyl diether, and the remaining two glycolipids are unidentified. The average nucleotide identity, in silico DNA-DNA hybridization, amino acid identity and percentage of conserved proteins values between the two strains were 88.5, 39.1, 89.3 and 72.8 %, respectively, much lower than the threshold values proposed as a species boundary. These values among the two strains and Haladaptatus members were 77.9-79.2, 22.0-23.5, 75.1-78.2 and 56.8-69.9 %, respectively, much lower than the recommended threshold values for species delimitation. These results suggested that strains PSR5[T] and PSR8[T] represent two novel species of Haladaptatus. Based on phenotypic, chemotaxonomic, genomic and phylogenetic properties, strains PSR5[T] (=CGMCC 1.16851[T]=JCM 34141[T]) and PSR8[T] (=CGMCC 1.17025[T]=JCM 34142[T]) represent two novel species of the genus Haladaptatus, for which the names Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov. are proposed.}, }
@article {pmid36253512, year = {2022}, author = {van Wolferen, M and Pulschen, AA and Baum, B and Gribaldo, S and Albers, SV}, title = {The cell biology of archaea.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1744-1755}, pmid = {36253512}, issn = {2058-5276}, support = {203276//Wellcome Trust/United Kingdom ; MC_UP_1201/27/MRC_/Medical Research Council/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Archaea ; Phylogeny ; *Biological Evolution ; Eukaryota ; Ecology ; }, abstract = {The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.}, }
@article {pmid36251741, year = {2022}, author = {Hofmann, M and Norris, PR and Malik, L and Schippers, A and Schmidt, G and Wolf, J and Neumann-Schaal, M and Hedrich, S}, title = {Metallosphaera javensis sp. nov., a novel species of thermoacidophilic archaea, isolated from a volcanic area.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {10}, pages = {}, doi = {10.1099/ijsem.0.005536}, pmid = {36251741}, issn = {1466-5034}, mesh = {*Archaea/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Iron ; Nucleotides ; Phylogeny ; Quinones ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sugars ; Sulfides ; *Sulfolobaceae ; Sulfur ; Sulfur Compounds ; }, abstract = {A novel thermoacidophilic archeaon, strain J1[T] (=DSM 112778[T],=JCM 34702[T]), was isolated from a hot pool in a volcanic area of Java, Indonesia. Cells of the strain were irregular, motile cocci of 1.0-1.2 µm diameter. Aerobic, organoheterotrophic growth with casamino acids was observed at an optimum temperature of 70 °C in a range of 55-78 °C and at an optimum pH of 3 in a range of 1.5 to 5. Various organic compounds were utilized, including a greater variety of sugars than has been reported for growth of other species of the genus. Chemolithoautotrophic growth was observed with reduced sulphur compounds, including mineral sulphides. Ferric iron was reduced during anaerobic growth with elemental sulphur. Cellular lipids were calditoglycerocaldarchaeol and caldarchaeol with some derivates. The organism contained the respiratory quinone caldariellaquinone. On the basis of phylogenetic and chemotaxonomic comparison with its closest relatives, it was concluded that strain J1[T] represents a novel species, for which the name Metallosphaera javensis is proposed. Low DNA-DNA relatedness values (16S rRNA gene <98.4%, average nucleotide identity (ANI) <80.1%) distinguished J1[T] from other species of the genus Metallosphaera and the DNA G+C content of 47.3% is the highest among the known species of the genus.}, }
@article {pmid36239851, year = {2022}, author = {Zheng, XW and Wu, ZP and Sun, YP and Wang, BB and Hou, J and Cui, HL}, title = {Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., Halorussus salinisoli sp. nov.: six extremely halophilic archaea isolated from solar saltern, salt lake and saline soil.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {3}, pages = {32}, pmid = {36239851}, issn = {1433-4909}, mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Esters ; Glycolipids ; *Halobacteriaceae ; *Lakes ; Nucleotides ; Phosphatidylglycerols ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; Sulfates ; }, abstract = {Six novel halophilic archaeal strains of XZYJT10[T], XZYJ18[T], XZYJT40[T], XZYJT49[T], YCN54[T] and LT46[T] were isolated from a solar saltern in Tibet, a salt lake in Shanxi, and a saline soil in Xinjiang, China. Sequence similarities of 16S rRNA and rpoB' genes among strains XZYJT10[T], XZYJ18[T], XZYJT40[T], XZYJT49[T], YCN54[T], LT46[T] and current members of Halorussus were 90.6-97.8% and 87.8-96.4%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among these six strains and current Halorussus members were in the range of 76.5-87.5% and 21.0-33.8%, respectively. These values were all below the species boundary threshold values. The phylogenomic tree based on 122 conserved archaeal protein marker genes revealed that the six novel strains formed individual distinct branches and clustered tightly with Halorussus members. Several phenotypic characteristics distinguished the six strains from current Halorussus members. Polar lipid analysis showed that the six novel strains contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and two to three glycolipids. Phenotypic, chemotaxonomic and phylogenetic properties showed that the six strains represented six novel species within the genus Halorussus, for which the names Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., and Halorussus salinisoli sp. nov. are proposed.}, }
@article {pmid36232866, year = {2022}, author = {Uzelac, M and Li, Y and Chakladar, J and Li, WT and Ongkeko, WM}, title = {Archaea Microbiome Dysregulated Genes and Pathways as Molecular Targets for Lung Adenocarcinoma and Squamous Cell Carcinoma.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36232866}, issn = {1422-0067}, mesh = {*Adenocarcinoma of Lung/pathology ; Archaea/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics ; *Carcinoma, Squamous Cell/pathology ; Female ; Humans ; *Lung Neoplasms/pathology ; Male ; *Microbiota/genetics ; }, abstract = {The human microbiome is a vast collection of microbial species that exist throughout the human body and regulate various bodily functions and phenomena. Of the microbial species that exist in the human microbiome, those within the archaea domain have not been characterized to the extent of those in more common domains, despite their potential for unique metabolic interaction with host cells. Research has correlated tumoral presence of bacterial microbial species to the development and progression of lung cancer; however, the impacts and influences of archaea in the microbiome remain heavily unexplored. Within the United States lung cancer remains highly fatal, responsible for over 100,000 deaths every year with a 5-year survival rate of roughly 22.9%. This project attempts to investigate specific archaeal species' correlation to lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) incidence, patient staging, death rates across individuals of varying ages, races, genders, and smoking-statuses, and potential molecular targets associated with archaea microbiome. Archaeal species abundance was assessed across lung tissue samples of 527 LUAD patients, 479 LUSC patients, and 99 healthy individuals. Nine archaeal species were found to be of significantly altered abundance in cancerous samples as compared to normal counterparts, 6 of which are common to both LUAD and LUSC subgroups. Several of these species are of the taxonomic class Thermoprotei or the phylum Euryarchaeota, both known to contain metabolic processes distinct from most bacterial species. Host-microbe metabolic interactions may be responsible for the observed correlation of these species' abundance with cancer incidence. Significant microbes were correlated to patient gene expression to reveal genes of altered abundance with respect to high and low archaeal presence. With these genes, cellular oncogenic signaling pathways were analyzed for enrichment across cancer and normal samples. In comparing gene expression between LUAD and adjacent normal samples, 2 gene sets were found to be significantly enriched in cancers. In LUSC comparison, 6 sets were significantly enriched in cancer, and 34 were enriched in normals. Microbial counts across healthy and cancerous patients were then used to develop a machine-learning based predictive algorithm, capable of distinguishing lung cancer patients from healthy normal with 99% accuracy.}, }
@article {pmid36229494, year = {2022}, author = {Jeter, VL and Schwarzwalder, AH and Rayment, I and Escalante-Semerena, JC}, title = {Structural studies of the phosphoribosyltransferase involved in cobamide biosynthesis in methanogenic archaea and cyanobacteria.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17175}, pmid = {36229494}, issn = {2045-2322}, support = {R35 GM130399/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Monophosphate ; Archaea/metabolism ; Aspartic Acid ; Cobamides/metabolism ; Crystallography, X-Ray ; *Cyanobacteria/metabolism ; *Euryarchaeota/metabolism ; Glutamates ; Ligands ; Pentosyltransferases/genetics/metabolism ; Phosphates/metabolism ; }, abstract = {Cobamides (Cbas) are coenzymes used by cells across all domains of life, but de novo synthesis is only found in some bacteria and archaea. Five enzymes assemble the nucleotide loop in the alpha phase of the corrin ring. Condensation of the activated ring and nucleobase yields adenosyl-Cba 5'-phosphate, which upon dephosphorylation yields the biologically active coenzyme (AdoCba). Base activation is catalyzed by a phosphoribosyltransferase (PRTase). The structure of the Salmonella enterica PRTase enzyme (i.e., SeCobT) is well-characterized, but archaeal PRTases are not. To gain insights into the mechanism of base activation by the PRTase from Methanocaldococcus jannaschii (MjCobT), we solved crystal structures of the enzyme in complex with substrate and products. We determined several structures: (i) a 2.2 Å structure of MjCobT in the absence of ligand (apo), (ii) structures of MjCobT bound to nicotinate mononucleotide (NaMN) and α-ribazole 5'-phosphate (α-RP) or α-adenylyl-5'-phosphate (α-AMP) at 2.3 and 1.4 Å, respectively. In MjCobT the general base that triggers the reaction is an aspartate residue (Asp 52) rather than a glutamate residue (E317) as in SeCobT. Notably, the dimer interface in MjCobT is completely different from that observed in SeCobT. Finally, entry PDB 3L0Z does not reflect the correct structure of MjCobT.}, }
@article {pmid36212815, year = {2022}, author = {Benito Merino, D and Zehnle, H and Teske, A and Wegener, G}, title = {Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {988871}, pmid = {36212815}, issn = {1664-302X}, abstract = {In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate-methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.}, }
@article {pmid36203131, year = {2022}, author = {Somee, MR and Amoozegar, MA and Dastgheib, SMM and Shavandi, M and Maman, LG and Bertilsson, S and Mehrshad, M}, title = {Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {690}, pmid = {36203131}, issn = {1471-2164}, mesh = {*Archaea ; Bacteria ; Biodegradation, Environmental ; Carbon/metabolism ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; *Petroleum/metabolism ; Phylogeny ; }, abstract = {BACKGROUND: Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. RESULTS: Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.<br><br>CONCLUSION: Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.}, }
@article {pmid36181435, year = {2022}, author = {Zhang, X and Huang, Y and Liu, Y and Xu, W and Pan, J and Zheng, X and Du, H and Zhang, C and Lu, Z and Zou, D and Liu, Z and Cai, M and Xiong, J and Zhu, Y and Dong, Z and Jiang, H and Dong, H and Jiang, J and Luo, Z and Huang, L and Li, M}, title = {An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales.}, journal = {Molecular biology and evolution}, volume = {39}, number = {10}, pages = {}, pmid = {36181435}, issn = {1537-1719}, mesh = {*Archaea/genetics/metabolism ; *Hydrogenase/chemistry/genetics/metabolism ; Sodium Chloride/metabolism ; Phylogeny ; Respiratory System/metabolism ; Amino Acids/genetics ; Antiporters/genetics/metabolism ; }, abstract = {Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.}, }
@article {pmid36160229, year = {2022}, author = {Meng, K and Chung, CZ and Söll, D and Krahn, N}, title = {Unconventional genetic code systems in archaea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1007832}, pmid = {36160229}, issn = {1664-302X}, support = {R35 GM122560/GM/NIGMS NIH HHS/United States ; }, abstract = {Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.}, }
@article {pmid36152750, year = {2022}, author = {Guo, LT and Amikura, K and Jiang, HK and Mukai, T and Fu, X and Wang, YS and O'Donoghue, P and Söll, D and Tharp, JM}, title = {Ancestral archaea expanded the genetic code with pyrrolysine.}, journal = {The Journal of biological chemistry}, volume = {298}, number = {11}, pages = {102521}, pmid = {36152750}, issn = {1083-351X}, support = {K99 GM141320/GM/NIGMS NIH HHS/United States ; R35 GM122560/GM/NIGMS NIH HHS/United States ; 165985//CIHR/Canada ; }, mesh = {*Amino Acyl-tRNA Synthetases/metabolism ; *Archaea/enzymology/genetics ; *Genetic Code ; *Lysine/analogs &amp; derivatives/genetics ; Methanosarcina ; RNA, Transfer/genetics ; }, abstract = {The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA[Pyl]) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA[Pyl] pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA[Pyl] and reveal the emergence of tRNA[Pyl] sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA[Pyl] species with the more common G73-containing tRNA[Pyl] will enable future efforts to engineer PylRS systems for further genetic code expansion.}, }
@article {pmid36150484, year = {2022}, author = {Guo, Z and Jalalah, M and Alsareii, SA and Harraz, FA and Thakur, N and Salama, ES}, title = {Biochar addition augmented the microbial community and aided the digestion of high-loading slaughterhouse waste: Active enzymes of bacteria and archaea.}, journal = {Chemosphere}, volume = {309}, number = {Pt 1}, pages = {136535}, doi = {10.1016/j.chemosphere.2022.136535}, pmid = {36150484}, issn = {1879-1298}, mesh = {Archaea/metabolism ; Biofuels ; Anaerobiosis ; Bioreactors ; Abattoirs ; Methane/metabolism ; *Hydrogenase/metabolism ; Bacteria/metabolism ; *Microbiota ; Fatty Acids, Volatile/metabolism ; *Lyases/metabolism ; Transaminases ; Digestion ; }, abstract = {The biogas production (BP), volatile fatty acids (VFAs), microbial communities, and microbes' active enzymes were studied upon the addition of biochar (0-1.5%) at 6% and 8% slaughterhouse waste (SHW) loadings. The 0.5% biochar enhanced BP by 1.5- and 1.6-folds in 6% and 8% SHW-loaded reactors, respectively. Increasing the biochar up to 1.5% caused a reduction in BP at 6% SHW. However, the BP from 8% of SHW was enhanced by 1.4-folds at 1.5% biochar. The VFAs production in all 0.5% biochar amended reactors was highly significant compared to control (p-value < 0.05). The biochar addition increased the bacterial and archaeal diversity at both 6% and 8% SHW loadings. The highest number of OTUs at 0.5% biochar were 567 and 525 in 6% and 8% SHW, respectively. Biochar prompted the Clostridium abundance and increased the lyases and transaminases involved in the degradation of lipids and protein, respectively. Biochar addition improved the Methanosaeta and Methanosphaera abundance in which the major enzymes were reductase and hydrogenase. The archaeal enzymes showed mixed acetoclastic and hydrogenotrophic methanogenesis.}, }
@article {pmid36144426, year = {2022}, author = {Pilotto, S and Werner, F}, title = {How to Shut Down Transcription in Archaea during Virus Infection.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144426}, issn = {2076-2607}, support = {/WT_/Wellcome Trust/United Kingdom ; 206166/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 202679/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Multisubunit RNA polymerases (RNAPs) carry out transcription in all domains of life; during virus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription with distinct outcomes for different host-virus combinations. These repressors serve as versatile molecular probes to study RNAP mechanisms, as well as aid the exploration of druggable sites for the development of new antibiotics. Here, we review the mechanisms and structural basis of RNAP inhibition by the viral repressor RIP and the crenarchaeal negative regulator TFS4, which follow distinct strategies. RIP operates by occluding the DNA-binding channel and mimicking the initiation factor TFB/TFIIB. RIP binds tightly to the clamp and locks it into one fixed position, thereby preventing conformational oscillations that are critical for RNAP function as it progresses through the transcription cycle. TFS4 engages with RNAP in a similar manner to transcript cleavage factors such as TFS/TFIIS through the NTP-entry channel; TFS4 interferes with the trigger loop and bridge helix within the active site by occlusion and allosteric mechanisms, respectively. The conformational changes in RNAP described above are universally conserved and are also seen in inactive dimers of eukaryotic RNAPI and several inhibited RNAP complexes of both bacterial and eukaryotic RNA polymerases, including inactive states that precede transcription termination. A comparison of target sites and inhibitory mechanisms reveals that proteinaceous repressors and RNAP-specific antibiotics use surprisingly common ways to inhibit RNAP function.}, }
@article {pmid36135934, year = {2022}, author = {Groult, B and Bredin, P and Lazar, CS}, title = {Ecological processes differ in community assembly of Archaea, Bacteria and Eukaryotes in a biogeographical survey of groundwater habitats in the Quebec region (Canada).}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5898-5910}, doi = {10.1111/1462-2920.16219}, pmid = {36135934}, issn = {1462-2920}, mesh = {Archaea/genetics ; Eukaryota ; Quebec ; RNA, Ribosomal, 16S ; Bacteria/genetics ; *Groundwater/microbiology ; *Microbiota ; }, abstract = {Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km[2] in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities.}, }
@article {pmid36125864, year = {2022}, author = {Pallen, MJ and Rodriguez-R, LM and Alikhan, NF}, title = {Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.005482}, pmid = {36125864}, issn = {1466-5034}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.}, }
@article {pmid36125771, year = {2022}, author = {Adam, PS and Bornemann, TLV and Probst, AJ}, title = {Progress and Challenges in Studying the Ecophysiology of Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2522}, number = {}, pages = {469-486}, pmid = {36125771}, issn = {1940-6029}, mesh = {Alkanes ; *Archaea/genetics ; *Genome, Archaeal ; Methane ; Phylogeny ; }, abstract = {It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.}, }
@article {pmid36125745, year = {2022}, author = {Thomsen, J and Weidenbach, K and Metcalf, WW and Schmitz, RA}, title = {Genetic Methods and Construction of Chromosomal Mutations in Methanogenic Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2522}, number = {}, pages = {105-117}, pmid = {36125745}, issn = {1940-6029}, mesh = {*Archaea ; *Hypoxanthine Phosphoribosyltransferase/genetics ; Mutation ; Purines ; }, abstract = {Genetic manipulation through markerless exchange enables the modification of several genomic regions without leaving a selection marker in the genome. Here, a method using hpt coding for hypoxanthine phosphoribosyltransferase as a counter selectable marker is described. For Methanosarcina species a chromosomal deletion of the hpt gene is firstly generated, which confers resistance to the purine analogue 8-aza-2,6-diaminopurine (8-ADP). In a second step, the reintroduction of the hpt gene on a plasmid leads to a selectable loss of 8-ADP resistance after a homologous recombination event (pop-in). A subsequent pop-out event restores the 8-ADP resistance and can generate chromosomal mutants with frequencies of about 50%.}, }
@article {pmid36125740, year = {2022}, author = {Forterre, P}, title = {Archaea: A Goldmine for Molecular Biologists and Evolutionists.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2522}, number = {}, pages = {1-21}, pmid = {36125740}, issn = {1940-6029}, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; Eukaryota/genetics ; Genome, Archaeal ; RNA, Ribosomal, 16S ; }, abstract = {The rebuttal of the prokaryote-eukaryote dichotomy and the elaboration of the three domains concept by Carl Woese and colleagues has been a breakthrough in biology. With the methodologies available at this time, they have shown that a single molecule, the 16S ribosomal RNA, could reveal the global organization of the living world. Later on, mining archaeal genomes led to major discoveries in archaeal molecular biology, providing a third model for comparative molecular biology. These analyses revealed the strong eukaryal flavor of the basic molecular fabric of Archaea and support rooting the universal tree between Bacteria and Arcarya (the clade grouping Archaea and Eukarya). However, in contradiction with this conclusion, it remains to understand why the archaeal and bacterial mobilomes are so similar and so different from the eukaryal one. These last years, the number of recognized archaea lineages (phyla?) has exploded. The archaeal nomenclature is now in turmoil and debates about the nature of the last universal common ancestor, the last archaeal common ancestor, and the topology of the tree of life are still going on. Interestingly, the expansion of the archaeal eukaryome, especially in the Asgard archaea, has provided new opportunities to study eukaryogenesis. In recent years, the application to Archaea of the new methodologies described in the various chapters of this book have opened exciting avenues to study the molecular biology and the physiology of these fascinating microorganisms.}, }
@article {pmid36125558, year = {2022}, author = {Chow, C and Padda, KP and Puri, A and Chanway, CP}, title = {An Archaic Approach to a Modern Issue: Endophytic Archaea for Sustainable Agriculture.}, journal = {Current microbiology}, volume = {79}, number = {11}, pages = {322}, pmid = {36125558}, issn = {1432-0991}, mesh = {Agriculture/methods ; Amino Acids/metabolism ; *Archaea/genetics ; *Coffee/metabolism ; Endophytes/genetics/metabolism ; Plant Growth Regulators/metabolism ; Plants ; }, abstract = {Archaea have existed for over 3.5 billion years, yet they were detected in the plant endosphere only in the recent past and still, not much is known about them. Archaeal endophytes may be important microorganisms for sustainable agriculture, particularly in the face of climate change and increasing food demand due to population growth. Recent advances in culture-independent methods of research have revealed a diverse abundance of archaea from the phyla Euryarchaeota, Crenarchaeaota, and Thaumarchaeota globally that are associated with significant crops such as maize, rice, coffee, and olive. Novel insights into the plant microbiome have revealed specific genes in archaea that may be involved in numerous plant metabolic functions including amino acid production and phytohormone modulation. This is the first review article to address what is known about archaea as endophytes, including their patterns of colonization and abundance in various parts of different crop plants grown under diverse environmental conditions. This review aims to facilitate mainstream discussions and encourage future research regarding the occurrence and role of endophytic archaea in plants, particularly in relation to agricultural applications.}, }
@article {pmid36111740, year = {2022}, author = {Yue, Y and Wang, F and Pan, J and Chen, XP and Tang, Y and Yang, Z and Ma, J and Li, M and Yang, M}, title = {Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {11}, pages = {}, doi = {10.1093/femsec/fiac109}, pmid = {36111740}, issn = {1574-6941}, mesh = {*Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Geologic Sediments/chemistry ; Nutrients ; China ; Phylogeny ; DNA, Archaeal/genetics ; }, abstract = {Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.}, }
@article {pmid36083447, year = {2022}, author = {Zhu, Q and Mirarab, S}, title = {Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {137-165}, pmid = {36083447}, issn = {1940-6029}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Software ; }, abstract = {Phylogenomics is the inference of phylogenetic trees based on multiple marker genes sampled in the genomes of interest. An important challenge in phylogenomics is the potential incongruence among the evolutionary histories of individual genes, which can be widespread in microorganisms due to the prevalence of horizontal gene transfer. This protocol introduces the procedures for building a phylogenetic tree of a large number of microbial genomes using a broad sampling of marker genes that are representative of whole-genome evolution. The protocol highlights the use of a gene tree summary method, which can effectively reconstruct the species tree while accounting for the topological conflicts among individual gene trees. The pipeline described in this protocol is scalable to tens of thousands of genomes while retaining high accuracy. We discussed multiple software tools, libraries, and scripts to enable convenient adoption of the protocol. The protocol is suitable for microbiology and microbiome studies based on public genomes and metagenomic data.}, }
@article {pmid36050385, year = {2022}, author = {Hoegenauer, C and Hammer, HF and Mahnert, A and Moissl-Eichinger, C}, title = {Methanogenic archaea in the human gastrointestinal tract.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {19}, number = {12}, pages = {805-813}, pmid = {36050385}, issn = {1759-5053}, mesh = {Humans ; *Archaea/physiology ; *Euryarchaeota ; Gastrointestinal Tract/microbiology ; Methane ; Bacteria ; }, abstract = {The human microbiome is strongly interwoven with human health and disease. Besides bacteria, viruses and eukaryotes, numerous archaea are located in the human gastrointestinal tract and are responsible for methane production, which can be measured in clinical methane breath analyses. Methane is an important readout for various diseases, including intestinal methanogen overgrowth. Notably, the archaea responsible for methane production are largely overlooked in human microbiome studies due to their non-bacterial biology and resulting detection issues. As such, their importance for health and disease remains largely unclear to date, in particular as not a single archaeal representative has been deemed to be pathogenic. In this Perspective, we discuss the current knowledge on the clinical relevance of methanogenic archaea. We explain the archaeal unique response to antibiotics and their negative and positive effects on human physiology, and present the current understanding of the use of methane as a diagnostic marker.}, }
@article {pmid36043790, year = {2022}, author = {Kuroda, K and Yamamoto, K and Nakai, R and Hirakata, Y and Kubota, K and Nobu, MK and Narihiro, T}, title = {Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0171122}, pmid = {36043790}, issn = {2150-7511}, mesh = {*Archaea/metabolism ; Symbiosis/genetics ; Wastewater ; Phylogeny ; In Situ Hybridization, Fluorescence ; Sewage ; Bacteria/genetics ; *Euryarchaeota ; Bioreactors ; Protein Sorting Signals/genetics ; }, abstract = {Each prokaryotic domain, Bacteria and Archaea, contains a large and diverse group of organisms characterized by their ultrasmall cell size and symbiotic lifestyles (potentially commensal, mutualistic, and parasitic relationships), namely, Candidatus Patescibacteria (also known as the Candidate Phyla Radiation/CPR superphylum) and DPANN archaea, respectively. Cultivation-based approaches have revealed that Ca. Patescibacteria and DPANN symbiotically interact with bacterial and archaeal partners and hosts, respectively, but that cross-domain symbiosis and parasitism have never been observed. By amending wastewater treatment sludge samples with methanogenic archaea, we observed increased abundances of Ca. Patescibacteria (Ca. Yanofskybacteria/UBA5738) and, using fluorescence in situ hybridization (FISH), discovered that nearly all of the Ca. Yanofskybacteria/UBA5738 cells were attached to Methanothrix (95.7 ± 2.1%) and that none of the cells were attached to other lineages, implying high host dependency and specificity. Methanothrix filaments (multicellular) with Ca. Yanofskybacteria/UBA5738 attached had significantly more cells with no or low detectable ribosomal activity (based on FISH fluorescence) and often showed deformations at the sites of attachment (based on transmission electron microscopy), suggesting that the interaction is parasitic. Metagenome-assisted metabolic reconstruction showed that Ca. Yanofskybacteria/UBA5738 lacks most of the biosynthetic pathways necessary for cell growth and universally conserves three unique gene arrays that contain multiple genes with signal peptides in the metagenome-assembled genomes of the Ca. Yanofskybacteria/UBA5738 lineage. The results shed light on a novel cross-domain symbiosis and inspire potential strategies for culturing CPR and DPANN. IMPORTANCE One highly diverse phylogenetic group of Bacteria, Ca. Patescibacteria, remains poorly understood, but, from the few cultured representatives and metagenomic investigations, they are thought to live symbiotically or parasitically with other bacteria or even with eukarya. We explored the possibility of symbiotic interactions with Archaea by amending wastewater treatment sludge samples that were rich in Ca. Patescibacteria and Archaea with an isolate archaeon that is closely related to a methanogen population abundant in situ (Methanothrix). This strategic cultivation successfully established enrichment cultures that were mainly comprised of Ca. Patescibacteria (family level lineage Ca. Yanofskybacteria/UBA5738) and Methanothrix, in which we found highly specific physical interactions between the two organisms. Microscopic observations based on transmission electron microscopy, target-specific fluorescence in situ hybridization, and metagenomic analyses showed evidence that the interaction is likely parasitic. The results show a novel cross-domain parasitism between Bacteria and Archaea and suggest that the amendment of host Archaea may be an effective approach in culturing novel Ca. Patescibacteria.}, }
@article {pmid36030953, year = {2022}, author = {Gou, Y and Song, Y and Yang, S and Yang, Y and Cheng, Y and Li, J and Zhang, T and Cheng, Y and Wang, H}, title = {Polycyclic aromatic hydrocarbon removal from subsurface soil mediated by bacteria and archaea under methanogenic conditions: Performance and mechanisms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {313}, number = {}, pages = {120023}, doi = {10.1016/j.envpol.2022.120023}, pmid = {36030953}, issn = {1873-6424}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; Carbon Dioxide/metabolism ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {In situ anoxic bioremediation is an easy-to-use technology to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated soil. Degradation of PAHs mediated by soil bacteria and archaea using CO2 as the electron acceptor is an important process for eliminating PAHs under methanogenic conditions; however, knowledge of the performance and mechanisms involved is poorly unveiled. In this study, the effectiveness and efficiency of NaHCO3 (CO2) as an electron acceptor to stimulate the degradation of PAHs by bacteria and archaea in highly contaminated soil were investigated. The results showed that CO2 addition (EC2000) promoted PAH degradation compared to soil without added CO2 (EC0), with 4.18%, 9.01%-8.05%, and 6.19%-12.45% increases for 2-, 3- and 4-ring PAHs after 250 days of incubation, respectively. Soil bacterial abundances increased with increasing incubation time, especially for EC2000 (2.90 × 10[8] g[-1] soil higher than EC0, p < 0.05). Different succession patterns of the soil bacterial and archaeal communities during PAH degradation were observed. According to the PCoA and ANOSIM results, the soil bacterial communities were greatly (ANOSIM: R = 0.7232, P = 0.001) impacted by electron acceptors, whereas significant differences in the archaeal communities were not observed (ANOSIM: R = 0.553, P = 0.001). Soil bacterial and archaeal co-occurrence network analyses showed that positive correlations outnumbered the negative correlations throughout the incubation period for both treatments (e.g., EC0 and EC2000), suggesting the prevalence of coexistence/cooperation within and between these two domains rather than competition. The higher complexity, connectance, edge, and node numbers in EC2000 revealed stronger linkage and a more stable co-occurrence network compared to EC0. The results of this study could improve the knowledge on the removal of PAHs and the responses of soil bacteria and archaea to CO2 application, as well as a scientific basis for the in situ anoxic bioremediation of PAH-contaminated industrial sites.}, }
@article {pmid36029340, year = {2022}, author = {Amores, GR and Zepeda-Ramos, G and García-Fajardo, LV and Hernández, E and Guillén-Navarro, K}, title = {The gut microbiome analysis of Anastrepha obliqua reveals inter-kingdom diversity: bacteria, fungi, and archaea.}, journal = {Archives of microbiology}, volume = {204}, number = {9}, pages = {579}, pmid = {36029340}, issn = {1432-072X}, mesh = {Animals ; Archaea ; Bacteria ; Fungi ; *Gastrointestinal Microbiome ; Male ; *Tephritidae ; }, abstract = {The fruit fly Anastrepha obliqua is an economically important pest. The sterile insect technique to control it involves mass production and release of sterile flies to reduce the reproduction of the wild population. As noted in different Tephritidae, the performance of sterile males may be affected by the assimilation of nutrients under mass-rearing conditions. In the wild, the fly's life cycle suggests the acquisition of different organisms that could modulate its fitness and physiology. For A. obliqua, there is no information regarding microorganisms other than bacteria. This study analyzed bacteria, fungal, and archaea communities in the A. obliqua gut through denaturing gradient gel electrophoresis (DGGE) profiles of 16S (using a different set of primers for bacteria and archaea) and 18S ribosomal DNA markers. We found that wild flies presented higher microbial diversity related to fructose assimilation than laboratory species, suggesting that microorganisms have led to a specialized metabolism to process nutrients associated with an artificial diet. We identified species that have not been previously described in this fruit fly, especially actinobacteria and archaea, by employing different primer sets aimed at the same molecular marker but targeting diverse hypervariable regions of 16S rDNA. The possibility that Archaea affect fly fitness should not be ignored. This report on the intestinal microbial (bacteria, archaea, and fungi) composition of A. obliqua contributes to our understanding of the role of microorganisms in the development and physiology of the flies.}, }
@article {pmid36009875, year = {2022}, author = {Alharbi, F and Knura, T and Siebers, B and Ma, K}, title = {Thermostable and O2-Insensitive Pyruvate Decarboxylases from Thermoacidophilic Archaea Catalyzing the Production of Acetaldehyde.}, journal = {Biology}, volume = {11}, number = {8}, pages = {}, pmid = {36009875}, issn = {2079-7737}, abstract = {Pyruvate decarboxylase (PDC) is a key enzyme involved in ethanol fermentation, and it catalyzes the decarboxylation of pyruvate to acetaldehyde and CO2. Bifunctional PORs/PDCs that also have additional pyruvate:ferredoxin oxidoreductase (POR) activity are found in hyperthermophiles, and they are mostly oxygen-sensitive and CoA-dependent. Thermostable and oxygen-stable PDC activity is highly desirable for biotechnological applications. The enzymes from the thermoacidophiles Saccharolobus (formerly Sulfolobus) solfataricus (Ss, Topt = 80 °C) and Sulfolobus acidocaldarius (Sa, Topt = 80 °C) were purified and characterized, and their biophysical and biochemical properties were determined comparatively. Both enzymes were shown to be heterodimeric, and their two subunits were determined by SDS-PAGE to be 37 ± 3 kDa and 65 ± 2 kDa, respectively. The purified enzymes from S. solfataricus and S. acidocaldarius showed both PDC and POR activities which were CoA-dependent, and they were thermostable with half-life times of 2.9 ± 1 and 1.1 ± 1 h at 80 °C, respectively. There was no loss of activity in the presence of oxygen. Optimal pH values for their PDC and POR activity were determined to be 7.9 and 8.6, respectively. In conclusion, both thermostable SsPOR/PDC and SaPOR/PDC catalyze the CoA-dependent production of acetaldehyde from pyruvate in the presence of oxygen.}, }
@article {pmid36005527, year = {2022}, author = {Grivard, A and Goubet, I and Duarte Filho, LMS and Thiéry, V and Chevalier, S and de Oliveira-Junior, RG and El Aouad, N and Guedes da Silva Almeida, JR and Sitarek, P and Quintans-Junior, LJ and Grougnet, R and Agogué, H and Picot, L}, title = {Archaea Carotenoids: Natural Pigments with Unexplored Innovative Potential.}, journal = {Marine drugs}, volume = {20}, number = {8}, pages = {}, pmid = {36005527}, issn = {1660-3397}, mesh = {*Archaea/metabolism ; Biotechnology ; *Carotenoids/metabolism ; Pigmentation ; }, abstract = {For more than 40 years, marine microorganisms have raised great interest because of their major ecological function and their numerous applications for biotechnology and pharmacology. Particularly, Archaea represent a resource of great potential for the identification of new metabolites because of their adaptation to extreme environmental conditions and their original metabolic pathways, allowing the synthesis of unique biomolecules. Studies on archaeal carotenoids are still relatively scarce and only a few works have focused on their industrial scale production and their biotechnological and pharmacological properties, while the societal demand for these bioactive pigments is growing. This article aims to provide a comprehensive review of the current knowledge on carotenoid metabolism in Archaea and the potential applications of these pigments in biotechnology and medicine. After reviewing the ecology and classification of these microorganisms, as well as their unique cellular and biochemical characteristics, this paper highlights the most recent data concerning carotenoid metabolism in Archaea, the biological properties of these pigments, and biotechnological considerations for their production at industrial scale.}, }
@article {pmid35992648, year = {2022}, author = {Yoshinaga, M and Nakayama, T and Inagaki, Y}, title = {A novel structural maintenance of chromosomes (SMC)-related protein family specific to Archaea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {913088}, pmid = {35992648}, issn = {1664-302X}, abstract = {The ATPases belonging to the structural maintenance of chromosomes (SMC) superfamily are involved in the maintenance of chromosome organization and dynamics, as well as DNA repair. The major proteins in this superfamily recognized to date are either conserved among the three domains of Life (i.e., SMC and Rad50) or specific to Bacteria (i.e., RecF, RecN, and MukB). In Archaea, no protein related to SMC (SMC-related protein) with a broad taxonomic distribution has been reported. Nevertheless, two SMC-related proteins, namely coalescin and Sph, have been identified in crenarchaea Sulfolobus spp. and the euryarchaeon Halobacterium salinarum, respectively, hinting that the diversity of SMC-related proteins has been overlooked in Archaea. In this study, we report a novel SMC-related protein that is distributed among broad archaeal lineages and termed "Archaea-specific SMC-related proteins" or "ASRPs." We further demonstrate that the ASRP family encloses both coalescin and Sph but the two proteins represent only a tip of the diversity of this family.}, }
@article {pmid35985606, year = {2022}, author = {Mafra, D and Ribeiro, M and Fonseca, L and Regis, B and Cardozo, LFMF and Fragoso Dos Santos, H and Emiliano de Jesus, H and Schultz, J and Shiels, PG and Stenvinkel, P and Rosado, A}, title = {Archaea from the gut microbiota of humans: Could be linked to chronic diseases?.}, journal = {Anaerobe}, volume = {77}, number = {}, pages = {102629}, doi = {10.1016/j.anaerobe.2022.102629}, pmid = {35985606}, issn = {1095-8274}, mesh = {Humans ; Archaea/genetics ; *Gastrointestinal Microbiome ; Methanobrevibacter/genetics ; *Euryarchaeota ; Methane ; Chronic Disease ; }, abstract = {Archaea comprise a unique domain of organisms with distinct biochemical and genetic differences from bacteria. Methane-forming archaea, methanogens, constitute the predominant group of archaea in the human gut microbiota, with Methanobrevibacter smithii being the most prevalent. However, the effect of methanogenic archaea and their methane production on chronic disease remains controversial. As perturbation of the microbiota is a feature of chronic conditions, such as cardiovascular disease, neurodegenerative diseases and chronic kidney disease, assessing the influence of archaea could provide a new clue to mitigating adverse effects associated with dysbiosis. In this review, we will discuss the putative role of archaea in the gut microbiota in humans and the possible link to chronic diseases.}, }
@article {pmid35968005, year = {2022}, author = {Peng, Y and Xie, T and Wu, Z and Zheng, W and Zhang, T and Howe, S and Chai, J and Deng, F and Li, Y and Zhao, J}, title = {Archaea: An under-estimated kingdom in livestock animals.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {973508}, pmid = {35968005}, issn = {2297-1769}, abstract = {Archaea are considered an essential group of gut microorganisms in both humans and animals. However, they have been neglected in previous studies, especially those involving non-ruminants. In this study, we re-analyzed published metagenomic and metatranscriptomic data sequenced from matched samples to explore the composition and the expression activity of gut archaea in ruminants (cattle and sheep) and monogastric animals (pig and chicken). Our results showed that the alpha and beta diversity of each host species, especially cattle and chickens, calculated from metagenomic and metatranscriptomic data were significantly different, suggesting that metatranscriptomic data better represent the functional status of archaea. We detected that the relative abundance of 17 (cattle), 7 (sheep), 20 (pig), and 2 (chicken) archaeal species were identified in the top 100 archaeal taxa when analyzing the metagenomic datasets, and these species were classified as the "active archaeal species" for each host species by comparison with corresponding metatranscriptomic data. For example, The expressive abundance in metatranscriptomic dataset of Methanosphaera cuniculi and Methanosphaera stadtmanae were 30- and 27-fold higher than that in metagenomic abundance, indicating their potentially important function in the pig gut. Here we aim to show the potential importance of archaea in the livestock digestive tract and encourage future research in this area, especially on the gut archaea of monogastric animals.}, }
@article {pmid35965098, year = {2022}, author = {Zhao, H and Zhang, L}, title = {Metagenome-assembled Genomes of Six Novel Ammonia-oxidizing Archaea (AOA) from Agricultural Upland Soil.}, journal = {Microbes and environments}, volume = {37}, number = {3}, pages = {}, pmid = {35965098}, issn = {1347-4405}, mesh = {*Ammonia/metabolism ; *Archaea ; Bacteria ; Metagenome ; Nitrites/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA), key players in agricultural upland soil nitrification, convert soil ammonium to nitrite. The microbial oxidation of ammonia to nitrite is an important part of the global biogeochemical nitrogen cycle. In the present study, we recovered six novel AOA metagenome-assembled genomes (MAGs) containing genes for carbon (C) fixation and nitrogen (N) metabolism by using a deep shotgun metagenomic sequencing strategy. We also found that these AOA MAGs possessed cobalamin synthesis genes, suggesting that AOA are vitamin suppliers in agricultural upland soil. Collectively, the present results deepen our understanding of the metabolic potential and phylogeny of AOA in agroecosystems.}, }
@article {pmid35922624, year = {2022}, author = {Ledesma, L and Hernandez-Guerrero, R and Perez-Rueda, E}, title = {Prediction of DNA-Binding Transcription Factors in Bacteria and Archaea Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2516}, number = {}, pages = {103-112}, pmid = {35922624}, issn = {1940-6029}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; DNA/metabolism ; *Genome, Archaeal/genetics ; Genome, Bacterial ; Humans ; *Transcription Factors/metabolism ; }, abstract = {DNA-binding transcription factors (TFs) play a central role in the gene expression of all organisms, from viruses to humans, including bacteria and archaea. The role of these proteins is the fate of gene expression in the context of environmental challenges. Because thousands of genomes have been sequenced to date, predictions of the encoded proteins are validated through the use of bioinformatics tools to obtain the necessary experimental, posterior knowledge. In this chapter, we describe three approaches to identify TFs in protein sequences. The first approach integrates the results of sequence comparisons and PFAM assignments, using as reference a manually curated collection of TFs. The second approach considers the prediction of DNA-binding structures, such as the classical helix-turn-helix (HTH); and the third approach considers a deep learning model. We suggest that all approaches must be considered together to increase the possibility of identifying new TFs in bacterial and archaeal genomes.}, }
@article {pmid35922623, year = {2022}, author = {Sybers, D and Charlier, D and Peeters, E}, title = {In Vitro Transcription Assay for Archaea Belonging to Sulfolobales.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2516}, number = {}, pages = {81-102}, pmid = {35922623}, issn = {1940-6029}, mesh = {*Archaea/genetics/metabolism ; *Archaeal Proteins/chemistry ; DNA-Binding Proteins/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Sulfolobales/genetics/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; }, abstract = {Archaeal transcription and its regulation are characterized by a mosaic of eukaryotic and bacterial features. Molecular analysis of the functioning of the archaeal RNA polymerase, basal transcription factors, and specific promoter-containing DNA templates allows to unravel the mechanisms of transcription regulation in archaea. In vitro transcription is a technique that allows the study of this process in a simplified and controlled environment less complex than the archaeal cell. In this chapter, we present an in vitro transcription methodology for the study of transcription in Sulfolobales. It is described how to purify the RNA polymerase and the basal transcription factors TATA-binding protein and transcription factor B of Saccharolobus solfataricus and how to perform in vitro transcription reactions and transcript detection. Application of this protocol for other archaeal species could require minor modifications to protein overexpression and purification conditions.}, }
@article {pmid35922619, year = {2022}, author = {Maruyama, H}, title = {Micrococcal Nuclease Digestion Assays for the Analysis of Chromosome Structure in Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2516}, number = {}, pages = {29-38}, pmid = {35922619}, issn = {1940-6029}, mesh = {*Archaea/genetics/metabolism ; Chromatin/genetics ; DNA/genetics ; Digestion ; *Micrococcal Nuclease/metabolism ; Nucleosomes ; }, abstract = {The digestion of chromosomes using micrococcal nuclease (MNase) enables the analysis of their fundamental structural units. For example, the digestion of eukaryotic chromatin using MNase results in laddered DNA fragments (~150 bp increment), which reflects the length of the DNA wrapped around regularly spaced nucleosomes. Here, we describe the application of MNase to examine the chromosome structure in Archaea. We used Thermococcus kodakarensis, a hyperthermophilic euryarchaeon that encodes proteins homologous to eukaryotic histones. Methods for chromosome extraction and agarose gel electrophoresis of MNase-digested DNA including small fragments (~30 bp) are also described.}, }
@article {pmid35922618, year = {2022}, author = {Rashid, FM and Detmar, L and Dame, RT}, title = {Chromosome Conformation Capture in Bacteria and Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2516}, number = {}, pages = {1-28}, pmid = {35922618}, issn = {1940-6029}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Chromatin/genetics ; *Chromosomes/genetics ; High-Throughput Nucleotide Sequencing/methods ; Nucleic Acid Conformation ; }, abstract = {The three-dimensional structure of the chromosome is encoded within its sequence and regulates activities such as replication and transcription. This necessitates the study of the spatial organization of the chromosome in relation to the underlying sequence. Chromosome conformation capture (3C) techniques are proximity ligation-based approaches that simplify the three-dimensional architecture of the chromosome into a one-dimensional library of hybrid ligation junctions. Deciphering the information contained in these libraries resolves chromosome architecture in a sequence-specific manner. This chapter describes the preparation of 3C libraries for bacteria and archaea. It details how the three-dimensional architecture of local chromatin can be extracted from the 3C library using qPCR (3C-qPCR), and it summarizes the processing of 3C libraries for next-generation sequencing (3C-Seq) for a study of global chromosome organization.}, }
@article {pmid35922580, year = {2022}, author = {Wang, BB and Sun, YP and Wu, ZP and Zheng, XW and Hou, J and Cui, HL}, title = {Halorientalis salina sp. nov., Halorientalis marina sp. nov., Halorientalis litorea sp. nov.: three extremely halophilic archaea isolated from a salt lake and coarse sea salt.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {3}, pages = {26}, pmid = {35922580}, issn = {1433-4909}, mesh = {Base Composition ; China ; DNA, Archaeal/genetics ; Glycolipids/metabolism ; *Halobacteriaceae ; *Lakes ; Phosphatidic Acids/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Three halophilic archaeal strains, NEN8[T], GDY88[T] and ZY14[T], were isolated from a salt lake in Tibet and coarse sea salt samples from Guangdong and Hebei, China, respectively. These strains formed three separate clades (showing 94.4-95.8% and 87.1-89.4% similarities, respectively) and then clustered with the current Halorientalis members (showing 90.7-97.6% and 87.0-91.2% similarities, respectively), as revealed by phylogenetic analyses based on 16S rRNA and rpoB' genes. The overall genome-related index, average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), average amino acid identity (AAI) and the percentage of conserved proteins (POCP) values, among the three strains and members of the genus Halorientalis were 76.0-88.0%, 21.3-37.2%, 69.0-88.3% and 57.7-78.1%, clearly below the threshold values for species demarcation. Strains NEN8[T], GDY88[T] and ZY14[T] could be distinguished from current Halorientalis species according to differential phenotypic characteristics. The major polar lipids of the three strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). In addition, mannosyl glucosyl diether (DGD-1) was detected in strain NEN8[T] and phosphatidic acid (PA), posssulfated galactosyl mannosyl glucosyl diether (S-TGD-1) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA) were observed in strain ZY14[T]. These results revealed that strains NEN8[T] (= CGMCC 1.17213[T] = JCM 34155[T]), GDY88[T] (= CGMCC 1.18548[T] = JCM 34481[T]) and ZY14[T] (= CGMCC 1.17178[T] = JCM 34154[T]) represent three novel species of the genus Halorientalis, for which the names Halorientalis salina sp. nov., Halorientalis marina sp. nov. and Halorientalis litorea sp. nov. are proposed.}, }
@article {pmid35917471, year = {2022}, author = {Wegener, G and Laso-Pérez, R and Orphan, VJ and Boetius, A}, title = {Anaerobic Degradation of Alkanes by Marine Archaea.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {553-577}, doi = {10.1146/annurev-micro-111021-045911}, pmid = {35917471}, issn = {1545-3251}, mesh = {*Alkanes/metabolism ; Anaerobiosis ; *Archaea ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Alkanes are saturated apolar hydrocarbons that range from their simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea.}, }
@article {pmid35905325, year = {2022}, author = {Rattanasriampaipong, R and Zhang, YG and Pearson, A and Hedlund, BP and Zhang, S}, title = {Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {31}, pages = {e2123193119}, pmid = {35905325}, issn = {1091-6490}, mesh = {*Ammonia/metabolism ; *Archaea/genetics ; *Diglycerides ; *Evolution, Molecular ; *Membrane Lipids ; Oxidation-Reduction ; Phylogeny ; Water ; }, abstract = {Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal and nonthermal behaviors of archaeal glycerol dialkyl glycerol tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX86) to the ratio of GDGTs with two and three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX86 and decrease GDGT-2/GDGT-3 when the ambient temperature increases. This presumed temperature-dependent (PTD) trend is observed in GDGTs derived from cultures of thermophilic and mesophilic AOA. The distribution of GDGTs in suspended particulate matter (SPM) and sediments collected from above the pycnocline-shallow water samples-also follows the PTD trend. These similar GDGT distributions between AOA cultures and shallow water environmental samples reflect shallow ecotypes of marine AOA. While there are currently no cultures of deep AOA clades, GDGTs derived from deep water SPM and marine sediment samples exhibit nonthermal behavior deviating from the PTD trend. The presence of deep AOA increases the GDGT-2/GDGT-3 ratio and distorts the temperature-controlled correlation between GDGT-2/GDGT-3 and TEX86. We then used Gaussian mixture models to statistically characterize these diagnostic patterns of modern AOA ecology from paleo-GDGT records to infer the evolution of marine AOA from the Mid-Mesozoic to the present. Long-term GDGT-2/GDGT-3 trends suggest a suppression of today's deep water marine AOA during the Mesozoic-early Cenozoic greenhouse climates. Our analysis provides invaluable insights into the evolutionary timeline and the expansion of AOA niches associated with major oceanographic and climate changes.}, }
@article {pmid35886964, year = {2022}, author = {Chong, PL and Chang, A and Yu, A and Mammedova, A}, title = {Vesicular and Planar Membranes of Archaea Lipids: Unusual Physical Properties and Biomedical Applications.}, journal = {International journal of molecular sciences}, volume = {23}, number = {14}, pages = {}, pmid = {35886964}, issn = {1422-0067}, mesh = {*Archaea ; Lipids ; *Liposomes ; Membranes ; Protons ; }, abstract = {Liposomes and planar membranes made of archaea or archaea-like lipids exhibit many unusual physical properties compared to model membranes composed of conventional diester lipids. Here, we review several recent findings in this research area, which include (1) thermosensitive archaeosomes with the capability to drastically change the membrane surface charge, (2) MthK channel's capability to insert into tightly packed tetraether black lipid membranes and exhibit channel activity with surprisingly high calcium sensitivity, and (3) the intercalation of apolar squalane into the midplane space of diether bilayers to impede proton permeation. We also review the usage of tetraether archaeosomes as nanocarriers of therapeutics and vaccine adjuvants, as well as the biomedical applications of planar archaea lipid membranes. The discussion on archaeosomal therapeutics is focused on partially purified tetraether lipid fractions such as the polar lipid fraction E (PLFE) and glyceryl caldityl tetraether (GCTE), which are the main components of PLFE with the sugar and phosphate removed.}, }
@article {pmid35880875, year = {2022}, author = {Boswinkle, K and McKinney, J and Allen, KD}, title = {Highlighting the Unique Roles of Radical S-Adenosylmethionine Enzymes in Methanogenic Archaea.}, journal = {Journal of bacteriology}, volume = {204}, number = {8}, pages = {e0019722}, pmid = {35880875}, issn = {1098-5530}, mesh = {Archaea/genetics/metabolism ; Catalysis ; *Greenhouse Gases/metabolism ; *Iron-Sulfur Proteins/metabolism ; S-Adenosylmethionine/chemistry/metabolism ; }, abstract = {Radical S-adenosylmethionine (SAM) enzymes catalyze an impressive variety of difficult biochemical reactions in various pathways across all domains of life. These metalloenzymes employ a reduced [4Fe-4S] cluster and SAM to generate a highly reactive 5'-deoxyadenosyl radical that is capable of initiating catalysis on otherwise unreactive substrates. Interestingly, the genomes of methanogenic archaea encode many unique radical SAM enzymes with underexplored or completely unknown functions. These organisms are responsible for the yearly production of nearly 1 billion tons of methane, a potent greenhouse gas as well as a valuable energy source. Thus, understanding the details of methanogenic metabolism and elucidating the functions of essential enzymes in these organisms can provide insights into strategies to decrease greenhouse gas emissions as well as inform advances in bioenergy production processes. This minireview provides an overview of the current state of the field regarding the functions of radical SAM enzymes in methanogens and discusses gaps in knowledge that should be addressed.}, }
@article {pmid35852729, year = {2022}, author = {Flusche, T and Rajan, R}, title = {Molecular Details of DNA Integration by CRISPR-Associated Proteins During Adaptation in Bacteria and Archaea.}, journal = {Advances in experimental medicine and biology}, volume = {}, number = {}, pages = {}, pmid = {35852729}, issn = {0065-2598}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in bacteria and archaea, where immunological memory is retained in the CRISPR locus as short pieces of the intruding nucleic acid, termed spacers. The adaptation to new infections occurs through the integration of a new spacer into the CRISPR array. For immune protection, spacers are transcribed into CRISPR RNAs (crRNA) that are used to guide the effector nuclease of the system in sequence-dependent target cleavage. Spacers originate as a prespacer from either DNA or RNA depending on the CRISPR-Cas system being observed, and the nearly universal Cas proteins, Cas1 and Cas2, insert the prespacer into the CRISPR locus during adaptation in all systems that contain them. The mechanism of site-specific prespacer integration varies across CRISPR classes and types, and distinct differences can even be found within the same subtype. In this review, the current knowledge on the mechanisms of prespacer integration in type II-A CRISPR-Cas systems will be described. Comparisons of the currently characterized type II-A systems show that distinct mechanisms exist within different members of this subtype and are correlated to sequence-specific interactions of Cas proteins and the DNA elements present in the CRISPR array. These observations indicate that nature has fine-tuned the mechanistic details while performing the basic step of DNA integration by Cas proteins, which offers unique advantages to develop Cas1-Cas2-based biotechnology.}, }
@article {pmid35811376, year = {2022}, author = {Villain, P and Catchpole, R and Forterre, P and Oberto, J and da Cunha, V and Basta, T}, title = {Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea.}, journal = {Molecular biology and evolution}, volume = {39}, number = {8}, pages = {}, pmid = {35811376}, issn = {1537-1719}, mesh = {*Archaea/genetics/metabolism ; Bacteria/genetics ; *DNA Gyrase/genetics ; DNA Topoisomerases, Type I/genetics ; Gene Transfer, Horizontal ; }, abstract = {DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, DNA gyrase has an essential role in the homeostatic regulation of supercoiling. While ubiquitous in bacteria, DNA gyrase was previously reported to have a patchy distribution in Archaea but its emergent function and evolutionary history in this domain of life remains elusive. In this study, we used phylogenomic approaches and an up-to date sequence dataset to establish global and archaea-specific phylogenies of DNA gyrases. The most parsimonious evolutionary scenario infers that DNA gyrase was introduced into the lineage leading to Euryarchaeal group II via a single horizontal gene transfer from a bacterial donor which we identified as an ancestor of Gracilicutes and/or Terrabacteria. The archaea-focused trees indicate that DNA gyrase spread from Euryarchaeal group II to some DPANN and Asgard lineages via rare horizontal gene transfers. The analysis of successful recent transfers suggests a requirement for syntropic or symbiotic/parasitic relationship between donor and recipient organisms. We further show that the ubiquitous archaeal Topoisomerase VI may have co-evolved with DNA gyrase to allow the division of labor in the management of topological constraints. Collectively, our study reveals the evolutionary history of DNA gyrase in Archaea and provides testable hypotheses to understand the prerequisites for successful establishment of DNA gyrase in a naive archaeon and the associated adaptations in the management of topological constraints.}, }
@article {pmid35810262, year = {2022}, author = {Ou, YF and Dong, HP and McIlroy, SJ and Crowe, SA and Hallam, SJ and Han, P and Kallmeyer, J and Simister, RL and Vuillemin, A and Leu, AO and Liu, Z and Zheng, YL and Sun, QL and Liu, M and Tyson, GW and Hou, LJ}, title = {Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis.}, journal = {The ISME journal}, volume = {16}, number = {10}, pages = {2373-2387}, pmid = {35810262}, issn = {1751-7370}, mesh = {Archaea/genetics/metabolism ; Cytochromes/genetics ; Cytochromes b/genetics/metabolism ; *Euryarchaeota/metabolism ; *Hydrogenase/metabolism ; Methane/metabolism ; Phylogeny ; }, abstract = {Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.}, }
@article {pmid35796992, year = {2022}, author = {Kern, M and Ferreira-Cerca, S}, title = {Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2533}, number = {}, pages = {229-246}, pmid = {35796992}, issn = {1940-6029}, mesh = {Alkynes/chemistry ; *Amino Acids/metabolism ; Archaea/metabolism ; *Azides/chemistry ; Click Chemistry/methods ; Proteins/chemistry ; Proteomics/methods ; }, abstract = {The study of protein production and degradation in a quantitative and time-dependent manner is a major challenge to better understand cellular physiological response. Among available technologies bioorthogonal noncanonical amino acid tagging (BONCAT) is an efficient approach allowing for time-dependent labeling of proteins through the incorporation of chemically reactive noncanonical amino acids like L-azidohomoalanine (L-AHA). The azide-containing amino-acid derivative enables a highly efficient and specific reaction termed click chemistry, whereby the azide group of the L-AHA reacts with a reactive alkyne derivate, like dibenzocyclooctyne (DBCO) derivatives, using strain-promoted alkyne-azide cycloaddition (SPAAC). Moreover, available DBCO containing reagents are versatile and can be coupled to fluorophore (e.g., Cy7) or affinity tag (e.g., biotin) derivatives, for easy visualization and affinity purification, respectively.Here, we describe a step-by-step BONCAT protocol optimized for the model archaeon Haloferax volcanii , but which is also suitable to harness other biological systems. Finally, we also describe examples of downstream visualization, affinity purification of L-AHA-labeled proteins and differential expression analysis.In conclusion, the following BONCAT protocol expands the available toolkit to explore proteostasis using time-resolved semiquantitative proteomic analysis in archaea .}, }
@article {pmid35773279, year = {2022}, author = {Buessecker, S and Palmer, M and Lai, D and Dimapilis, J and Mayali, X and Mosier, D and Jiao, JY and Colman, DR and Keller, LM and St John, E and Miranda, M and Gonzalez, C and Gonzalez, L and Sam, C and Villa, C and Zhuo, M and Bodman, N and Robles, F and Boyd, ES and Cox, AD and St Clair, B and Hua, ZS and Li, WJ and Reysenbach, AL and Stott, MB and Weber, PK and Pett-Ridge, J and Dekas, AE and Hedlund, BP and Dodsworth, JA}, title = {An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3773}, pmid = {35773279}, issn = {2041-1723}, mesh = {Anaerobiosis ; *Archaea/metabolism ; Metagenome ; Phylogeny ; *Tungsten ; }, abstract = {Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.}, }
@article {pmid35770746, year = {2022}, author = {Cai, M and Tang, X}, title = {Human Archaea and Associated Metabolites in Health and Disease.}, journal = {Biochemistry}, volume = {61}, number = {24}, pages = {2835-2840}, doi = {10.1021/acs.biochem.2c00232}, pmid = {35770746}, issn = {1520-4995}, abstract = {Trillions of microorganisms, including bacteria, archaea, fungi, and viruses, live in or on the human body. Microbe-microbe and microbe-host interactions are often influenced by diffusible and microbe-associated small molecules. Over the past few years, it has become evident that these interactions have a substantial impact on human health and disease. In this Perspective, we summarize the research involving the discovery of methanogenic and non-methanogenic archaea associated with the human body. In particular, we emphasize the importance of some archaeal metabolites in mediating intra- and interspecies interactions in the ecological environment of the human body. A deep understanding of the archaeal metabolites as well as their biological functions may reveal in more detail whether and how archaea are involved in maintaining human health and/or causing certain diseases.}, }
@article {pmid35765181, year = {2022}, author = {Kropp, C and Lipp, J and Schmidt, AL and Seisenberger, C and Linde, M and Hinrichs, KU and Babinger, P}, title = {Identification of acetylated diether lipids in halophilic Archaea.}, journal = {MicrobiologyOpen}, volume = {11}, number = {3}, pages = {e1299}, pmid = {35765181}, issn = {2045-8827}, mesh = {*Archaea/metabolism ; *Bacillales ; Ethers/chemistry/metabolism ; Mass Spectrometry ; Terpenes/metabolism ; }, abstract = {As a hallmark of Archaea, their cell membranes are comprised of ether lipids. However, Archaea-type ether lipids have recently been identified in Bacteria as well, with a somewhat different composition: In Bacillales, sn-glycerol 1-phosphate is etherified with one C35 isoprenoid chain, which is longer than the typical C20 chain in Archaea, and instead of a second isoprenoid chain, the product heptaprenylglyceryl phosphate becomes dephosphorylated and afterward diacetylated by the O-acetyltransferase YvoF. Interestingly, database searches have revealed YvoF homologs in Halobacteria (Archaea), too. Here, we demonstrate that YvoF from Haloferax volcanii can acetylate geranylgeranylglycerol in vitro. Additionally, we present the first-time identification of acetylated diether lipids in H. volcanii and Halobacterium salinarum by mass spectrometry. A variety of different acetylated lipids, namely acetylated archaeol, and acetylated archaetidylglycerol, were found, suggesting that halobacterial YvoF has a broad substrate range. We suppose that the acetyl group might serve to modify the polarity of the lipid headgroup, with still unknown biological effects.}, }
@article {pmid35761090, year = {2022}, author = {Banciu, HL and Gridan, IM and Zety, AV and Baricz, A}, title = {Asgard archaea in saline environments.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {2}, pages = {21}, pmid = {35761090}, issn = {1433-4909}, mesh = {*Archaea ; Eukaryotic Cells/metabolism ; *Genome, Archaeal ; Metagenome ; Phylogeny ; }, abstract = {Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.}, }
@article {pmid35760837, year = {2022}, author = {Rambo, IM and Langwig, MV and Leão, P and De Anda, V and Baker, BJ}, title = {Genomes of six viruses that infect Asgard archaea from deep-sea sediments.}, journal = {Nature microbiology}, volume = {7}, number = {7}, pages = {953-961}, pmid = {35760837}, issn = {2058-5276}, mesh = {*Archaea/genetics/metabolism ; Eukaryota/genetics ; Genome, Archaeal ; Metagenome ; Phylogeny ; *Viruses/genetics ; }, abstract = {Asgard archaea are globally distributed prokaryotic microorganisms related to eukaryotes; however, viruses that infect these organisms have not been described. Here, using metagenome sequences recovered from deep-sea hydrothermal sediments, we characterize six relatively large (up to 117 kb) double-stranded DNA (dsDNA) viral genomes that infected two Asgard archaeal phyla, Lokiarchaeota and Helarchaeota. These viruses encode Caudovirales-like structural proteins, as well as proteins distinct from those described in known archaeal viruses. Their genomes contain around 1-5% of genes associated with eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs) and appear to be capable of semi-autonomous genome replication, repair, epigenetic modifications and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. Genomic analysis of these Asgard viruses reveals that they contain features of both prokaryotic and eukaryotic viruses, and provides insights into their potential infection and host interaction mechanisms.}, }
@article {pmid35759872, year = {2022}, author = {Garcia, PS and Gribaldo, S and Borrel, G}, title = {Diversity and Evolution of Methane-Related Pathways in Archaea.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {727-755}, doi = {10.1146/annurev-micro-041020-024935}, pmid = {35759872}, issn = {1545-3251}, mesh = {*Archaea ; *Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase complex (Mcr). Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.}, }
@article {pmid35751084, year = {2022}, author = {Xiong, X and Rao, Y and Tu, X and Wang, Z and Gong, J and Yang, Y and Wu, H and Liu, X}, title = {Gut archaea associated with bacteria colonization and succession during piglet weaning transitions.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {243}, pmid = {35751084}, issn = {1746-6148}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Mucorales ; *Physical Conditioning, Animal ; Swine ; Weaning ; }, abstract = {BACKGROUND: Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods.<br><br>RESULTS: We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3.<br><br>CONCLUSION: Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions.}, }
@article {pmid35743947, year = {2022}, author = {Doytchinov, VV and Dimov, SG}, title = {Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {35743947}, issn = {2075-1729}, abstract = {Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.}, }
@article {pmid35741701, year = {2022}, author = {Ding, R and Yang, N and Liu, J}, title = {The Osmoprotectant Switch of Potassium to Compatible Solutes in an Extremely Halophilic Archaea Halorubrum kocurii 2020YC7.}, journal = {Genes}, volume = {13}, number = {6}, pages = {}, pmid = {35741701}, issn = {2073-4425}, mesh = {Betaine/metabolism ; *Halobacteriales ; *Halorubrum ; Potassium/metabolism ; Sodium Chloride/metabolism ; Trehalose ; }, abstract = {The main osmoadaptive mechanisms of extremely halophilic archaea include the "salt-in" strategy and the "compatible solutes" strategy. Here we report the osmoadaptive mechanism of an extremely halophilic archaea H. kocurii 2020YC7, isolated from a high salt environment sample. Genomic data revealed that strain 2020YC7 harbors genes trkA, trkH, kch for K[+] uptake, kefB for K[+] output, treS for trehalose production from polysaccharide, and betaine/carnitine/choline transporter family gene for glycine betaine uptake. Strain 2020YC7 could accumulate 8.17 to 28.67 μmol/mg protein K[+] in a defined medium, with its content increasing along with the increasing salinity from 100 to 200 g/L. When exogenous glycine betaine was added, glycine betaine functioned as the primary osmotic solute between 200 and 250 g/L NaCl, which was accumulated up to 15.27 mg/mg protein in 2020YC7 cells. RT-qPCR results completely confirmed these results. Notably, the concentrations of intracellular trehalose decreased from 5.26 to 2.61 mg/mg protein as the NaCl increased from 50 to 250 g/L. In combination with this result, the transcript level of gene treS, which catalyzes the production of trehalose from polysaccharide, was significantly up-regulated at 50-100 g/L NaCl. Therefore, trehalose does not act as an osmotic solute at high NaCl concentrations (more than 100 g/L) but at relatively low NaCl concentrations (50-100 g/L). And we propose that the degradation of cell wall polysaccharide, as a source of trehalose in a low-salt environment, may be one of the reasons for the obligate halophilic characteristics of strain 2020YC7.}, }
@article {pmid35720372, year = {2022}, author = {Krawczyk, KT and Locht, C and Kowalewicz-Kulbat, M}, title = {Halophilic Archaea Halorhabdus Rudnickae and Natrinema Salaciae Activate Human Dendritic Cells and Orient T Helper Cell Responses.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {833635}, pmid = {35720372}, issn = {1664-3224}, mesh = {Cytokines ; Dendritic Cells ; *Halobacteriaceae ; Humans ; *Interleukin-13/pharmacology ; T-Lymphocytes, Helper-Inducer ; }, abstract = {Halophilic archaea are procaryotic organisms distinct from bacteria, known to thrive in hypersaline environments, including salt lakes, salterns, brines and salty food. They have also been identified in the human microbiome. The biological significance of halophiles for human health has rarely been examined. The interactions between halophilic archaea and human dendritic cells (DCs) and T cells have not been identified so far. Here, we show for the first time that the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae activate human monocyte-derived DCs, induce DC maturation, cytokine production and autologous T cell activation. In vitro both strains induced DC up-regulation of the cell-surface receptors CD86, CD80 and CD83, and cytokine production, including IL-12p40, IL-10 and TNF-α, but not IL-23 and IL-12p70. Furthermore, autologous CD4[+] T cells produced significantly higher amounts of IFN-γ and IL-13, but not IL-17A when co-cultured with halophile-stimulated DCs in comparison to T cells co-cultured with unstimulated DCs. IFN-γ was almost exclusively produced by naïve T cells, while IL-13 was produced by both naïve and memory CD4[+] T cells. Our findings thus show that halophilic archaea are recognized by human DCs and are able to induce a balanced cytokine response. The immunomodulatory functions of halophilic archaea and their potential ability to re-establish the immune balance may perhaps participate in the beneficial effects of halotherapies.}, }
@article {pmid35706137, year = {2022}, author = {Hu, W and Hou, Q and Delgado-Baquerizo, M and Stegen, JC and Du, Q and Dong, L and Ji, M and Sun, Y and Yao, S and Gong, H and Xiong, J and Xia, R and Liu, J and Aqeel, M and Akram, MA and Ran, J and Deng, J}, title = {Continental-scale niche differentiation of dominant topsoil archaea in drylands.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5483-5497}, doi = {10.1111/1462-2920.16099}, pmid = {35706137}, issn = {1462-2920}, mesh = {*Archaea/genetics ; *Ecosystem ; Soil Microbiology ; Ammonia ; Soil ; Oxidation-Reduction ; Nitrification ; Phylogeny ; }, abstract = {Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e. deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world.}, }
@article {pmid35697693, year = {2022}, author = {Hatano, T and Palani, S and Papatziamou, D and Salzer, R and Souza, DP and Tamarit, D and Makwana, M and Potter, A and Haig, A and Xu, W and Townsend, D and Rochester, D and Bellini, D and Hussain, HMA and Ettema, TJG and Löwe, J and Baum, B and Robinson, NP and Balasubramanian, M}, title = {Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3398}, pmid = {35697693}, issn = {2041-1723}, support = {203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; WT101885MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaea/genetics/metabolism ; *Endosomal Sorting Complexes Required for Transport/metabolism ; *Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; Ubiquitin/genetics ; }, abstract = {The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, in processes that include ubiquitin-mediated multivesicular body formation, membrane repair, cytokinetic abscission, and virus exit from host cells. This ESCRT system appears to have simpler, ancient origins, since many archaeal species possess homologues of ESCRT-III and Vps4, the components that execute the final membrane scission reaction, where they have been shown to play roles in cytokinesis, extracellular vesicle formation and viral egress. Remarkably, metagenome assemblies of Asgard archaea, the closest known living relatives of eukaryotes, were recently shown to encode homologues of the entire cascade involved in ubiquitin-mediated membrane remodelling, including ubiquitin itself, components of the ESCRT-I and ESCRT-II subcomplexes, and ESCRT-III and Vps4. Here, we explore the phylogeny, structure, and biochemistry of Asgard homologues of the ESCRT machinery and the associated ubiquitylation system. We provide evidence for the ESCRT-I and ESCRT-II subcomplexes being involved in ubiquitin-directed recruitment of ESCRT-III, as it is in eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin for the ubiquitin-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.}, }
@article {pmid35695998, year = {2022}, author = {Verma, D and Kumar, V and Satyanarayana, T}, title = {Genomic attributes of thermophilic and hyperthermophilic bacteria and archaea.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {38}, number = {8}, pages = {135}, pmid = {35695998}, issn = {1573-0972}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genes, Archaeal ; Genomics ; Metagenome ; Phylogeny ; }, abstract = {Thermophiles and hyperthermophiles are immensely useful in understanding the evolution of life, besides their utility in environmental and industrial biotechnology. Advancements in sequencing technologies have revolutionized the field of microbial genomics. The massive generation of data enhances the sequencing coverage multi-fold and allows to analyse the entire genomic features of microbes efficiently and accurately. The mandate of a pure isolate can also be bypassed where whole metagenome-assembled genomes and single cell-based sequencing have fulfilled the majority of the criteria to decode various attributes of microbial genomes. A boom has, therefore, been seen in analysing the extremophilic bacteria and archaea using sequence-based approaches. Due to extensive sequence analysis, it becomes easier to understand the gene flow and their evolution among the members of bacteria and archaea. For instance, sequencing unveiled that Thermotoga maritima shares around 24% of genes of archaeal origin. Comparative and functional genomics provide an analytical view to understanding the microbial diversity of thermophilic bacteria and archaea, their interactions with other microbes, their adaptations, gene flow, and evolution over time. In this review, the genomic features of thermophilic bacteria and archaea are dealt with comprehensively.}, }
@article {pmid35667126, year = {2022}, author = {Gophna, U and Altman-Price, N}, title = {Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {481-502}, doi = {10.1146/annurev-micro-040820-124627}, pmid = {35667126}, issn = {1545-3251}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea-specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research.}, }
@article {pmid35665142, year = {2022}, author = {Selim, S and Akhtar, N and Hagagy, N and Alanazi, A and Warrad, M and El Azab, E and Elamir, MYM and Al-Sanea, MM and Jaouni, SKA and Abdel-Mawgoud, M and Shah, AA and Abdelgawad, H}, title = {Selection of Newly Identified Growth-Promoting Archaea Haloferax Species With a Potential Action on Cobalt Resistance in Maize Plants.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {872654}, pmid = {35665142}, issn = {1664-462X}, abstract = {Soil contamination with cobalt (Co) negatively impacts plant growth and production. To combat Co toxicity, plant growth-promoting microorganisms for improving plant growth are effectively applied. To this end, unclassified haloarchaeal species strain NRS_31 (OL912833), belonging to Haloferax genus, was isolated, identified for the first time, and applied to mitigate the Co phytotoxic effects on maize plants. This study found that high Co levels in soil lead to Co accumulation in maize leaves. Co accumulation in the leaves inhibited maize growth and photosynthetic efficiency, inducing oxidative damage in the tissue. Interestingly, pre-inoculation with haloarchaeal species significantly reduced Co uptake and mitigated the Co toxicity. Induced photosynthesis improved sugar metabolism, allocating more carbon to defend against Co stress. Concomitantly, the biosynthetic key enzymes involved in sucrose (sucrose-P-synthase and invertases) and proline (pyrroline-5- carboxylate synthetase (P5CS), pyrroline-5-carboxylate reductase (P5CR)) biosynthesis significantly increased to maintain plant osmotic potential. In addition to their osmoregulation potential, soluble sugars and proline can contribute to maintaining ROS hemostasis. Maize leaves managed their oxidative homeostasis by increasing the production of antioxidant metabolites (such as phenolics and tocopherols) and increasing the activity of ROS-scavenging enzymes (such as POX, CAT, SOD, and enzymes involved in the AsA/GSH cycle). Inside the plant tissue, to overcome heavy Co toxicity, maize plants increased the synthesis of heavy metal-binding ligands (metallothionein, phytochelatins) and the metal detoxifying enzymes (glutathione S transferase). Overall, the improved ROS homeostasis, osmoregulation, and Co detoxification systems were the basis underlying Co oxidative stress, mitigating haloarchaeal treatment's impact.}, }
@article {pmid35660788, year = {2022}, author = {Lim, JK and Yang, JI and Kim, YJ and Park, YJ and Kim, YH}, title = {Bioconversion of CO to formate by artificially designed carbon monoxide:formate oxidoreductase in hyperthermophilic archaea.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {539}, pmid = {35660788}, issn = {2399-3642}, mesh = {*Carbon Monoxide/metabolism ; Formate Dehydrogenases/genetics/metabolism ; Formates/metabolism ; Hydrogen/metabolism ; *Thermococcus/genetics/metabolism ; }, abstract = {Ferredoxin-dependent metabolic engineering of electron transfer circuits has been developed to enhance redox efficiency in the field of synthetic biology, e.g., for hydrogen production and for reduction of flavoproteins or NAD(P)[+]. Here, we present the bioconversion of carbon monoxide (CO) gas to formate via a synthetic CO:formate oxidoreductase (CFOR), designed as an enzyme complex for direct electron transfer between non-interacting CO dehydrogenase and formate dehydrogenase using an electron-transferring Fe-S fusion protein. The CFOR-introduced Thermococcus onnurineus mutant strains showed CO-dependent formate production in vivo and in vitro. The maximum formate production rate from purified CFOR complex and specific formate productivity from the bioreactor were 2.2 ± 0.2 μmol/mg/min and 73.1 ± 29.0 mmol/g-cells/h, respectively. The CO-dependent CO2 reduction/formate production activity of synthetic CFOR was confirmed, indicating that direct electron transfer between two unrelated dehydrogenases was feasible via mediation of the FeS-FeS fusion protein.}, }
@article {pmid35651488, year = {2022}, author = {Zhong, L and Qing, J and Liu, M and Cai, X and Li, G and Li, FY and Chen, G and Xu, X and Xue, K and Wang, Y}, title = {Fungi and Archaea Control Soil N2O Production Potential in Chinese Grasslands Rather Than Bacteria.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {844663}, pmid = {35651488}, issn = {1664-302X}, abstract = {Nitrous oxide (N2O) is a powerful greenhouse gas and the predominant stratospheric ozone-depleting substance. Soil is a major source of N2O but remains largely uncertain due to the complicated processes of nitrification and denitrification performed by various groups of microbes such as bacteria, fungi, and archaea. We used incubation experiments to measure the total fungal, archaeal, and bacterial N2O production potential and the microbial functional genes in soils along 3,000 km Chinese grassland transect, including meadow steppe, typical steppe, desert steppe, alpine meadow, and alpine steppe. The results indicated that fungi, archaea, and bacteria contributed 25, 34, and 19% to nitrification and 46, 29, and 15% to denitrification, respectively. The AOA and AOB genes were notably correlated with the total nitrification enzyme activity (TNEA), whereas both narG and nirK genes were significantly correlated with total denitrification enzyme activity (TDEA) at p < 0.01. The correlations between AOA and ANEA (archaeal nitrification enzyme activity), AOB and BNEA (bacterial nitrification enzyme activity), and narG, nirK, and BDEA (bacterial denitrification enzyme activity) showed higher coefficients than those between the functional genes and TNEA/TDEA. The structural equation modeling (SEM) results showed that fungi are dominant in N2O production processes, followed by archaea in the northern Chinese grasslands. Our findings indicate that the microbial functional genes are powerful predictors of the N2O production potential, after distinguishing bacterial, fungal, and archaeal processes. The key variables of N2O production and the nitrogen (N) cycle depend on the dominant microbial functional groups in the N-cycle in soils.}, }
@article {pmid35639688, year = {2022}, author = {Thevasundaram, K and Gallagher, JJ and Cherng, F and Chang, MCY}, title = {Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {23}, pages = {e2118638119}, pmid = {35639688}, issn = {1091-6490}, support = {T32 GM066698/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/metabolism ; Carbon Cycle ; Carbon Dioxide/metabolism ; Chemoautotrophic Growth ; *Euryarchaeota/metabolism ; }, abstract = {The conversion of CO2 to value-added products allows both capture and recycling of greenhouse gas emissions. While plants and other photosynthetic organisms play a key role in closing the global carbon cycle, their dependence on light to drive carbon fixation can be limiting for industrial chemical synthesis. Methanogenic archaea provide an alternative platform as an autotrophic microbial species capable of non-photosynthetic CO2 fixation, providing a potential route to engineered microbial fermentation to synthesize chemicals from CO2 without the need for light irradiation. One major challenge in this goal is to connect upstream carbon-fixation pathways with downstream biosynthetic pathways, given the distinct differences in metabolism between archaea and typical heterotrophs. We engineered the model methanogen, Methanococcus maripaludis, to divert acetyl-coenzyme A toward biosynthesis of value-added chemicals, including the bioplastic polyhydroxybutyrate (PHB). A number of studies implicated limitations in the redox pool, with NAD(P)(H) pools in M. maripaludis measured to be <15% of that of Escherichia coli, likely since methanogenic archaea utilize F420 and ferredoxins instead. Multiple engineering strategies were used to precisely target and increase the cofactor pool, including heterologous expression of a synthetic nicotinamide salvage pathway as well as an NAD+-dependent formate dehydrogenase from Candida boidinii. Engineered strains of M. maripaludis with improved NADH pools produced up to 171 ± 4 mg/L PHB and 24.0 ± 1.9% of dry cell weight. The metabolic engineering strategies presented in this study broaden the utility of M. maripaludis for sustainable chemical synthesis using CO2 and may be transferable to related archaeal species.}, }
@article {pmid35633707, year = {2022}, author = {Zheng, J and Tao, L and Dini-Andreote, F and Luan, L and Kong, P and Xue, J and Zhu, G and Xu, Q and Jiang, Y}, title = {Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {911799}, pmid = {35633707}, issn = {1664-302X}, abstract = {Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics.}, }
@article {pmid35630397, year = {2022}, author = {Liu, H and Zhou, P and Cheung, S and Lu, Y and Liu, H and Jing, H}, title = {Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630397}, issn = {2076-2607}, abstract = {Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with [15]N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; therefore, this physical forcing should be considered in the future assessment of the global nitrogen budgets and biogeochemical nitrogen cycles.}, }
@article {pmid35625610, year = {2022}, author = {Pastor, MM and Sakrikar, S and Rodriguez, DN and Schmid, AK}, title = {Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.}, journal = {Biomolecules}, volume = {12}, number = {5}, pages = {}, pmid = {35625610}, issn = {2218-273X}, support = {T32 GM136627/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics/metabolism ; RNA, Messenger/genetics ; *RNA, Ribosomal/genetics/metabolism ; RNA-Seq ; Sequence Analysis, RNA/methods ; }, abstract = {Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The high rRNA:mRNA ratio (80-90%: ~10%) in prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results in low sequence coverage of mRNA, and therefore, requires a substantially higher number of replicate samples and/or sequencing reads to achieve statistically reliable conclusions regarding the significance of differential gene expression between case and control samples. Here, we show that after the discontinuation of the previous version of RiboZero (Illumina, San Diego, CA, USA) that was useful in partially or completely depleting rRNA from archaea, archaeal transcriptomics studies have experienced a slowdown. To overcome this limitation, here, we analyze the efficiency for four different hybridization-based kits from three different commercial suppliers, each with two sets of sequence-specific probes to remove rRNA from four different species of halophilic archaea. We conclude that the key for transcriptomic success with the currently available tools is the probe-specificity for the rRNA sequence hybridization. With this paper, we provide insights into the archaeal community for selecting certain reagents and strategies over others depending on the archaeal species of interest. These methods yield improved RNA-seq sensitivity and enhanced detection of low abundance transcripts.}, }
@article {pmid35623507, year = {2022}, author = {Fonseca de Souza, L and Alvarez, DO and Domeignoz-Horta, LA and Gomes, FV and de Souza Almeida, C and Merloti, LF and Mendes, LW and Andreote, FD and Bohannan, BJM and Mazza Rodrigues, JL and Nüsslein, K and Tsai, SM}, title = {Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 2}, pages = {156225}, doi = {10.1016/j.scitotenv.2022.156225}, pmid = {35623507}, issn = {1879-1026}, mesh = {Animals ; *Archaea ; Cattle ; *Methane ; Poaceae/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest-to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. We also assessed changes in the soil microbial community structure of both bare (bulk) and rhizospheric pasture soils through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that soil liming to increasing pH compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Liming reduced the relative abundance of Beijerinckiacea family in forest soils, which account for many known methanotrophs. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, compared to bare (bulk) pasture soil.}, }
@article {pmid35618771, year = {2022}, author = {Badel, C and Samson, RY and Bell, SD}, title = {Chromosome organization affects genome evolution in Sulfolobus archaea.}, journal = {Nature microbiology}, volume = {7}, number = {6}, pages = {820-830}, pmid = {35618771}, issn = {2058-5276}, support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/genetics ; Chromosomes ; Evolution, Molecular ; Replication Origin ; *Sulfolobus/genetics ; }, abstract = {In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.}, }
@article {pmid35616996, year = {2022}, author = {Bao, CX and Li, SY and Xin, YJ and Hou, J and Cui, HL}, title = {Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov., Natrinema amylolyticum sp. nov. and Haloterrigena alkaliphila sp. nov., four extremely halophilic archaea isolated from salt mine, saline soil and salt lake.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005385}, pmid = {35616996}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; *Halobacteriaceae ; *Lakes ; Phosphatidic Acids ; Phosphatidylglycerols ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; }, abstract = {Four halophilic archaeal strains, YPL8[T], SLN56[T], LT61[T] and KZCA68[T], were isolated from a salt mine, saline soil and a salt lake located in different regions of China. Sequence similarities of 16S rRNA and rpoB' genes among strains YPL8[T], SLN56[T], LT61[T] and the current members of Natrinema were 94.1-98.2 % and 89.3-95.1 %, respectively, while these values among strain KZCA68[T] and the current members of Haloterrigena were 97.2-97.4 % and 91.7-91.9 %, respectively. The average nucleotide identity, in silico DNA-DNA hybridization and average amino acid identity values among these four strains and their closely related species were all lower than the threshold values for species boundary. All four strains were unable to hydrolyse casein, gelatin, or Tween 80. Strain YPL8[T] contained phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), disulfated mannosyl glucosyl diether (S2-DGD) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). Strain SLN56[T] contained PA, PG, phosphatidylglycerol sulphate (PGS), PGP-Me, S-DGD-1, S2-DGD and S-DGD-PA. Strain LT61[T] contained PA, PG, PGS, PGP-Me, S-DGD-1 and S2-DGD. The phospholipids of strain KZCA68[T] were PA, PG and PGP-Me. These results showed that strains YPL8[T] (=CGMCC 1.13883[T]=JCM 31181[T]), SLN56[T] (=CGMCC 1.14945[T]=JCM 30832[T]) and LT61[T] (=CGMCC 1.14942[T]=JCM 30668[T]) represent novel species of the genus Natrinema, for which the names, Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov. and Natrinema amylolyticum sp. nov. are proposed. Strain KZCA68[T] (=CGMCC 1.17211[T]=JCM 34158[T]) represents a novel species of Haloterrigena, for which the name Haloterrigena alkaliphila sp. nov. is proposed.}, }
@article {pmid35615789, year = {2022}, author = {Dyksma, S and Gallert, C}, title = {Effect of magnetite addition on transcriptional profiles of syntrophic Bacteria and Archaea during anaerobic digestion of propionate in wastewater sludge.}, journal = {Environmental microbiology reports}, volume = {14}, number = {4}, pages = {664-678}, doi = {10.1111/1758-2229.13080}, pmid = {35615789}, issn = {1758-2229}, mesh = {Anaerobiosis ; *Archaea/genetics ; Bacteria/genetics ; *Euryarchaeota/genetics ; Ferrosoferric Oxide/pharmacology ; Formates/pharmacology ; Methane ; Propionates ; Sewage ; Wastewater ; }, abstract = {Anaerobic digestion (AD) is an important technology for the effective conversion of waste and wastewater to methane. Here, syntrophic bacteria transfer molecular hydrogen (H2), formate, or directly supply electrons (direct interspecies electron transfer, DIET) to the methanogens. Evidence is accumulating that the methanation of short-chain fatty acids can be enhanced by the addition of conductive material to the anaerobic digester, which has often been attributed to the stimulation of DIET. Since little is known about the transcriptional response of a complex AD microbial community to the addition of conductive material, we added magnetite to propionate-fed laboratory-scale reactors that were inoculated with wastewater sludge. Compared to the control reactors, the magnetite-amended reactors showed improved methanation of propionate. A genome-centric metatranscriptomics approach identified the active SCFA-oxidizing bacteria that affiliated with Firmicutes, Desulfobacterota and Cloacimonadota. The transcriptional profiles revealed that the syntrophic bacteria transferred acetate, H2 and formate to acetoclastic and hydrogenotrophic methanogens, whereas transcription of potential determinants for DIET such as conductive pili and outer-membrane cytochromes did not significantly change with magnetite addition. Overall, changes in the transcriptional profiles of syntrophic Bacteria and Archaea in propionate-fed lab-scale reactors amended with magnetite refute a major role of DIET in the studied system.}, }
@article {pmid35610383, year = {2022}, author = {Pierangeli, GMF and Domingues, MR and Choueri, RB and Hanisch, WS and Gregoracci, GB and Benassi, RF}, title = {Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35610383}, issn = {1432-184X}, abstract = {Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.}, }
@article {pmid35607968, year = {2022}, author = {Semler, AC and Fortney, JL and Fulweiler, RW and Dekas, AE}, title = {Cold Seeps on the Passive Northern U.S. Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {11}, pages = {e0046822}, pmid = {35607968}, issn = {1098-5336}, mesh = {*Archaea/metabolism ; Geologic Sediments/microbiology ; Methane/metabolism ; Methanosarcinales/genetics ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/microbiology ; }, abstract = {Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Atlantic Margin (USAM). We sampled in and around four USAM seeps and combined pore water geochemistry measurements with amplicon sequencing of 16S rRNA and mcrA (DNA and RNA) to investigate the microbial communities present, their assembly processes, and how they compare to communities at previously studied sites. We found that the USAM seeps contained communities consistent with the canonical seep microbiome at the class and order levels but differed markedly at the sequence variant level, especially within the anaerobic methanotrophic (ANME) archaea. The ANME populations were highly uneven, with just a few dominant mcrA sequence variants at each seep. Interestingly, the USAM seeps did not form a distinct phylogenetic cluster when compared with other previously described seeps around the world. Consistent with this, we found only a very weak (though statistically significant) distance-decay trend in seep community similarity across a global data set. Ecological assembly indices suggest that the USAM seep communities were assembled primarily deterministically, in contrast to the surrounding nonseep sediments, where stochastic processes dominated. Together, our results suggest that the primary driver of seep microbial community composition is local geochemistry-specifically methane, sulfide, nitrate, acetate, and ammonium concentrations-rather than the geologic context, the composition of nearby seeps, or random events of dispersal. IMPORTANCE Cold seeps are now known to be widespread features of passive continental margins, including the northern U.S. Atlantic Margin (USAM). Methane seepage is expected to intensify at these relatively shallow seeps as bottom waters warm and underlying methane hydrates dissociate. While methanotrophic microbial communities might reduce or prevent methane release, microbial communities on passive margins have rarely been characterized. In this study, we investigated the Bacteria and Archaea at four cold seeps on the northern USAM and found that despite being colocated on the same continental slope, the communities significantly differ by site at the sequence variant level, particularly methane-cycling community members. Differentiation by site was not observed in similarly spaced background sediments, raising interesting questions about the dispersal pathways of cold seep microorganisms. Understanding the genetic makeup of these discrete seafloor ecosystems and how their microbial communities develop will be increasingly important as the climate changes.}, }
@article {pmid35605022, year = {2022}, author = {Martinez-Gutierrez, CA and Aylward, FO}, title = {Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales.}, journal = {PLoS genetics}, volume = {18}, number = {5}, pages = {e1010220}, pmid = {35605022}, issn = {1553-7404}, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; Genome Size ; Phylogeny ; }, abstract = {The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel's lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.}, }
@article {pmid35604119, year = {2022}, author = {Popp, PF and Gumerov, VM and Andrianova, EP and Bewersdorf, L and Mascher, T and Zhulin, IB and Wolf, D}, title = {Phyletic Distribution and Diversification of the Phage Shock Protein Stress Response System in Bacteria and Archaea.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0134821}, pmid = {35604119}, issn = {2379-5077}, support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; }, abstract = {Maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protein protection networks that connect stress perception, transmembrane signal transduction, and mediation of cellular responses upon cell envelope stress. The phage shock protein (Psp) stress response is one such conserved protection network. Most knowledge about the Psp response derives from studies in the Gram-negative model bacterium Escherichia coli, where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of the Proteobacteria, Actinobacteria, and Firmicutes. However, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and describe that the predicted Psp systems deviate dramatically from the known prototypes. The core proteins PspA and PspC have been integrated into various (often phylum-specifically) conserved protein networks during evolution. Based on protein domain-based and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system for Psp networks in bacteria and archaea. We validate our approach by performing a comprehensive in vivo protein interaction study of Psp domains identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected protein network. Our study highlights the diversity of Psp domain organizations and potentially diverse functions across the plethora of the microbial landscape, thus laying the ground for studies beyond known Psp functions in underrepresented organisms. IMPORTANCE The PspA protein domain is found in all domains of life, highlighting its central role in Psp networks. To date, all insights into the core functions of Psp responses derive mainly from protein network blueprints representing only three bacterial phyla. Despite large overlaps in function and regulation, the evolutionary diversity of Psp networks remains largely elusive. Here, we present an unbiased protein domain- and genomic context-centered approach that describes and classifies Psp systems. Our results suggest so-far-unknown Psp-associated roles with other protein networks giving rise to new functions. We demonstrate the applicability of our approach by dissecting the Psp protein network present in Bacillus subtilis and demonstrate Psp domains working in concert with other cell envelope stress response systems. We find that the Psp-like protein universe reflects a surprising diversity within the bacterial and archaeal microbial world.}, }
@article {pmid35602962, year = {2022}, author = {Wu, J and Hong, Y and He, X and Liu, X and Ye, J and Jiao, L and Li, Y and Wang, Y and Ye, F and Yang, Y and Du, J}, title = {Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea.}, journal = {iScience}, volume = {25}, number = {5}, pages = {104333}, pmid = {35602962}, issn = {2589-0042}, abstract = {The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.}, }
@article {pmid35544775, year = {2022}, author = {Tunçkanat, T and Gendron, A and Sadler, Z and Neitz, A and Byquist, S and Lie, TJ and Allen, KD}, title = {Lysine 2,3-Aminomutase and a Newly Discovered Glutamate 2,3-Aminomutase Produce β-Amino Acids Involved in Salt Tolerance in Methanogenic Archaea.}, journal = {Biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.biochem.2c00014}, pmid = {35544775}, issn = {1520-4995}, abstract = {Many methanogenic archaea synthesize β-amino acids as osmolytes that allow survival in high salinity environments. Here, we investigated the radical S-adenosylmethionine (SAM) aminomutases involved in the biosynthesis of N[ε]-acetyl-β-lysine and β-glutamate in Methanococcus maripaludis C7. Lysine 2,3-aminomutase (KAM), encoded by MmarC7_0106, was overexpressed and purified from Escherichia coli, followed by biochemical characterization. In the presence of l-lysine, SAM, and dithionite, this archaeal KAM had a kcat = 14.3 s[-1] and a Km = 19.2 mM. The product was shown to be 3(S)-β-lysine, which is like the well-characterized Clostridium KAM as opposed to the E. coli KAM that produces 3(R)-β-lysine. We further describe the function of MmarC7_1783, a putative radical SAM aminomutase with a ∼160 amino acid extension at its N-terminus. Bioinformatic analysis of the possible substrate-binding residues suggested a function as glutamate 2,3-aminomutase, which was confirmed here through heterologous expression in a methanogen followed by detection of β-glutamate in cell extracts. β-Glutamate has been known to serve as an osmolyte in select methanogens for a long time, but its biosynthetic origin remained unknown until now. Thus, this study defines the biosynthetic routes for β-lysine and β-glutamate in M. maripaludis and expands the importance and diversity of radical SAM enzymes in all domains of life.}, }
@article {pmid35508560, year = {2022}, author = {Fisk, LM and Barton, L and Maccarone, LD and Jenkins, SN and Murphy, DV}, title = {Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7299}, pmid = {35508560}, issn = {2045-2322}, mesh = {Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Betaproteobacteria/metabolism ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Seasons ; Soil/chemistry ; Soil Microbiology ; Water/metabolism ; }, abstract = {Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.}, }
@article {pmid35500274, year = {2022}, author = {Lemaire, ON and Wagner, T}, title = {A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea.}, journal = {Biochemistry}, volume = {61}, number = {10}, pages = {805-821}, pmid = {35500274}, issn = {1520-4995}, mesh = {*Alkanes/metabolism ; Anaerobiosis ; *Archaea/chemistry ; Catalysis ; Mesna/metabolism ; Methane/metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Phylogeny ; }, abstract = {Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO2 by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.}, }
@article {pmid35489791, year = {2022}, author = {Glodowska, M and Welte, CU and Kurth, JM}, title = {Metabolic potential of anaerobic methane oxidizing archaea for a broad spectrum of electron acceptors.}, journal = {Advances in microbial physiology}, volume = {80}, number = {}, pages = {157-201}, doi = {10.1016/bs.ampbs.2022.01.003}, pmid = {35489791}, issn = {2162-5468}, mesh = {Anaerobiosis ; *Archaea/metabolism ; Electrons ; Ferric Compounds/metabolism ; Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; }, abstract = {Methane (CH4) is a potent greenhouse gas significantly contributing to the climate warming we are currently facing. Microorganisms play an important role in the global CH4 cycle that is controlled by the balance between anaerobic production via methanogenesis and CH4 removal via methanotrophic oxidation. Research in recent decades advanced our understanding of CH4 oxidation, which until 1976 was believed to be a strictly aerobic process. Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is now known to be an important sink of CH4 in marine ecosystems. Furthermore, in 2006 it was discovered that anaerobic CH4 oxidation can also be coupled to nitrate reduction (N-DAMO), demonstrating that AOM may be much more versatile than previously thought and linked to other electron acceptors. In consequence, an increasing number of studies in recent years showed or suggested that alternative electron acceptors can be used in the AOM process including Fe[III], Mn[IV], As[V], Cr[VI], Se[VI], Sb[V], V[V], and Br[V]. In addition, humic substances as well as biochar and perchlorate (ClO4[-]) were suggested to mediate AOM. Anaerobic methanotrophic archaea, the so-called ANME archaea, are key players in the AOM process, yet we are still lacking deeper understanding of their metabolism, electron acceptor preferences and their interaction with other microbial community members. It is still not clear whether ANME archaea can oxidize CH4 and reduce metallic electron acceptors independently or via electron transfer to syntrophic partners, interspecies electron transfer, nanowires or conductive pili. Therefore, the aim of this review is to summarize and discuss the current state of knowledge about ANME archaea, focusing on their physiology, metabolic flexibility and potential to use various electron acceptors.}, }
@article {pmid35437913, year = {2022}, author = {Campbell, BC and Greenfield, P and Gong, S and Barnhart, EP and Midgley, DJ and Paulsen, IT and George, SC}, title = {Methanogenic archaea in subsurface coal seams are biogeographically distinct: an analysis of metagenomically-derived mcrA sequences.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {4065-4078}, doi = {10.1111/1462-2920.16014}, pmid = {35437913}, issn = {1462-2920}, mesh = {Animals ; Archaea/metabolism ; Coal/microbiology ; *Euryarchaeota/genetics ; *Greenhouse Gases/metabolism ; Methane/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Soil ; }, abstract = {The production of methane as an end-product of organic matter degradation in the absence of other terminal electron acceptors is common, and has often been studied in environments such as animal guts, soils and wetlands due to its potency as a greenhouse gas. To date, however, the study of the biogeographic distribution of methanogens across coal seam environments has been minimal. Here, we show that coal seams are host to a diverse range of methanogens, which are distinctive to each geological basin. Based on comparisons to close relatives from other methanogenic environments, the dominant methanogenic pathway in these basins is hydrogenotrophic, with acetoclastic being a second major pathway in the Surat Basin. Finally, mcrA and 16S rRNA gene primer biases were predominantly seen to affect the detection of Methanocellales, Methanomicrobiales and Methanosarcinales taxa in this study. Subsurface coal methanogenic community distributions and pathways presented here provide insights into important metabolites and bacterial partners for in situ coal biodegradation.}, }
@article {pmid35422794, year = {2022}, author = {Kamruzzaman, M and Yan, A and Castro-Escarpulli, G}, title = {Editorial: CRISPR-Cas Systems in Bacteria and Archaea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {887778}, pmid = {35422794}, issn = {1664-302X}, }
@article {pmid35420474, year = {2022}, author = {He, W and Gao, H and Wu, D and Jiang, S and Huang, W and Chen, C and Deng, Z and Xiong, L and Wu, G and Wang, L}, title = {Structural and Functional Analysis of DndE Involved in DNA Phosphorothioation in the Haloalkaliphilic Archaea Natronorubrum bangense JCM10635.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0071622}, pmid = {35420474}, issn = {2150-7511}, mesh = {DNA/metabolism ; DNA, Bacterial/metabolism ; *DNA, Superhelical/metabolism ; Escherichia coli/genetics/metabolism ; *Halobacteriaceae/genetics/metabolism ; Oxygen/metabolism ; Sulfur/metabolism ; }, abstract = {Phosphorothioate (PT) modification, a sequence-specific modification that replaces the nonbridging oxygen atom with sulfur in a DNA phosphodiester through the gene products of dndABCDE or sspABCD, is widely distributed in prokaryotes. DNA PT modification functions together with gene products encoded by dndFGH, pbeABCD, or sspE to form defense systems that can protect against invasion by exogenous DNA particles. While the functions of the multiple enzymes in the PT system have been elucidated, the exact role of DndE in the PT process is still obscure. Here, we solved the crystal structure of DndE from the haloalkaliphilic archaeal strain Natronorubrum bangense JCM10635 at a resolution of 2.31 Å. Unlike the tetrameric conformation of DndE in Escherichia coli B7A, DndE from N. bangense JCM10635 exists in a monomeric conformation and can catalyze the conversion of supercoiled DNA to nicked or linearized products. Moreover, DndE exhibits preferential binding affinity to nicked DNA by virtue of the R19- and K23-containing positively charged surface. This work provides insight into how DndE functions in PT modification and the potential sulfur incorporation mechanism of DNA PT modification. IMPORTANCE DndABCDE proteins have been demonstrated to catalyze DNA PT modification with the nonbridging oxygen in the DNA sugar-phosphate backbone replaced by sulfur. In the PT modification pathway, DndA exerts cysteine desulfurase activity capable of catalyzing the mobilization of sulfur from l-cysteine, which involves the ion-sulfur cluster assembly of DndC. This is regarded as the initial step of the DNA PT modification. Moreover, DndD has ATPase activity in vitro, which is believed to provide energy for the oxygen-sulfur swap, while the function of DndE is unknown. However, the exact function of the key enzyme DndE remains to be elucidated. By determining the structure of DndE from the haloalkaliphilic strain Natronorubrum bangense JCM10635, we showed that the archaeal DndE adopts a monomer conformation. Notably, DndE can introduce nicks to supercoiled DNA and exhibits a binding preference for nicked DNA; the nicking is believed to be the initial step for DNA to facilitate the sulfur incorporation.}, }
@article {pmid35408816, year = {2022}, author = {Huang, C and Liu, X and Chen, Y and Zhou, J and Li, W and Ding, N and Huang, L and Chen, J and Zhang, Z}, title = {A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea.}, journal = {International journal of molecular sciences}, volume = {23}, number = {7}, pages = {}, pmid = {35408816}, issn = {1422-0067}, mesh = {Archaea/metabolism ; DNA/chemistry ; DNA, Single-Stranded ; *DNA-Binding Proteins/metabolism ; *Sulfolobus/genetics ; }, abstract = {The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA binding protein family highly conserved in Sulfolobaceae. Sul7s from Sulfolobus islandicus binds ssDNA with an affinity approximately 15-fold higher than that for dsDNA in vitro. It prefers binding oligo(dT)30 over oligo(dC)30 or a dG-rich 30-nt oligonucleotide, and barely binds oligo(dA)30. Further, binding by Sul7s inhibits DNA strand annealing, but shows little effect on the melting temperature of DNA duplexes. The solution structure of Sul7s determined by NMR shows a winged helix-turn-helix fold, consisting of three α-helices, three β-strands, and two short wings. It interacts with ssDNA via a large positively charged binding surface, presumably resulting in ssDNA deformation. Our results shed significant light on not only non-OB fold single-stranded DNA binding proteins in Archaea, but also the divergence of the winged-helix proteins in both function and structure during evolution.}, }
@article {pmid35405221, year = {2022}, author = {Yang, P and Tang, KW and Tong, C and Lai, DYF and Wu, L and Yang, H and Zhang, L and Tang, C and Hong, Y and Zhao, G}, title = {Changes in sediment methanogenic archaea community structure and methane production potential following conversion of coastal marsh to aquaculture ponds.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {305}, number = {}, pages = {119276}, doi = {10.1016/j.envpol.2022.119276}, pmid = {35405221}, issn = {1873-6424}, mesh = {Aquaculture ; Archaea ; Ecosystem ; Methane ; *Ponds ; *Wetlands ; }, abstract = {Widespread conversion of coastal wetlands into aquaculture ponds in coastal region often results in degradation of the wetland ecosystems, but its effects on sediment's potential to produce greenhouse gases remain unclear. Using field sampling, incubation experiments and molecular analysis, we studied the sediment CH4 production potential and the relevant microbial communities in a brackish marsh and the nearby aquaculture ponds in the Min River Estuary in southeastern China. Sediment CH4 production potential was higher in the summer and autumn months than in spring and winter months, and it was significantly correlated with sediment carbon content among all environmental variables. The mean sediment CH4 production potential in the aquaculture ponds (20.1 ng g[-1] d[-1]) was significantly lower than that in the marsh (45.2 ng g[-1] d[-1]). While Methanobacterium dominated in both habitats (41-59%), the overall composition of sediment methanogenic archaea communities differed significantly between the two habitats (p < 0.05) and methanogenic archaea alpha diversity was lower in the aquaculture ponds (p < 0.01). Network analysis revealed that interactions between sediment methanogenic archaea were much weaker in the ponds than in the marsh. Overall, these findings suggest that conversion of marsh land to aquaculture ponds significantly altered the sediment methanogenic archaea community structure and diversity and lowered the sediment's capacity to produce CH4.}, }
@article {pmid35402889, year = {2022}, author = {Al-Ajeel, S and Spasov, E and Sauder, LA and McKnight, MM and Neufeld, JD}, title = {Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems.}, journal = {Water research X}, volume = {15}, number = {}, pages = {100131}, pmid = {35402889}, issn = {2589-9147}, abstract = {Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.}, }
@article {pmid35384236, year = {2022}, author = {Vuong, P and Moreira-Grez, B and Wise, MJ and Whiteley, AS and Kumaresan, D and Kaur, P}, title = {From rags to enriched: metagenomic insights into ammonia-oxidizing archaea following ammonia enrichment of a denuded oligotrophic soil ecosystem.}, journal = {Environmental microbiology}, volume = {24}, number = {7}, pages = {3097-3110}, pmid = {35384236}, issn = {1462-2920}, mesh = {*Ammonia/metabolism ; *Archaea/metabolism ; Bacteria ; Ecosystem ; Metagenome ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; }, abstract = {Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavourable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia-oxidizing archaea (AOA) can be considered one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates.}, }
@article {pmid35380107, year = {2022}, author = {Gupta, D and Shalvarjian, KE and Nayak, DD}, title = {An Archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35380107}, issn = {2050-084X}, mesh = {*Archaea/metabolism ; Cytochromes/metabolism ; Electron Transport/genetics ; Methane/metabolism ; *Methanosarcina/genetics ; }, abstract = {c-Type cytochromes (cyt c) are proteins that undergo post-translational modification to covalently bind heme, which allows them to facilitate redox reactions in electron transport chains across all domains of life. Genomic evidence suggests that cyt c are involved in electron transfer processes among the Archaea, especially in members that produce or consume the potent greenhouse gas methane. However, neither the maturation machinery for cyt c in Archaea nor their role in methane metabolism has ever been functionally characterized. Here, we have used CRISPR-Cas9 genome editing tools to map a distinct pathway for cyt c biogenesis in the model methanogenic archaeon Methanosarcina acetivorans, and have also identified substrate-specific functional roles for cyt c during methanogenesis. Although the cyt c maturation machinery from M. acetivorans is universally conserved in the Archaea, our evolutionary analyses indicate that different clades of Archaea acquired this machinery through multiple independent horizontal gene transfer events from different groups of Bacteria. Overall, we demonstrate the convergent evolution of a novel Archaea-specific cyt c maturation machinery and its physiological role during methanogenesis, a process which contributes substantially to global methane emissions.}, }
@article {pmid35369442, year = {2022}, author = {Thirumalaisamy, G and Malik, PK and Trivedi, S and Kolte, AP and Bhatta, R}, title = {Effect of Long-Term Supplementation With Silkworm Pupae Oil on the Methane Yield, Ruminal Protozoa, and Archaea Community in Sheep.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {780073}, pmid = {35369442}, issn = {1664-302X}, abstract = {Supplementation with lipids and oils is one of the most efficient strategies for reducing enteric methane emission. However, high costs and adverse impacts on fiber degradation restrict the use of conventional oils. Silkworm pupae, a non-conventional oil source rarely used for human consumption in India, could be one of the cheaper alternatives for methane mitigation. The objective of this study was to investigate the effect on sheep of long-term supplementation (180 days) of silkworm pupae oil (SWPO) with two distinct supplementation regimes (daily and biweekly) on daily enteric methane emission, methane yield, nutrient digestibility, rumen fermentation, ruminal archaea community composition, and protozoal population. The effect of the discontinuation of oil supplementation on enteric methane emission was also investigated. Eighteen adult male sheep, randomly divided into three groups (n = 6), were provisioned with a mixed diet consisting of 10.1% crude protein (CP) and 11.7 MJ/kg metabolizable energy formulated using finger millet straw and concentrate in a 55:45 ratio. SWPO was supplemented at 2% of dry matter intake (DMI) in test groups either daily (CON) or biweekly (INT), while no oil was supplemented in the control group (CTR). DMI (p = 0.15) and CP (p = 0.16) in the CON and INT groups were similar to that of the CTR group; however, the energy intake (MJ/kg) in the supplemented groups (CON and INT) was higher (p < 0.001) than in CTR. In the CON group, body weight gain (kg, p = 0.02) and average daily gain (g, p = 0.02) were both higher than in the CTR. The daily methane emission in the CON (17.5 g/day) and INT (18.0 g/day) groups was lower (p = 0.01) than the CTR group (23.6 g/day), indicating a reduction of 23-25% due to SWPO supplementation. Similarly, compared with the CTR group, methane yields (g/kg DMI) in test groups were also significantly lower (p < 0.01). The transient nature of the anti-methanogenic effect of SWPO was demonstrated in the oil discontinuation study, where daily methane emission reverted to pre-supplementation levels after a short period. The recorded methanogens were affiliated to the families Methanobacteriaceae, Methanomassilliicoccaceae, and Methanosarcinaceae. The long-term supplementation of oil did not induce any significant change in the rumen archaeal community, whereas minor species such as Group3b exhibited differing abundance among the groups. Methanobrevibacter, irrespective of treatment, was the largest genus, while Methanobrevibacter gottschalkii was the dominant species. Oil supplementation in CON and INT compared with CTR decreased (p < 0.01) the numbers of total protozoa (× 10[7] cells/ml), Entodiniomorphs (× 10[7] cells/ml), and Holotrichs (× 10[6] cells/ml). SWPO continuous supplementation (CON group) resulted in the largest reduction in enteric methane emission and relatively higher body weight gain (p = 0.02) in sheep.}, }
@article {pmid35347497, year = {2022}, author = {Yuan, B and Wu, W and Yue, S and Zou, P and Yang, R and Zhou, X}, title = {Community structure, distribution pattern, and influencing factors of soil Archaea in the construction area of a large-scale photovoltaic power station.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {25}, number = {3}, pages = {571-586}, pmid = {35347497}, issn = {1618-1905}, mesh = {*Archaea/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The photovoltaic power station in Qinghai has been built for 8 years; however, its impact on the regional soil ecological environment has not been studied in depth. To reveal the structure and distribution pattern of archaeal communities in desert soil under the influence of a large photovoltaic power station, a comparative study was carried out between the soil affected by photovoltaic panels and the bare land samples outside the photovoltaic station in Gonghe, Qinghai Province. The abundance, community structure, diversity, and distribution characteristics of archaea were analyzed by quantitative PCR and Illumina-MiSeq high-throughput sequencing, and the main environmental factors affecting the variation in soil archaeal community were identified by RDA. The contribution rate of environmental factors and human factors to microbial community diversity was quantitatively evaluated by VPA. The results showed that there was no significant difference in soil nutrients and other physicochemical factors between the photovoltaic power station and bare land. Thaumarchaeota was the dominant archaeal phylum in the area, accounting for more than 99% of archaeal phylum, while at the level of genus, Nitrososphaera was the dominant archaeal genera. There was no significant difference in archaeal community structure between and under different types of PV panels. The analysis has shown that the construction of a photovoltaic station has little effect on the community structure of soil archaea in a desert area, and it was speculated that the selection of niche played a leading role in the distribution pattern of soil archaeal community. This study provides the basis for a scientific understanding of the characteristics and distribution patterns of soil archaeal communities affected by the construction of a photovoltaic power station.}, }
@article {pmid35340443, year = {2022}, author = {Schiller, H and Young, C and Schulze, S and Tripepi, M and Pohlschroder, M}, title = {A Twist to the Kirby-Bauer Disk Diffusion Susceptibility Test: an Accessible Laboratory Experiment Comparing Haloferax volcanii and Escherichia coli Antibiotic Susceptibility to Highlight the Unique Cell Biology of Archaea.}, journal = {Journal of microbiology &amp; biology education}, volume = {23}, number = {1}, pages = {}, pmid = {35340443}, issn = {1935-7877}, abstract = {Archaea, once thought to only live in extreme environments, are present in many ecosystems, including the human microbiome, and they play important roles ranging from nutrient cycling to bioremediation. Yet this domain is often overlooked in microbiology classes and rarely included in laboratory exercises. Excluding archaea from high school and undergraduate curricula prevents students from learning the uniqueness and importance of this domain. Here, we have modified a familiar and popular microbiology experiment-the Kirby-Bauer disk diffusion antibiotic susceptibility test-to include, together with the model bacterium Escherichia coli, the model archaeon Haloferax volcanii. Students will learn the differences and similarities between archaea and bacteria by using antibiotics that target, for example, the bacterial peptidoglycan cell wall or the ribosome. Furthermore, the experiment provides a platform to reiterate basic cellular biology concepts that students may have previously discussed. We have developed two versions of this experiment, one designed for an undergraduate laboratory curriculum and the second, limited to H. volcanii, that high school students can perform in their classrooms. This nonpathogenic halophile can be cultured aerobically at ambient temperature in high-salt media, preventing contamination, making the experiment low-cost and safe for use in the high school setting.}, }
@article {pmid35336099, year = {2022}, author = {Cisek, AA and Bąk, I and Stefańska, I and Binek, M}, title = {Selection and Optimization of High-Yielding DNA Isolation Protocol for Quantitative Analyses of Methanogenic Archaea.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336099}, issn = {2076-2607}, abstract = {Methanogenic archaea are a functionally important component of the intestinal microbiota of humans and animals, participating in the utilization of detrimental hydrogen produced during gut fermentation. Despite this, archaeal DNA has rarely been found in intestinal microbiome analyses, which prompts the need to optimize detecting procedures of these microorganisms, including the DNA isolation step. Three commercially available kits for DNA isolation and one extra purification kit that removes PCR inhibitors were evaluated on chicken droppings. In addition, different variants of mechanical lysis and a double elution were tested to ensure the maximum efficiency of DNA isolation from archaea as well as bacteria. A quantitative real-time PCR was used to monitor the optimization progress. As a result, the combination of the selected Genomic Mini AX Bacteria+ kit with a 2-min-long sonication by ultrasonic probe and enzymatic pretreatment gave excellent extraction efficiency rates for DNA of methanogenic archaea (an approximate 50-fold increase compared to the standard enzymatic lysis described by the producer) and, at the same time, provided optimal protection of DNA extracted from bacteria susceptible to enzymatic lysis. The presented results indicate that the optimized protocol allows for highly efficient extraction of total DNA, which is well-suited for quantitative microbial analyses by real-time PCR.}, }
@article {pmid35323924, year = {2022}, author = {Klein, T and Poghosyan, L and Barclay, JE and Murrell, JC and Hutchings, MI and Lehtovirta-Morley, LE}, title = {Cultivation of ammonia-oxidising archaea on solid medium.}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, pmid = {35323924}, issn = {1574-6968}, support = {BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Agar ; *Ammonia ; *Archaea/genetics ; Culture Media ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; }, abstract = {Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: 'Candidatus Nitrosocosmicus franklandus C13', Nitrososphaera viennensis EN76 and 'Candidatus Nitrosotalea sinensis Nd2'. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both 'Ca. N. franklandus C13' and N. viennensis EN76 tolerated Phytagel™ while the acidophilic 'Ca. N. sinensis Nd2' was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel™ and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from 'Ca. N. franklandus C13' and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.}, }
@article {pmid35276174, year = {2022}, author = {Wang, JT and Zhang, YB and Xiao, Q and Zhang, LM}, title = {Archaea is more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats.}, journal = {The Science of the total environment}, volume = {827}, number = {}, pages = {154417}, doi = {10.1016/j.scitotenv.2022.154417}, pmid = {35276174}, issn = {1879-1026}, mesh = {*Archaea ; Bacteria ; Forests ; *Microbiota ; Nitrogen/analysis ; Phosphorus/analysis ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Phosphorus deficiency is a critical limit on the cycling of carbon (C), nitrogen (N) and phosphorus (P) in forest ecosystems. Despite the pivotal roles of microbes in driving the biogeochemical cycling of C/N/P, our knowledge on the relationships of soil bacteria and archaea to P deficiency in forest ecosystems remains scarce. Here, we studied 110 acidic soils (average pH 4.5) collected across 700-km subtropical forests with a gradient of available phosphorus (AP) ranging from 0.21 to 17.6 mg/kg. We analyzed the soil C/N/P stoichiometry and studied soil bacterial and archaeal diversity/abundance via high throughput sequencing and qPCR approaches. Our results show that soil P decoupled with N or C when below 3 mg/kg but coupled with C and N when above 3 mg/kg. Archaeal diversity and abundance were significantly higher in low AP (< 3 mg/kg) soils than in high AP (>3 mg/kg) soils, while bacterial were less changed. Compared with bacteria, archaea are more strongly related with soil stoichiometry (C:N, C:P, N:P), especially when AP was less than 3 mg/kg. Taxonomic and functional composition analysis further confirmed that archaeal rather than bacterial taxonomic composition was significantly related with functional composition of microbial communities. Taken together, our results show that archaea are more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats and suggest a niche differentiation of soil bacteria and archaea in regulating the soil C/N/P cycling in subtropical forests.}, }
@article {pmid35270425, year = {2022}, author = {Xu, A and Li, L and Xie, J and Gopalakrishnan, S and Zhang, R and Luo, Z and Cai, L and Liu, C and Wang, L and Anwar, S and Jiang, Y}, title = {Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {5}, pages = {}, pmid = {35270425}, issn = {1660-4601}, mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Fertilization ; Fertilizers ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha[-1] yr[-1]) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha[-1] (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 10[7] to 1.05 × 10[7] copies g[-1] dry soil, while AOB abundance increased from 3.63 × 10[7] up to a maximum of 8.24 × 10[7] copies g[-1] dry soil with the N105 treatment (105 kg N ha[-1] yr[-1]). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha[-1] yr[-1] was optimum for the AOB community and wheat yield in the semi-arid area.}, }
@article {pmid35260828, year = {2022}, author = {Klotz, F and Kitzinger, K and Ngugi, DK and Büsing, P and Littmann, S and Kuypers, MMM and Schink, B and Pester, M}, title = {Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels.}, journal = {The ISME journal}, volume = {16}, number = {6}, pages = {1647-1656}, pmid = {35260828}, issn = {1751-7370}, mesh = {Ammonia/metabolism ; *Archaea/genetics/metabolism ; Ecosystem ; Lakes ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Deep oligotrophic lakes sustain large populations of the class Nitrososphaeria (Thaumarchaeota) in their hypolimnion. They are thought to be the key ammonia oxidizers in this habitat, but their impact on N-cycling in lakes has rarely been quantified. We followed this archaeal population in one of Europe's largest lakes, Lake Constance, for two consecutive years using metagenomics and metatranscriptomics combined with stable isotope-based activity measurements. An abundant (8-39% of picoplankton) and transcriptionally active archaeal ecotype dominated the nitrifying community. It represented a freshwater-specific species present in major inland water bodies, for which we propose the name "Candidatus Nitrosopumilus limneticus". Its biomass corresponded to 12% of carbon stored in phytoplankton over the year´s cycle. Ca. N. limneticus populations incorporated significantly more ammonium than most other microorganisms in the hypolimnion and were driving potential ammonia oxidation rates of 6.0 ± 0.9 nmol l[‒1] d[‒1], corresponding to potential cell-specific rates of 0.21 ± 0.11 fmol cell[-1] d[-1]. At the ecosystem level, this translates to a maximum capacity of archaea-driven nitrification of 1.76 × 10[9] g N-ammonia per year or 11% of N-biomass produced annually by phytoplankton. We show that ammonia-oxidizing archaea play an equally important role in the nitrogen cycle of deep oligotrophic lakes as their counterparts in marine ecosystems.}, }
@article {pmid35246355, year = {2022}, author = {Ithurbide, S and Gribaldo, S and Albers, SV and Pende, N}, title = {Spotlight on FtsZ-based cell division in Archaea.}, journal = {Trends in microbiology}, volume = {30}, number = {7}, pages = {665-678}, doi = {10.1016/j.tim.2022.01.005}, pmid = {35246355}, issn = {1878-4380}, mesh = {*Archaea/metabolism ; *Bacteria/metabolism ; Bacterial Proteins/genetics/metabolism ; Cell Division ; Eukaryota/metabolism ; }, abstract = {Compared with the extensive knowledge on cell division in model eukaryotes and bacteria, little is known about how archaea divide. Interestingly, both endosomal sorting complex required for transport (ESCRT)-based and FtsZ-based cell division systems are found in members of the Archaea. In the past couple of years, several studies have started to shed light on FtsZ-based cell division processes in members of the Euryarchaeota. In this review we highlight recent findings in this emerging field of research. We present current knowledge of the cell division machinery of halophiles which relies on two FtsZ proteins, and we compare it with that of methanobacteria, which relies on only one FtsZ. Finally, we discuss how these differences relate to the distinct cell envelopes of these two archaeal model systems.}, }
@article {pmid35221208, year = {2023}, author = {Stevens, KM and Warnecke, T}, title = {Histone variants in archaea - An undiscovered country.}, journal = {Seminars in cell &amp; developmental biology}, volume = {135}, number = {}, pages = {50-58}, doi = {10.1016/j.semcdb.2022.02.016}, pmid = {35221208}, issn = {1096-3634}, mesh = {Humans ; *Histones/genetics ; *Archaea/genetics/chemistry ; Nucleosomes/genetics ; Chromatin ; Eukaryotic Cells ; }, abstract = {Exchanging core histones in the nucleosome for paralogous variants can have important functional ramifications. Many of these variants, and their physiological roles, have been characterized in exquisite detail in model eukaryotes, including humans. In comparison, our knowledge of histone biology in archaea remains rudimentary. This is true in particular for our knowledge of histone variants. Many archaea encode several histone genes that differ in sequence, but do these paralogs make distinct, adaptive contributions to genome organization and regulation in a manner comparable to eukaryotes? Below, we review what we know about histone variants in archaea at the level of structure, regulation, and evolution. In all areas, our knowledge pales when compared to the wealth of insight that has been gathered for eukaryotes. Recent findings, however, provide tantalizing glimpses into a rich and largely undiscovered country that is at times familiar and eukaryote-like and at times strange and uniquely archaeal. We sketch a preliminary roadmap for further exploration of this country; an undertaking that may ultimately shed light not only on chromatin biology in archaea but also on the origin of histone-based chromatin in eukaryotes.}, }
@article {pmid35220398, year = {2022}, author = {Yin, X and Zhou, G and Cai, M and Zhu, QZ and Richter-Heitmann, T and Aromokeye, DA and Liu, Y and Nimzyk, R and Zheng, Q and Tang, X and Elvert, M and Li, M and Friedrich, MW}, title = {Catabolic protein degradation in marine sediments confined to distinct archaea.}, journal = {The ISME journal}, volume = {16}, number = {6}, pages = {1617-1626}, pmid = {35220398}, issn = {1751-7370}, mesh = {*Archaea/genetics/metabolism ; Carbon/metabolism ; *Geologic Sediments ; Peptide Hydrolases/metabolism ; Phylogeny ; Proteolysis ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating [13]C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.}, }
@article {pmid35189237, year = {2022}, author = {Li, M and He, H and Mi, T and Zhen, Y}, title = {Spatiotemporal dynamics of ammonia-oxidizing archaea and bacteria contributing to nitrification in sediments from Bohai Sea and South Yellow Sea, China.}, journal = {The Science of the total environment}, volume = {825}, number = {}, pages = {153972}, doi = {10.1016/j.scitotenv.2022.153972}, pmid = {35189237}, issn = {1879-1026}, mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Geologic Sediments/microbiology ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; }, abstract = {Nitrification is a central process in nitrogen cycle in the ocean. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play significant roles in ammonia oxidation which is the first and rate-limiting step in nitrification, and their differential contribution to nitrification is an important issue, attracting extensive attention. In this study, based on the quantification of archaeal and bacterial amoA gene and the measurement of potential nitrification rate (PNR), we investigated the spatiotemporal dynamics of PNRs and the amoA gene abundance and transcript abundance of aerobic ammonia oxidizers in surface sediments collected in summer and spring across ~900 km of the Bohai Sea and Yellow Sea in China. The results revealed that the contribution of AOA to nitrification was greater than that of AOB in coastal sediments, probably due to salinity and ammonia concentration. Besides, seasons had significant effect on amoA gene abundance and transcript abundance, especially for AOA, while both seasons and sea areas had significant influence on PNR of AOA and AOB. Further analysis showed complex relationships among amoA gene abundances, transcript abundances and PNRs. More importantly, both spatial (geographic distance) and environmental factors were vital in explaining the variations of ammonia-oxidizing microorganism abundances and the PNRs.}, }
@article {pmid35181078, year = {2022}, author = {Wei, W and Hu, X and Yang, S and Wang, K and Zeng, C and Hou, Z and Cui, H and Liu, S and Zhu, L}, title = {Denitrifying halophilic archaea derived from salt dominate the degradation of nitrite in salted radish during pickling.}, journal = {Food research international (Ottawa, Ont.)}, volume = {152}, number = {}, pages = {110906}, doi = {10.1016/j.foodres.2021.110906}, pmid = {35181078}, issn = {1873-7145}, mesh = {China ; Nitrates ; *Nitrites/metabolism ; Nitrogen/metabolism ; *Raphanus/chemistry ; }, abstract = {Salted radish is a popular high-salinity table food in China, and nitrite is always generated during the associated pickling process. However, this nitrite can be naturally degraded, and the underlying mechanism is unknown. Here, we identified the microbial groups that dominate the natural degradation of nitrite in salted radish and clarified the related metabolic mechanism. Based on dynamic monitoring of pH and the concentrations of nitrogen compounds as well as high-throughput sequencing analysis of the structural succession of microbial communities in the tested salted radish, we determined that the halophilic archaea derived from pickling salt dominate the natural degradation of nitrite via denitrification. Based on isolation, identification, nitrite reduction assays, and genome annotation, we further determined that Haloarcula, Halolamina, and Halobacterium were the key genera. These halophilic archaea might cope with high salt stress through the "salt-in" mechanism with the assistance of the accumulation of potassium ions, obtain electrons necessary for "truncated denitrification" from the metabolism of extracellular glucose absorbed from salted radish, and efficiently reduce nitrite to nitrogen, bypassing nitrite generation from nitrate reduction. The present study provides important information for the prevention and control of nitrite hazards in salted vegetables with high salinity, such as salted radish.}, }
@article {pmid35165305, year = {2022}, author = {Xu, B and Li, F and Cai, L and Zhang, R and Fan, L and Zhang, C}, title = {A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {49}, pmid = {35165305}, issn = {2052-4463}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Estuaries ; Genome ; *Microbiota/genetics ; Rivers ; *Viruses/genetics ; }, abstract = {Estuaries are one of the most important coastal ecosystems. While microbiomes and viromes have been separately investigated in some estuaries, few studies holistically deciphered the genomes and connections of viruses and their microbial hosts along an estuarine salinity gradient. Here we applied deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary, one of China's largest estuaries with strong anthropogenic impacts. Overall, 1,205 non-redundant prokaryotic genomes with ≥50% completeness and ≤10% contamination, and 78,502 non-redundant viral-like genomes were generated from samples of three size fractions and five salinity levels. Phylogenomic analysis and taxonomy classification show that majority of these estuarine prokaryotic and viral genomes are novel at species level according to public databases. Potential connections between the microbial and viral populations were further investigated by host-virus matching. These combined microbial and viral genomes provide an important complement of global marine genome datasets and should greatly facilitate our understanding of microbe-virus interactions, evolution and their implications in estuarine ecosystems.}, }
@article {pmid35165204, year = {2022}, author = {Schorn, S and Ahmerkamp, S and Bullock, E and Weber, M and Lott, C and Liebeke, M and Lavik, G and Kuypers, MMM and Graf, JS and Milucka, J}, title = {Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {9}, pages = {}, pmid = {35165204}, issn = {1091-6490}, mesh = {Aerobiosis ; Alismatales/*metabolism ; Anaerobiosis ; Euryarchaeota/classification/*metabolism ; Geologic Sediments ; Mediterranean Sea ; Methane/*metabolism ; Microbiota ; Oxidation-Reduction ; Phylogeny ; Species Specificity ; }, abstract = {Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m[-2] ⋅ d[-1] Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.}, }
@article {pmid35145493, year = {2021}, author = {Chen, S and Tao, J and Chen, Y and Wang, W and Fan, L and Zhang, C}, title = {Interactions Between Marine Group II Archaea and Phytoplankton Revealed by Population Correlations in the Northern Coast of South China Sea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {785532}, pmid = {35145493}, issn = {1664-302X}, abstract = {Marine Group II (MGII) archaea (Poseidoniales) are the most abundant surface marine planktonic archaea and are widely distributed in both coastal and pelagic waters. The factors affecting their distribution and activity are poorly understood. MGII archaea have the metabolic potential to utilize algae-derived organic matter and are frequently observed in high abundance during or following phytoplankton blooms, suggesting that they are key players of the marine food web. In this study, we studied interactions between MGII archaea and the diverse taxa of phytoplankton in the northern coast of South China Sea. Non-metric multidimensional scaling and cluster analyses demonstrated distinct MGII community patterns in the Pearl River plume (PRP) and the open regions of the northern South China Sea (ONSCS), with MGIIb dominating the former and MGIIa and MGIIb showing remarkable variations in the latter for the same sampling season. Nevertheless, positive correlations (Pearson correlation: R > 0.8 and P < 0.01) in absolute abundances of ribosomal RNA (rRNA)-derived complementary DNA and rRNA genes from network analyses were found between MGII archaea and phytoplankton (cyanobacteria, haptophytes, and stramenopiles in both PRP and ONSCS) among different particle size fractions, indicating their intrinsic relationships under changing environmental conditions. The results of this study may shed light on the multiple interactions between co-existing species in the micro-niches of different oceanic regions.}, }
@article {pmid35142133, year = {2022}, author = {Cui, L and Fan, X and Zheng, Y}, title = {[Enhanced heterologous expression of the cytochrome c from uncultured anaerobic methanotrophic archaea].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {38}, number = {1}, pages = {226-237}, doi = {10.13345/j.cjb.210193}, pmid = {35142133}, issn = {1872-2075}, mesh = {Anaerobiosis ; Archaea/metabolism ; *Cytochromes c/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; Heme/metabolism ; }, abstract = {Cytochrome c is a type of heme proteins that are widely distributed in living organisms. It consists of heme and apocytochrome c, and has potential applications in bioelectronics, biomedicine and pollutant degradation. However, heterologous overexpression of cytochrome c is still challenging. To date, expression of the cytochrome c from uncultured anaerobic methanotrophic archaea has not been reported, and nothing is known about the function of this cytochrome c. A his tagged cytochrome c was successfully expressed in E. coli by introducing a thrombin at the N-terminus of CytC4 and co-expressing CcmABCDEFGH, which is responsible for the maturation of cytochrome c. Shewanella oneidensis, which naturally has enzymes for cytochrome c maturation, was then used as a host to further increase the expression of CytC4. Indeed, a significantly higher expression of CytC4 was achieved in S. oneidensis when compared with in E. coli. The successful heterologous overexpression of CytC4 will facilitate the exploitation of its physiological functions and biotechnological applications.}, }
@article {pmid35126338, year = {2021}, author = {Hedlund, BP and Zhang, C and Wang, F and Rinke, C and Martin, WF}, title = {Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {827229}, pmid = {35126338}, issn = {1664-302X}, }
@article {pmid35101434, year = {2022}, author = {Liu, BB and Govindan, R and Muthuchamy, M and Cheng, S and Li, X and Ye, L and Wang, LY and Guo, SX and Li, WJ and Alharbi, NS and M Khaled, J and Kadaikunnan, S}, title = {Halophilic archaea and their extracellular polymeric compounds in the treatment of high salt wastewater containing phenol.}, journal = {Chemosphere}, volume = {294}, number = {}, pages = {133732}, doi = {10.1016/j.chemosphere.2022.133732}, pmid = {35101434}, issn = {1879-1298}, mesh = {Archaea/metabolism ; Extracellular Polymeric Substance Matrix/metabolism ; *Phenol/metabolism ; Phenols ; *Wastewater ; }, abstract = {Phenol is one of the major organic pollutants in high salt industrial wastewaters. The biological treatment of such waste using microorganisms is considered to be a cost-effective and eco-friendly method. However, in this process, salt tolerance of microorganisms is one of the main limiting factors. Halophilic microorganisms, especially halophilic archaea are thought to be appropriate for such treatment. To develop a novel effective biological method for high salt phenol wastewater treatment, the influence of phenol in high salt phenol wastewater on halophilic archaea and their extracellular polymeric substances (EPS) should be investigated. In the present study, using phenol enrichment method, 75 halophilic archaeal strains were isolated from Wuyongbulake salt lake sediment sample. The majority of the identified strains were phenol-tolerant. Six strains with high phenol tolerance were chosen, and the phenol scavenging effect was observed in the microbial suspension, supernatant, and EPS. It was noticed that the phenol degradation rate of suspensions of both strains 869-1, and 121-1 in salt water exhibited the highest rates of 83.7%, while the supernatant of strain 869-1 reached the highest rate of 78.2%. When combined with the comprehensive analysis of the artificial wastewater simulation experiment, it was discovered that in the artificial wastewater containing phenol, the phenol degradation rate of suspension of strain A387 exhibited the highest rates of 55.74% both, and supernatant of strain 630-3 reached the highest rate of 62.3%. The EPS produced by strains A00135, 558-1, 869-1, 121-1 and A387 removed 100% phenol within 96 h, and the phenol removal efficiency of EPS produced by 869-1 reached 56.1% under an artificial wastewater simulation experiment with high salt (15%NaCl) condition. The present study suggests that halophilic archaea and their EPS play an important role in phenol degradation. This approach could be potentially used for industrial high-salt wastewater treatment.}, }
@article {pmid35098330, year = {2022}, author = {Shen, LD and Geng, CY and Ren, BJ and Jin, JH and Huang, HC and Liu, X and Yang, WT and Yang, YL and Liu, JQ and Tian, MH}, title = {Detection and Quantification of Candidatus Methanoperedens-Like Archaea in Freshwater Wetland Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35098330}, issn = {1432-184X}, abstract = {Candidatus Methanoperedens-like archaea, which can use multiple electron acceptors (nitrate, iron, manganese, and sulfate) for anaerobic methane oxidation, could play an important role in reducing methane emissions from freshwater wetlands. Currently, very little is known about the distribution and community composition of Methanoperedens-like archaea in freshwater wetlands, particularly based on their alpha subunit of methyl-coenzyme M reductase (mcrA) genes. Here, the community composition, diversity, and abundance of Methanoperedens-like archaea were investigated in a freshwater wetland through high-throughput sequencing and quantitative PCR on their mcrA genes. A large number of Methanoperedens-like mcrA gene sequences (119,250) were recovered, and a total of 31 operational taxonomic units (OTUs) were generated based on 95% sequence similarity cut-off. The majority of Methanoperedens-like sequences can be grouped into three distinct clusters that were closely associated with the known Methanoperedens species which can couple anaerobic methane oxidation to nitrate or iron reduction. The community composition of Methanoperedens-like archaea differed significantly among different sampling sites, and their mcrA gene abundance was 1.49 × 10[6] ~ 4.62 × 10[6] copies g[-1] dry soil in the examined wetland. In addition, the community composition of Methanoperedens-like archaea was significantly affected by the soil water content, and the archaeal abundance was significantly positively correlated with the water content. Our results suggest that the mcrA gene is a good biomarker for detection and quantification of Methanoperedens-like archaea, and provide new insights into the distribution and environmental regulation of these archaea in freshwater wetlands.}, }
@article {pmid35076275, year = {2022}, author = {Rasmussen, AN and Francis, CA}, title = {Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0127021}, pmid = {35076275}, issn = {2379-5077}, abstract = {Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of "Candidatus Nitrosomarinus catalina" SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)-the largest estuary on the west coast of North America-and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.}, }
@article {pmid35069467, year = {2021}, author = {Rodríguez-Gijón, A and Nuy, JK and Mehrshad, M and Buck, M and Schulz, F and Woyke, T and Garcia, SL}, title = {A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {761869}, pmid = {35069467}, issn = {1664-302X}, abstract = {Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.}, }
@article {pmid35052563, year = {2021}, author = {Neira, G and Vergara, E and Cortez, D and Holmes, DS}, title = {A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {35052563}, issn = {2076-3921}, abstract = {Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (·OH) and superoxide (O2[-]). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.}, }
@article {pmid35049347, year = {2022}, author = {McMahon, FT and Lonergan, CM and Gilmore, BF and Megaw, J}, title = {Draft Genome Sequences of Halobacterium sp. Strains KA-4 and KA-6, Two Extremely Halophilic Archaea Isolated from a Triassic Salt Deposit in Northern Ireland.}, journal = {Microbiology resource announcements}, volume = {11}, number = {1}, pages = {e0116521}, pmid = {35049347}, issn = {2576-098X}, abstract = {Here, we report the draft genome sequences of Halobacterium sp. strains KA-4 and KA-6. These extremely halophilic archaea were isolated from a Triassic halite deposit in Northern Ireland. Based on 16S sequence identity, they were deemed to be closely related strains of Halobacterium noricense but with some notable phenotypic differences.}, }
@article {pmid35040218, year = {2022}, author = {Papenfort, K and Woodson, SA and Schmitz, RA and Winkler, WC}, title = {Special Issue: Regulating with RNA in Microbes: In conjunction with the 6th Meeting on Regulating with RNA in Bacteria and Archaea.}, journal = {Molecular microbiology}, volume = {117}, number = {1}, pages = {1-3}, doi = {10.1111/mmi.14867}, pmid = {35040218}, issn = {1365-2958}, support = {R13 AI147570/AI/NIAID NIH HHS/United States ; R13 AI154714/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Evolution, Molecular ; *RNA Processing, Post-Transcriptional ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Untranslated/*genetics ; RNA-Binding Proteins/genetics/*metabolism ; }, }
@article {pmid35027677, year = {2022}, author = {Wu, F and Speth, DR and Philosof, A and Crémière, A and Narayanan, A and Barco, RA and Connon, SA and Amend, JP and Antoshechkin, IA and Orphan, VJ}, title = {Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes.}, journal = {Nature microbiology}, volume = {7}, number = {2}, pages = {200-212}, pmid = {35027677}, issn = {2058-5276}, mesh = {Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Flow ; *Genome, Archaeal ; Metagenomics ; Phylogeny ; Prokaryotic Cells/*metabolism ; }, abstract = {Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.}, }
@article {pmid35022241, year = {2022}, author = {Sakai, HD and Nur, N and Kato, S and Yuki, M and Shimizu, M and Itoh, T and Ohkuma, M and Suwanto, A and Kurosawa, N}, title = {Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {3}, pages = {}, pmid = {35022241}, issn = {1091-6490}, mesh = {Archaea/classification/cytology/*genetics/*physiology ; Coculture Techniques ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Archaeal ; Genomics ; Nanoarchaeota ; Phylogeny ; Symbiosis/*genetics/*physiology ; }, abstract = {Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum "Candidatus Micrarchaeota" (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera-Metallosphaera, Acidianus, and Saccharolobus-originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions.}, }
@article {pmid35021862, year = {2022}, author = {Salter, TL and Magee, BA and Waite, JH and Sephton, MA}, title = {Mass Spectrometric Fingerprints of Bacteria and Archaea for Life Detection on Icy Moons.}, journal = {Astrobiology}, volume = {22}, number = {2}, pages = {143-157}, doi = {10.1089/ast.2020.2394}, pmid = {35021862}, issn = {1557-8070}, mesh = {Archaea ; Bacteria ; *Exobiology/methods ; Extraterrestrial Environment/chemistry ; Mass Spectrometry ; *Moon ; }, abstract = {The icy moons of the outer Solar System display evidence of subsurface liquid water and, therefore, potential habitability for life. Flybys of Saturn's moon Enceladus by the Cassini spacecraft have provided measurements of material from plumes that suggest hydrothermal activity and the presence of organic matter. Jupiter's moon Europa may have similar plumes and is the target for the forthcoming Europa Clipper mission that carries a high mass resolution and high sensitivity mass spectrometer, called the MAss Spectrometer for Planetary EXploration (MASPEX), with the capability for providing detailed characterization of any organic materials encountered. We have performed a series of experiments using pyrolysis-gas chromatography-mass spectrometry to characterize the mass spectrometric fingerprints of microbial life. A range of extremophile Archaea and Bacteria have been analyzed and the laboratory data converted to MASPEX-type signals. Molecular characteristics of protein, carbohydrate, and lipid structures were detected, and the characteristic fragmentation patterns corresponding to these different biological structures were identified. Protein pyrolysis fragments included phenols, nitrogen heterocycles, and cyclic dipeptides. Oxygen heterocycles, such as furans, were detected from carbohydrates. Our data reveal how mass spectrometry on Europa Clipper can aid in the identification of the presence of life, by looking for characteristic bacterial fingerprints that are similar to those from simple Earthly organisms.}, }
@article {pmid34987183, year = {2022}, author = {Diamond, S and Lavy, A and Crits-Christoph, A and Matheus Carnevali, PB and Sharrar, A and Williams, KH and Banfield, JF}, title = {Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs).}, journal = {The ISME journal}, volume = {16}, number = {5}, pages = {1348-1362}, pmid = {34987183}, issn = {1751-7370}, mesh = {Ammonia/metabolism ; *Archaea/metabolism ; Carbon/metabolism ; Copper/metabolism ; *Euryarchaeota/metabolism ; Mixed Function Oxygenases/genetics ; Phylogeny ; Soil ; }, abstract = {Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.}, }
@article {pmid34986784, year = {2022}, author = {Aouad, M and Flandrois, JP and Jauffrit, F and Gouy, M and Gribaldo, S and Brochier-Armanet, C}, title = {A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {1}, pmid = {34986784}, issn = {2730-7182}, mesh = {*Archaea/genetics ; *Eukaryota ; Phylogeny ; }, abstract = {BACKGROUND: The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal.<br><br>RESULTS: We analyzed sub-sets of full supermatrices&#xa0;covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study.<br><br>CONCLUSIONS: We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.}, }
@article {pmid34986141, year = {2022}, author = {Chadwick, GL and Skennerton, CT and Laso-Pérez, R and Leu, AO and Speth, DR and Yu, H and Morgan-Lang, C and Hatzenpichler, R and Goudeau, D and Malmstrom, R and Brazelton, WJ and Woyke, T and Hallam, SJ and Tyson, GW and Wegener, G and Boetius, A and Orphan, VJ}, title = {Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea.}, journal = {PLoS biology}, volume = {20}, number = {1}, pages = {e3001508}, pmid = {34986141}, issn = {1545-7885}, mesh = {Anaerobiosis ; *Archaea/genetics/metabolism ; *Electrons ; Genomics ; Geologic Sediments/microbiology ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; Sulfates/metabolism ; }, abstract = {The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.}, }
@article {pmid34984789, year = {2022}, author = {Chazan, A and Rozenberg, A and Mannen, K and Nagata, T and Tahan, R and Yaish, S and Larom, S and Inoue, K and Béjà, O and Pushkarev, A}, title = {Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {110-121}, doi = {10.1111/1462-2920.15890}, pmid = {34984789}, issn = {1462-2920}, mesh = {*Actinobacteria/genetics ; Archaea/genetics ; *Chloroflexi ; Fresh Water ; Metagenomics ; Rhodopsins, Microbial ; }, abstract = {The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional metagenomics on samples from two freshwater environments. These HeRs originated from diverse prokaryotic groups: Actinobacteria, Chloroflexi and Archaea. Heterologously expressed HeRs absorbed light in the green and yellow wavelengths (543-562 nm) and their photocycles exhibited diverse kinetic characteristics. To approach the physiological function of the HeRs, we used our environmental clones along with thousands of microbial genomes to analyze genes neighbouring HeRs. The strongest association was found with the DegV family involved in activation of fatty acids, which allowed us to hypothesize that HeRs might be involved in light-induced membrane lipid modifications.}, }
@article {pmid34962596, year = {2021}, author = {Li, SY and Xin, YJ and Bao, CX and Hou, J and Cui, HL}, title = {Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {1}, pages = {6}, pmid = {34962596}, issn = {1433-4909}, mesh = {Base Composition ; China ; DNA, Archaeal ; Glycolipids ; *Halobacteriaceae/genetics ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; }, abstract = {Three halophilic archaeal strains, Gai1-5[T], SEDH52[T] and SQT7-1[T] were isolated from Gaize salt lake and Xiadi salt lake in Tibet, and saline soil from Xinjiang, respectively. Phylogenetic analysis based on 16S rRNA gene and rpoB' gene sequences showed that these three strains formed different branches separating them from Haloprofundus halophilus NK23[T] (97.7-98.3% similarities for 16S rRNA gene and 94.7-94.8% similarities for rpoB' gene, respectively) and Haloprofundus marisrubri SB9[T] (94.7-96.4% similarities for 16S rRNA gene and 92.3-93.2% similarities for rpoB' gene, respectively). Several phenotypic characteristics distinguish the strains Gai1-5[ T], SEDH52[T] and SQT7-1[T] from Haloprofundus halophilus NK23[T] and Haloprofundus marisrubri SB9[T]. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values among the three strains and current Haloprofundus members were in the range of 83.3-88.3% and 27.2-35.7%, respectively, far below the species boundary threshold values. The major polar lipids of three strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol sulphate (PGS), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), mannosyl glucosyl diether-phosphatidic acid (DGD-PA) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). These results showed that strains Gai1-5[T] (= CGMCC 1.16079[T] = JCM 33561[T]), SQT7-1[T] (= CGMCC 1.16063[T] = JCM 33553[ T]) and SEDH52[T] (= CGMCC 1.17434[T]) represented three novel species in the genus Haloprofundus, for which the names Haloprofundus salilacus sp. nov., Haloprofundus salinisoli sp. nov., and Haloprofundus halobius sp. nov. are proposed.}, }
@article {pmid34948099, year = {2021}, author = {De Falco, M and De Felice, M}, title = {Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea.}, journal = {International journal of molecular sciences}, volume = {22}, number = {24}, pages = {}, pmid = {34948099}, issn = {1422-0067}, mesh = {*Archaea/genetics/metabolism ; *DNA Breaks, Double-Stranded ; *DNA Repair ; *DNA, Archaeal/genetics/metabolism ; *Genomic Instability ; Humans ; }, abstract = {All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.}, }
@article {pmid34927901, year = {2021}, author = {Otzen, DE and Dueholm, MS and Najarzadeh, Z and Knowles, TPJ and Ruggeri, FS}, title = {In situ Sub-Cellular Identification of Functional Amyloids in Bacteria and Archaea by Infrared Nanospectroscopy.}, journal = {Small methods}, volume = {5}, number = {6}, pages = {e2001002}, doi = {10.1002/smtd.202001002}, pmid = {34927901}, issn = {2366-9608}, mesh = {Amyloid/chemistry/*isolation &amp; purification/*metabolism ; Amyloidogenic Proteins/chemistry/isolation &amp; purification/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Bacterial Outer Membrane ; Biofilms ; Escherichia coli/metabolism ; Escherichia coli Proteins ; Humans ; Protein Structure, Secondary ; Pseudomonas/metabolism ; }, abstract = {Formation of amyloid structures is originally linked to human disease. However, amyloid materials are found extensively in the animal and bacterial world where they stabilize intra- and extra-cellular environments like biofilms or cell envelopes. To date, functional amyloids have largely been studied using optical microscopy techniques in vivo, or after removal from their biological context for higher-resolution studies in vitro. Furthermore, conventional microscopies only indirectly identify amyloids based on morphology or unspecific amyloid dyes. Here, the high chemical and spatial (≈20 nm) resolution of Infrared Nanospectroscopy (AFM-IR) to investigate functional amyloid from Escherichia coli (curli), Pseudomonas (Fap), and the Archaea Methanosaeta (MspA) in situ is exploited. It is demonstrated that AFM-IR identifies amyloid protein within single intact cells through their cross β-sheet secondary structure, which has a unique spectroscopic signature in the amide I band of protein. Using this approach, nanoscale-resolved chemical images and spectra of purified curli and Methanosaeta cell wall sheaths are provided. The results highlight significant differences in secondary structure between E. coli cells with and without curli. Taken together, these results suggest that AFM-IR is a new and powerful label-free tool for in situ investigations of the biophysical state of functional amyloid and biomolecules in general.}, }
@article {pmid34917055, year = {2021}, author = {Lu, S and Liu, X and Liu, C and Cheng, G and Zhou, R and Li, Y}, title = {A Review of Ammonia-Oxidizing Archaea and Anaerobic Ammonia-Oxidizing Bacteria in the Aquaculture Pond Environment in China.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {775794}, pmid = {34917055}, issn = {1664-302X}, abstract = {The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.}, }
@article {pmid34910467, year = {2021}, author = {Wang, Y and Xu, J and Cui, D and Kong, L and Chen, S and Xie, W and Zhang, C}, title = {Classification and Identification of Archaea Using Single-Cell Raman Ejection and Artificial Intelligence: Implications for Investigating Uncultivated Microorganisms.}, journal = {Analytical chemistry}, volume = {93}, number = {51}, pages = {17012-17019}, doi = {10.1021/acs.analchem.1c03495}, pmid = {34910467}, issn = {1520-6882}, mesh = {*Artificial Intelligence ; In Situ Hybridization, Fluorescence ; *Lipids ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Archaea can produce special cellular components such as polyhydroxyalkanoates, carotenoids, rhodopsin, and ether lipids, which have valuable applications in medicine and green energy production. Most of the archaeal species are uncultivated, posing challenges to investigating their biomarker components and biochemical properties. In this study, we applied Raman spectroscopy to examine the biological characteristics of nine archaeal isolates, including halophilic archaea (Haloferax larsenii, Haloarcula argentinensis, Haloferax mediterranei, Halomicrobium mukohataei, Halomicrobium salinus, Halorussus sp., Natrinema gari), thermophilic archaea (Sulfolobus acidocaldarius), and marine group I (MGI) archaea (Nitrosopumilus maritimus). Linear discriminant analysis of the Raman spectra allowed visualization of significant separations among the nine archaeal isolates. Machine-learning classification models based on support vector machine achieved accuracies of 88-100% when classifying the nine archaeal species. The predicted results were validated by DNA sequencing analysis of cells isolated from the mixture by Raman-activated cell sorting. Raman spectra of uncultured archaea (MGII) were also obtained based on Raman spectroscopy and fluorescence in situ hybridization. The results combining multiple Raman-based techniques indicated that MGII may have the ability to produce lipids distinct from other archaeal species. Our study provides a valuable approach for investigating and classifying archaea, especially uncultured species, at the single-cell level.}, }
@article {pmid34894218, year = {2022}, author = {Stevens, KM and Hocher, A and Warnecke, T}, title = {Deep Conservation of Histone Variants in Thermococcales Archaea.}, journal = {Genome biology and evolution}, volume = {14}, number = {1}, pages = {}, pmid = {34894218}, issn = {1759-6653}, support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; MC-A658-5TY40/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Archaea/genetics/metabolism ; Chromatin ; *Histones/genetics ; Nucleosomes/genetics ; Phylogeny ; *Thermococcales/genetics/metabolism ; }, abstract = {Histones are ubiquitous in eukaryotes where they assemble into nucleosomes, binding and wrapping DNA to form chromatin. One process to modify chromatin and regulate DNA accessibility is the replacement of histones in the nucleosome with paralogous variants. Histones are also present in archaea but whether and how histone variants contribute to the generation of different physiologically relevant chromatin states in these organisms remains largely unknown. Conservation of paralogs with distinct properties can provide prima facie evidence for defined functional roles. We recently revealed deep conservation of histone paralogs with different properties in the Methanobacteriales, but little is known experimentally about these histones. In contrast, the two histones of the model archaeon Thermococcus kodakarensis, HTkA and HTkB, have been examined in some depth, both in vitro and in vivo. HTkA and HTkB exhibit distinct DNA-binding behaviors and elicit unique transcriptional responses when deleted. Here, we consider the evolution of HTkA/B and their orthologs across the order Thermococcales. We find histones with signature HTkA- and HTkB-like properties to be present in almost all Thermococcales genomes. Phylogenetic analysis indicates the presence of one HTkA- and one HTkB-like histone in the ancestor of Thermococcales and long-term maintenance of these two paralogs throughout Thermococcales diversification. Our results support the notion that archaea and eukaryotes have convergently evolved histone variants that carry out distinct adaptive functions. Intriguingly, we also detect more highly diverged histone-fold proteins, related to those found in some bacteria, in several Thermococcales genomes. The functions of these bacteria-type histones remain unknown, but structural modeling suggests that they can form heterodimers with HTkA/B-like histones.}, }
@article {pmid34871608, year = {2022}, author = {Liu, Y and Wang, Q and Pan, Q and Zhou, X and Peng, Z and Jahng, D and Yang, B and Pan, X}, title = {Ventilation induced evolution pattern of archaea, fungi, bacteria and their potential roles during co-bioevaporation treatment of concentrated landfill leachate and food waste.}, journal = {Chemosphere}, volume = {289}, number = {}, pages = {133122}, doi = {10.1016/j.chemosphere.2021.133122}, pmid = {34871608}, issn = {1879-1298}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bioreactors ; Food ; Fungi/genetics ; *Refuse Disposal ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; }, abstract = {To obtain a favorable aeration type in co-bioevaporation treatment of concentrated landfill leachate and food waste, and to deeply understand the co-bioevaporation mechanisms, the temporal evolution differences of archaea, fungi and bacteria as well as the related microbial metabolism genes and functional enzymes under intermittent ventilation (IV) and continuous ventilation (CV) were investigated. Results through metagenomics analysis showed that the less sufficient oxygen and longer thermophilic phase in IV stimulated the vigorous growth of archaea, while CV was beneficial for fungal growth. Even genes of carbohydrates and lipids metabolism and ATP-associated enzymes (enzyme 2.7.13.3 and 3.6.4.12), as well as peptidoglycan biosynthesis enzyme (enzyme 3.4.16.4), were more abundant in CV, IV hold better DNA repair ability, higher microbial viability, and less dehydrogenase sensitivity to temperatures due to the critical contribution of Pseudomonas (3.1-45.9%). Furthermore, IV consumed a similar amount of heat for water evaporation with nearly half of the ventilation of CV and was a favorable aeration type in the practical application of co-bioevaporation.}, }
@article {pmid34850144, year = {2021}, author = {Yen, CY and Lin, MG and Chen, BW and Ng, IW and Read, N and Kabli, AF and Wu, CT and Shen, YY and Chen, CH and Barillà, D and Sun, YJ and Hsiao, CD}, title = {Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly.}, journal = {Nucleic acids research}, volume = {49}, number = {22}, pages = {13150-13164}, pmid = {34850144}, issn = {1362-4962}, support = {BB/M007839/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R006369/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/chemistry/genetics/metabolism ; Adenosine Triphosphate/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; Chromatin/genetics/metabolism/ultrastructure ; *Chromosome Segregation ; Chromosomes, Archaeal/*genetics ; Crystallography, X-Ray ; DNA, Archaeal/chemistry/*genetics/metabolism ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Microscopy, Electron ; Models, Molecular ; Multiprotein Complexes/chemistry/metabolism/ultrastructure ; Mutation ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Sulfolobus solfataricus/*genetics/metabolism ; }, abstract = {Genome segregation is a vital process in all organisms. Chromosome partitioning remains obscure in Archaea, the third domain of life. Here, we investigated the SegAB system from Sulfolobus solfataricus. SegA is a ParA Walker-type ATPase and SegB is a site-specific DNA-binding protein. We determined the structures of both proteins and those of SegA-DNA and SegB-DNA complexes. The SegA structure revealed an atypical, novel non-sandwich dimer that binds DNA either in the presence or in the absence of ATP. The SegB structure disclosed a ribbon-helix-helix motif through which the protein binds DNA site specifically. The association of multiple interacting SegB dimers with the DNA results in a higher order chromatin-like structure. The unstructured SegB N-terminus plays an essential catalytic role in stimulating SegA ATPase activity and an architectural regulatory role in segrosome (SegA-SegB-DNA) formation. Electron microscopy results also provide a compact ring-like segrosome structure related to chromosome organization. These findings contribute a novel mechanistic perspective on archaeal chromosome segregation.}, }
@article {pmid34846953, year = {2022}, author = {Vavilin, VA and Lokshina, LY and Rytov, SV}, title = {Anaerobic oxidation of methane coupled with sulphate reduction: high concentration of methanotrophic archaea might be responsible for low stable isotope fractionation factors in methane.}, journal = {Isotopes in environmental and health studies}, volume = {58}, number = {1}, pages = {44-59}, doi = {10.1080/10256016.2021.2000405}, pmid = {34846953}, issn = {1477-2639}, mesh = {Anaerobiosis ; *Archaea ; Factor VII ; Geologic Sediments ; Isotopes ; *Methane ; Oxidation-Reduction ; Sulfates ; }, abstract = {The changes in δ[13]CH4 and δ[12]C[1]H3[2]H during sulphate-dependent anaerobic oxidation of methane (AOM) were described using dynamic modelling. The batch sulphate-dependent AOM at the nearly linear dynamics of methane oxidation with different enriched cultures originating from three marine sediments was simulated. The traditional Rayleigh equation for carbon and hydrogen stable isotopes in methane was derived from the basic dynamic isotope equation. The general and reduced models, taking into account the reaction stoichiometry and based on balances of chemical elements and their isotopes, describes a redistribution of stable isotope values in the sulphate-dependent AOM process. It was shown that AOM is the first and rate-limiting step in the whole AOM + SR (sulphate reduction) process. The different fractionation factors of carbon and hydrogen isotopes in methane were obtained for three marine sediments. It was concluded that during incubation the highest concentration of methanotrophic archaea might be responsible for the lowest fractionation factors of stable isotopes of carbon and hydrogen in methane. The interpretation of this phenomenon was suggested. Different concentrations of methanotrophic archaea can lead to variations of isotope fractionation factors.}, }
@article {pmid34841354, year = {2021}, author = {Tan, RSG and Zhou, M and Li, F and Guan, LL}, title = {Identifying active rumen epithelial associated bacteria and archaea in beef cattle divergent in feed efficiency using total RNA-seq.}, journal = {Current research in microbial sciences}, volume = {2}, number = {}, pages = {100064}, pmid = {34841354}, issn = {2666-5174}, abstract = {To date, the role of ruminal epithelial attached microbiota in cattle feed efficiency is undefined. In this study, we aimed to characterize transcriptionally active bacteria and archaea attached to the rumen epithelial wall and to determine whether they differ in cattle with varied feed efficiency. RNA-sequencing was performed to obtain the rumen epithelial transcriptomes from 9 of the most efficient (low RFI) and 9 of the most inefficient (high RFI) animals. The bacteria and archaea 16S rRNA transcripts were identified using an in-house developed pipeline, enriched from filtered reads that did not map to the bovine genome. Archaea from unclassified genera belonging to the Euryarchaeota phylum showed the most activity on the rumen epithelium of low RFI (81.3 ± 1.9%) and high RFI (76.4 ± 3.0%) steers. Bacteria from the Succinivibrionaceae family showed the greatest activity of bacteria on the low RFI (28.7 ± 9.0%) and high RFI (33.9± 8.8%) epithelium. Of the bacterial families, Campylobacteraceae and Neisseriaceae had significantly greater activity on the low RFI epithelium (p < 0.05) and are known to play a role in oxygen scavenging. Greater activity of rumen epithelial attached oxygen scavenging bacteria may provide more optimal feed fermentation conditions, which contributes to high fermentation efficiency in the rumen.}, }
@article {pmid34827555, year = {2021}, author = {Amin, K and Tranchimand, S and Benvegnu, T and Abdel-Razzak, Z and Chamieh, H}, title = {Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology.}, journal = {Biomolecules}, volume = {11}, number = {11}, pages = {}, pmid = {34827555}, issn = {2218-273X}, mesh = {Biotechnology ; *Glycoside Hydrolases ; Temperature ; }, abstract = {Hyperthermophilic Archaea colonizing unnatural habitats of extremes conditions such as volcanoes and deep-sea hydrothermal vents represent an unmeasurable bioresource for enzymes used in various industrial applications. Their enzymes show distinct structural and functional properties and are resistant to extreme conditions of temperature and pressure where their mesophilic homologs fail. In this review, we will outline carbohydrate-active enzymes (CAZymes) from hyperthermophilic Archaea with specific focus on the two largest families, glycoside hydrolases (GHs) and glycosyltransferases (GTs). We will present the latest advances on these enzymes particularly in the light of novel accumulating data from genomics and metagenomics sequencing technologies. We will discuss the contribution of these enzymes from hyperthermophilic Archaea to industrial applications and put the emphasis on newly identifed enzymes. We will highlight their common biochemical and distinct features. Finally, we will overview the areas that remain to be explored to identify novel promising hyperthermozymes.}, }
@article {pmid34825404, year = {2022}, author = {Coker, OO}, title = {Non-bacteria microbiome (virus, fungi, and archaea) in gastrointestinal cancer.}, journal = {Journal of gastroenterology and hepatology}, volume = {37}, number = {2}, pages = {256-262}, doi = {10.1111/jgh.15738}, pmid = {34825404}, issn = {1440-1746}, mesh = {Archaea ; Fungi ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/microbiology/prevention &amp; control ; Humans ; Viruses ; }, abstract = {The gastrointestinal tract houses millions of microbes collectively referred to as the gut microbiome. The gut microbes comprise of bacteria, viruses, fungi, archaea, and microscopic eukaryotes, which co-evolved or colonize the gut forming complex symbiotic and mutualistic relationships. A state of homeostasis is required between host and gut microbiome relationship to maintain several host beneficial processes. Alterations in the taxonomic and functional composition of the gut microbes are associated with several human diseases including gastrointestinal cancers. Owed to their overwhelming abundance and ease of characterization, several studies focus on the role of bacteria in gastrointestinal cancers. There is however growing evidence that non-bacteria gut microbes are associated with the pathogenesis of gastrointestinal cancers. This review details the association of non-bacteria gut microbes including fungi, viruses, and archaea and their potential manipulation in the prevention and treatment of human gastrointestinal cancers.}, }
@article {pmid34808316, year = {2022}, author = {Fan, Q and Fan, X and Fu, P and Li, Y and Zhao, Y and Hua, D}, title = {Anaerobic digestion of wood vinegar wastewater using domesticated sludge: Focusing on the relationship between organic degradation and microbial communities (archaea, bacteria, and fungi).}, journal = {Bioresource technology}, volume = {347}, number = {}, pages = {126384}, doi = {10.1016/j.biortech.2021.126384}, pmid = {34808316}, issn = {1873-2976}, mesh = {Acetic Acid ; Anaerobiosis ; Archaea ; Bacteria ; Bioreactors ; Fungi ; Methane ; Methanol ; *Microbiota ; *Sewage ; Wastewater ; }, abstract = {Thermochemical process of biomass is one of the promising renewable energy technologies; however, the by-product (wood vinegar wastewater) is rich in refractory organics, which is harmful to the environment and inhibits the conversion efficiency of microorganisms. Consequently, the dominant functional microbial communities corresponding to the various substrate were obtained through the continuous domestication, and the relationship between the dominant functional communities and the degradation of organic compounds was comprehensively analyzed. The bacterial community was absolutely dominant (approximately 85%), while archaea and fungi had similar relative abundance. The diversity showed that glucose was not conducive to the development of microbial diversity, while the substrate containing wood vinegar wastewater showed the opposite trend. The functional analysis revealed that the enrichment of bacteria associated with the hydrolysis and acidification of organics increased in the domestication process. Glucose facilitated hydrogen-trophic methanogenesis as the main methanogenic pathway in the methanogenic stage.}, }
@article {pmid34803972, year = {2021}, author = {Durán-Viseras, A and Sánchez-Porro, C and Ventosa, A}, title = {Genomic Insights Into New Species of the Genus Halomicroarcula Reveals Potential for New Osmoadaptative Strategies in Halophilic Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {751746}, pmid = {34803972}, issn = {1664-302X}, abstract = {Metagenomic studies on prokaryotic diversity of hypersaline soils from the Odiel saltmarshes, South-west Spain, revealed a high proportion of genomic sequences not related to previously cultivated taxa, that might be related to haloarchaea with a high environmental and nutritional flexibility. In this study, we used a culturomics approach in order to isolate new haloarchaeal microorganisms from these hypersaline soils. Four haloarchaeal strains, designated strains F24A[T], F28, F27[T], and F13[T], phylogenetically related to the genus Halomicroarcula, were isolated and characterized in detail. The phylogenomic tree based on the 100 orthologous single-copy genes present in the genomes of these four strains as well as those of the type strains of the species Halomicroarcula pellucida CECT 7537[T], Halomicroarcula salina JCM 18369[T] and Halomicroarcula limicola JCM 18640[T], that were determined in this study, revealed that these four new isolates clustered on three groups, with strains F24A[T] and F28 within a single cluster, and altogether with the species of Halomicroarcula. Additionally, Orthologous Average Nucleotide Identity (OrthoANI), digital DNA-DNA hybridization (dDDH) and Average Amino-acid Identity (AAI) values, likewise phenotypic characteristics, including their polar lipids profiles, permitted to determine that they represent three new species, for which we propose the names Halomicroarcula rubra sp. nov. (type strain F13[T]), Halomicroarcula nitratireducens sp. nov. (type strain F27[T]) and Halomicroarcula salinisoli sp. nov. (type strain F24A[T]). An in deep comparative genomic analysis of species of the genus Halomicroarcula, including their metabolism, their capability to biosynthesize secondary metabolites and their osmoregulatory adaptation mechanisms was carried out. Although they use a salt-in strategy, the identification of the complete pathways for the biosynthesis of the compatible solutes trehalose and glycine betaine, not identified before in any other haloarchaea, might suggest alternative osmoadaptation strategies for this group. This alternative osmoregulatory mechanism would allow this group of haloarchaea to be versatile and eco-physiologically successful in hypersaline environments and would justify the capability of the species of this genus to grow not only on environments with high salt concentrations [up to 30% (w/v) salts], but also under intermediate to low salinities.}, }
@article {pmid34796612, year = {2022}, author = {Saghaï, A and Banjeree, S and Degrune, F and Edlinger, A and García-Palacios, P and Garland, G and van der Heijden, MGA and Herzog, C and Maestre, FT and Pescador, DS and Philippot, L and Rillig, MC and Romdhane, S and Hallin, S}, title = {Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {341-356}, doi = {10.1111/1462-2920.15830}, pmid = {34796612}, issn = {1462-2920}, mesh = {*Ammonia ; *Archaea ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.}, }
@article {pmid34790173, year = {2021}, author = {Trouche, B and Brandt, MI and Belser, C and Orejas, C and Pesant, S and Poulain, J and Wincker, P and Auguet, JC and Arnaud-Haond, S and Maignien, L}, title = {Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {702016}, pmid = {34790173}, issn = {1664-302X}, abstract = {Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.}, }
@article {pmid34777272, year = {2021}, author = {Satari, L and Guillén, A and Latorre-Pérez, A and Porcar, M}, title = {Beyond Archaea: The Table Salt Bacteriome.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {714110}, pmid = {34777272}, issn = {1664-302X}, abstract = {Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.}, }
@article {pmid34740642, year = {2022}, author = {Zou, W and Lang, M and Zhang, L and Liu, B and Chen, X}, title = {Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil.}, journal = {The Science of the total environment}, volume = {811}, number = {}, pages = {151402}, doi = {10.1016/j.scitotenv.2021.151402}, pmid = {34740642}, issn = {1879-1026}, mesh = {Ammonia ; *Archaea/genetics ; *Betaproteobacteria ; Ecosystem ; Fertilization ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha[-1] for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.}, }
@article {pmid34737728, year = {2021}, author = {Vázquez-Campos, X and Kinsela, AS and Bligh, MW and Payne, TE and Wilkins, MR and Waite, TD}, title = {Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {732575}, pmid = {34737728}, issn = {1664-302X}, abstract = {During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.}, }
@article {pmid34725736, year = {2021}, author = {Sutter, JM and Johnsen, U and Reinhardt, A and Schönheit, P}, title = {Correction to: Pentose degradation in archaea: Halorhabdus species degrade D-xylose, L-arabinose and D-ribose via bacterial-type pathways.}, journal = {Extremophiles : life under extreme conditions}, volume = {25}, number = {5-6}, pages = {527}, doi = {10.1007/s00792-021-01248-7}, pmid = {34725736}, issn = {1433-4909}, }
@article {pmid34721370, year = {2021}, author = {Liu, LJ and Jiang, Z and Wang, P and Qin, YL and Xu, W and Wang, Y and Liu, SJ and Jiang, CY}, title = {Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {768283}, pmid = {34721370}, issn = {1664-302X}, abstract = {The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.}, }
@article {pmid34691003, year = {2021}, author = {Anchal,  and Kaushik, V and Goel, M}, title = {Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {751049}, pmid = {34691003}, issn = {1664-302X}, abstract = {Cis-trans isomerization of the peptide bond prior to proline is an intrinsically slow process but plays an essential role in protein folding. In vivo cis-trans isomerization reaction is catalyzed by Peptidyl-prolyl isomerase (PPIases), a category of proteins widely distributed among all the three domains of life. The present study is majorly focused on the distribution of different types of PPIases in the archaeal domain. All the three hitherto known families of PPIases (namely FKBP, Cyclophilin and parvulin) were studied to identify the evolutionary conservation across the phylum archaea. The basic function of cyclophilin, FKBP and parvulin has been conserved whereas the sequence alignment suggested variations in each clade. The conserved residues within the predicted motif of each family are unique. The available protein structures of different PPIase across various domains were aligned to ascertain the structural variation in the catalytic site. The structural alignment of native PPIase proteins among various groups suggested that the apo-protein may have variable conformations but when bound to their specific inhibitors, they attain similar active site configuration. This is the first study of its kind which explores the distribution of archaeal PPIases, along with detailed structural and functional analysis of each type of PPIase found in archaea.}, }
@article {pmid34688753, year = {2022}, author = {Wunderer, M and Markt, R and Lackner, N and Wagner, AO}, title = {The glutamyl tail length of the cofactor F420 in the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus.}, journal = {The Science of the total environment}, volume = {809}, number = {}, pages = {151112}, doi = {10.1016/j.scitotenv.2021.151112}, pmid = {34688753}, issn = {1879-1026}, mesh = {Methane ; *Methanomicrobiaceae/enzymology ; Methanosarcina/*enzymology ; Riboflavin/analogs &amp; derivatives ; }, abstract = {The cofactor F420 is synthesized by many different organisms and as a redox cofactor, it plays a crucial role in the redox reactions of catabolic and biosynthetic metabolic pathways. It consists of a deazaflavin structure, which is linked via lactate to an oligoglutamate chain, that can vary in length. In the present study, the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus were cultivated on different carbon sources and their coenzyme F420 composition has been assayed by reversed-phase ion-pair high-performance liquid chromatography with fluorometric detection regarding both, overall cofactor F420 production and distribution of F420 glutamyl tail length. In Methanosarcina thermophila cultivated on methanol, acetate, and a mixture of acetate and methanol, the most abundant cofactors were F420-5 and F420-4, whereby the last digit refers to the number of expressed glutamyl rests. By contrast, in the obligate CO2 reducing Methanoculleus thermophilus the most abundant cofactors were F420-3 and F420-4. In Methanosarcina thermophila, the relative proportions of the expressed F420 tail length changed during batch growth on all three carbon sources. Over time F420-3 and F420-4 decreased while F420-5 and F420-6 increased in their relative proportion in comparison to total F420 content. In contrast, in Methanoculleus thermophilus the relative abundance of the different F420 cofactors remained stable. It was also possible to differentiate the two methanogenic Archaea based on the glutamyl tail length of the cofactor F420. The cofactor F420-5 in concentrations >2% could only be assigned to Methanosarcina thermophila. In all four variants a trend for a positive correlation between the DNA concentration and the total concentration of the cofactor could be shown. Except for the variant Methanosarcinathermophila with acetate as sole carbon source the same could be shown between the concentration of the mcrA gene copy number and the total concentration of the cofactor.}, }
@article {pmid34666825, year = {2021}, author = {Wang, B and Liu, N and Yang, M and Wang, L and Liang, X and Liu, CQ}, title = {Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China's coastal wetlands.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {19}, pmid = {34666825}, issn = {2524-6372}, abstract = {Planktonic bacteria and archaea play a key role in maintaining ecological functions in aquatic ecosystems; however, their biogeographic patterns and underlying mechanisms have not been well known in coastal wetlands including multiple types and at a large space scale. Therefore, planktonic bacteria and archaea and related environmental factors were investigated in twenty-one wetlands along China's coast to understand the above concerns. The results indicated that planktonic bacteria had different biogeographic pattern from planktonic archaea, and both patterns were not dependent on the wetland's types. Deterministic selection shapes the former's community structure, whereas stochastic processes regulate the latter's, being consistent with the fact that planktonic archaea have a larger niche breadth than planktonic bacteria. Planktonic bacteria and archaea co-occur, and their co-occurrence rather than salinity is more important in shaping their community structure although salinity is found to be a main environmental deterministic factor in the coastal wetland waters. This study highlights the role of planktonic bacteria-archaea co-occurrence on their biogeographic patterns, and thus provides a new insight into studying underlying mechanisms of microbial biogeography in coastal wetlands.}, }
@article {pmid34665251, year = {2021}, author = {Westoby, M and Nielsen, DA and Gillings, MR and Gumerov, VM and Madin, JS and Paulsen, IT and Tetu, SG}, title = {Strategic traits of bacteria and archaea vary widely within substrate-use groups.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {11}, pages = {}, doi = {10.1093/femsec/fiab142}, pmid = {34665251}, issn = {1574-6941}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genome Size ; Phenotype ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.}, }
@article {pmid34661841, year = {2022}, author = {Ye, H and Tang, C and Cao, Y and Li, X and Huang, P}, title = {Contribution of ammonia-oxidizing archaea and bacteria to nitrification under different biogeochemical factors in acidic soils.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {12}, pages = {17209-17222}, doi = {10.1007/s11356-021-16887-8}, pmid = {34661841}, issn = {1614-7499}, mesh = {Ammonia/chemistry ; *Archaea/genetics ; Bacteria/genetics ; Ecosystem ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Nitrification in soils is an essential process that involves archaeal and bacterial ammonia-oxidizers. Despite its importance, the relative contributions of soil factors to the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their nitrification performances are seldom discussed. The aim of this study was to determine the effects of AOA and AOB abundance and different environmental conditions (pH, TC, TN, moisture, and temperature) on nitrification performance. The soils of the long-term fertilized tea orchards and forests were sampled in the field, and nitrification experiments were conducted in the laboratory. The acid soils were collected from the field and used in laboratory incubation experiments to calculate the nitrification rate, including the net nitrification rate (NN rate), nitrification potential (NP), and nitrification kinetics. The basic parameters, different forms of nitrogen content, and AOA and AOB amoA gene copies were also analyzed. Compared with the forest soil, the tea orchard soil had a lower pH and higher nitrogen content (p < 0.05). The AOA and AOB abundance in the soils of the forests and tea orchards were pH-dependent. The NN rate and NP had good relationships with AOA or AOB in the forest soil; however, poor relationships were observed in the tea orchard soil. When pH < 4, the performances of AOA and AOB were restricted by pH and the environment, especially in long-term fertilized farmlands. Long-term fertilization can cause soil acidification, which regulates the abundance of AOA and AOB and their nitrifying ability. The soil environment rather than AOA or AOB could control nitrification in long-term fertilized farmlands with a pH below 4. These findings could improve fertilization efficiency and control nutrient runoff in hilly agricultural ecosystems.}, }
@article {pmid34655277, year = {2022}, author = {Chouhan, BPS and Gade, M and Martinez, D and Toledo-Patino, S and Laurino, P}, title = {Implications of divergence of methionine adenosyltransferase in archaea.}, journal = {FEBS open bio}, volume = {12}, number = {1}, pages = {130-145}, pmid = {34655277}, issn = {2211-5463}, mesh = {*Archaea/genetics/metabolism ; Catalytic Domain ; Methionine ; *Methionine Adenosyltransferase/chemistry/genetics/metabolism ; S-Adenosylmethionine/chemistry ; }, abstract = {Methionine adenosyltransferase (MAT) catalyzes the biosynthesis of S-adenosyl methionine from l-methionine and ATP. MAT enzymes are ancient, believed to share a common ancestor, and are highly conserved in all three domains of life. However, the sequences of archaeal MATs show considerable divergence compared with their bacterial and eukaryotic counterparts. Furthermore, the structural significance and functional significance of this sequence divergence are not well understood. In the present study, we employed structural analysis and ancestral sequence reconstruction to investigate archaeal MAT divergence. We observed that the dimer interface containing the active site (which is usually well conserved) diverged considerably between the bacterial/eukaryotic MATs and archaeal MAT. A detailed investigation of the available structures supports the sequence analysis outcome: The protein domains and subdomains of bacterial and eukaryotic MAT are more similar than those of archaea. Finally, we resurrected archaeal MAT ancestors. Interestingly, archaeal MAT ancestors show substrate specificity, which is lost during evolution. This observation supports the hypothesis of a common MAT ancestor for the three domains of life. In conclusion, we have demonstrated that archaeal MAT is an ideal system for studying an enzyme family that evolved differently in one domain compared with others while maintaining the same catalytic activity.}, }
@article {pmid34650523, year = {2021}, author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, RK}, title = {Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {701414}, pmid = {34650523}, issn = {1664-302X}, abstract = {Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus-host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance.}, }
@article {pmid34628131, year = {2021}, author = {Castro, I and Costa, H and Turgeman-Grott, I and Allers, T and Mendo, S and Caetano, T}, title = {The lanthipeptide biosynthetic clusters of the domain Archaea.}, journal = {Microbiological research}, volume = {253}, number = {}, pages = {126884}, doi = {10.1016/j.micres.2021.126884}, pmid = {34628131}, issn = {1618-0623}, mesh = {*Archaea/genetics ; Eukaryota ; Euryarchaeota ; *Peptides/genetics ; }, abstract = {Research on Archaea's secondary metabolites is still lagging behind that of Bacteria and Eukarya. Our goal was to contribute to this knowledge gap by analyzing the lanthipeptide's clusters in Archaea. As previously proposed, Archaea encodes only class II synthetases (LanMs), which we found to be confined to the class Halobacteria (also known as haloarchaea). In total, we analyzed the phylogeny and the domains of 42 LanMs. Four types were identified, and the majority of them belong to the CCG group due to their cyclization domain, which includes LanMs of Cyanobacteria. Putative cognate peptides were predicted for most of LanMs and are a very diverse group of molecules that share a Kx(Y/F)(D/E)xx(F/Y) motif in their leader peptides. According to their homology, some of them were categorized into subfamilies, including Halolancins, Haladacins, Haloferaxcins and Halobiforcins. Many LanM genes were associated with mobile genetic elements, and their vicinities mainly encode ABC and MFS transporters, tailoring enzymes and uncharacterized proteins. Our results suggest that the biosynthesis of lanthipeptides in haloarchaea can entail distinct enzymology that must lead to the production of peptides with novel structures and unpredicted biological and ecological roles. Finally, an Haloferax mediterranei knockout, lacking its three lanM genes, was generated, and it was concluded that its antimicrobial activity is not primarily related to the production of lanthipeptides.}, }
@article {pmid34606606, year = {2021}, author = {Payne, LJ and Todeschini, TC and Wu, Y and Perry, BJ and Ronson, CW and Fineran, PC and Nobrega, FL and Jackson, SA}, title = {Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types.}, journal = {Nucleic acids research}, volume = {49}, number = {19}, pages = {10868-10878}, pmid = {34606606}, issn = {1362-4962}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Antibiosis/*genetics ; Archaea/classification/*genetics/metabolism/virology ; Archaeal Proteins/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism/virology ; Bacterial Proteins/*genetics/metabolism ; Bacteriophages/*genetics/growth &amp; development ; CRISPR-Cas Systems ; DNA Helicases/genetics/metabolism ; DNA Modification Methylases/genetics/metabolism ; Markov Chains ; Phylogeny ; *Software ; Terminology as Topic ; }, abstract = {To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).}, }
@article {pmid34578152, year = {2021}, author = {Krawczyk, A and Salamon, D and Kowalska-Duplaga, K and Bogiel, T and Gosiewski, T}, title = {Association of Fungi and Archaea of the Gut Microbiota with Crohn's Disease in Pediatric Patients-Pilot Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34578152}, issn = {2076-0817}, abstract = {The composition of bacteria is often altered in Crohn's disease (CD), but its connection to the disease is not fully understood. Gut archaea and fungi have recently been suggested to play a role as well. In our study, the presence and number of selected species of fungi and archaea in pediatric patients with CD and healthy controls were evaluated. Stool samples were collected from children with active CD (n = 54), non-active CD (n = 37) and control subjects (n = 33). The prevalence and the number of selected microorganisms were assessed by real-time PCR. The prevalence of Candida tropicalis was significantly increased in active CD compared to non-active CD and the control group (p = 0.011 and p = 0.036, respectively). The number of Malassezia spp. cells was significantly lower in patients with active CD compared to the control group, but in non-active CD, a significant increase was observed (p = 0.005 and p = 0.020, respectively). There were no statistically significant differences in the colonization by archaea. The obtained results indicate possible correlations with the course of the CD; however, further studies of the entire archeobiome and the mycobiome are necessary in order to receive a complete picture.}, }
@article {pmid34575103, year = {2021}, author = {Merkel, AY and Chernyh, NA and Pimenov, NV and Bonch-Osmolovskaya, EA and Slobodkin, AI}, title = {Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {34575103}, issn = {2075-1729}, abstract = {Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.}, }
@article {pmid34543104, year = {2022}, author = {Weidenbach, K and Gutt, M and Cassidy, L and Chibani, C and Schmitz, RA}, title = {Small Proteins in Archaea, a Mainly Unexplored World.}, journal = {Journal of bacteriology}, volume = {204}, number = {1}, pages = {e0031321}, pmid = {34543104}, issn = {1098-5530}, mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Gene Expression Regulation, Archaeal/*physiology ; Genome, Archaeal ; }, abstract = {In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.}, }
@article {pmid34535658, year = {2021}, author = {Blombach, F and Fouqueau, T and Matelska, D and Smollett, K and Werner, F}, title = {Promoter-proximal elongation regulates transcription in archaea.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5524}, pmid = {34535658}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; WT 207446/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {CRISPR-Cas Systems/genetics ; DNA/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Oxidative Stress/genetics ; *Promoter Regions, Genetic ; Regression Analysis ; Sulfolobus solfataricus/*genetics/growth &amp; development ; *Transcription Elongation, Genetic ; }, abstract = {Recruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.}, }
@article {pmid34531846, year = {2021}, author = {Lin, T and Zhang, L and Wu, M and Jiang, D and Li, Z and Yang, Z}, title = {Repair of Hypoxanthine in DNA Revealed by DNA Glycosylases and Endonucleases From Hyperthermophilic Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {736915}, pmid = {34531846}, issn = {1664-302X}, abstract = {Since hyperthermophilic Archaea (HA) thrive in high-temperature environments, which accelerate the rates of deamination of base in DNA, their genomic stability is facing a severe challenge. Hypoxanthine (Hx) is one of the common deaminated bases in DNA. Generally, replication of Hx in DNA before repaired causes AT → GC mutation. Biochemical data have demonstrated that 3-methyladenine DNA glycosylase II (AlkA) and Family V uracil DNA glycosylase (UDG) from HA could excise Hx from DNA, thus triggering a base excision repair (BER) process for Hx repair. Besides, three endonucleases have been reported from HA: Endonuclease V (EndoV), Endonuclease Q (EndoQ), and Endonuclease NucS (EndoNucS), capable of cleaving Hx-containing DNA, thereby providing alternative pathways for Hx repair. Both EndoV and EndoQ could cleave one DNA strand with Hx, thus forming a nick and further initiating an alternative excision repair (AER) process for the follow-up repair. By comparison, EndoNucS cleaves both strands of Hx-containing DNA in a restriction endonuclease manner, thus producing a double-stranded break (DSB). This created DSB might be repaired by homologous recombination (HR) or by a combination activity of DNA polymerase (DNA pol), flap endonuclease 1 (FEN1), and DNA ligase (DNA lig). Herein, we reviewed the most recent advances in repair of Hx in DNA triggered by DNA glycosylases and endonucleases from HA, and proposed future research directions.}, }
@article {pmid34526983, year = {2021}, author = {Franke, JD and Fuerst, JA and Poole, AM}, title = {Editorial: Structure, Function and Evolution of Complex Cellular Organization in Bacteria and Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {751416}, pmid = {34526983}, issn = {1664-302X}, }
@article {pmid34516368, year = {2021}, author = {Pallen, MJ}, title = {The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {71}, number = {9}, pages = {}, pmid = {34516368}, issn = {1466-5034}, mesh = {*Archaea/classification ; *Bacteria/classification ; Phylogeny ; Terminology as Topic ; }, abstract = {The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.}, }
@article {pmid34509601, year = {2021}, author = {Kumar, V and Singh, B and van Belkum, MJ and Diep, DB and Chikindas, ML and Ermakov, AM and Tiwari, SK}, title = {Halocins, natural antimicrobials of Archaea: Exotic or special or both?.}, journal = {Biotechnology advances}, volume = {53}, number = {}, pages = {107834}, doi = {10.1016/j.biotechadv.2021.107834}, pmid = {34509601}, issn = {1873-1899}, mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents/pharmacology ; *Archaea ; Sodium Chloride ; }, abstract = {Haloarchaea are adapted to survive under extreme saline conditions by accumulating osmolytes and salts to counteract the high osmotic pressure in their habitats. As a consequence, their proteins have evolved to remain active, or even most active, at very high ionic strength. Halocins are proteinaceous antimicrobial substances that are ribosomally-synthesized by haloarchaea and they provide the producers an advantage in the competition for nutrients and ecological niches. These antimicrobials are stable at high temperature, elevated salt concentrations, and alkaline pH conditions. These properties have endowed them with great potential in diverse biotechnological applications, which involve extreme processing conditions (such as high salt concentrations, high pressure, or high temperatures). They kill target cells by inhibition of Na[+]/H[+] antiporter in the membrane or modification/disruption of the cell membrane leading to cell lysis. In general, the taxonomy of haloarchaea and their typical phenotypic and genotypic characteristics are well studied; however, information regarding their halocins, especially aspects related to genetics, biosynthetic pathways, mechanism of action, and structure-function relationship is very limited. A few studies have demonstrated the potential applications of halocins in the preservation of salted food products and brine-cured hides in leather industries, protecting the myocardium from ischemia and reperfusion injury, as well as from life-threatening diseases such as cardiac arrest and cancers. In recent years, genome mining has been an essential tool to decipher the genetic basis of halocin biosynthesis. Nevertheless, this is likely the tip of the iceberg as genome analyses have revealed many putative halocins in databases waiting for further investigation. Identification and characterization of this source of halocins may lead to antimicrobials for future therapeutics and/or food preservation. Hence, the present review analyzes different aspects of halocins such as biosynthesis, mechanism of action against target cells, and potential biotechnological applications.}, }
@article {pmid34491083, year = {2021}, author = {Li, L and Zhang, W and Zhang, S and Song, L and Sun, Q and Zhang, H and Xiang, H and Dong, X}, title = {Bacteria and Archaea Synergistically Convert Glycine Betaine to Biogenic Methane in the Formosa Cold Seep of the South China Sea.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0070321}, pmid = {34491083}, issn = {2379-5077}, abstract = {Cold seeps are globally widespread seafloor ecosystems that feature abundant methane production and flourishing chemotrophic benthic communities. Chemical evidence indicates that cold seep methane is largely biogenic; however, the primary methane-producing organisms and associated pathways involved in methanogenesis remain elusive. This work detected methane production when glycine betaine (GBT) or trimethylamine (TMA) was added to the sediment microcosms of the Formosa cold seep, South China Sea. The methane production was suppressed by antibiotic inhibition of bacteria, while GBT was accumulated. This suggests that the widely used osmoprotectant GBT could be converted to cold seep biogenic methane via the synergistic activity of bacteria and methanogenic archaea because archaea are not sensitive to antibiotics and no bacteria are known to produce ample methane (mM). 16S rRNA gene diversity analyses revealed that the predominant bacterial and archaeal genera in the GBT-amended methanogenic microcosms included Oceanirhabdus and Methanococcoides. Moreover, metagenomic analyses detected the presence of grdH and mtgB genes that are involved in GBT reduction and demethylation, respectively. Two novel species were obtained, including bacterium Oceanirhabdus seepicola, which reduces GBT to TMA, and a methanogenic archaeon, Methanococcoides seepicolus, which produces methane from TMA and GBT. The two strains reconstituted coculture efficiently converted GBT to methane at 18°C; however, at 4°C addition of dimethylglycine (DMG), the GBT demethylation product, was necessary. Therefore, this work demonstrated that GBT is the precursor not only of the biogenic methane but also of the cryoprotectant DMG to the microorganisms at the Formosa cold seep. IMPORTANCE Numerous cold seeps have been found in global continental margins where methane is enriched in pore waters that are forced upward from sediments. Therefore, high concerns have been focused on the methane-producing organisms and the metabolic pathways in these environments because methane is a potent greenhouse gas. In this study, GBT was identified as the main precursor for methane in the Formosa cold seep of the South China Sea. Further, synergism of bacteria and methanogenic archaea was identified in GBT conversion to methane via the GBT reduction pathway, while methanogen-mediated GBT demethylation to methane was also observed. In addition, GBT-demethylated product dimethyl glycine acted as a cryoprotectant that promoted the cold seep microorganisms at cold temperatures. GBT is an osmoprotectant that is widely used by marine organisms, and therefore, the GBT-derived methanogenic pathway reported here could be widely distributed among global cold seep environments.}, }
@article {pmid34490397, year = {2021}, author = {Hu, D and Yang, J and Qi, Y and Li, B and Li, K and Mok, KM}, title = {Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {708512}, pmid = {34490397}, issn = {2297-1769}, abstract = {Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.}, }
@article {pmid34489912, year = {2021}, author = {Makarova, KS and Wolf, YI and Karamycheva, S and Koonin, EV}, title = {A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {721392}, pmid = {34489912}, issn = {1664-302X}, abstract = {Molecular mechanisms involved in biological conflicts and self vs nonself recognition in archaea remain poorly characterized. We apply phylogenomic analysis to identify a hypervariable gene module that is widespread among Thermococcales. These loci consist of an upstream gene coding for a large protein containing several immunoglobulin (Ig) domains and unique combinations of downstream genes, some of which also contain Ig domains. In the large Ig domain containing protein, the C-terminal Ig domain sequence is hypervariable, apparently, as a result of recombination between genes from different Thermococcales. To reflect the hypervariability, we denote this gene module VARTIG (VARiable Thermococcales IG). The overall organization of the VARTIG modules is similar to the organization of Polymorphic Toxin Systems (PTS). Archaeal genomes outside Thermococcales encode a variety of Ig domain proteins, but no counterparts to VARTIG and no Ig domains with comparable levels of variability. The specific functions of VARTIG remain unknown but the identified features of this system imply three testable hypotheses: (i) involvement in inter-microbial conflicts analogous to PTS, (ii) role in innate immunity analogous to the vertebrate complement system, and (iii) function in self vs nonself discrimination analogous to the vertebrate Major Histocompatibility Complex. The latter two hypotheses seem to be of particular interest given the apparent analogy to the vertebrate immunity.}, }
@article {pmid34487604, year = {2022}, author = {Haiming, T and Chao, L and Kaikai, C and Lihong, S and Li, W and Weiyan, L and Xiaoping, X and Ke, W}, title = {Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field.}, journal = {Journal of applied microbiology}, volume = {132}, number = {2}, pages = {1307-1318}, doi = {10.1111/jam.15289}, pmid = {34487604}, issn = {1365-2672}, mesh = {Ammonia ; Archaea/genetics ; *Betaproteobacteria ; Nitrification ; *Oryza ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {AIMS: The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5 years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction.<br><br>METHODS AND RESULTS: The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management.<br><br>CONCLUSIONS: The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition.<br><br>The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.}, }
@article {pmid34464803, year = {2022}, author = {Cai, M and Yin, X and Tang, X and Zhang, C and Zheng, Q and Li, M}, title = {Metatranscriptomics reveals different features of methanogenic archaea among global vegetated coastal ecosystems.}, journal = {The Science of the total environment}, volume = {802}, number = {}, pages = {149848}, doi = {10.1016/j.scitotenv.2021.149848}, pmid = {34464803}, issn = {1879-1026}, mesh = {*Archaea/genetics ; *Ecosystem ; Methane ; Methanosarcinaceae ; Methanosarcinales ; Phylogeny ; }, abstract = {Vegetated coastal ecosystems (VCEs; i.e., mangroves, saltmarshes, and seagrasses) represent important sources of natural methane emission. Despite recent advances in the understanding of novel taxa and pathways associated with methanogenesis in these ecosystems, the key methanogenic players and the contribution of different substrates to methane formation remain elusive. Here, we systematically investigate the community and activity of methanogens using publicly available metatranscriptomes at a global scale together with our in-house metatranscriptomic dataset. Taxonomic profiling reveals that 13 groups of methanogenic archaea were transcribed in the investigated VCEs, and they were predominated by Methanosarcinales. Among these VCEs, methanogens exhibited all the three known methanogenic pathways in some mangrove sediments, where methylotrophic methanogens Methanosarcinales/Methanomassiliicoccales grew on diverse methyl compounds and coexisted with hydrogenotrophic (mainly Methanomicrobiales) and acetoclastic (mainly Methanothrix) methanogens. Contrastingly, the predominant methanogenic pathway in saltmarshes and seagrasses was constrained to methylotrophic methanogenesis. These findings reveal different archaeal methanogens in VCEs and suggest the potentially distinct methanogenesis contributions in these VCEs to the global warming.}, }
@article {pmid34442741, year = {2021}, author = {Koirala, A and Brözel, VS}, title = {Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442741}, issn = {2076-2607}, abstract = {The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.}, }
@article {pmid34436605, year = {2021}, author = {Martinez-Gutierrez, CA and Aylward, FO}, title = {Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea.}, journal = {Molecular biology and evolution}, volume = {38}, number = {12}, pages = {5514-5527}, pmid = {34436605}, issn = {1537-1719}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Biological Evolution ; Phylogeny ; Uncertainty ; }, abstract = {Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, and many inter-phylum and inter-domain evolutionary relationships remain unclear. Here, we benchmark different marker genes often used in constructing multidomain phylogenetic trees of bacteria and archaea and present a set of marker genes that perform best for multidomain trees constructed from concatenated alignments. We use recently-developed Tree Certainty metrics to assess the confidence of our results and to obviate the complications of traditional bootstrap-based metrics. Given the vastly disparate number of genomes available for different phyla of bacteria and archaea, we also assessed the impact of taxon sampling on multidomain tree construction. Our results demonstrate that biases between the representation of different taxonomic groups can dramatically impact the topology of resulting trees. Inspection of our highest-quality tree supports the division of most bacteria into Terrabacteria and Gracilicutes, with Thermatogota and Synergistota branching earlier from these superphyla. This tree also supports the inclusion of the Patescibacteria within the Terrabacteria as a sister group to the Chloroflexota instead of as a basal-branching lineage. For the Archaea, our tree supports three monophyletic lineages (DPANN, Euryarchaeota, and TACK/Asgard), although we note the basal placement of the DPANN may still represent an artifact caused by biased sequence composition. Our findings provide a robust and standardized framework for multidomain phylogenetic reconstruction that can be used to evaluate inter-phylum relationships and assess uncertainty in conflicting topologies of the Tree of Life.}, }
@article {pmid34394058, year = {2021}, author = {Kostygov, AY and Alves, JMP and Yurchenko, V}, title = {Editorial: Symbioses Between Protists and Bacteria/Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {709184}, pmid = {34394058}, issn = {1664-302X}, }
@article {pmid34391833, year = {2021}, author = {Moghimipour, E and Abedishirehjin, S and Baghbadorani, MA and Handali, S}, title = {Bacteria and Archaea: A new era of cancer therapy.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {338}, number = {}, pages = {1-7}, doi = {10.1016/j.jconrel.2021.08.019}, pmid = {34391833}, issn = {1873-4995}, mesh = {*Antineoplastic Agents ; Archaea ; Bacteria ; Drug Delivery Systems ; Nanotechnology ; *Neoplasms/drug therapy ; }, abstract = {Cancer is one of the most important mortality in the world. The major drawbacks of chemotherapy are the poor absorption of drugs into tumor tissues and development of resistance against anti-cancer agents. To overcome these limitations, the use of microorganisms has been extensively considered in the treatment of cancer. Microorganisms (bacteria/Archaea) secrete different bioactive compounds that can efficiently inhibit cancer cells growth. Biological nanocarriers derived from microorganisms including outer membrane vesicles (OMVs), bacterial ghosts (BGs) and archaeosomes have also been considered as drug delivery systems. Conjugation of drug loaded nanocarriers to bacteria strongly kills the cancer cells after internalization through the bacteria. Merging of microbiology and nanotechnology may provide versatile microbial nano-hybrids for promising treatment of cancer. This strategy causes more amount of drug to enter into cancer cells. In this review, we present evidence that microorganism, their derivatives as well as their intervention with nanotechnology can be a powerful vehicle for eradication cancer.}, }
@article {pmid34379636, year = {2021}, author = {Acharya, S and Dahal, A and Bhattarai, HK}, title = {Evolution and origin of sliding clamp in bacteria, archaea and eukarya.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0241093}, pmid = {34379636}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Archaea/*genetics ; Bacteria/*genetics ; DNA/genetics ; DNA Replication/genetics ; DNA-Directed DNA Polymerase/genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Firmicutes/genetics ; Phylogeny ; Proliferating Cell Nuclear Antigen/genetics ; Pyrococcus furiosus/genetics ; }, abstract = {The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize the conservation of protein sequence among sliding clamps. In this paper, we have used PSI blast to the second iteration in NCBI to show a statistically significant sequence homology between Pyrococcus furiosus PCNA and Kallipyga gabonensis beta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.}, }
@article {pmid34378142, year = {2022}, author = {Xie, R and Wang, Y and Huang, D and Hou, J and Li, L and Hu, H and Zhao, X and Wang, F}, title = {Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes.}, journal = {Science China. Life sciences}, volume = {65}, number = {4}, pages = {818-829}, pmid = {34378142}, issn = {1869-1889}, mesh = {*Archaea/genetics/metabolism ; *Eukaryota/genetics ; Eukaryotic Cells/metabolism ; Phylogeny ; }, abstract = {The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr- and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota, respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.}, }
@article {pmid34367583, year = {2021}, author = {Wu, D and Zhao, C and Bai, H and Feng, F and Sui, X and Sun, G}, title = {Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China.}, journal = {Ecology and evolution}, volume = {11}, number = {15}, pages = {10396-10408}, pmid = {34367583}, issn = {2045-7758}, abstract = {Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla-Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.}, }
@article {pmid34367089, year = {2021}, author = {Londei, P and Ferreira-Cerca, S}, title = {Ribosome Biogenesis in Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {686977}, pmid = {34367089}, issn = {1664-302X}, abstract = {Making ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding the genetic information contained in messenger RNAs into proteins, their biogenesis shows an intriguing degree of variability across the tree of life. In this review, we summarize our knowledge on the least understood ribosome biogenesis pathway: the archaeal one. Furthermore, we highlight some evolutionary conserved and divergent molecular features of making ribosomes across the tree of life.}, }
@article {pmid34364295, year = {2021}, author = {Xiao, L and Liu, G and Gong, F and Cai, Z and Li, Y}, title = {The reductive carboxylation activity of heterotetrameric pyruvate synthases from hyperthermophilic archaea.}, journal = {Biochemical and biophysical research communications}, volume = {572}, number = {}, pages = {151-156}, doi = {10.1016/j.bbrc.2021.07.091}, pmid = {34364295}, issn = {1090-2104}, mesh = {Archaea/*enzymology ; Carboxylic Acids/metabolism ; Oxidation-Reduction ; Pyruvate Synthase/*metabolism ; }, abstract = {Pyruvate synthase (pyruvate:ferredoxin oxidoreductase, PFOR) catalyzes the interconversion of acetyl-CoA and pyruvate, but the reductive carboxylation activities of heterotetrameric PFORs remain largely unknown. In this study, we cloned, expressed, and purified selected six heterotetrameric PFORs from hyperthermophilic archaea. The reductive carboxylation activities of these heterotetrameric PFORs were measured at 70 °C and the ratio of reductive carboxylation activity to oxidative decarboxylation activity (red/ox ratio) were calculated. Four out of six showed reductive decarboxylation activities. Among them, the PFORpfm from Pyrolobus fumarii showed the highest reductive carboxylation activities and the highest red/ox ratio, which were 54.32 mU/mg and 0.51, respectively. The divergence of the reductive carboxylation activities and the red/ox ratios of heterotetrameric PFORs in hyperthermophilic archaea indicate the diversity of the functions of PFOR over long-term evolution. This can help us better understand the autotrophic CO2 fixation process in thermal vent, or in other CO2-rich high temperature habitat.}, }
@article {pmid34359268, year = {2021}, author = {Deng, F and Li, Y and Peng, Y and Wei, X and Wang, X and Howe, S and Yang, H and Xiao, Y and Li, H and Zhao, J and Li, Y}, title = {The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {7}, pages = {}, pmid = {34359268}, issn = {2076-2615}, abstract = {Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.}, }
@article {pmid34354121, year = {2021}, author = {Clark, IM and Hughes, DJ and Fu, Q and Abadie, M and Hirsch, PR}, title = {Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15905}, pmid = {34354121}, issn = {2045-2322}, support = {BBS/E/C/00005196/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/000I0310/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Ammonia/analysis ; Archaea/*genetics ; Bacteria/*genetics ; Fertilizers/analysis ; Genetic Variation/genetics ; Metagenome/genetics ; Metagenomics/methods ; Nitrification/*genetics/physiology ; Nitrites/analysis ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes-permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soil from the experimental sites (microcosms amended or not with DCD at concentrations inhibitory to AOB but not AOA), was highest in arable samples and lower in all assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.}, }
@article {pmid34350672, year = {2021}, author = {Wakai, M and Hayashi, S and Chiba, Y and Koike, S and Nagashima, K and Kobayashi, Y}, title = {Growth and morphologic response of rumen methanogenic archaea and bacteria to cashew nut shell liquid and its alkylphenol components.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {92}, number = {1}, pages = {e13598}, doi = {10.1111/asj.13598}, pmid = {34350672}, issn = {1740-0929}, mesh = {*Anacardium ; Animals ; Archaea ; Bacteria ; Methane ; Nuts ; *Rumen ; }, abstract = {The growth and morphology of rumen methanogenic archaea (15 strains of 10 species in 5 genera, including 7 strains newly isolated in the present study) and bacteria (14 species in 12 genera) were investigated using unsupplemented in vitro pure cultures and cultures supplemented with cashew nut shell liquid (CNSL) and its phenolic compound components, anti-methanogenic agents for ruminant animals. Growth of most of the methanogens tested was inhibited by CNSL and alkylphenols at different concentrations ranging from 1.56 to 12.5 μg/ml. Of the alkylphenols tested, anacardic acid exhibited the most potent growth inhibition. Three gram-negative bacterial species involved in propionate production were resistant to CNSL and alkylphenols (>50 μg/ml). All the methanogens and bacteria that were sensitive to CNSL and alkylphenols exhibited altered morphology; disruption of the cell surface was notable, possibly due to surfactant activity of the tested materials. Cells division was inhibited in some organisms, with cell elongation and unclear septum formation observed. These results indicate that CNSL and alkylphenols, particularly anacardic acid, inhibit both rumen bacteria and methanogens in a selective manner, which could help mitigate rumen methane generation.}, }
@article {pmid34347515, year = {2021}, author = {French, E and Kozlowski, JA and Bollmann, A}, title = {Competition between Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {20}, pages = {e0103821}, pmid = {34347515}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Archaea/genetics/growth &amp; development/*metabolism ; Fresh Water/*microbiology ; *Microbial Interactions ; Nitrosomonas/genetics/growth &amp; development/*metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {In the environment, nutrients are rarely available in a constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of AOA (AOA-AC1) and AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp., and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. strain Is79, belonged to the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM, and AOB-G5-7 was dominant at 500 μM. These findings indicate that during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. IMPORTANCE Nitrification is an important process in the global nitrogen cycle. The first step, ammonia oxidation to nitrite, can be carried out by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and that AOB are more abundant when the ammonium availability increases. These results will help to predict potential shifts in the community composition of ammonia oxidizers in the environment due to changes in ammonium availability.}, }
@article {pmid34346295, year = {2021}, author = {Santos, MVD and Goes, RHTB and Takiya, CS and Cabral, LDS and Mombach, MA and Oliveira, RT and Silva, NGD and Anschau, DG and Freitas Júnior, JE and de Araújo, MLGML and Gandra, JR}, title = {Effect of increasing doses of chitosan to grazing beef steers on the relative population and transcript abundance of Archaea and cellulolytic and amylolytic bacterias.}, journal = {Animal biotechnology}, volume = {}, number = {}, pages = {1-7}, doi = {10.1080/10495398.2021.1954936}, pmid = {34346295}, issn = {1532-2378}, abstract = {This paper aims to investigate the influence of increasing chitosan doses on the relative proportion and abundance of cellulotytic, amylolytic bacteria, and Archaea transcripts for grazing cattle. Five rumen cannulated crossbread steers [3.6 months and 300 ± 25 kg body LW (live weight), mean ± standard deviation] were used in a 5 × 5 latin square design, randomly assigned to treatment sequence containing chitosan added to 0, 400, 800, 1200, or 1600 mg/kg concentrate. There was the effect of chitosan on the population of Fibrobacter succinogenes, Ruminococcus albus, and Archaea. The lowest population of these bacteria of 576.60 mg/kg DM (dry matter), 1010.40 mg/kg DM, and 634.80 mg/kg DM were noted when chitosan was added at levels of 3.87, 4.16, and 3.52. Except for Ruminococcus albus, which was not affected by increasing chitosan doses, supplementation of this additive in the concentrate quadratically increased the relative abundance of Fibrobacter succinogenes and Archaea Supplemental 740 mg CHI/kg concentrate for grazing steers receiving concentrate at 150 grams/100 kg LW is recommended to promote minimal effect on the relative population and abundance of cellulolytics and amylomatics and to restrict Archaea growth.}, }
@article {pmid34343555, year = {2022}, author = {Zhu, J and Yan, X and Zhou, L and Li, N and Liao, C and Wang, X}, title = {Insight of bacteria and archaea in Feammox community enriched from different soils.}, journal = {Environmental research}, volume = {203}, number = {}, pages = {111802}, doi = {10.1016/j.envres.2021.111802}, pmid = {34343555}, issn = {1096-0953}, mesh = {*Ammonium Compounds ; Archaea ; Bacteria ; Ferric Compounds ; Nitrogen/analysis ; Oxidation-Reduction ; *Soil ; Soil Microbiology ; }, abstract = {Anaerobic ammonium oxidation coupled to Fe(III) reduction, known as Feammox, is a newly discovered nitrogen-cycling process, which serves an important role in the pathways of nitrogen loss in the environment. However, the specific types of microorganisms involved in Feammox currently remain unclear. In this study, we selected two groups of soil samples (paddy and mine), from considerably different habitats in South China, to acclimate Feammox colonies. The Paddy Group had a shorter lag period than the Mine Group, while the ammonium transformation rate was nearly equal in both groups in the mature period. The emergence of the Feammox activity was found to be associated with the increased abundance of iron-reducing bacteria, especially Clostridium_sensu_stricto_12, Desulfitobacterium, Thermoanaerobaculum, Anaeromyxobacter and Geobacter. Ammonium oxidizing archaea and methanogens were dominant among the known archaea. These findings extend our knowledge of the microbial community composition of the potential Feammox microbes from soils under different environmental conditions, which broadens our understanding of this important Fe/N transformation process.}, }
@article {pmid34327792, year = {2021}, author = {Li, C and Hambright, KD and Bowen, HG and Trammell, MA and Grossart, HP and Burford, MA and Hamilton, DP and Jiang, H and Latour, D and Meyer, EI and Padisák, J and Zamor, RM and Krumholz, LR}, title = {Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6503-6519}, doi = {10.1111/1462-2920.15691}, pmid = {34327792}, issn = {1462-2920}, mesh = {Archaea/genetics ; *Euryarchaeota/genetics ; Eutrophication ; Lakes/microbiology ; Methane ; *Microcystis/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Global warming and eutrophication contribute to the worldwide increase in cyanobacterial blooms, and the level of cyanobacterial biomass is strongly associated with rises in methane emissions from surface lake waters. Hence, methane-metabolizing microorganisms may be important for modulating carbon flow in cyanobacterial blooms. Here, we surveyed methanogenic and methanotrophic communities associated with floating Microcystis aggregates in 10 lakes spanning four continents, through sequencing of 16S rRNA and functional marker genes. Methanogenic archaea (mainly Methanoregula and Methanosaeta) were detectable in 5 of the 10 lakes and constituted the majority (~50%-90%) of the archaeal community in these lakes. Three of the 10 lakes contained relatively more abundant methanotrophs than the other seven lakes, with the methanotrophic genera Methyloparacoccus, Crenothrix, and an uncultured species related to Methylobacter dominating and nearly exclusively found in each of those three lakes. These three are among the five lakes in which methanogens were observed. Operational taxonomic unit (OTU) richness and abundance of methanotrophs were strongly positively correlated with those of methanogens, suggesting that their activities may be coupled. These Microcystis-aggregate-associated methanotrophs may be responsible for a hitherto overlooked sink for methane in surface freshwaters, and their co-occurrence with methanogens sheds light on the methane cycle in cyanobacterial aggregates.}, }
@article {pmid34316016, year = {2022}, author = {Jung, MY and Sedlacek, CJ and Kits, KD and Mueller, AJ and Rhee, SK and Hink, L and Nicol, GW and Bayer, B and Lehtovirta-Morley, L and Wright, C and de la Torre, JR and Herbold, CW and Pjevac, P and Daims, H and Wagner, M}, title = {Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {272-283}, pmid = {34316016}, issn = {1751-7370}, mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; }, abstract = {Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that-like for AOB-ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.}, }
@article {pmid34286299, year = {2021}, author = {Coutinho, FH and Zaragoza-Solas, A and López-Pérez, M and Barylski, J and Zielezinski, A and Dutilh, BE and Edwards, R and Rodriguez-Valera, F}, title = {RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.}, journal = {Patterns (New York, N.Y.)}, volume = {2}, number = {7}, pages = {100274}, pmid = {34286299}, issn = {2666-3899}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; }, abstract = {Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644 protein clusters to assign hosts to complete or fragmented genomes of viruses of Archaea and Bacteria. RaFAH displayed performance comparable with that of other methods for virus-host prediction in three different benchmarks encompassing viruses from RefSeq, single amplified genomes, and metagenomes. RaFAH was applied to assembled metagenomic datasets of uncultured viruses from eight different biomes of medical, biotechnological, and environmental relevance. Our analyses led to the identification of 537 sequences of archaeal viruses representing unknown lineages, whose genomes encode novel auxiliary metabolic genes, shedding light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.}, }
@article {pmid34285362, year = {2022}, author = {Yu, H and Skennerton, CT and Chadwick, GL and Leu, AO and Aoki, M and Tyson, GW and Orphan, VJ}, title = {Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {168-177}, pmid = {34285362}, issn = {1751-7370}, mesh = {Anaerobiosis ; *Archaea/metabolism ; Geologic Sediments/microbiology ; Humans ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; *Sulfates/metabolism ; }, abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.}, }
@article {pmid34282942, year = {2021}, author = {Umbach, AK and Stegelmeier, AA and Neufeld, JD}, title = {Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0064221}, pmid = {34282942}, issn = {2379-5077}, abstract = {Although previous research demonstrates that skin-associated archaea are rarely detected within human skin microbiome data, exist at relatively low abundance, and are primarily affiliated with the Methanobacteriota and Halobacteriota phyla, other studies suggest that archaea are consistently detected and relatively abundant on human skin, with skin "archaeomes" dominated by putative ammonia oxidizers of the Nitrososphaeria class (Thermoproteota phylum, formerly Thaumarchaeota). Here, we evaluated new and existing 16S rRNA gene sequence data sourced from mammalian skin and skin-associated surfaces and generated with two commonly used universal prokaryotic primer sets to assess archaeal prevalence, relative abundance, and taxonomic distribution. Archaeal 16S rRNA gene sequences were detected in only 17.5% of 1,688 samples by high-throughput sequence data, with most of the archaeon-positive samples associated with nonhuman mammalian skin. Only 5.9% of human-associated skin sample data sets contained sequences affiliated with archaeal 16S rRNA genes. When detected, the relative abundance of sequences affiliated with archaeal amplicon sequence variants (ASVs) was less than 1% for most mammalian skin samples and did not exceed 2% for any samples. Although several computer keyboard microbial profiles were dominated by Nitrososphaeria sequences, all other skin microbiome data sets tested were primarily composed of sequences affiliated with Methanobacteriota and Halobacteriota phyla. Our findings revise downward recent estimates of human skin archaeal distributions and relative abundances, especially those affiliated with the Nitrososphaeria, reflecting a limited and infrequent archaeal presence within the mammalian skin microbiome. IMPORTANCE The current state of research on mammalian skin-associated archaea is limited, with the few papers focusing on potential skin archaeal communities often in disagreement with each other. As such, there is no consensus on the prevalence or taxonomic composition of archaea on mammalian skin. Mammalian skin health is in part influenced by its complex microbiota and consortium of bacteria and potential archaea. Without a clear foundational analysis and characterization of the mammalian skin archaeome, it will be difficult for future research to explore the potential impact of skin-associated archaea on skin health and function. The current work provides a much-needed analysis of the mammalian skin archaeome and contributes to building a foundation from which further discussion and exploration of the skin archaeome might continue.}, }
@article {pmid34276623, year = {2021}, author = {Dong, Y and Shan, Y and Xia, K and Shi, L}, title = {The Proposed Molecular Mechanisms Used by Archaea for Fe(III) Reduction and Fe(II) Oxidation.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {690918}, pmid = {34276623}, issn = {1664-302X}, abstract = {Iron (Fe) is the fourth most abundant element in the Earth's crust where ferrous Fe [Fe(II)] and ferric Fe [Fe(III)] can be used by archaea for energy conservation. In these archaea-Fe interactions, Fe(III) serves as terminal electron acceptor for anaerobic respiration by a variety of archaea, while Fe(II) serves as electron donor and/or energy sources for archaeal growth. As no Fe is incorporated into the archaeal cells, these redox reactions are referred to as dissimilatory Fe(III) reduction and Fe(II) oxidation, respectively. Dissimilatory Fe(III)-reducing archaea (FeRA) and Fe(II)-oxidizing archaea (FeOA) are widespread on Earth where they play crucial roles in biogeochemical cycling of not only Fe, but also carbon and sulfur. To reduce extracellular Fe(III) (oxyhydr)oxides, some FeRA transfer electrons directly to the Fe(III) (oxyhydr)oxides most likely via multiheme c-type cytochromes (c-Cyts). These multiheme c-Cyts may form the pathways similar to those found in bacteria for transferring electrons from the quinone/quinol pool in the cytoplasmic membrane to the Fe(III) (oxyhydr)oxides external to the archaeal cells. Use of multiheme c-Cyts for extracellular Fe(III) reduction by both Domains of Archaea and Bacteria emphasizes an ancient mechanism of extracellular electron transfer, which is well conserved. Other FeRA, however, reduce Fe(III) (oxyhydr)oxides indirectly via electron shuttles. Similarly, it is proposed that FeOA use pathways to oxidize Fe(II) on the surface of the cytoplasmic membrane and then to transfer the released electrons across the cytoplasmic membrane inward to the O2 and NAD[+] in the cytoplasm. In this review, we focus on the latest understandings of the molecular mechanisms used by FeRA and FeOA for Fe(III) reduction and Fe(II) oxidation, respectively.}, }
@article {pmid34267287, year = {2021}, author = {Wang, L and Huang, D}, title = {Soil ammonia-oxidizing archaea in a paddy field with different irrigation and fertilization managements.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {14563}, pmid = {34267287}, issn = {2045-2322}, mesh = {Agricultural Irrigation/*methods ; Ammonia/*metabolism ; Archaea/*metabolism ; China ; Crenarchaeota/metabolism ; *Fertilizers ; Hydrogen-Ion Concentration ; Oryza/growth &amp; development ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Because ammonia-oxidizing archaea (AOA) are ubiquitous and highly abundant in almost all terrestrial soils, they play an important role in soil nitrification. However, the changes in the structure and function of AOA communities and their edaphic drivers in paddy soils under different fertilization and irrigation regimes remain unclear. In this study, we investigated AOA abundance, diversity and activity in acid paddy soils by a field experiment. Results indicated that the highest potential ammonia oxidation (PAO) (0.011 μg NO 2 [-] -N g[-1] d.w.day[-1]) was found in T2 (optimal irrigation and fertilization)-treated soils, whereas the lowest PAO (0.004 μg NO 2 [-] -N g[-1] d.w.day[-1]) in T0 (traditional irrigation)- treated soils. Compared with the T0-treated soil, the T2 treatment significantly (P < 0.05) increased AOA abundances. Furthermore, the abundance of AOA was significantly (P < 0.01) positively correlated with pH, soil organic carbon (SOC), and PAO. Meanwhile, pH and SOC content were significantly (P < 0.05) higher in the T2-treated soil than those in the T1 (traditional irrigation and fertilization)- treated soil. In addition, these two edaphic factors further influenced the AOA community composition. The AOA phylum Crenarchaeota was mainly found in the T2-treated soils. Phylogenetic analysis revealed that most of the identified OTUs of AOA were mainly affiliated with Crenarchaeota. Furthermore, the T2 treatment had higher rice yield than the T0 and T1 treatments. Together, our findings confirm that T2 might ameliorate soil chemical properties, regulate the AOA community structure, increase the AOA abundance, enhance PAO and consequently maintain rice yields in the present study.}, }
@article {pmid34253852, year = {2022}, author = {Jørgensen, BB}, title = {Do methanogenic archaea cause reductive pyrite dissolution in subsurface sediments?.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {1-2}, pmid = {34253852}, issn = {1751-7370}, mesh = {*Archaea/genetics ; *Euryarchaeota ; Iron ; Solubility ; Sulfides ; }, }
@article {pmid34248899, year = {2021}, author = {Christakis, CA and Barkay, T and Boyd, ES}, title = {Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {682605}, pmid = {34248899}, issn = {1664-302X}, abstract = {Mercury (Hg) is a highly toxic element due to its high affinity for protein sulfhydryl groups, which upon binding, can destabilize protein structure and decrease enzyme activity. Prokaryotes have evolved enzymatic mechanisms to detoxify inorganic Hg and organic Hg (e.g., MeHg) through the activities of mercuric reductase (MerA) and organomercury lyase (MerB), respectively. Here, the taxonomic distribution and evolution of MerAB was examined in 84,032 archaeal and bacterial genomes, metagenome assembled genomes, and single-cell genomes. Homologs of MerA and MerB were identified in 7.8 and 2.1% percent of genomes, respectively. MerA was identified in the genomes of 10 archaeal and 28 bacterial phyla previously unknown to code for this functionality. Likewise, MerB was identified in 2 archaeal and 11 bacterial phyla previously unknown to encode this functionality. Surprisingly, homologs of MerB were identified in a number of genomes (∼50% of all MerB-encoding genomes) that did not encode MerA, suggesting alternative mechanisms to detoxify Hg(II) once it is generated in the cytoplasm. Phylogenetic reconstruction of MerA place its origin in thermophilic Thermoprotei (Crenarchaeota), consistent with high levels of Hg(II) in geothermal environments, the natural habitat of this archaeal class. MerB appears to have been recruited to the mer operon relatively recently and likely among a mesophilic ancestor of Euryarchaeota and Thaumarchaeota. This is consistent with the functional dependence of MerB on MerA and the widespread distribution of mesophilic microorganisms that methylate Hg(II) at lower temperature. Collectively, these results expand the taxonomic and ecological distribution of mer-encoded functionalities, and suggest that selection for Hg(II) and MeHg detoxification is dependent not only on the availability and type of mercury compounds in the environment but also the physiological potential of the microbes who inhabit these environments. The expanded diversity and environmental distribution of MerAB identify new targets to prioritize for future research.}, }
@article {pmid34245190, year = {2022}, author = {Wang, S and Narsing Rao, MP and Wei, D and Sun, L and Fang, BZ and Li, WQ and Yu, LH and Li, WJ}, title = {Complete genome sequencing and comparative genome analysis of the extremely halophilic archaea, Haloterrigena daqingensis.}, journal = {Biotechnology and applied biochemistry}, volume = {69}, number = {4}, pages = {1482-1488}, doi = {10.1002/bab.2220}, pmid = {34245190}, issn = {1470-8744}, mesh = {DNA, Archaeal/genetics ; *Halobacteriaceae/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {In the present study, we report the complete genome sequencing of Haloterrigena daqingensis species. The genome of H. daqingensis JX313[T] consisted of a circular chromosome with three plasmids. The genome size and G+C content were estimated to be 3835796 bp and 61.7%, respectively. A total of 4158 genes were predicted with six rRNAs and 45 tRNAs. Metabolic pathway analysis suggests that H. daqingensis JX313[T] codes for all the necessary genes responsible to sustain its life at saline environment. The pan-genome analysis suggests that the number of singleton-gene between H. daqingensis and other Haloterrigena species varied. The study not only helps us understand H. daqingensis strategy for dealing with high stress, but it also provides an overview of its genomic makeup.}, }
@article {pmid34217274, year = {2021}, author = {Kakuk, B and Wirth, R and Maróti, G and Szuhaj, M and Rakhely, G and Laczi, K and Kovács, KL and Bagi, Z}, title = {Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics.}, journal = {Microbial cell factories}, volume = {20}, number = {1}, pages = {127}, pmid = {34217274}, issn = {1475-2859}, mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Carbon Dioxide/metabolism ; Fermentation ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Hydrogen/*metabolism ; Metagenome ; Metagenomics ; Methane/*biosynthesis ; Methanomicrobiaceae/genetics/*metabolism ; Methanosarcina/genetics/*metabolism ; Microbiota ; *Transcriptome ; }, abstract = {BACKGROUND: The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies.<br><br>RESULTS: The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10&#xa0;min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria.<br><br>CONCLUSIONS: External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.}, }
@article {pmid34213183, year = {2020}, author = {Wang, X and He, Z and Li, X and Song, Q and Zou, X and Song, X and Feng, L}, title = {[Comparison of pretreatment methods in lipid analysis and ultra-performance liquid chromatography-mass spectrometry analysis of archaea].}, journal = {Se pu = Chinese journal of chromatography}, volume = {38}, number = {8}, pages = {914-922}, doi = {10.3724/SP.J.1123.2019.12009}, pmid = {34213183}, issn = {1000-8713}, mesh = {*Archaea/chemistry ; Chromatography, High Pressure Liquid ; *Lipidomics ; Lipids/*analysis ; Mass Spectrometry ; Pyrococcus/chemistry ; Reproducibility of Results ; }, abstract = {Archaea are single-cell microorganisms, structurally and biochemically similar to bacteria and fungi. Most of them live in extreme environments, such as high salt, extremely acidic, extremely hot, and anaerobicenvironments. The membrane structure and related metabolic pathways of archaea are different from those of other microorganisms. Therefore, studying the lipid metabolism of archaea is of great significance for exploring the life activities in extreme environments. As the first step in lipidomic analysis, lipid extraction and pretreatment methods play an important role, as they influence the accuracy and reliability of the final results. We harnessed ultra-performance liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS) to detect the total normal lipids. The hyperthermophilic archaeon Pyrococcus yayanosii was selected as the model. The Bligh-Dyer acidic method, Folch method, methyl tert-butyl ether (MTBE) method, and solid-phase extraction (SPE) method were compared by multi-component analysis in terms of extraction efficiency, reproducibility, and extraction discrimination. Comprehensive analysis revealed that the SPE and MTBE methods showed the best extraction repeatability and extraction efficiency, and were suitable for high-throughput microbial lipid extraction. Finally, normal lipid components of P. yayanosii were comprehensively analyzed by SPE coupled with UPLC-HRMS. A total of 1402 lipid components were identified. This article aims to provide a reference for non-targeted lipidomic analysis of archaea and other microorganisms towards understanding their lipid metabolism.}, }
@article {pmid34207561, year = {2021}, author = {Abellan-Schneyder, I and Siebert, A and Hofmann, K and Wenning, M and Neuhaus, K}, title = {Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34207561}, issn = {2076-2607}, abstract = {Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.}, }
@article {pmid34202810, year = {2021}, author = {Pfeiffer, F and Dyall-Smith, M}, title = {Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea.}, journal = {Genes}, volume = {12}, number = {7}, pages = {}, pmid = {34202810}, issn = {2073-4425}, mesh = {Archaeal Proteins/classification/*genetics ; Halobacteriales/classification/*genetics ; Haloferax volcanii/*genetics ; Molecular Sequence Annotation ; }, abstract = {BACKGROUND: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii.<br><br>RESULTS: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials.<br><br>CONCLUSIONS: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.}, }
@article {pmid34190386, year = {2022}, author = {Tamisier, M and Schmidt, M and Vogt, C and Kümmel, S and Stryhanyuk, H and Musat, N and Richnow, HH and Musat, F}, title = {Iron corrosion by methanogenic archaea characterized by stable isotope effects and crust mineralogy.}, journal = {Environmental microbiology}, volume = {24}, number = {2}, pages = {583-595}, doi = {10.1111/1462-2920.15658}, pmid = {34190386}, issn = {1462-2920}, mesh = {*Archaea ; Carbon Isotopes/analysis ; Corrosion ; *Euryarchaeota ; Iron ; Isotopes ; Methane ; }, abstract = {Carbon and hydrogen stable isotope effects associated with methane formation by the corrosive archaeon Methanobacterium strain IM1 were determined during growth with hydrogen and iron. Isotope analyses were complemented by structural, elemental and molecular composition analyses of corrosion crusts. During growth with H2 , strain IM1 formed methane with average δ[13] C of -43.5‰ and δ[2] H of -370‰. Corrosive growth led to methane more depleted in [13] C, with average δ[13] C ranging from -56‰ to -64‰ during the early and the late growth phase respectively. The corresponding δ[2] H were less impacted by the growth phase, with average values ranging from -316 to -329‰. The stable isotope fractionation factors, α 13 C CO 2 / CH 4 , were 1.026 and 1.042 for hydrogenotrophic and corrosive growth respectively. Corrosion crusts formed by strain IM1 have a domed structure, appeared electrically conductive and were composed of siderite, calcite and iron sulfide, the latter formed by precipitation of sulfide (from culture medium) with ferrous iron generated during corrosion. Strain IM1 cells were found attached to crust surfaces and encrusted deep inside crust domes. Our results may assist to diagnose methanogens-induced corrosion in the field and suggest that intrusion of sulfide in anoxic settings may stimulate corrosion by methanogenic archaea via formation of semiconductive crusts.}, }
@article {pmid34158628, year = {2021}, author = {Zhao, R and Mogollón, JM and Roerdink, DL and Thorseth, IH and Økland, I and Jørgensen, SL}, title = {Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments.}, journal = {The ISME journal}, volume = {15}, number = {12}, pages = {3657-3667}, pmid = {34158628}, issn = {1751-7370}, mesh = {*Ammonia ; *Archaea/genetics ; Bacteria ; Geologic Sediments ; Nitrification ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Energy/power availability is regarded as one of the ultimate controlling factors of microbial abundance in the deep biosphere, where fewer cells are found in habitats of lower energy availability. A critical assumption driving the proportional relationship between total cell abundance and power availability is that the cell-specific power requirement keeps constant or varies over smaller ranges than other variables, which has yet to be validated. Here we present a quantitative framework to determine the cell-specific power requirement of the omnipresent ammonia-oxidizing archaea (AOA) in eight sediment cores with 3-4 orders of magnitude variations of organic matter flux and oxygen penetration depth. Our results show that despite the six orders of magnitude variations in the rates and power supply of nitrification and AOA abundances across these eight cores, the cell-specific power requirement of AOA from different cores and depths overlaps within the narrow range of 10[-19]-10[-17] W cell[-1], where the lower end may represent the basal power requirement of microorganisms persisting in subseafloor sediments. In individual cores, AOA also exhibit similar cell-specific power requirements, regardless of the AOA population size or sediment depth/age. Such quantitative insights establish a relationship between the power supply and the total abundance of AOA, and therefore lay a foundation for a first-order estimate of the standing stock of AOA in global marine oxic sediments.}, }
@article {pmid34153824, year = {2021}, author = {Chen, Z and Liu, WS and Zhong, X and Zheng, M and Fei, YH and He, H and Ding, K and Chao, Y and Tang, YT and Wang, S and Qiu, R}, title = {Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China.}, journal = {Water research}, volume = {201}, number = {}, pages = {117331}, doi = {10.1016/j.watres.2021.117331}, pmid = {34153824}, issn = {1879-2448}, mesh = {*Archaea/genetics ; China ; Genome, Archaeal ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.}, }
@article {pmid34151666, year = {2021}, author = {Ziegler, CA and Freddolino, PL}, title = {The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {56}, number = {4}, pages = {373-400}, pmid = {34151666}, issn = {1549-7798}, support = {R35 GM128637/GM/NIGMS NIH HHS/United States ; T32 GM007544/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Leucine-Responsive Regulatory Protein/genetics/*metabolism ; }, abstract = {Since the discovery of the Escherichia coli leucine-responsive regulatory protein (Lrp) almost 50 years ago, hundreds of Lrp homologs have been discovered, occurring in 45% of sequenced bacteria and almost all sequenced archaea. Lrp-like proteins are often referred to as the feast/famine regulatory proteins (FFRPs), reflecting their common regulatory roles. Acting as either global or local transcriptional regulators, FFRPs detect the environmental nutritional status by sensing small effector molecules (usually amino acids) and regulate the expression of genes involved in metabolism, virulence, motility, nutrient transport, stress tolerance, and antibiotic resistance to implement appropriate behaviors for the specific ecological niche of each organism. Despite FFRPs' complexity, a significant role in gene regulation, and prevalence throughout prokaryotes, the last comprehensive review on this family of proteins was published about a decade ago. In this review, we integrate recent notable findings regarding E. coli Lrp and other FFRPs across bacteria and archaea with previous observations to synthesize a more complete view on the mechanistic details and biological roles of this ancient class of transcription factors.}, }
@article {pmid34149676, year = {2021}, author = {De Lise, F and Strazzulli, A and Iacono, R and Curci, N and Di Fenza, M and Maurelli, L and Moracci, M and Cobucci-Ponzano, B}, title = {Programmed Deviations of Ribosomes From Standard Decoding in Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {688061}, pmid = {34149676}, issn = {1664-302X}, abstract = {Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.}, }
@article {pmid34145392, year = {2021}, author = {Kurth, JM and Nobu, MK and Tamaki, H and de Jonge, N and Berger, S and Jetten, MSM and Yamamoto, K and Mayumi, D and Sakata, S and Bai, L and Cheng, L and Nielsen, JL and Kamagata, Y and Wagner, T and Welte, CU}, title = {Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds.}, journal = {The ISME journal}, volume = {15}, number = {12}, pages = {3549-3565}, pmid = {34145392}, issn = {1751-7370}, mesh = {*Euryarchaeota/enzymology/genetics ; Methane/*metabolism ; *Methyltransferases/genetics ; }, abstract = {Methane-generating archaea drive the final step in anaerobic organic compound mineralization and dictate the carbon flow of Earth's diverse anoxic ecosystems in the absence of inorganic electron acceptors. Although such Archaea were presumed to be restricted to life on simple compounds like hydrogen (H2), acetate or methanol, an archaeon, Methermicoccus shengliensis, was recently found to convert methoxylated aromatic compounds to methane. Methoxylated aromatic compounds are important components of lignin and coal, and are present in most subsurface sediments. Despite the novelty of such a methoxydotrophic archaeon its metabolism has not yet been explored. In this study, transcriptomics and proteomics reveal that under methoxydotrophic growth M. shengliensis expresses an O-demethylation/methyltransferase system related to the one used by acetogenic bacteria. Enzymatic assays provide evidence for a two step-mechanisms in which the methyl-group from the methoxy compound is (1) transferred on cobalamin and (2) further transferred on the C1-carrier tetrahydromethanopterin, a mechanism distinct from conventional methanogenic methyl-transfer systems which use coenzyme M as final acceptor. We further hypothesize that this likely leads to an atypical use of the methanogenesis pathway that derives cellular energy from methyl transfer (Mtr) rather than electron transfer (F420H2 re-oxidation) as found for methylotrophic methanogenesis.}, }
@article {pmid34145390, year = {2021}, author = {Murali, R and Gennis, RB and Hemp, J}, title = {Evolution of the cytochrome bd oxygen reductase superfamily and the function of CydAA' in Archaea.}, journal = {The ISME journal}, volume = {15}, number = {12}, pages = {3534-3548}, pmid = {34145390}, issn = {1751-7370}, support = {R01 AI148160/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/enzymology/*genetics ; Archaeal Proteins/*genetics ; Cytochrome b Group/*genetics ; Electron Transport Chain Complex Proteins/*genetics ; Evolution, Molecular ; Oxidation-Reduction ; *Oxidoreductases/genetics ; Oxygen ; }, abstract = {Cytochrome bd-type oxygen reductases (cytbd) belong to one of three enzyme superfamilies that catalyze oxygen reduction to water. They are widely distributed in Bacteria and Archaea, but the full extent of their biochemical diversity is unknown. Here we used phylogenomics to identify three families and several subfamilies within the cytbd superfamily. The core architecture shared by all members of the superfamily consists of four transmembrane helices that bind two active site hemes, which are responsible for oxygen reduction. While previously characterized cytochrome bd-type oxygen reductases use quinol as an electron donor to reduce oxygen, sequence analysis shows that only one of the identified families has a conserved quinol binding site. The other families are missing this feature, suggesting that they use an alternative electron donor. Multiple gene duplication events were identified within the superfamily, resulting in significant evolutionary and structural diversity. The CydAA' cytbd, found exclusively in Archaea, is formed by the co-association of two superfamily paralogs. We heterologously expressed CydAA' from Caldivirga maquilingensis and demonstrated that it performs oxygen reduction with quinol as an electron donor. Strikingly, CydAA' is the first isoform of cytbd containing only b-type hemes shown to be active when isolated from membranes, demonstrating that oxygen reductase activity in this superfamily is not dependent on heme d.}, }
@article {pmid34142100, year = {2021}, author = {Takemata, N and Bell, SD}, title = {Chromosome conformation capture assay combined with biotin enrichment for hyperthermophilic archaea.}, journal = {STAR protocols}, volume = {2}, number = {2}, pages = {100576}, pmid = {34142100}, issn = {2666-1667}, support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; }, mesh = {Biotin/*metabolism ; *Chromosomes, Archaeal ; Genes, Archaeal ; Sequence Analysis, DNA/methods ; Sulfolobus acidocaldarius/genetics/*metabolism ; }, abstract = {Chromosome organization in archaea has long been enigmatic due, in part, to the typically small cell size of archaea and the extremophilic nature of many of the model archaeal species studies, rendering live-cell imaging technically challenging. To circumvent these problems, we recently applied chromosome conformation capture combined with biotin enrichment and deep sequencing (Hi-C) to members of hyperthermophilic archaeal genus Sulfolobus. Our optimized Hi-C protocol described here permits delineation of how Sulfolobus species organize their chromosomes. For complete details on the use and execution of this protocol, please refer to Takemata et al. (2019).}, }
@article {pmid34140936, year = {2021}, author = {Castelle, CJ and Méheust, R and Jaffe, AL and Seitz, K and Gong, X and Baker, BJ and Banfield, JF}, title = {Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {660052}, pmid = {34140936}, issn = {1664-302X}, abstract = {DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 3,197 genomes including 569 newly reconstructed genomes. Protein family content clearly separates the final set of 390 DPANN genomes from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.}, }
@article {pmid34138841, year = {2021}, author = {Schulze, S and Pfeiffer, F and Garcia, BA and Pohlschroder, M}, title = {Comprehensive glycoproteomics shines new light on the complexity and extent of glycosylation in archaea.}, journal = {PLoS biology}, volume = {19}, number = {6}, pages = {e3001277}, pmid = {34138841}, issn = {1545-7885}, support = {P01 CA196539/CA/NCI NIH HHS/United States ; R01 AI118891/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Archaeal Proteins/chemistry/*metabolism ; Biological Assay ; Cell Shape/drug effects ; Databases, Protein ; Glycopeptides/chemistry/*metabolism ; Glycoproteins/chemistry/*metabolism ; Glycosylation/drug effects ; Haloferax volcanii/drug effects/*metabolism ; Mutation/genetics ; Phenotype ; Phylogeny ; Proteomics ; Sodium Chloride/pharmacology ; }, abstract = {Glycosylation is one of the most complex posttranslational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility, and mating. However, comprehensive glycoproteomic analyses are largely missing in prokaryotes. Here, we extend the phenotypic characterization of N-glycosylation pathway mutants in Haloferax volcanii and provide a detailed glycoproteome for this model archaeon through the mass spectrometric analysis of intact glycopeptides. Using in-depth glycoproteomic datasets generated for the wild-type (WT) and mutant strains as well as a reanalysis of datasets within the Archaeal Proteome Project (ArcPP), we identify the largest archaeal glycoproteome described so far. We further show that different N-glycosylation pathways can modify the same glycosites under the same culture conditions. The extent and complexity of the Hfx. volcanii N-glycoproteome revealed here provide new insights into the roles of N-glycosylation in archaeal cell biology.}, }
@article {pmid34119867, year = {2021}, author = {Shen, LD and Yang, YL and Liu, JQ and Hu, ZH and Liu, X and Tian, MH and Yang, WT and Jin, JH and Wang, HY and Wang, YY and Wu, HS}, title = {Different responses of ammonia-oxidizing archaea and bacteria in paddy soils to elevated CO2 concentration.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {286}, number = {}, pages = {117558}, doi = {10.1016/j.envpol.2021.117558}, pmid = {34119867}, issn = {1873-6424}, mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; Carbon Dioxide ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {The elevated atmospheric CO2 concentration is well known to have an important effect on soil nutrient cycling. Ammonia oxidation, mediated by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is the rate-limiting step in soil nitrification, which controls the availability of two key soil nutrients (ammonium and nitrate) for crops. Until now, how the AOA and AOB communities in paddy soils respond to elevated CO2 remains largely unknown. Here, we examined the communities of AOA and AOB and nitrification potential at both surface (0-5 cm) and subsurface (5-10 cm) soil layers of paddy fields under three different CO2 treatments, including CK (ambient CO2 concentration), LT (CK + 160 ppm of CO2) and HT (CK + 200 ppm of CO2). The elevated CO2 was found to have a greater impact on the community structure of AOB than that of AOA in surface soils as revealed by high-throughput sequencing of their amoA genes. However, no obvious variation of AOA or AOB communities was observed in subsurface soils among different CO2 treatments. The abundance of AOA and AOB, and nitrification potential were significantly increased in surface soils under elevated CO2. The variation of AOB abundance correlated well with the variation of nitrification potential. The soil water content and dissolved organic carbon content had important impacts on the dynamic of AOB communities and nitrification potential. Overall, our results showed different responses of AOA and AOB communities to elevated CO2 in paddy ecosystems, and AOB were more sensitive to the rising CO2 concentration.}, }
@article {pmid34113850, year = {2021}, author = {Takemata, N and Bell, SD}, title = {High-resolution analysis of chromosome conformation in hyperthermophilic archaea.}, journal = {STAR protocols}, volume = {2}, number = {2}, pages = {100562}, pmid = {34113850}, issn = {2666-1667}, support = {R01 GM135178/GM/NIGMS NIH HHS/United States ; }, mesh = {*Chromosomes ; DNA, Archaeal/genetics ; High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction/methods ; Sulfolobus/*genetics ; }, abstract = {Chromosome conformation capture (3C) techniques are emerging as promising approaches to study genome organization in Archaea, the least understood domain of life in terms of chromosome biology. Here, we describe a 3C technique combined with deep sequencing for the hyperthermophilic archaeal genus Sulfolobus. Instead of using restriction enzymes compatible with fill-in labeling, this protocol uses the 4-bp blunt cutter AluI to generate high-resolution (up to 2 kb) contact maps from Sulfolobus species. For complete details on the use and execution of this protocol, please refer to Takemata and Bell (2021).}, }
@article {pmid34113328, year = {2021}, author = {Garnier, F and Couturier, M and Débat, H and Nadal, M}, title = {Archaea: A Gold Mine for Topoisomerase Diversity.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {661411}, pmid = {34113328}, issn = {1664-302X}, abstract = {The control of DNA topology is a prerequisite for all the DNA transactions such as DNA replication, repair, recombination, and transcription. This global control is carried out by essential enzymes, named DNA-topoisomerases, that are mandatory for the genome stability. Since many decades, the Archaea provide a significant panel of new types of topoisomerases such as the reverse gyrase, the type IIB or the type IC. These more or less recent discoveries largely contributed to change the understanding of the role of the DNA topoisomerases in all the living world. Despite their very different life styles, Archaea share a quasi-homogeneous set of DNA-topoisomerases, except thermophilic organisms that possess at least one reverse gyrase that is considered a marker of the thermophily. Here, we discuss the effect of the life style of Archaea on DNA structure and topology and then we review the content of these essential enzymes within all the archaeal diversity based on complete sequenced genomes available. Finally, we discuss their roles, in particular in the processes involved in both the archaeal adaptation and the preservation of the genome stability.}, }
@article {pmid34112969, year = {2021}, author = {Payne, D and Spietz, RL and Boyd, ES}, title = {Reductive dissolution of pyrite by methanogenic archaea.}, journal = {The ISME journal}, volume = {15}, number = {12}, pages = {3498-3507}, pmid = {34112969}, issn = {1751-7370}, mesh = {*Archaea/genetics ; Iron ; Solubility ; *Sulfides ; }, abstract = {The formation and fate of pyrite (FeS2) modulates global iron, sulfur, carbon, and oxygen biogeochemical cycles and has done so since early in Earth's geological history. A longstanding paradigm is that FeS2 is stable at low temperature and is unavailable to microorganisms in the absence of oxygen and oxidative weathering. Here, we show that methanogens can catalyze the reductive dissolution of FeS2 at low temperature (≤38 °C) and utilize dissolution products to meet cellular iron and sulfur demands associated with the biosynthesis of simple and complex co-factors. Direct access to FeS2 is required to catalyze its reduction and/or to assimilate iron monosulfide that likely forms through coupled reductive dissolution and precipitation, consistent with close associations observed between cells and FeS2. These findings demonstrate that FeS2 is bioavailable to anaerobic methanogens and can be mobilized in low temperature anoxic environments. Given that methanogens evolved at least 3.46 Gya, these data indicate that the microbial contribution to the iron and sulfur cycles in ancient and contemporary anoxic environments may be more complex and robust than previously recognized, with impacts on the sources and sinks of iron and sulfur and other bio-essential and thiophilic elements such as nickel and cobalt.}, }
@article {pmid34099860, year = {2021}, author = {Watanabe, S and Murase, Y and Watanabe, Y and Sakurai, Y and Tajima, K}, title = {Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {687}, pmid = {34099860}, issn = {2399-3642}, mesh = {Aconitate Hydratase/*chemistry ; Agrobacterium tumefaciens/chemistry/*enzymology ; Catalytic Domain ; Crystallography, X-Ray ; Evolution, Molecular ; Models, Molecular ; Protein Conformation ; Thermococcus/chemistry/*enzymology ; }, abstract = {Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.}, }
@article {pmid34088904, year = {2021}, author = {Pende, N and Sogues, A and Megrian, D and Sartori-Rupp, A and England, P and Palabikyan, H and Rittmann, SKR and Graña, M and Wehenkel, AM and Alzari, PM and Gribaldo, S}, title = {SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3214}, pmid = {34088904}, issn = {2041-1723}, mesh = {Archaeal Proteins/chemistry/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Cell Cycle ; Cell Division/genetics/*physiology ; Conserved Sequence ; Crystallography, X-Ray ; Evolution, Molecular ; Methanobrevibacter/genetics/*metabolism/ultrastructure ; Microscopy, Electron, Transmission ; Models, Molecular ; Phylogeny ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Quaternary ; Recombinant Proteins/genetics/metabolism/ultrastructure ; }, abstract = {Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.}, }
@article {pmid34065163, year = {2021}, author = {Vázquez-Madrigal, AS and Barbachano-Torres, A and Arellano-Plaza, M and Kirchmayr, MR and Finore, I and Poli, A and Nicolaus, B and De la Torre Zavala, S and Camacho-Ruiz, RM}, title = {Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {34065163}, issn = {2076-2607}, abstract = {The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3'-sn-glycerol-1'-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea.}, }
@article {pmid34060911, year = {2021}, author = {McNichol, J and Berube, PM and Biller, SJ and Fuhrman, JA}, title = {Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0056521}, pmid = {34060911}, issn = {2379-5077}, abstract = {Small subunit rRNA (SSU rRNA) amplicon sequencing can quantitatively and comprehensively profile natural microbiomes, representing a critically important tool for studying diverse global ecosystems. However, results will only be accurate if PCR primers perfectly match the rRNA of all organisms present. To evaluate how well marine microorganisms across all 3 domains are detected by this method, we compared commonly used primers with >300 million rRNA gene sequences retrieved from globally distributed marine metagenomes. The best-performing primers compared to 16S rRNA of bacteria and archaea were 515Y/926R and 515Y/806RB, which perfectly matched over 96% of all sequences. Considering cyanobacterial and chloroplast 16S rRNA, 515Y/926R had the highest coverage (99%), making this set ideal for quantifying marine primary producers. For eukaryotic 18S rRNA sequences, 515Y/926R also performed best (88%), followed by V4R/V4RB (18S rRNA specific; 82%)-demonstrating that the 515Y/926R combination performs best overall for all 3 domains. Using Atlantic and Pacific Ocean samples, we demonstrate high correspondence between 515Y/926R amplicon abundances (generated for this study) and metagenomic 16S rRNA (median R[2] = 0.98, n = 272), indicating amplicons can produce equally accurate community composition data compared with shotgun metagenomics. Our analysis also revealed that expected performance of all primer sets could be improved with minor modifications, pointing toward a nearly completely universal primer set that could accurately quantify biogeochemically important taxa in ecosystems ranging from the deep sea to the surface. In addition, our reproducible bioinformatic workflow can guide microbiome researchers studying different ecosystems or human health to similarly improve existing primers and generate more accurate quantitative amplicon data. IMPORTANCE PCR amplification and sequencing of marker genes is a low-cost technique for monitoring prokaryotic and eukaryotic microbial communities across space and time but will work optimally only if environmental organisms match PCR primer sequences exactly. In this study, we evaluated how well primers match globally distributed short-read oceanic metagenomes. Our results demonstrate that primer sets vary widely in performance, and that at least for marine systems, rRNA amplicon data from some primers lack significant biases compared to metagenomes. We also show that it is theoretically possible to create a nearly universal primer set for diverse saline environments by defining a specific mixture of a few dozen oligonucleotides, and present a software pipeline that can guide rational design of primers for any environment with available meta'omic data.}, }
@article {pmid34027477, year = {2021}, author = {Cockram, C and Thierry, A and Koszul, R}, title = {Generation of gene-level resolution chromosome contact maps in bacteria and archaea.}, journal = {STAR protocols}, volume = {2}, number = {2}, pages = {100512}, pmid = {34027477}, issn = {2666-1667}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Chromosome Mapping ; Chromosomes, Archaeal/*genetics ; Chromosomes, Bacterial/*genetics ; Genome, Archaeal ; Genome, Bacterial ; }, abstract = {Chromosome conformation capture (Hi-C) has become a routine method for probing the 3D organization of genomes. However, when applied to bacteria and archaea, current protocols are expensive and limited in their resolution. By dissecting the different steps of published eukaryotic and prokaryotic Hi-C protocols, we have developed a cost- and time-effective approach to generate high-resolution (down to 500 bp - 1 kb) contact matrices of both bacteria and archaea genomes. For complete details on the use and execution of this protocol, please refer to Cockram et al. (2020).}, }
@article {pmid34027378, year = {2021}, author = {Inkinen, J and Siponen, S and Jayaprakash, B and Tiwari, A and Hokajärvi, AM and Pursiainen, A and Ikonen, J and Kauppinen, A and Miettinen, IT and Paananen, J and Torvinen, E and Kolehmainen, M and Pitkänen, T}, title = {Diverse and active archaea communities occur in non-disinfected drinking water systems-Less activity revealed in disinfected and hot water systems.}, journal = {Water research X}, volume = {12}, number = {}, pages = {100101}, pmid = {34027378}, issn = {2589-9147}, abstract = {The knowledge about the members of active archaea communities in DWDS is limited. The current understanding is based on high-throughput 16S ribosomal RNA gene (DNA-based) amplicon sequencing that reveals the diversity of active, dormant, and dead members of the prokaryote (bacteria, archaea) communities. The sequencing primers optimized for bacteria community analysis may underestimate the share of the archaea community. This study characterized archaea communities at five full-scale drinking water distribution systems (DWDS), representing a variety of drinking water production units (A-E); A&amp;B use artificially recharged non-disinfected groundwater (ARG), the other DWDS's supplied water disinfected by using ultraviolet (UV) light and chlorine compounds, C&amp;D were surface waterworks and E was a ground waterworks. For the first time for archaea community analyses, this study employed the archaea-specific high-throughput sequencing primers for 16S ribosomal RNA (rRNA) as a target (reverse-transcribed cDNA; an RNA-based approach) in addition to the previously used 16S rRNA gene target (rDNA; a DNA-based approach) to reveal the active fraction of the archaea present in DWDS. The archaea community structure in varying environmental conditions in the water and biofilm of the five DWDSs were investigated by taking into consideration the system properties (cold or hot water system) and water age (distance from the treatment plants) in samples from each season of one year. The RNA-based archaea amplicon reads were obtained mostly from cold water samples from DWDSs (A-B) distributing water without disinfection where the DNA-based and RNA-based analysis created separate clusters in a weighted beta-diversity analysis. The season and location in DWDS A further affected the diversity of these archaea communities as was seen by different clusters in beta-diversity plots. The recovery of archaea reads was not adequate for analysis in any of the disinfected samples in DWDSs C-E or non-disinfected hot water in DWDSs A-B when utilizing RNA-based template. The metabolically active archaea community of DWDSs thus seemed to be effectively controlled by disinfection of water and in the hot water systems by the temperature. All biofilms regardless of DWDS showed lower species richness values (mainly Nitrososphaeria class) than non-disinfected water from DWDSs A-B where several archaea classes occurred (e.g. Woesearchaeia, Nitrososphaeria, Micrarchaeia, Methanomicrobia, Iairchaeia, Bathyarchaeia) indicating only part of the archaea members were able to survive in biofilms. Thus, Archaea has been shown as a significant part of normal DWDS biota, and their role especially in non-disinfected DWDS may be more important than previously considered.}, }
@article {pmid34026962, year = {2020}, author = {Bomberg, M and Miettinen, H}, title = {Data on the optimization of an archaea-specific probe-based qPCR assay.}, journal = {Data in brief}, volume = {33}, number = {}, pages = {106610}, pmid = {34026962}, issn = {2352-3409}, abstract = {Estimation of archaeal numbers by use of fluorescent DNA binding dyes is challenging, because primers targeting the archaeal 16SrRNA genes readily also bind to bacterial 16S rRNA gene sequences, especially when the relative abundance of bacteria is greater than that of archaea. In order to increase specificity, we optimized a fluorescent probe-based assay using previously published archaeal primers and probe. The assay was tested on genomic DNA of pure bacterial and archaeal cultures and optimized using PCR amplicons of the archaeal pure cultures. The used bacterial strains showed slight amplification using the fluorescent dye assay, whereas all archaeal strains could be amplified with the archaea primers used. Due to differences in genome size and number of 16S rRNA gene copies between the tested archaeal strains, the amplification level varied greatly between the strains. Therefore, we also tested the amplification using PCR amplified fragments of the archaeal 16S rRNA genes. The tests with the archaeal 16S rRNA gene amplicons showed good amplification, although the amplification efficiency still varied between archaeal strains. The qPCR assay was used to estimate the archaeal numbers in process water of a multi-metal mine's metallurgical plant [1] and will be used in similar future microbiological analysis included in the H2020 ITERAMS project (Grant agreement# 730480).}, }
@article {pmid34026831, year = {2021}, author = {Lei, L and Burton, ZF}, title = {Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria.}, journal = {Frontiers in molecular biosciences}, volume = {8}, number = {}, pages = {651134}, pmid = {34026831}, issn = {2296-889X}, abstract = {DNA template-dependent multi-subunit RNA polymerases (RNAPs) found in all three domains of life and some viruses are of the two-double-Ψ-β-barrel (DPBB) type. The 2-DPBB protein format is also found in some RNA template-dependent RNAPs and a major replicative DNA template-dependent DNA polymerase (DNAP) from Archaea (PolD). The 2-DPBB family of RNAPs and DNAPs probably evolved prior to the last universal common cellular ancestor (LUCA). Archaeal Transcription Factor B (TFB) and bacterial σ factors include homologous strings of helix-turn-helix units. The consequences of TFB-σ homology are discussed in terms of the evolution of archaeal and bacterial core promoters. Domain-specific DPBB loop inserts functionally connect general transcription factors to the RNAP active site. Archaea appear to be more similar to LUCA than Bacteria. Evolution of bacterial σ factors from TFB appears to have driven divergence of Bacteria from Archaea, splitting the prokaryotic domains.}, }
@article {pmid34019119, year = {2021}, author = {Naitam, MG and Kaushik, R}, title = {Archaea: An Agro-Ecological Perspective.}, journal = {Current microbiology}, volume = {78}, number = {7}, pages = {2510-2521}, pmid = {34019119}, issn = {1432-0991}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Rhizosphere ; Soil ; *Soil Microbiology ; }, abstract = {Microorganisms inhabiting bulk soil and rhizosphere play an important role in soil biogeochemical cycles leading to enhanced plant growth and productivity. In this context, the role of bacteria is well established, however, not much reports are available about the role archaea plays in this regard. Literature suggests that archaea also play a greater role in nutrient cycling of carbon, nitrogen, sulfur, and other minerals, possess various plant growth promoting attributes, and can impart tolerance to various abiotic stresses (especially osmotic and oxidative) in areas of high salinity, low and high temperatures and hydrogen ion concentrations. Thermoacidophilic archaea have been found to potentially involve in bioleaching of mineral ores and bioremediation of chemical pollutants and aromatic compounds. Looking at immense potential of archaea in promoting plant growth, alleviating abiotic stresses, and remediating contaminated sites, detailed studies are required to establish their role in different ecological processes, and their interactions in rhizosphere with plant and other microflora (bacteria and fungi) in different ecosystems. In this review, a brief discussion on archaea from the agro-ecological point of view is presented.}, }
@article {pmid34017110, year = {2021}, author = {Graham, F}, title = {Daily briefing: Enigmatic archaea might be key to complex life.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-021-01366-4}, pmid = {34017110}, issn = {1476-4687}, }
@article {pmid33997611, year = {2021}, author = {Clemmons, BA and Schneider, LG and Melchior, EA and Lindholm-Perry, AK and Hales, KE and Wells, JE and Freetly, HC and Hansen, SL and Drewnoski, ME and Hartman, SJ and Myer, PR}, title = {The effects of feeding ferric citrate on ruminal bacteria, methanogenic archaea and methane production in growing beef steers.}, journal = {Access microbiology}, volume = {3}, number = {1}, pages = {acmi000180}, pmid = {33997611}, issn = {2516-8290}, abstract = {Methane produced by cattle is one of the contributors of anthropogenic greenhouse gas. Methods to lessen methane emissions from cattle have been met with varying success; thus establishing consistent methods for decreasing methane production are imperative. Ferric iron may possibly act to decrease methane by acting as an alternative electron acceptor. The objective of this study was to assess the effect of ferric citrate on the rumen bacterial and archaeal communities and its impact on methane production. In this study, eight steers were used in a repeated Latin square design with 0, 250, 500 or 750 mg Fe/kg DM of ferric iron (as ferric citrate) in four different periods. Each period consisted of a 16 day adaptation period and 5 day sampling period. During each sampling period, methane production was measured, and rumen content was collected for bacterial and archaeal community analyses. Normally distributed data were analysed using a mixed model ANOVA using the GLIMMIX procedure of SAS, and non-normally distributed data were analysed in the same manner following ranking. Ferric citrate did not have any effect on bacterial community composition, methanogenic archaea nor methane production (P>0.05). Ferric citrate may not be a viable option to observe a ruminal response for decreases in enteric methane production.}, }
@article {pmid33995325, year = {2021}, author = {Weixlbaumer, A and Grünberger, F and Werner, F and Grohmann, D}, title = {Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {661827}, pmid = {33995325}, issn = {1664-302X}, abstract = {The lack of a nucleus is the defining cellular feature of bacteria and archaea. Consequently, transcription and translation are occurring in the same compartment, proceed simultaneously and likely in a coupled fashion. Recent cryo-electron microscopy (cryo-EM) and tomography data, also combined with crosslinking-mass spectrometry experiments, have uncovered detailed structural features of the coupling between a transcribing bacterial RNA polymerase (RNAP) and the trailing translating ribosome in Escherichia coli and Mycoplasma pneumoniae. Formation of this supercomplex, called expressome, is mediated by physical interactions between the RNAP-bound transcription elongation factors NusG and/or NusA and the ribosomal proteins including uS10. Based on the structural conservation of the RNAP core enzyme, the ribosome, and the universally conserved elongation factors Spt5 (NusG) and NusA, we discuss requirements and functional implications of transcription-translation coupling in archaea. We furthermore consider additional RNA-mediated and co-transcriptional processes that potentially influence expressome formation in archaea.}, }
@article {pmid33993308, year = {2021}, author = {Yang, Y and Zhang, C and Lenton, TM and Yan, X and Zhu, M and Zhou, M and Tao, J and Phelps, TJ and Cao, Z}, title = {The Evolution Pathway of Ammonia-Oxidizing Archaea Shaped by Major Geological Events.}, journal = {Molecular biology and evolution}, volume = {38}, number = {9}, pages = {3637-3648}, pmid = {33993308}, issn = {1537-1719}, mesh = {*Ammonia/metabolism ; *Archaea/genetics/metabolism ; Bacteria/genetics ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {Primordial nitrification processes have been studied extensively using geochemical approaches, but the biological origination of nitrification remains unclear. Ammonia-oxidizing archaea (AOA) are widely distributed nitrifiers and implement the rate-limiting step in nitrification. They are hypothesized to have been important players in the global nitrogen cycle in Earth's early history. We performed systematic phylogenomic and marker gene analyses to elucidate the diversification timeline of AOA evolution. Our results suggested that the AOA ancestor experienced terrestrial geothermal environments at ∼1,165 Ma (1,928-880 Ma), and gradually evolved into mesophilic soil at ∼652 Ma (767-554 Ma) before diversifying into marine settings at ∼509 Ma (629-412 Ma) and later into shallow and deep oceans, respectively. Corroborated by geochemical evidence and modeling, the timing of key diversification nodes can be linked to the global magmatism and glaciation associated with the assembly and breakup of the supercontinent Rodinia, and the later oxygenation of the deep ocean. Results of this integrated study shed light on the geological forces that may have shaped the evolutionary pathways of the AOA, which played an important role in the ancient global nitrogen cycle.}, }
@article {pmid33976787, year = {2021}, author = {Westoby, M and Nielsen, DA and Gillings, MR and Litchman, E and Madin, JS and Paulsen, IT and Tetu, SG}, title = {Cell size, genome size, and maximum growth rate are near-independent dimensions of ecological variation across bacteria and archaea.}, journal = {Ecology and evolution}, volume = {11}, number = {9}, pages = {3956-3976}, pmid = {33976787}, issn = {2045-7758}, abstract = {Among bacteria and archaea, maximum relative growth rate, cell diameter, and genome size are widely regarded as important influences on ecological strategy. Via the most extensive data compilation so far for these traits across all clades and habitats, we ask whether they are correlated and if so how. Overall, we found little correlation among them, indicating they should be considered as independent dimensions of ecological variation. Nor was correlation evident within particular habitat types. A weak nonlinearity (6% of variance) was found whereby high maximum growth rates (temperature-adjusted) tended to occur in the midrange of cell diameters. Species identified in the literature as oligotrophs or copiotrophs were clearly separated on the dimension of maximum growth rate, but not on the dimensions of genome size or cell diameter.}, }
@article {pmid33941062, year = {2021}, author = {Mikhaylina, AO and Nikonova, EY and Kostareva, OS and Piendl, W and Erlacher, M and Tishchenko, SV}, title = {Characterization of Regulatory Elements of L11 and L1 Operons in Thermophilic Bacteria and Archaea.}, journal = {Biochemistry. Biokhimiia}, volume = {86}, number = {4}, pages = {397-408}, doi = {10.1134/S0006297921040027}, pmid = {33941062}, issn = {1608-3040}, support = {P 30486/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Haloarcula marismortui/*genetics/metabolism ; Hot Temperature ; Operon/*genetics ; *Regulatory Sequences, Nucleic Acid ; Ribosomal Proteins/*genetics ; Thermotoga maritima/*genetics/metabolism ; Thermus thermophilus/*genetics/metabolism ; }, abstract = {Ribosomal protein L1 is a conserved two-domain protein that is involved in formation of the L1 stalk of the large ribosomal subunit. When there are no free binding sites available on the ribosomal 23S RNA, the protein binds to the specific site on the mRNA of its own operon (L11 operon in bacteria and L1 operon in archaea) preventing translation. Here we show that the regulatory properties of the r-protein L1 and its domain I are conserved in the thermophilic bacteria Thermus and Thermotoga and in the halophilic archaeon Haloarcula marismortui. At the same time the revealed features of the operon regulation in thermophilic bacteria suggest presence of two regulatory regions.}, }
@article {pmid33935987, year = {2021}, author = {Schnakenberg, A and Aromokeye, DA and Kulkarni, A and Maier, L and Wunder, LC and Richter-Heitmann, T and Pape, T and Ristova, PP and Bühring, SI and Dohrmann, I and Bohrmann, G and Kasten, S and Friedrich, MW}, title = {Electron Acceptor Availability Shapes Anaerobically Methane Oxidizing Archaea (ANME) Communities in South Georgia Sediments.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {617280}, pmid = {33935987}, issn = {1664-302X}, abstract = {Anaerobic methane oxidizing archaea (ANME) mediate anaerobic oxidation of methane (AOM) in marine sediments and are therefore important for controlling atmospheric methane concentrations in the water column and ultimately the atmosphere. Numerous previous studies have revealed that AOM is coupled to the reduction of different electron acceptors such as sulfate, nitrate/nitrite or Fe(III)/Mn(IV). However, the influence of electron acceptor availability on the in situ ANME community composition in sediments remains largely unknown. Here, we investigated the electron acceptor availability and compared the microbial in situ communities of three methane-rich locations offshore the sub-Antarctic island South Georgia, by Illumina sequencing and qPCR of mcrA genes. The methanic zone (MZ) sediments of Royal Trough and Church Trough comprised high sulfide concentrations of up to 4 and 19 mM, respectively. In contrast, those of the Cumberland Bay fjord accounted for relatively high concentrations of dissolved iron (up to 186 μM). Whereas the ANME community in the sulfidic sites Church Trough and Royal Trough mainly comprised members of the ANME-1 clade, the order-level clade "ANME-1-related" (Lever and Teske, 2015) was most abundant in the iron-rich site in Cumberland Bay fjord, indicating that the availability of electron acceptors has a strong selective effect on the ANME community. This study shows that potential electron acceptors for methane oxidation may serve as environmental filters to select for the ANME community composition and adds to a better understanding of the global importance of AOM.}, }
@article {pmid33911286, year = {2021}, author = {Liu, Y and Makarova, KS and Huang, WC and Wolf, YI and Nikolskaya, AN and Zhang, X and Cai, M and Zhang, CJ and Xu, W and Luo, Z and Cheng, L and Koonin, EV and Li, M}, title = {Expanded diversity of Asgard archaea and their relationships with eukaryotes.}, journal = {Nature}, volume = {593}, number = {7860}, pages = {553-557}, pmid = {33911286}, issn = {1476-4687}, mesh = {Archaea/*classification ; Biological Evolution ; Eukaryota ; *Genome, Archaeal ; Metagenomics ; *Phylogeny ; }, abstract = {Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes[1-5]. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)[6-8]. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that-to our knowledge-have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead-depending on the choice of species and conserved genes used to build the phylogeny-supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota-Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal 'eukaryome' in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer.}, }
@article {pmid33907062, year = {2021}, author = {Kitamura, R and Kozaki, T and Ishii, K and Iigo, M and Kurokura, T and Yamane, K and Maeda, I and Iwabuchi, K and Saito, T}, title = {Utilizing Cattle Manure Compost Increases Ammonia Monooxygenase A Gene Expression and Ammonia-oxidizing Activity of Both Bacteria and Archaea in Biofiltration Media for Ammonia Deodorization.}, journal = {Microbes and environments}, volume = {36}, number = {2}, pages = {}, pmid = {33907062}, issn = {1347-4405}, mesh = {Ammonia/metabolism ; Animals ; Archaea/classification/*enzymology/genetics/metabolism ; Archaeal Proteins/genetics/*metabolism ; Bacteria/classification/*enzymology/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; Cattle ; Composting ; Filtration ; Manure/analysis/*microbiology ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; Phylogeny ; }, abstract = {Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.}, }
@article {pmid33901216, year = {2021}, author = {Płaza, G and Jałowiecki, &#x141; and Głowacka, D and Hubeny, J and Harnisz, M and Korzeniewska, E}, title = {Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250514}, pmid = {33901216}, issn = {1932-6203}, mesh = {Archaea/*isolation &amp; purification ; Bacteria/isolation &amp; purification ; *Biodiversity ; Cities ; *Microbiota ; Phylogeny ; Principal Component Analysis ; *Water Purification ; }, abstract = {Due to limited description of the role and diversity of archaea in WWTPs, the aim of the study was to analyze microbial community structures and diversities with particular regard to Archaea in the samples taken from different stages of the full-scale municipal wastewater treatment plant and effluent receiving water (upstream and downstream discharge point). Our study was focused on showing how the treatment processes influenced the Eubacteria and Archaea composition. Alpha and Beta diversity were used to evaluate the microbial diversity changes in the collected samples. Proteobacteria was the largest fraction ranging from 28% to 67% with 56% relative abundance across all samples. Archaea were present in all stages of WWTP ranged from 1 to 8%. Among the Archaea, two groups of methanogens, acetoclastic (Methanosarcina, Methanosaeta) and hydrogenotrophic methanogens (Methanospirillium, Methanoculleus, Methanobrevibacter) were dominant in the technological stages. The obtained results indicate that the treated wastewater did not significantly affect eubacterial and archaeal composition in receiving water. However, differences in richness, diversity and microbial composition of Eubacteria and Archaea between the wastewater samples taken from the primary and secondary treatment were observed.}, }
@article {pmid33896087, year = {2021}, author = {Westoby, M and Gillings, MR and Madin, JS and Nielsen, DA and Paulsen, IT and Tetu, SG}, title = {Trait dimensions in bacteria and archaea compared to vascular plants.}, journal = {Ecology letters}, volume = {24}, number = {7}, pages = {1487-1504}, doi = {10.1111/ele.13742}, pmid = {33896087}, issn = {1461-0248}, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Ecology ; Phenotype ; Plants ; }, abstract = {Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so-called 'trait ecology'-strategy description reframed along measurable trait dimensions-has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate-yield trade-off that is analogous to the acquisitive-conservative spectrum in plants, though underpinned by different trade-offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade-offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate-use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate-use pathways. This indicates they convey information complementary to substrate use.}, }
@article {pmid33892429, year = {2021}, author = {Thema, M and Weidlich, T and Kaul, A and Böllmann, A and Huber, H and Bellack, A and Karl, J and Sterner, M}, title = {Optimized biological CO2-methanation with a pure culture of thermophilic methanogenic archaea in a trickle-bed reactor.}, journal = {Bioresource technology}, volume = {333}, number = {}, pages = {125135}, doi = {10.1016/j.biortech.2021.125135}, pmid = {33892429}, issn = {1873-2976}, mesh = {Bioreactors ; *Carbon Dioxide ; *Euryarchaeota ; Hydrogen ; Methane ; }, abstract = {In this study, a fully automated process converting hydrogen and carbon dioxide to methane in a high temperature trickle-bed reactor was developed from lab scale to field test level. The reactor design and system performance was optimized to yield high methane content in the product gas for direct feed-in to the gas grid. The reaction was catalyzed by a pure culture of Methanothermobacter thermoautotrophicus IM5, which formed a biofilm on ceramic packing elements. During 600 h in continuous and semi-continuous operation in countercurrent flow, the 0.05 m[3] reactor produced up to95.3 % of methane at a methane production rate of 0.35 [Formula: see text] . Adding nitrogen as carrier gas during startup, foam control and dosing of ammonium and sodium sulfide as nitrogen and sulfur source were important factors for process automation.}, }
@article {pmid33851978, year = {2021}, author = {Grinter, R and Greening, C}, title = {Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {5}, pages = {}, pmid = {33851978}, issn = {1574-6976}, mesh = {*Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biosynthetic Pathways ; *Euryarchaeota/metabolism ; Humans ; Riboflavin/metabolism ; }, abstract = {Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.}, }
@article {pmid33847950, year = {2021}, author = {Taib, N and Gribaldo, S and MacNeill, SA}, title = {Single-Stranded DNA-Binding Proteins in the Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2281}, number = {}, pages = {23-47}, pmid = {33847950}, issn = {1940-6029}, mesh = {Archaea/classification/genetics/*metabolism ; Archaeal Proteins/chemistry/metabolism ; DNA Repair ; DNA Replication ; DNA, Archaeal/metabolism ; DNA, Single-Stranded/chemistry/*metabolism ; DNA-Binding Proteins/*chemistry/*metabolism ; Models, Molecular ; Phylogeny ; Protein Binding ; Protein Domains ; Species Specificity ; }, abstract = {Single-stranded (ss) DNA-binding proteins are found in all three domains of life where they play vital roles in nearly all aspects of DNA metabolism by binding to and stabilizing exposed ssDNA and acting as platforms onto which DNA-processing activities can assemble. The ssDNA-binding factors SSB and RPA are extremely well conserved across bacteria and eukaryotes, respectively, and comprise one or more OB-fold ssDNA-binding domains. In the third domain of life, the archaea, multiple types of ssDNA-binding protein are found with a variety of domain architectures and subunit compositions, with OB-fold ssDNA-binding domains being a characteristic of most, but not all. This chapter summarizes current knowledge of the distribution, structure, and biological function of the archaeal ssDNA-binding factors, highlighting key features shared between clades and those that distinguish the proteins of different clades from one another. The likely cellular functions of the proteins are discussed and gaps in current knowledge identified.}, }
@article {pmid33828536, year = {2021}, author = {Gao, K and Lu, Y}, title = {Putative Extracellular Electron Transfer in Methanogenic Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {611739}, pmid = {33828536}, issn = {1664-302X}, abstract = {It has been suggested that a few methanogens are capable of extracellular electron transfers. For instance, Methanosarcina barkeri can directly capture electrons from the coexisting microbial cells of other species. Methanothrix harundinacea and Methanosarcina horonobensis retrieve electrons from Geobacter metallireducens via direct interspecies electron transfer (DIET). Recently, Methanobacterium, designated strain YSL, has been found to grow via DIET in the co-culture with Geobacter metallireducens. Methanosarcina acetivorans can perform anaerobic methane oxidation and respiratory growth relying on Fe(III) reduction through the extracellular electron transfer. Methanosarcina mazei is capable of electromethanogenesis under the conditions where electron-transfer mediators like H2 or formate are limited. The membrane-bound multiheme c-type cytochromes (MHC) and electrically-conductive cellular appendages have been assumed to mediate the extracellular electron transfer in bacteria like Geobacter and Shewanella species. These molecules or structures are rare but have been recently identified in a few methanogens. Here, we review the current state of knowledge for the putative extracellular electron transfers in methanogens and highlight the opportunities and challenges for future research.}, }
@article {pmid33821466, year = {2021}, author = {Chuphal, N and Singha, KP and Sardar, P and Sahu, NP and Shamna, N and Kumar, V}, title = {Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics?.}, journal = {Probiotics and antimicrobial proteins}, volume = {13}, number = {6}, pages = {1668-1695}, pmid = {33821466}, issn = {1867-1314}, mesh = {Animal Feed/*microbiology ; *Archaea/genetics ; *Probiotics ; }, abstract = {The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.}, }
@article {pmid33807612, year = {2021}, author = {Gonzalez-Bosquet, J and Pedra-Nobre, S and Devor, EJ and Thiel, KW and Goodheart, MJ and Bender, DP and Leslie, KK}, title = {Bacterial, Archaea, and Viral Transcripts (BAVT) Expression in Gynecological Cancers and Correlation with Regulatory Regions of the Genome.}, journal = {Cancers}, volume = {13}, number = {5}, pages = {}, pmid = {33807612}, issn = {2072-6694}, support = {R01 CA99908/NH/NIH HHS/United States ; R01 CA184101/NH/NIH HHS/United States ; }, abstract = {Bacteria, archaea, and viruses are associated with numerous human cancers. To date, microbiome variations in transcription have not been evaluated relative to upper female genital tract cancer risk. Our aim was to assess differences in bacterial, archaea, and viral transcript (BAVT) expression between different gynecological cancers and normal fallopian tubes. In this case-control study we performed RNA sequencing on 12 normal tubes, 112 serous ovarian cancers (HGSC) and 62 endometrioid endometrial cancers (EEC). We used the centrifuge algorithm to classify resultant transcripts into four indexes: bacterial, archaea, viral, and human genomes. We then compared BAVT expression from normal samples, HGSC and EEC. T-test was used for univariate comparisons (correcting for multiple comparison) and lasso for multivariate modelling. For validation we performed DNA sequencing of normal tubes in comparison to HGSC and EEC BAVTs in the TCGA database. Pathway analyses were carried out to evaluate the function of significant BAVTs. Our results show that BAVT expression levels vary between different gynecological cancers. Finally, we mapped some of these BAVTs to the human genome. Numerous map locations were close to regulatory genes and long non-coding RNAs based on the pathway enrichment analysis. BAVTs may affect gynecological cancer risk and may be part of potential targets for cancer therapy.}, }
@article {pmid33798878, year = {2021}, author = {Fan, C and Zhang, W and Chen, X and Li, N and Li, W and Wang, Q and Duan, P and Chen, M}, title = {Residual effects of four-year amendments of organic material on N2O production driven by ammonia-oxidizing archaea and bacteria in a tropical vegetable soil.}, journal = {The Science of the total environment}, volume = {781}, number = {}, pages = {146746}, doi = {10.1016/j.scitotenv.2021.146746}, pmid = {33798878}, issn = {1879-1026}, mesh = {*Ammonia ; *Archaea ; Bacteria ; Ecosystem ; Fertilizers/analysis ; Nitrification ; Oxidation-Reduction ; Soil ; Soil Microbiology ; Vegetables ; }, abstract = {Organic material (OM) applied to cropland not only enhances soil fertility but also profoundly affects soil nitrogen cycling. However, little is known about the relative contributions of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrous oxide (N2O) production during ammonia oxidation in response to the additions of diverse types of OMs in the tropical soil for vegetable production. Herein, the soils were sampled from a tropical vegetable field subjected to 4-year consecutive amendments of straw or manure. All the soils were amended with ammonium sulfate ((NH4)2SO4, applied at a dose of 150 mg N kg[-1]) and incubated aerobically for four weeks under 50% water holding capacity. 1-octyne or acetylene inhibition technique was used to differentiate the relative contributions of AOA and AOB to N2O production. Results showed that AOA dominated N2O production in soil managements of unfertilized control (CK), chemical fertilization (NPK), and NPK with straw (NPKS), whereas AOB contributed more in soil under NPK with manure (NPKM). Straw addition stimulated AOA-dependent N2O production by 94.8% despite the decreased AOA-amoA abundance. Moreover, manure incorporation triggered both AOA- and AOB-dependent N2O production by 147.2% and 233.7%, respectively, accompanied with increased AOA and AOB abundances. Those stimulating effects were stronger for AOB, owing to its sensitivity to the alleviated soil acidification and decreased soil C/N ratio. Our findings highlight the stimulated N2O emissions during ammonia oxidation by historical OM amendments in tropical vegetable soil, with the magnitude of those priming effects dependent on the types of OM, and appropriate measures need to be taken to counter this challenge in tropical agriculture ecosystems.}, }
@article {pmid33782110, year = {2021}, author = {Liu, J and Cvirkaite-Krupovic, V and Baquero, DP and Yang, Y and Zhang, Q and Shen, Y and Krupovic, M}, title = {Virus-induced cell gigantism and asymmetric cell division in archaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {15}, pages = {}, pmid = {33782110}, issn = {1091-6490}, mesh = {Archaeal Proteins/metabolism ; Archaeal Viruses/*pathogenicity ; *Asymmetric Cell Division ; CRISPR-Cas Systems ; Endosomal Sorting Complexes Required for Transport/metabolism ; Giant Cells/*metabolism/virology ; Sulfolobales/genetics/physiology/*virology ; }, abstract = {Archaeal viruses represent one of the most mysterious parts of the global virosphere, with many virus groups sharing no evolutionary relationship to viruses of bacteria or eukaryotes. How these viruses interact with their hosts remains largely unexplored. Here we show that nonlytic lemon-shaped virus STSV2 interferes with the cell cycle control of its host, hyperthermophilic and acidophilic archaeon Sulfolobus islandicus, arresting the cell cycle in the S phase. STSV2 infection leads to transcriptional repression of the cell division machinery, which is homologous to the eukaryotic endosomal sorting complexes required for transport (ESCRT) system. The infected cells grow up to 20-fold larger in size, have 8,000-fold larger volume compared to noninfected cells, and accumulate massive amounts of viral and cellular DNA. Whereas noninfected Sulfolobus cells divide symmetrically by binary fission, the STSV2-infected cells undergo asymmetric division, whereby giant cells release normal-sized cells by budding, resembling the division of budding yeast. Reinfection of the normal-sized cells produces a new generation of giant cells. If the CRISPR-Cas system is present, the giant cells acquire virus-derived spacers and terminate the virus spread, whereas in its absence, the cycle continues, suggesting that CRISPR-Cas is the primary defense system in Sulfolobus against STSV2. Collectively, our results show how an archaeal virus manipulates the cell cycle, transforming the cell into a giant virion-producing factory.}, }
@article {pmid33776986, year = {2021}, author = {Teske, A and Amils, R and Ramírez, GA and Reysenbach, AL}, title = {Editorial: Archaea in the Environment: Views on Archaeal Distribution, Activity, and Biogeography.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {667596}, pmid = {33776986}, issn = {1664-302X}, }
@article {pmid33776984, year = {2021}, author = {Czekay, DP and Kothe, U}, title = {H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {654370}, pmid = {33776984}, issn = {1664-302X}, abstract = {During ribosome synthesis, ribosomal RNA is modified through the formation of many pseudouridines and methylations which contribute to ribosome function across all domains of life. In archaea and eukaryotes, pseudouridylation of rRNA is catalyzed by H/ACA small ribonucleoproteins (sRNPs) utilizing different H/ACA guide RNAs to identify target uridines for modification. H/ACA sRNPs are conserved in archaea and eukaryotes, as they share a common general architecture and function, but there are also several notable differences between archaeal and eukaryotic H/ACA sRNPs. Due to the higher protein stability in archaea, we have more information on the structure of archaeal H/ACA sRNPs compared to eukaryotic counterparts. However, based on the long history of yeast genetic and other cellular studies, the biological role of H/ACA sRNPs during ribosome biogenesis is better understood in eukaryotes than archaea. Therefore, this review provides an overview of the current knowledge on H/ACA sRNPs from archaea, in particular their structure and function, and relates it to our understanding of the roles of eukaryotic H/ACA sRNP during eukaryotic ribosome synthesis and beyond. Based on this comparison of our current insights into archaeal and eukaryotic H/ACA sRNPs, we discuss what role archaeal H/ACA sRNPs may play in the formation of ribosomes.}, }
@article {pmid33771626, year = {2021}, author = {Orona-Navar, A and Aguilar-Hernández, I and Nigam, KDP and Cerdán-Pasarán, A and Ornelas-Soto, N}, title = {Alternative sources of natural pigments for dye-sensitized solar cells: Algae, cyanobacteria, bacteria, archaea and fungi.}, journal = {Journal of biotechnology}, volume = {332}, number = {}, pages = {29-53}, doi = {10.1016/j.jbiotec.2021.03.013}, pmid = {33771626}, issn = {1873-4863}, mesh = {*Archaea ; Carotenoids ; *Cyanobacteria ; Fungi ; Plants ; }, abstract = {Dye-sensitized solar cells have been of great interest in photovoltaic technology due to their capacity to convert energy at a low cost. The use of natural pigments means replacing expensive chemical synthesis processes by easily extractable pigments that are non-toxic and environmentally friendly. Although most of the pigments used for this purpose are obtained from higher plants, there are potential alternative sources that have been underexploited and have shown encouraging results, since pigments can also be obtained from organisms like bacteria, cyanobacteria, microalgae, yeast, and molds, which have the potential of being cultivated in bioreactors or optimized by biotechnological processes. The aforementioned organisms are sources of diverse sensitizers like photosynthetic pigments, accessory pigments, and secondary metabolites such as chlorophylls, bacteriochlorophylls, carotenoids, and phycobiliproteins. Moreover, retinal proteins, photosystems, and reaction centers from these organisms can also act as sensitizers. In this review, the use of natural sensitizers extracted from algae, cyanobacteria, bacteria, archaea, and fungi is assessed. The reported photoconversion efficiencies vary from 0.001 % to 4.6 % for sensitizers extracted from algae and microalgae, 0.004 to 1.67 % for bacterial sensitizers, 0.07-0.23 % for cyanobacteria, 0.09 to 0.049 % for archaea and 0.26-2.3 % for pigments from fungi.}, }
@article {pmid33753464, year = {2021}, author = {Galperin, MY and Wolf, YI and Garushyants, SK and Vera Alvarez, R and Koonin, EV}, title = {Non-essential ribosomal proteins in bacteria and archaea identified using COGs.}, journal = {Journal of bacteriology}, volume = {203}, number = {11}, pages = {}, pmid = {33753464}, issn = {1098-5530}, abstract = {Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.IMPORTANCEIn many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 16 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in Escherichia coli and Bacillus subtilis These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.}, }
@article {pmid33726663, year = {2021}, author = {Bize, A and Midoux, C and Mariadassou, M and Schbath, S and Forterre, P and Da Cunha, V}, title = {Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {186}, pmid = {33726663}, issn = {1471-2164}, support = {340440/ERC_/European Research Council/International ; }, mesh = {*Archaea/genetics ; Ecosystem ; Phylogeny ; Plasmids ; *Viruses/genetics ; }, abstract = {BACKGROUND: K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors.<br><br>RESULTS: For cells, the 5-mer profiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-mer profile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikingly retain the specific imprint of their own viral or plasmid taxonomic family in their 5-mer profile.<br><br>CONCLUSION: This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected only recent host transfer events, suggesting the fast evolution of short k-mer profiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.}, }
@article {pmid33720296, year = {2021}, author = {Zhang, C and Meckenstock, RU and Weng, S and Wei, G and Hubert, CRJ and Wang, JH and Dong, X}, title = {Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {5}, pages = {}, doi = {10.1093/femsec/fiab045}, pmid = {33720296}, issn = {1574-6941}, mesh = {Anaerobiosis ; *Archaea/genetics ; Bacteria/genetics ; *Fumarates ; Geologic Sediments ; Hydrocarbons ; Phylogeny ; }, abstract = {Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.}, }
@article {pmid33694023, year = {2021}, author = {Jain, A and Krishnan, KP}, title = {Marine Group-II archaea dominate particle-attached as well as free-living archaeal assemblages in the surface waters of Kongsfjorden, Svalbard, Arctic Ocean.}, journal = {Antonie van Leeuwenhoek}, volume = {114}, number = {5}, pages = {633-647}, pmid = {33694023}, issn = {1572-9699}, mesh = {*Archaea/genetics ; Ecosystem ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater ; Svalbard ; }, abstract = {Marine archaea are a significant component of the global oceanic ecosystems, including the polar oceans. However, only a few attempts have been made to study archaea in the high Arctic fjords. Given the importance of Archaea in carbon and nitrogen cycling, it is imperative to explore their diversity and community composition in the high Arctic fjords, such as Kongsfjorden (Svalbard). In the present study, we evaluated archaeal diversity and community composition in the size-fractionated microbial population, viz-a-viz free-living (FL; 0.2-3 μm) and particle-attached (PA; > 3 μm) using archaeal V3-V4 16S rRNA gene amplicon sequencing. Our results indicate that the overall archaeal community in the surface water of Kongsfjorden was dominated by the members of the marine group-II (MGII) archaea, followed by the MGI group members, including Nitrosopumilaceae and Nitrososphaeraceae. Although a clear niche partitioning between PA and FL archaeal communities was not observed, 2 OTUs among 682 OTUs, and 3 ASVs out of 1932 ASVs were differentially abundant among the fractions. OTU001/ASV0002, classified as MGIIa, was differentially abundant in the PA fraction. OTU006/ASV0006/ASV0010 affiliated with MGIIb were differentially abundant in the FL fraction. Particulate organic nitrogen and C:N ratio were the most significant variables (P < 0.05) explaining the observed variation in the FL and PA archaeal communities, respectively. These results indicate an exchange between archaeal communities or a generalist lifestyle switching between FL and PA fractions. Besides, the particles' elemental composition (carbon and nitrogen) seems to play an essential role in shaping the PA archaeal communities in the surface waters of Kongsfjorden.}, }
@article {pmid33674723, year = {2021}, author = {Mauerhofer, LM and Zwirtmayr, S and Pappenreiter, P and Bernacchi, S and Seifert, AH and Reischl, B and Schmider, T and Taubner, RS and Paulik, C and Rittmann, SKR}, title = {Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {289}, pmid = {33674723}, issn = {2399-3642}, mesh = {Amino Acid Motifs ; High-Throughput Screening Assays ; *Industrial Microbiology ; Kinetics ; Membrane Glycoproteins/metabolism ; Methane/*metabolism ; Methanocaldococcaceae/growth &amp; development/*metabolism ; Methanocaldococcus/growth &amp; development/*metabolism ; Oxidoreductases/metabolism ; Pressure ; Renewable Energy ; }, abstract = {Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyr[α444] Gly[α445] Tyr[α446] in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH4 production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.}, }
@article {pmid33637253, year = {2021}, author = {Zheng, M and He, S and Feng, Y and Wang, M and Liu, YX and Dang, C and Wang, J}, title = {Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems.}, journal = {Journal of environmental sciences (China)}, volume = {102}, number = {}, pages = {273-282}, doi = {10.1016/j.jes.2020.09.039}, pmid = {33637253}, issn = {1001-0742}, mesh = {Ammonia ; *Archaea/genetics ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; *Water Purification ; }, abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two microbial groups mediating nitrification, yet little is presently known about their abundances and community structures at the transcriptional level in wastewater treatment systems (WWTSs). This is a significant issue, as the numerical abundance of AOA or AOB at the gene level may not necessarily represent their functional role in ammonia oxidation. Using amoA genes as molecular markers, this study investigated the transcriptional abundance and community structure of active AOA and AOB in 14 WWTSs. Quantitative PCR results indicated that the transcriptional abundances of AOB amoA (averaged: 1.6 × 10[8] copies g[-1] dry sludge) were higher than those of AOA (averaged: 3.4 × 10[7] copies g[-1] dry sludge) in all WWTSs despite several higher abundances of AOA amoA at the gene level. Moreover, phylogenetic analysis demonstrated that Nitrosomonas europaea and unknown clusters accounted for 37.66% and 49.96% of the total AOB amoA transcripts, respectively, suggesting their dominant role in driving ammonia oxidation. Meanwhile, AOA amoA transcripts were only successfully retrieved from 3 samples, and the Nitrosospaera sister cluster dominated, accounting for 83.46%. Finally, the substrate utilization kinetics of different AOA and AOB species might play a fundamental role in shaping their niche differentiation, community composition, and functional activity. This study provides a basis for evaluating the relative contributions of ammonia-oxidizing microorganisms (AOMs) to nitrogen conversions in WWTSs.}, }
@article {pmid33624267, year = {2021}, author = {Kim, JG and Gazi, KS and Awala, SI and Jung, MY and Rhee, SK}, title = {Ammonia-oxidizing archaea in biological interactions.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {298-310}, pmid = {33624267}, issn = {1976-3794}, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Phylogeny ; }, abstract = {The third domain Archaea was known to thrive in extreme or anoxic environments based on cultivation studies. Recent metagenomics-based approaches revealed a widespread abundance of archaea, including ammonia-oxidizing archaea (AOA) of Thaumarchaeota in non-extreme and oxic environments. AOA alter nitrogen species availability by mediating the first step of chemolithoautotrophic nitrification, ammonia oxidation to nitrite, and are important primary producers in ecosystems, which affects the distribution and activity of other organisms in ecosystems. Thus, information on the interactions of AOA with other cohabiting organisms is a crucial element in understanding nitrogen and carbon cycles in ecosystems as well as the functioning of whole ecosystems. AOA are self-nourishing, and thus interactions of AOA with other organisms can often be indirect and broad. Besides, there are possibilities of specific and obligate interactions. Mechanisms of interaction are often not clearly identified but only inferred due to limited knowledge on the interaction factors analyzed by current technologies. Here, we overviewed different types of AOA interactions with other cohabiting organisms, which contribute to understanding AOA functions in ecosystems.}, }
@article {pmid33620581, year = {2021}, author = {Sorokin, DY and Roman, P and Kolganova, TV}, title = {Halo(natrono)archaea from hypersaline lakes can utilize sulfoxides other than DMSO as electron acceptors for anaerobic respiration.}, journal = {Extremophiles : life under extreme conditions}, volume = {25}, number = {2}, pages = {173-180}, pmid = {33620581}, issn = {1433-4909}, mesh = {Anaerobiosis ; *Dimethyl Sulfoxide ; Electrons ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S ; Respiration ; Russia ; Siberia ; }, abstract = {Dimethylsulfoxide (DMSO) has long been known to support anaerobic respiration in a few species of basically aerobic extremely halophilic euryarchaea living in hypersaline lakes. Recently, it has also been shown to be utilized as an additional electron acceptor in basically anaerobic sulfur-reducing haloarchaea. Here we investigated whether haloarchaea would be capable of anaerobic respiration with other two sulfoxides, methionine sulfoxide (MSO) and tetramethylene sulfoxide (TMSO). For this, anaerobic enrichment cultures were inoculated with sediments from hypersaline salt and soda lakes in southwestern Siberia and southern Russia. Positive enrichments were obtained for both MSO and TMSO with yeast extract but not with formate or acetate as the electron donor. Two pure cultures obtained from salt lakes, either with MSO or TMSO, were obligate anaerobes closely related to sulfur-reducing Halanaeroarchaeum sulfurireducens, although the type strain of this genus was unable to utilize any sulfoxides. Two pure cultures isolated from soda lakes were facultatively anaerobic alkaliphilic haloarchaea using O2, sulfur and sulfoxides as the electron acceptors. One isolate was identical to the previously described sulfur-reducing Natrarchaeobaculum sulfurireducens, while another one, enriched at lower alkalinity, is forming a new species in the genus Halobiforma. Since all isolates enriched with either MSO or TMSO were able to respire all three sulfoxides including DMSO and the corresponding activities were cross-induced, it suggest that a single enzyme of the DMSO-reductase family with a broad substrate specificity is responsible for various sulfoxide-dependent respiration in haloarchaea.}, }
@article {pmid33608296, year = {2021}, author = {Cai, R and Zhang, J and Liu, R and Sun, C}, title = {Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {9}, pages = {}, pmid = {33608296}, issn = {1098-5336}, mesh = {Amino Acids/biosynthesis ; Archaea/*genetics/metabolism ; Genome, Archaeal ; Glucose/metabolism ; Hydrothermal Vents/*microbiology ; Metagenome ; Nucleotides/biosynthesis ; Phylogeny ; }, abstract = {Due to their unique metabolism and important ecological roles, deep-sea hydrothermal archaea have attracted great scientific interest. Among these archaea, DPANN superphylum archaea are widely distributed in hydrothermal vent environments. However, DPANN metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes among 43 reconstructed genomes obtained from deep-sea hydrothermal vent sediments. Phylogenetic analysis suggests 6 phyla, comprised of Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum we have designated Kexuearchaeota These are included in the 20 DPANN archaeal members, indicating their broad diversity in this special environment. Analyses of their metabolism reveal deficiencies due to their reduced genome size, including gluconeogenesis and de novo nucleotide and amino acid biosynthesis. However, DPANN archaea possess alternate strategies to address these deficiencies. DPANN archaea also have the potential to assimilate nitrogen and sulfur compounds, indicating an important ecological role in the hydrothermal vent system.IMPORTANCE DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play. In this study, we obtained 20 high-quality metagenome-assembled genomes (MAGs) corresponding to 6 phyla of the DPANN group (Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum designated Kexuearchaeota). Further metagenomic analyses provided insights on the metabolism and ecological functions of DPANN archaea to adapt to deep-sea hydrothermal environments. Our study contributes to a deeper understanding of their special lifestyles and should provide clues to cultivate this important archaeal group in the future.}, }
@article {pmid33584634, year = {2021}, author = {Distaso, MA and Bargiela, R and Brailsford, FL and Williams, GB and Wright, S and Lunev, EA and Toshchakov, SV and Yakimov, MM and Jones, DL and Golyshin, PN and Golyshina, OV}, title = {Corrigendum: High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {633015}, doi = {10.3389/fmicb.2021.633015}, pmid = {33584634}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2020.576520.].}, }
@article {pmid33582288, year = {2021}, author = {Starke, R and Siles, JA and Fernandes, MLP and Schallert, K and Benndorf, D and Plaza, C and Jehmlich, N and Delgado-Baquerizo, M and Bastida, F}, title = {The structure and function of soil archaea across biomes.}, journal = {Journal of proteomics}, volume = {237}, number = {}, pages = {104147}, doi = {10.1016/j.jprot.2021.104147}, pmid = {33582288}, issn = {1876-7737}, mesh = {*Archaea/genetics ; Ecosystem ; RNA, Ribosomal, 16S ; *Soil ; Soil Microbiology ; }, abstract = {We lack a predictive understanding of the environmental drivers determining the structure and function of archaeal communities as well as the proteome associated with these important soil organisms. Here, we characterized the structure (by 16S rRNA gene sequencing) and function (by metaproteomics) of archaea from 32 soil samples across terrestrial ecosystems with contrasting climate and vegetation types. Our multi-"omics" approach unveiled that genes from Nitrosophaerales and Thermoplasmata dominated soils collected from four continents, and that archaea comprise 2.3 ± 0.3% of microbial proteins in these soils. Aridity positively correlated with the proportion of Nitrosophaerales genes and the number of archaeal proteins. The interaction of climate x vegetation shaped the functional profile of the archaeal community. Our study provides novel insights into the structure and function of soil archaea across climates, and highlights that these communities may be influenced by increasing global aridity.}, }
@article {pmid33561735, year = {2021}, author = {Shalvarjian, KE and Nayak, DD}, title = {Transcriptional regulation of methanogenic metabolism in archaea.}, journal = {Current opinion in microbiology}, volume = {60}, number = {}, pages = {8-15}, doi = {10.1016/j.mib.2021.01.005}, pmid = {33561735}, issn = {1879-0364}, mesh = {*Archaea/genetics ; Gene Expression Regulation, Archaeal ; *Methane ; Methanococcus/genetics ; Methanosarcina/genetics ; }, abstract = {Methanogenesis is a widespread metabolism of evolutionary and environmental importance that is likely to have originated on early Earth. Microorganisms that perform methanogenesis, termed methanogens, belong exclusively to the domain Archaea. Despite maintaining eukaryotic transcription machinery and homologs of bacterial regulators, archaeal transcription and gene regulation appear to be distinct from either domain. While genes involved in methanogenic metabolism have been identified and characterized, their regulation in response to both extracellular and intracellular signals is less understood. Here, we review recent reports on transcriptional regulation of methanogenesis using two model methanogens, Methanococcus maripaludis and Methanosarcina acetivorans, and highlight directions for future research in this nascent field.}, }
@article {pmid33558390, year = {2021}, author = {Kuprat, T and Ortjohann, M and Johnsen, U and Schönheit, P}, title = {Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii.}, journal = {Journal of bacteriology}, volume = {203}, number = {8}, pages = {}, pmid = {33558390}, issn = {1098-5530}, mesh = {Acetate-CoA Ligase/genetics/metabolism ; Acetates/*metabolism ; Acetyl Coenzyme A/metabolism ; Archaeal Proteins/genetics/metabolism ; Glucose/*metabolism ; Haloferax volcanii/*enzymology/genetics/growth &amp; development/metabolism ; Phosphoenolpyruvate Carboxylase/genetics/metabolism ; Phosphoglycerate Mutase/genetics/metabolism ; Phosphopyruvate Hydratase/genetics/metabolism ; Pyruvic Acid/metabolism ; }, abstract = {The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. Following our previous studies on key enzymes of this pathway, we now focus on the characterization of enzymes involved in 3-phosphoglycerate conversion to pyruvate, in anaplerosis, and in acetyl coenzyme A (acetyl-CoA) formation from pyruvate. These enzymes include phosphoglycerate mutase, enolase, pyruvate kinase, phosphoenolpyruvate carboxylase, and pyruvate-ferredoxin oxidoreductase. The essential function of these enzymes were shown by transcript analyses and growth experiments with respective deletion mutants. Furthermore, we show that H. volcanii-during aerobic growth on glucose-excreted significant amounts of acetate, which was consumed in the stationary phase (acetate switch). The enzyme catalyzing the conversion of acetyl-CoA to acetate as part of the acetate overflow mechanism, an ADP-forming acetyl-CoA synthetase (ACD), was characterized. The functional involvement of ACD in acetate formation and of AMP-forming acetyl-CoA synthetases (ACSs) in activation of excreted acetate was proven by using respective deletion mutants. Together, the data provide a comprehensive analysis of enzymes of the spED pathway and of anaplerosis and report the first genetic evidence of the functional involvement of enzymes of the acetate switch in archaea.IMPORTANCE In this work, we provide a comprehensive analysis of glucose degradation via the semiphosphorylative Entner-Doudoroff pathway in the haloarchaeal model organism Haloferax volcanii The study includes transcriptional analyses, growth experiments with deletion mutants. and characterization of all enzymes involved in the conversion of 3-phosphoglycerate to acetyl coenzyme A (acetyl-CoA) and in anaplerosis. Phylogenetic analyses of several enzymes indicate various lateral gene transfer events from bacteria to haloarchaea. Furthermore, we analyzed the key players involved in the acetate switch, i.e., in the formation (overflow) and subsequent consumption of acetate during aerobic growth on glucose. Together, the data provide novel aspects of glucose degradation, anaplerosis, and acetate switch in H. volcanii and thus expand our understanding of the unusual sugar metabolism in archaea.}, }
@article {pmid33556662, year = {2021}, author = {Du, H and Sun, T and Liu, Y and An, S and Xie, H and Wang, D and Igarashi, Y and Imanaka, T and Luo, F and Ma, M}, title = {Bacteria and archaea involved in anaerobic mercury methylation and methane oxidation in anaerobic sulfate-rich reactors.}, journal = {Chemosphere}, volume = {274}, number = {}, pages = {129773}, doi = {10.1016/j.chemosphere.2021.129773}, pmid = {33556662}, issn = {1879-1298}, mesh = {Anaerobiosis ; Animals ; *Archaea/genetics ; Bacteria/genetics ; *Mercury ; Methane ; Methylation ; Oxidation-Reduction ; Phylogeny ; Sulfates ; Swine ; }, abstract = {The identification of dominant microbes in anaerobic mercury (Hg) methylation, methylmercury (MeHg) demethylation, and methane oxidation as sulfate-reducing bacteria, methanogens or, probably, anaerobic methanotrophic archaea (ANMEs) is of great interest. To date, however, the interrelationship of bacteria and archaea involved in these processes remains unclear. Here, we demonstrated the dynamics of microorganisms participating in these processes. Anaerobic fixed-bed reactors were operated with swine manure and sludge to produce methane stably, and then, sulfate (reactor C), sulfate and Hg(II) (reactor H), and sulfate and MeHg (reactor M) were added, and the reactors were operated for 120 d, divided equally into four periods, P1-P4. The bacterial compositions changed nonsignificantly, whereas Methanosaeta in reactors H and M decreased significantly, revealing that it was irrelevant for Hg transformation. The abundances of Syntrophomonadaceae, Methanoculleus, Candidatus Methanogranum and Candidatus Methanoplasma increased continuously with time; these species probably functioned in these processes, but further evidence is needed. Desulfocella and Desulfobacterium dominated first but eventually almost vanished, while the dominant archaeal genera Methanogenium, Methanoculleus and Methanocorpusculum were closely related to ANME-1 and ANME-2. PLS-DA results indicated that both bacteria and archaea in different periods in the three reactors were clustered separately, implying that the microbial compositions in the same periods were similar and changed markedly with time.}, }
@article {pmid33555973, year = {2020}, author = {Makarova, KS and Wolf, YI and Shmakov, SA and Liu, Y and Li, M and Koonin, EV}, title = {Unprecedented Diversity of Unique CRISPR-Cas-Related Systems and Cas1 Homologs in Asgard Archaea.}, journal = {The CRISPR journal}, volume = {3}, number = {3}, pages = {156-163}, pmid = {33555973}, issn = {2573-1602}, mesh = {Archaea/classification/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Endonucleases/genetics ; Genome, Archaeal ; Metagenome ; Phylogeny ; }, abstract = {The principal function of archaeal and bacterial CRISPR-Cas systems is antivirus adaptive immunity. However, recent genome analyses identified a variety of derived CRISPR-Cas variants at least some of which appear to perform different functions. Here, we describe a unique repertoire of CRISPR-Cas-related systems that we discovered by searching archaeal metagenome-assemble genomes of the Asgard superphylum. Several of these variants contain extremely diverged homologs of Cas1, the integrase involved in CRISPR adaptation as well as casposon transposition. Strikingly, the diversity of Cas1 in Asgard archaea alone is greater than that detected so far among the rest of archaea and bacteria. The Asgard CRISPR-Cas derivatives also encode distinct forms of Cas4, Cas5, and Cas7 proteins, and/or additional nucleases. Some of these systems are predicted to perform defense functions, but possibly not programmable ones, whereas others are likely to represent previously unknown mobile genetic elements.}, }
@article {pmid33554274, year = {2021}, author = {Zhu, D and Shen, G and Wang, Z and Han, R and Long, Q and Gao, X and Xing, J and Li, Y and Wang, R}, title = {Distinctive distributions of halophilic Archaea across hypersaline environments within the Qaidam Basin of China.}, journal = {Archives of microbiology}, volume = {203}, number = {5}, pages = {2029-2042}, pmid = {33554274}, issn = {1432-072X}, mesh = {China ; *Ecosystem ; *Environmental Microbiology ; Euryarchaeota/*classification/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/microbiology ; }, abstract = {Halophilic Archaea are widely distributed globally in hypersaline environments. However, little is known of how dominant halophilic archaeal genera are distributed across environments and how they may co-associate across ecosystems. Here, the archaeal community composition and diversity from hypersaline environments (> 300 g/L salinity; total of 33 samples) in the Qaidam Basin of China were investigated using high-throughput Illumina sequencing of 16S rRNA genes. The archaeal communities (total of 3,419 OTUs) were dominated by the class Halobacteria (31.7-99.6% relative abundances) within the phylum Euryarchaeota (90.8-99.9%). Five predominant taxa, including Halorubrum, Halobacterium, Halopenitus, Methanothrix, and Halomicrobium, were observed across most samples. However, several distinct genera were associated with individual samples and were inconsistently distributed across samples, which contrast with previous studies of hypersaline archaeal communities. Additionally, co-occurrence network analysis indicated that five network clusters were present and potentially reflective of interspecies interactions among the environments, including three clusters (clusters II, III, and IV) comprising halophilic archaeal taxa within the Halobacteriaceae and Haloferacaceae families. In addition, two other clusters (clusters I and V) were identified that comprised methanogens. Finally, salinity comprising ionic concentrations (in the order of Na[+] > Ca[2+] > Mg[2+]) and pH were most correlated with taxonomic distributions across sample sites.}, }
@article {pmid33545473, year = {2021}, author = {Wei, H and Lin, X}, title = {Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum.}, journal = {The Science of the total environment}, volume = {771}, number = {}, pages = {144824}, doi = {10.1016/j.scitotenv.2020.144824}, pmid = {33545473}, issn = {1879-1026}, mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Estuaries ; Humans ; Oxidation-Reduction ; Phylogeny ; Rivers ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g[-1] d[-1], mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 10[6] and 2.4 ± 3.54 × 10[6] copies g[-1], respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4[+]) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4[+] consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.}, }
@article {pmid33539079, year = {2021}, author = {Wang, Y and Qin, W and Jiang, X and Ju, F and Mao, Y and Zhang, A and Stahl, DA and Zhang, T}, title = {Seasonal Prevalence of Ammonia-Oxidizing Archaea in a Full-Scale Municipal Wastewater Treatment Plant Treating Saline Wastewater Revealed by a 6-Year Time-Series Analysis.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {4}, pages = {2662-2673}, doi = {10.1021/acs.est.0c07703}, pmid = {33539079}, issn = {1520-5851}, mesh = {Ammonia ; *Archaea/genetics ; Bacteria/genetics ; Extracellular Polymeric Substance Matrix ; Hong Kong ; Oxidation-Reduction ; Phylogeny ; Prevalence ; RNA, Ribosomal, 16S/genetics ; Seasons ; Wastewater ; *Water Purification ; }, abstract = {Although several molecular-based studies have demonstrated the involvement of ammonia-oxidizing archaea (AOA) in ammonia oxidation in wastewater treatment plants (WWTPs), factors affecting the persistence and growth of AOA in these engineered systems have not been resolved. Here, we show a seasonal prevalence of AOA in a full-scale WWTP (Shatin, Hong Kong SAR) over a 6-year period of observation, even outnumbering ammonia-oxidizing bacteria in the seasonal peaks in 3 years, which may be due to the high bioavailable copper concentrations. Comparative analysis of three metagenome-assembled genomes of group I.1a AOA obtained from the activated sludge and 16S rRNA gene sequences recovered from marine sediments suggested that the seawater used for toilet flushing was the primary source of the WWTP AOA. A rare AOA population in the estuarine source water became transiently abundant in the WWTP with a metagenome-based relative abundance of up to 1.3% over three seasons of observation. Correlation-based network analysis revealed a robust co-occurrence relationship between these AOA and organisms potentially active in nitrite oxidation. Moreover, a strong correlation between the dominant AOA and an abundant proteobacterial organism suggested that capacity for extracellular polymeric substance production by the proteobacterium could provide a niche for AOA within bioaggregates. Together, the study highlights the importance of long-term observation in identifying biotic and abiotic factors governing population dynamics in open systems such as full-scale WWTPs.}, }
@article {pmid33538376, year = {2021}, author = {Sorokin, DY and Messina, E and Smedile, F and La Cono, V and Hallsworth, JE and Yakimov, MM}, title = {Carbohydrate-dependent sulfur respiration in halo(alkali)philic archaea.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3789-3808}, doi = {10.1111/1462-2920.15421}, pmid = {33538376}, issn = {1462-2920}, mesh = {*Alkalies ; *Archaea ; Carbohydrates ; Phylogeny ; Respiration ; Sulfur ; }, abstract = {Archaea are environmentally ubiquitous on Earth, and their extremophilic and metabolically versatile phenotypes make them useful as model systems for astrobiology. Here, we reveal a new functional group of halo(natrono)archaea able to utilize alpha-d-glucans (amylopectin, amylose and glycogen), sugars, and glycerol as electron donors and carbon sources for sulfur respiration. They are facultative anaerobes enriched from hypersaline sediments with either amylopectin, glucose or glycerol as electron/carbon sources and elemental sulfur as the terminal electron acceptor. They include 10 strains of neutrophilic haloarchaea from circum pH-neutral lakes and one natronoarchaeon from soda-lake sediments. The neutrophilic isolates can grow by fermentation, although addition of S[0] or dimethyl sulfoxide increased growth rate and biomass yield (with a concomitant decrease in H2). Natronoarchaeal isolate AArc-S grew only by respiration, either anaerobically with S[0] or thiosulfate as the terminal electron acceptor, or aerobically. Through genome analysis of five representative strains, we detected the full set of enzymes required for the observed catabolic and respiratory phenotypes. These findings provide evidence that sulfur-respiring haloarchaea partake in biogeochemical sulfur cycling, linked to terminal anaerobic carbon mineralization in hypersaline anoxic habitats. We discuss the implications for life detection in analogue environments such as the polar subglacial brine-lakes of Mars.}, }
@article {pmid33527146, year = {2021}, author = {Ali, MM and Khanom, A and Nahar, K and Ali, MY and Azad, MAK and Rahman, MM}, title = {Effect of Manure Application on Net Nitrification Rates, Heavy Metal Concentrations and Nitrifying Archaea/Bacteria in Soils.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {106}, number = {4}, pages = {707-713}, pmid = {33527146}, issn = {1432-0800}, mesh = {Ammonia ; *Archaea ; Bacteria/genetics ; Manure ; *Metals, Heavy ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {In this study, we determined the effect of manure application on net nitrification rates (NNRs), heavy metal concentrations (HMCs), and abundance of ammonia-oxidizing archaea (AOA)/bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soil. HMCs were measured by atomic absorption spectroscopy. Abundance of AOA, AOB, and NOB was enumerated by q-PCR. NNRs ranged from 2.8 to 14.7 mg kg[-1] h[-1] and were significantly (p < 0.05) increased in manure soils as compared to control soils. NNRs were affected by pH 7 and temperature 30°C. Cd, Fe and Pb concentrations were classified as excessively polluted, moderate contamination and slight pollution, respectively, in the manure soils. NNRs and concentrations of Fe and Pb were significantly (p < 0.00) positive correlated, but Cu and Cd were significantly (p < 0.00) negative correlated with NNRs. Application of manure significantly (p < 0.05) increased HMCs (Fe, Cu, and Pb), which have indirect and direct effects on NNRs and nitrifying bacteria.}, }
@article {pmid33519774, year = {2020}, author = {DeLong, EF}, title = {Exploring Marine Planktonic Archaea: Then and Now.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {616086}, pmid = {33519774}, issn = {1664-302X}, abstract = {In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.}, }
@article {pmid33501490, year = {2021}, author = {Mueller, RC and Peach, JT and Skorupa, DJ and Copié, V and Bothner, B and Peyton, BM}, title = {An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaa246}, pmid = {33501490}, issn = {1574-6941}, mesh = {*Archaea/genetics ; Bacteria ; Ecology ; Ecosystem ; *Hot Springs ; Phylogeny ; }, abstract = {The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi-omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.}, }
@article {pmid33499367, year = {2021}, author = {Tittes, C and Schwarzer, S and Quax, TEF}, title = {Viral Hijack of Filamentous Surface Structures in Archaea and Bacteria.}, journal = {Viruses}, volume = {13}, number = {2}, pages = {}, pmid = {33499367}, issn = {1999-4915}, mesh = {Archaea/*virology ; Archaeal Viruses/*physiology ; Bacteria/*virology ; Bacteriophages/*physiology ; Cytoskeleton/*virology ; Fimbriae Proteins ; Fimbriae, Bacterial/virology ; Flagella/virology ; }, abstract = {The bacterial and archaeal cell surface is decorated with filamentous surface structures that are used for different functions, such as motility, DNA exchange and biofilm formation. Viruses hijack these structures and use them to ride to the cell surface for successful entry. In this review, we describe currently known mechanisms for viral attachment, translocation, and entry via filamentous surface structures. We describe the different mechanisms used to exploit various surface structures bacterial and archaeal viruses. This overview highlights the importance of filamentous structures at the cell surface for entry of prokaryotic viruses.}, }
@article {pmid33495623, year = {2021}, author = {He, C and Keren, R and Whittaker, ML and Farag, IF and Doudna, JA and Cate, JHD and Banfield, JF}, title = {Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems.}, journal = {Nature microbiology}, volume = {6}, number = {3}, pages = {354-365}, pmid = {33495623}, issn = {2058-5276}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Agriculture ; Archaea/classification/*physiology/ultrastructure ; Bacteria/classification/ultrastructure ; *Bacterial Physiological Phenomena ; Cell Adhesion ; Cell Proliferation ; *Ecosystem ; Groundwater/chemistry/*microbiology ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.}, }
@article {pmid33476388, year = {2021}, author = {Lewis, AM and Recalde, A and Bräsen, C and Counts, JA and Nussbaum, P and Bost, J and Schocke, L and Shen, L and Willard, DJ and Quax, TEF and Peeters, E and Siebers, B and Albers, SV and Kelly, RM}, title = {The biology of thermoacidophilic archaea from the order Sulfolobales.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {4}, pages = {}, pmid = {33476388}, issn = {1574-6976}, support = {GM008776-16/NH/NIH HHS/United States ; T32 GM008776/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; T32 AI007392/AI/NIAID NIH HHS/United States ; }, mesh = {*Archaea/genetics ; Biology ; Iron ; *Sulfolobales ; }, abstract = {Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.}, }
@article {pmid33469805, year = {2021}, author = {Lyu, Z}, title = {Back to the Source: Molecular Identification of Methanogenic Archaea as Markers of Colonic Methane Production.}, journal = {Digestive diseases and sciences}, volume = {66}, number = {11}, pages = {3661-3664}, pmid = {33469805}, issn = {1573-2568}, mesh = {*Archaea/genetics ; *Euryarchaeota ; Humans ; Methane ; }, }
@article {pmid33462984, year = {2021}, author = {Kevorkian, RT and Callahan, S and Winstead, R and Lloyd, KG}, title = {ANME-1 archaea may drive methane accumulation and removal in estuarine sediments.}, journal = {Environmental microbiology reports}, volume = {13}, number = {2}, pages = {185-194}, doi = {10.1111/1758-2229.12926}, pmid = {33462984}, issn = {1758-2229}, mesh = {Anaerobiosis ; *Archaea ; Geologic Sediments/microbiology ; *Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {ANME-1 archaea subsist on the very low energy of anaerobic oxidation of methane (AOM). Most marine sediments shift from net AOM in the sulfate methane transition zone (SMTZ) to methanogenesis in the methane zone (MZ) below it. In White Oak River estuarine sediments, ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but none of the putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Our meta-analysis of public data showed only ANME-1 expressed methanogenic genes during both net AOM and net methanogenesis in an enrichment culture. We conclude that ANME-1 perform AOM in the SMTZ and methanogenesis in the MZ of White Oak River sediments. This metabolic flexibility may expand habitable zones in extraterrestrial environments, since it enables greater energy yields in a fluctuating energetic landscape.}, }
@article {pmid33462601, year = {2021}, author = {Garg, SG and Kapust, N and Lin, W and Knopp, M and Tria, FDK and Nelson-Sathi, S and Gould, SB and Fan, L and Zhu, R and Zhang, C and Martin, WF}, title = {Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea.}, journal = {Genome biology and evolution}, volume = {13}, number = {1}, pages = {}, pmid = {33462601}, issn = {1759-6653}, mesh = {Archaea/*genetics ; Ecosystem ; Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; *Genome, Archaeal ; Genomics ; *Metagenome ; Metagenomics ; *Phylogeny ; Ribosomal Proteins/*classification/*genetics ; }, abstract = {Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.}, }
@article {pmid33453701, year = {2021}, author = {Tao, R and Li, J and Hu, B and Chu, G}, title = {Mitigating N2O emission by synthetic inhibitors mixed with urea and cattle manure application via inhibiting ammonia-oxidizing bacteria, but not archaea, in a calcareous soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {273}, number = {}, pages = {116478}, doi = {10.1016/j.envpol.2021.116478}, pmid = {33453701}, issn = {1873-6424}, abstract = {Synthetic inhibitors and organic amendment have been proposed for mitigating greenhouse gas N2O emissions. However, their combined effect on the N2O emissions and ammonia-oxidizer (ammonia-oxidizing bacteria and archaea, AOB and AOA) communities remains unclear in calcareous soils under climate warming. We conducted two incubation experiments (25 and 35 °C) to examine how N2O emissions and AOA and AOB communities responded to organic amendment (urea plus cattle manure, UCM), and in combination with urease (N-(n-butyl) thiophosphoric triamide, NBPT) and nitrification inhibitor (nitrapyrin). The treatments of UCM + nitrapyrin and UCM + nitrapyrin + NBPT significantly lowered total N2O emissions by average 64.5 and 71.05% at 25 and 35 °C, respectively, compared with UCM treatment. AOB gene abundance and α-diversity (Chao1 and Shannon indices) were significantly increased by the application of urea and manure (P < 0.05). However, relative to UCM treatment, nitrapyrin addition treatments decreased AOB gene abundance and Chao 1 index by average 115.4 and 30.4% at 25 and 35 °C, respectively. PCA analysis showed that UCM or UCM plus nitrapyrin notably shifted AOB structure at both temperatures. However, fertilization had little effects on AOA community (P > 0.05). Potential nitrification rate (PNR) was greatly decreased by nitrapyrin addition, and PNR significantly positively correlated with AOB gene abundance (P = 0.0179 at 25 °C and P = 0.0029 at 35 °C) rather than AOA (P > 0.05). Structural equation model analysis showed that temperature directly increased AOA abundance but decrease AOB abundance, while fertilization indirectly influenced AOB community by altering soil NH4[+], pH and SOC. In conclusion, the combined application of organic amendment, NBPT and nitrapyrin significantly lowered N2O emissions via reducing AOB community in calcareous soil even at high temperature. Our findings provide a solid theoretical basis in mitigating N2O emissions from calcareous soil under climate warming.}, }
@article {pmid33452484, year = {2021}, author = {Zhang, JW and Dong, HP and Hou, LJ and Liu, Y and Ou, YF and Zheng, YL and Han, P and Liang, X and Yin, GY and Wu, DM and Liu, M and Li, M}, title = {Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway.}, journal = {The ISME journal}, volume = {15}, number = {6}, pages = {1826-1843}, pmid = {33452484}, issn = {1751-7370}, mesh = {Acyl Coenzyme A ; *Alkanes ; *Archaea/genetics ; Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Succinic Acid ; }, abstract = {Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood-Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.}, }
@article {pmid33452028, year = {2021}, author = {Aldridge, J and Carr, S and Weber, KA and Buan, NR}, title = {Anaerobic Production of Isoprene by Engineered Methanosarcina Species Archaea.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {6}, pages = {}, pmid = {33452028}, issn = {1098-5336}, mesh = {Anaerobiosis ; Butadienes ; Hemiterpenes/*biosynthesis ; Methanol/metabolism ; Methanosarcina/genetics/*metabolism ; Mevalonic Acid ; Microorganisms, Genetically-Modified/metabolism ; }, abstract = {Isoprene is a valuable petrochemical used for a wide variety of consumer goods, such as adhesives and synthetic rubber. We were able to achieve a high yield of renewable isoprene by taking advantage of the naturally high-flux mevalonate lipid synthesis pathway in anaerobic methane-producing archaea (methanogens). Our study illustrates that by genetically manipulating Methanosarcina species methanogens, it is possible to create organisms that grow by producing the hemiterpene isoprene. Mass balance measurements show that engineered methanogens direct up to 4% of total carbon flux to isoprene, demonstrating that methanogens produce higher isoprene yields than engineered yeast, bacteria, or cyanobacteria, and from inexpensive feedstocks. Expression of isoprene synthase resulted in increased biomass and changes in gene expression that indicate that isoprene synthesis depletes membrane precursors and redirects electron flux, enabling isoprene to be a major metabolic product. Our results demonstrate that methanogens are a promising engineering chassis for renewable isoprene synthesis.IMPORTANCE A significant barrier to implementing renewable chemical technologies is high production costs relative to those for petroleum-derived products. Existing technologies using engineered organisms have difficulty competing with petroleum-derived chemicals due to the cost of feedstocks (such as glucose), product extraction, and purification. The hemiterpene monomer isoprene is one such chemical that cannot currently be produced using cost-competitive renewable biotechnologies. To reduce the cost of renewable isoprene, we have engineered methanogens to synthesize it from inexpensive feedstocks such as methane, methanol, acetate, and carbon dioxide. The "isoprenogen" strains we developed have potential to be used for industrial production of inexpensive renewable isoprene.}, }
@article {pmid33444853, year = {2021}, author = {Yang, Y and Herbold, CW and Jung, MY and Qin, W and Cai, M and Du, H and Lin, JG and Li, X and Li, M and Gu, JD}, title = {Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.}, journal = {Water research}, volume = {191}, number = {}, pages = {116798}, doi = {10.1016/j.watres.2020.116798}, pmid = {33444853}, issn = {1879-2448}, mesh = {Ammonia ; *Archaea/genetics ; Bacteria ; Copper ; Ions ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; *Water Pollutants, Chemical ; }, abstract = {Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.}, }
@article {pmid33434266, year = {2021}, author = {Knüppel, R and Trahan, C and Kern, M and Wagner, A and Grünberger, F and Hausner, W and Quax, TEF and Albers, SV and Oeffinger, M and Ferreira-Cerca, S}, title = {Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea.}, journal = {Nucleic acids research}, volume = {49}, number = {3}, pages = {1662-1687}, pmid = {33434266}, issn = {1362-4962}, support = {PJT 386315//CIHR/Canada ; }, mesh = {Archaea/*enzymology/genetics ; Cell Movement ; Crenarchaeota/enzymology ; Euryarchaeota/enzymology ; Haloferax volcanii/enzymology ; Methyltransferases/*metabolism/physiology ; Protein Biosynthesis ; RNA, Archaeal/chemistry/*metabolism ; RNA, Ribosomal/chemistry/*metabolism ; Ribosome Subunits, Small, Archaeal/enzymology ; }, abstract = {Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.}, }
@article {pmid33432457, year = {2021}, author = {Wang, YF and Gu, JD and Dick, RP and Han, W and Yang, HX and Liao, HQ and Zhou, Y and Meng, H}, title = {Distribution of ammonia-oxidizing archaea and bacteria along an engineered coastal ecosystem in subtropical China.}, journal = {Ecotoxicology (London, England)}, volume = {30}, number = {8}, pages = {1769-1779}, pmid = {33432457}, issn = {1573-3017}, mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Ecosystem ; Humans ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the crucial players in nitrogen cycle. Both AOA and AOB were examined along a gradient of human activity in a coastal ecosystem from intertidal zone, grassland, and Casuarina equisetifolia forest to farmland. Results showed that the farmland soils had noticeably higher nitrate-N, available P than soils in the other three sites. Generally, AOA and AOB community structures varied across sites. The farmland mainly had Nitrosotalea-like AOA, intertidal zone was dominated by Nitrosopumilus AOA, while grassland and C. equisetifolia forest primarily harbored Nitrososphaera-like AOA. The farmland and C. equisetifolia forest owned Nitrosospira-like AOB, intertidal zone possessed Nitrosomonas-like AOB, and no AOB was detected in the grassland. AOA abundance was significantly greater than AOB in this coastal ecosystem (p < 0.05, n = 8). AOB diversity and abundance in the farmland were significantly higher than those in the other three sites (p < 0.05, n = 2). The biodiversity and abundance of AOA were not significantly correlated with any soil property (p < 0.05, n = 8). However, the diversity of AOB was significantly correlated with pH, available P and total P (p < 0.05, n = 6). The abundance of AOB was significantly correlated with pH, nitrite, available N, available P and total P (p < 0.05, n = 6). This study suggested that the community structures of AOA and AOB vary in the different parts in the bio-engineered coastal ecosystem and agricultural activity appears to influence these nitrifiers.}, }
@article {pmid33385817, year = {2021}, author = {Zheng, T and Li, W and Ma, Y and Liu, J}, title = {Time-based succession existed in rural sewer biofilms: Bacterial communities, sulfate-reducing bacteria and methanogenic archaea, and sulfide and methane generation.}, journal = {The Science of the total environment}, volume = {765}, number = {}, pages = {144397}, doi = {10.1016/j.scitotenv.2020.144397}, pmid = {33385817}, issn = {1879-1026}, mesh = {*Archaea ; Bacteria ; Biofilms ; Family Characteristics ; *Methane ; Sewage ; Sulfates ; Sulfides ; }, abstract = {Rural sewers are applied widely to collect rural sewage and biofilm characteristics in rural sewers may be different with municipal sewers. The succession of bacteria communities, sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) need to be studied since rural sewers have a potential risk of sulfide and methane accumulation. In this study, lab-scale rural sewer facilities were established to analyze the characteristics of sewer biofilm and the generation of sulfide and methane. The results indicate that the variation tendency of biofilm thickness in rural sewers was different with municipal sewers. Time-based bacterial succession existed in rural sewer biofilms and the predominant genus was changed from Acinetobacter (approximately 19.10%) to Pseudomonas (approximately 12.61%). SRB (mean 1.49 × 10[6]dsrA copies/cm[2]) were abundant than MA (mean 2.57 × 10[5]mcrA copies/cm[2]) while MA were eliminated gradually in rural sewer biofilms. The tendency of sulfide and methane generation was similar with the number variation of SRB and MA, indicating sulfide accumulation might be more serious trouble than methane accumulation in a long-run rural sewer. Overall, this study deeply analyzed the succession of rural sewer biofilms and found that MA and methane were automatically inhibited in rural sewers.}, }
@article {pmid33383035, year = {2021}, author = {Laursen, SP and Bowerman, S and Luger, K}, title = {Archaea: The Final Frontier of Chromatin.}, journal = {Journal of molecular biology}, volume = {433}, number = {6}, pages = {166791}, pmid = {33383035}, issn = {1089-8638}, support = {/HHMI/Howard Hughes Medical Institute/United States ; F32 GM137496/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Archaea/classification/*genetics/metabolism ; Archaeal Proteins/*chemistry/genetics/metabolism ; Chromatin/chemistry/metabolism/*ultrastructure ; Conserved Sequence ; DNA, Archaeal/*chemistry/genetics/metabolism ; DNA-Binding Proteins/*chemistry/genetics/metabolism ; Histones/*chemistry/genetics/metabolism ; Nucleic Acid Conformation ; Phylogeny ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Multimerization ; }, abstract = {The three domains of life employ various strategies to organize their genomes. Archaea utilize features similar to those found in both eukaryotic and bacterial chromatin to organize their DNA. In this review, we discuss the current state of research regarding the structure-function relationships of several archaeal chromatin proteins (histones, Alba, Cren7, and Sul7d). We address individual structures as well as inferred models for higher-order chromatin formation. Each protein introduces a unique phenotype to chromatin organization, and these structures are put into the context of in vivo and in vitro data. We close by discussing the present gaps in knowledge that are preventing further studies of the organization of archaeal chromatin, on both the organismal and domain level.}, }
@article {pmid33343547, year = {2020}, author = {Kuprat, T and Johnsen, U and Ortjohann, M and Schönheit, P}, title = {Acetate Metabolism in Archaea: Characterization of an Acetate Transporter and of Enzymes Involved in Acetate Activation and Gluconeogenesis in Haloferax volcanii.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {604926}, pmid = {33343547}, issn = {1664-302X}, abstract = {The haloarchaeon Haloferax volcanii grows on acetate as sole carbon and energy source. The genes and proteins involved in uptake and activation of acetate and in gluconeogenesis were identified and analyzed by characterization of enzymes and by growth experiments with the respective deletion mutants. (i) An acetate transporter of the sodium: solute-symporter family (SSF) was characterized by kinetic analyses of acetate uptake into H. volcanii cells. The functional involvement of the transporter was proven with a Δssf mutant. (ii) Four paralogous AMP-forming acetyl-CoA synthetases that belong to different phylogenetic clades were shown to be functionally involved in acetate activation. (iii) The essential involvement of the glyoxylate cycle as an anaplerotic sequence was concluded from growth experiments with an isocitrate lyase knock-out mutant excluding the operation of the methylaspartate cycle reported for Haloarcula species. (iv) Enzymes involved in phosphoenolpyruvate synthesis from acetate, namely two malic enzymes and a phosphoenolpyruvate synthetase, were identified and characterized. Phylogenetic analyses of haloarchaeal malic enzymes indicate a separate evolutionary line distinct from other archaeal homologs. The exclusive function of phosphoenolpyruvate synthetase in gluconeogenesis was proven by the respective knock-out mutant. Together, this is a comprehensive study of acetate metabolism in archaea.}, }
@article {pmid33329506, year = {2020}, author = {Skretas, G and Ventura, S}, title = {Editorial: Protein Aggregation and Solubility in Microorganisms (Archaea, Bacteria and Unicellular Eukaryotes): Implications and Applications.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {620239}, pmid = {33329506}, issn = {1664-302X}, }
@article {pmid33329479, year = {2020}, author = {Schwarz, TS and Berkemer, SJ and Bernhart, SH and Weiß, M and Ferreira-Cerca, S and Stadler, PF and Marchfelder, A}, title = {Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {594838}, pmid = {33329479}, issn = {1664-302X}, abstract = {In all three domains of life, tRNA genes contain introns that must be removed to yield functional tRNA. In archaea and eukarya, the first step of this process is catalyzed by a splicing endonuclease. The consensus structure recognized by the splicing endonuclease is a bulge-helix-bulge (BHB) motif which is also found in rRNA precursors. So far, a systematic analysis to identify all biological substrates of the splicing endonuclease has not been carried out. In this study, we employed CRISPRi to repress expression of the splicing endonuclease in the archaeon Haloferax volcanii to identify all substrates of this enzyme. Expression of the splicing endonuclease was reduced to 1% of its normal level, resulting in a significant extension of lag phase in H. volcanii growth. In the repression strain, 41 genes were down-regulated and 102 were up-regulated. As an additional approach in identifying new substrates of the splicing endonuclease, we isolated and sequenced circular RNAs, which identified excised introns removed from tRNA and rRNA precursors as well as from the 5' UTR of the gene HVO_1309. In vitro processing assays showed that the BHB sites in the 5' UTR of HVO_1309 and in a 16S rRNA-like precursor are processed by the recombinant splicing endonuclease. The splicing endonuclease is therefore an important player in RNA maturation in archaea.}, }
@article {pmid33329440, year = {2020}, author = {Distaso, MA and Bargiela, R and Brailsford, FL and Williams, GB and Wright, S and Lunev, EA and Toshchakov, SV and Yakimov, MM and Jones, DL and Golyshin, PN and Golyshina, OV}, title = {High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {576520}, pmid = {33329440}, issn = {1664-302X}, abstract = {Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.}, }
@article {pmid33325687, year = {2021}, author = {Stein, LY and Klotz, MG and Lancaster, KM and Nicol, GW and Qin, W and Schleper, C and Stahl, D and Ward, BB and Yoon, S}, title = {Comment on"A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea" by Lan Wu, Xueming Chen, Wei Wei, Yiwen Liu, Dongbo Wang, and Bing-Jie Ni.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {1}, pages = {797-798}, doi = {10.1021/acs.est.0c06792}, pmid = {33325687}, issn = {1520-5851}, mesh = {*Ammonia ; *Archaea ; Nitrification ; Nitrous Oxide ; Oxidation-Reduction ; }, }
@article {pmid33325686, year = {2021}, author = {Wu, L and Wei, W and Ni, BJ}, title = {Response to Comment on "A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea".}, journal = {Environmental science &amp; technology}, volume = {55}, number = {1}, pages = {799-800}, doi = {10.1021/acs.est.0c08136}, pmid = {33325686}, issn = {1520-5851}, mesh = {*Ammonia ; *Archaea ; Nitrification ; Nitrous Oxide ; Oxidation-Reduction ; }, }
@article {pmid33320181, year = {2021}, author = {Thomès, L and Lescure, A}, title = {Mosaic Evolution of the Phosphopantothenate Biosynthesis Pathway in Bacteria and Archaea.}, journal = {Genome biology and evolution}, volume = {13}, number = {2}, pages = {}, pmid = {33320181}, issn = {1759-6653}, mesh = {Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Biosynthetic Pathways/genetics ; Coenzyme A/*biosynthesis ; *Evolution, Molecular ; Genes, Bacterial ; Symbiosis ; }, abstract = {Phosphopantothenate is a precursor to synthesis of coenzyme A, a molecule essential to many metabolic pathways. Organisms of the archaeal phyla were shown to utilize a different phosphopantothenate biosynthetic pathway from the eukaryotic and bacterial one. In this study, we report that symbiotic bacteria from the group Candidatus poribacteria present enzymes of the archaeal pathway, namely pantoate kinase and phosphopantothenate synthetase, mirroring what was demonstrated for Picrophilus torridus, an archaea partially utilizing the bacterial pathway. Our results not only support the ancient origin of the coenzyme A pathway in the three domains of life but also highlight its complex and dynamic evolution. Importantly, this study helps to improve protein annotation for this pathway in the C. poribacteria group and other related organisms.}, }
@article {pmid33316511, year = {2021}, author = {Ding, J and Zeng, RJ}, title = {Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea.}, journal = {The Science of the total environment}, volume = {757}, number = {}, pages = {143928}, doi = {10.1016/j.scitotenv.2020.143928}, pmid = {33316511}, issn = {1879-1026}, mesh = {Anaerobiosis ; *Archaea ; Bioreactors ; Denitrification ; *Methane ; Nitrites ; Oxidation-Reduction ; }, abstract = {Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.}, }
@article {pmid33288720, year = {2020}, author = {Stevens, KM and Swadling, JB and Hocher, A and Bang, C and Gribaldo, S and Schmitz, RA and Warnecke, T}, title = {Histone variants in archaea and the evolution of combinatorial chromatin complexity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {52}, pages = {33384-33395}, pmid = {33288720}, issn = {1091-6490}, support = {MC_UP_1102/7/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acids/genetics ; Archaea/*genetics ; Chromatin/*metabolism ; DNA/metabolism ; *Evolution, Molecular ; *Genetic Variation ; Histones/chemistry/*genetics/metabolism ; Molecular Dynamics Simulation ; Mutation/genetics ; Phylogeny ; Protein Binding ; }, abstract = {Nucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Posttranslational modifications are reversibly added or removed and core histones exchanged for paralogous variants, in concert with changing demands on transcription and genome accessibility. Histones are also common in archaea. Their role in genome regulation, however, and the capacity of individual paralogs to assemble into histone-DNA complexes with distinct properties remain poorly understood. Here, we combine structural modeling with phylogenetic analysis to shed light on archaeal histone paralogs, their evolutionary history, and capacity to generate combinatorial chromatin states through hetero-oligomeric assembly. Focusing on the human commensal Methanosphaera stadtmanae as a model archaeal system, we show that the heteromeric complexes that can be assembled from its seven histone paralogs vary substantially in DNA binding affinity and tetramer stability. Using molecular dynamics simulations, we go on to identify unique paralogs in M. stadtmanae and Methanobrevibacter smithii that are characterized by unstable interfaces between dimers. We propose that these paralogs act as capstones that prevent stable tetramer formation and extension into longer oligomers characteristic of model archaeal histones. Importantly, we provide evidence from phylogeny and genome architecture that these capstones, as well as other paralogs in the Methanobacteriales, have been maintained for hundreds of millions of years following ancient duplication events. Taken together, our findings indicate that at least some archaeal histone paralogs have evolved to play distinct and conserved functional roles, reminiscent of eukaryotic histone variants. We conclude that combinatorially complex histone-based chromatin is not restricted to eukaryotes and likely predates their emergence.}, }
@article {pmid33288384, year = {2021}, author = {Pallen, MJ and Telatin, A and Oren, A}, title = {The Next Million Names for Archaea and Bacteria.}, journal = {Trends in microbiology}, volume = {29}, number = {4}, pages = {289-298}, doi = {10.1016/j.tim.2020.10.009}, pmid = {33288384}, issn = {1878-4380}, support = {BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Metagenomics ; *Phylogeny ; }, abstract = {Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come.}, }
@article {pmid33276555, year = {2020}, author = {Urbonavičius, J and Tauraitė, D}, title = {Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea.}, journal = {Biomolecules}, volume = {10}, number = {12}, pages = {}, pmid = {33276555}, issn = {2218-273X}, support = {S-MIP-19-61//Lietuvos Mokslo Taryba/International ; }, mesh = {Archaea/*genetics/*metabolism ; Guanosine/*analogs &amp; derivatives/biosynthesis ; RNA, Transfer/*genetics ; }, abstract = {Tricyclic wyosine derivatives are present at position 37 in tRNA[Phe] of both eukaryotes and archaea. In eukaryotes, five different enzymes are needed to form a final product, wybutosine (yW). In archaea, 4-demethylwyosine (imG-14) is an intermediate for the formation of three different wyosine derivatives, yW-72, imG, and mimG. In this review, current knowledge regarding the archaeal enzymes involved in this process and their reaction mechanisms are summarized. The experiments aimed to elucidate missing steps in biosynthesis pathways leading to the formation of wyosine derivatives are suggested. In addition, the chemical synthesis pathways of archaeal wyosine nucleosides are discussed, and the scheme for the formation of yW-86 and yW-72 is proposed. Recent data demonstrating that wyosine derivatives are present in the other tRNA species than those specific for phenylalanine are discussed.}, }
@article {pmid33274598, year = {2021}, author = {More, KD and Wuchter, C and Irigoien, X and Tierney, JE and Giosan, L and Grice, K and Coolen, MJL}, title = {Subseafloor Archaea reflect 139 kyrs of paleodepositional changes in the northern Red Sea.}, journal = {Geobiology}, volume = {19}, number = {2}, pages = {162-172}, doi = {10.1111/gbi.12421}, pmid = {33274598}, issn = {1472-4669}, mesh = {*Archaea/genetics ; DNA, Archaeal/genetics ; *Euryarchaeota ; Geologic Sediments ; Indian Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The vertical distribution of subseafloor archaeal communities is thought to be primarily controlled by in situ conditions in sediments such as the availability of electron acceptors and donors, although sharp community shifts have also been observed at lithological boundaries suggesting that at least a subset of vertically stratified Archaea form a long-term genetic record of coinciding environmental conditions that occurred at the time of sediment deposition. To substantiate this possibility, we performed a highly resolved 16S rRNA gene survey of vertically stratified archaeal communities paired with paleo-oceanographic proxies in a sedimentary record from the northern Red Sea spanning the last glacial-interglacial cycle (i.e., marine isotope stages 1-6; MIS1-6). Our results show a strong significant correlation between subseafloor archaeal communities and drastic paleodepositional changes associated with glacial low vs. interglacial high stands (ANOSIM; R = .73; p = .001) and only a moderately strong correlation with lithological changes. Bathyarchaeota, Lokiarchaeota, MBGA, and DHVEG-1 were the most abundant identified archaeal groups. Whether they represented ancient cell lines from the time of deposition or migrated to the specific sedimentary horizons after deposition remains speculative. However, we show that the majority of sedimentary archaeal tetraether membrane lipids were of allochthonous origin and not produced in situ. Slow post-burial growth under energy-limited conditions would explain why the downcore distribution of these dominant archaeal groups still indirectly reflect changes in the paleodepositional environment that prevailed during the analyzed marine isotope stages. In addition, archaea seeded from the overlying water column such as Thaumarchaeota and group II and III Euryarchaeota, which were likely not have been able to subsist after burial, were identified from a lower abundance of preserved sedimentary DNA signatures, and represented direct markers of paleoenvironmental changes in the Red Sea spanning the last six marine isotope stages.}, }
@article {pmid33272134, year = {2022}, author = {Kumar, V and Behl, A and Shoaib, R and Abid, M and Shevtsov, M and Singh, S}, title = {Comparative structural insight into prefoldin subunints of archaea and eukaryotes with special emphasis on unexplored prefoldin of Plasmodium falciparum.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {40}, number = {8}, pages = {3804-3818}, doi = {10.1080/07391102.2020.1850527}, pmid = {33272134}, issn = {1538-0254}, mesh = {*Archaea/metabolism ; Chaperonins/metabolism ; Eukaryota/metabolism ; Humans ; *Malaria ; Molecular Chaperones/chemistry ; Plasmodium falciparum/genetics/metabolism ; }, abstract = {Prefoldin (PFD) is a heterohexameric molecular chaperone which bind unfolded proteins and subsequently deliver them to a group II chaperonin for correct folding. Although there is structural and functional information available for humans and archaea PFDs, their existence and functions in malaria parasite remains uncharacterized. In the present review, we have collected the available information on prefoldin family members of archaea and humans and attempted to analyze unexplored PFD subunits of Plasmodium falciparum (Pf). Our review enhances the understanding of probable functions, structure and mechanism of substrate binding of Pf prefoldin by comparing with the available information of its homologs in archaea and H. sapiens. Three PfPFD out of six and a Pf prefoldin-like protein are reported to be essential for parasite survival that signifies their importance in malaria parasite biology. Transcriptome analyses suggest that PfPFD subunits are up-regulated at the mRNA level during asexual and sexual stages of parasite life cycle. Our in silico analysis suggested several pivotal proteins like myosin E, cytoskeletal protein (tubulin), merozoite surface protein and ring exported protein 3 as their interacting partners. Based on structural information of archaeal and H. sapiens PFDs, P. falciparum counterparts have been modelled and key interface residues were identified that are critical for oligomerization of PfPFD subunits. We collated information on PFD-substrate binding and PFD-chaperonin interaction in detail to understand the mechanism of substrate delivery in archaea and humans. Overall, our review enables readers to view the PFD family comprehensively. Communicated by Ramaswamy H. SarmaAbbreviations: HSP: Heat shock proteins; CCT: Chaperonin containing TCP-1; PFD: Prefoldin; PFLP: Prefoldin like protein; PfPFD: Plasmodium falciparum prefoldin; Pf: Plasmodium falciparum; H. sapiens: Homo sapiens; M. thermoautotrophicus: Methanobacterium thermoautotrophicus; P. horikoshii: Pyrococcus horikoshii.}, }
@article {pmid33271237, year = {2021}, author = {Pfeifer, K and Ergal, &#x130; and Koller, M and Basen, M and Schuster, B and Rittmann, SKR}, title = {Archaea Biotechnology.}, journal = {Biotechnology advances}, volume = {47}, number = {}, pages = {107668}, doi = {10.1016/j.biotechadv.2020.107668}, pmid = {33271237}, issn = {1873-1899}, support = {P 29399/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Archaea/genetics ; Bacteria ; *Biotechnology ; Fungi ; *Industrial Microbiology ; Polyhydroxyalkanoates ; }, abstract = {Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic organisms under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in early to advanced development stages, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future of sustainable bioprocessing, and to illustrate their physiological and biotechnological potential.}, }
@article {pmid33264986, year = {2021}, author = {Cai, Y and Zheng, Z and Wang, X}, title = {Obstacles faced by methanogenic archaea originating from substrate-driven toxicants in anaerobic digestion.}, journal = {Journal of hazardous materials}, volume = {403}, number = {}, pages = {123938}, doi = {10.1016/j.jhazmat.2020.123938}, pmid = {33264986}, issn = {1873-3336}, mesh = {Ammonia ; Anaerobiosis ; *Archaea/genetics ; *Bioreactors ; Methane ; }, abstract = {Anaerobic digestion (AD) is used to treat waste and produce bioenergy. However, toxicants, which originate from the substrate, can inhibit or damage the digestion process. Methanogenic archaea (MA), which are the executor in the methanogenesis stage, are more sensitive than bacteria to these toxicants. This review discusses the effects of substrate-driven toxicants, namely, antibiotics, H2S and sulfate, heavy metals (HMs), long-chain fatty acids (LCFAs), and ammonia nitrogen, on the activity of MAs, methanogenic pathways, and the inter-genus succession of MAs. The adverse effects of these five toxicants on MA include effects on pH, damages to cell membranes, the prevention of protein synthesis, changes in hydrogen partial pressure, a reduction in the bioavailability of trace elements, and hindrance of mass transfer. These effects cause a reduction in MA activity and the succession of MAs and methanogenic pathways, which affect AD performance. Under the stress of these toxicants, succession occurs among HA (hydrogenotrophic methanogen), AA (acetoclastic methanogen), and MM (methylotrophic methanogen), especially HA gradually replaces AA as the dominant MA. Simultaneously, the dominant methanogenic pathway also changes from the aceticlastic pathway to other methanogenic pathways. A comprehensive understanding of the impact of toxicants on MA permits more specific targeting when developing strategies to mitigate or eliminate the effects of these toxicants.}, }
@article {pmid33264482, year = {2021}, author = {Wilkens, D and Meusinger, R and Hein, S and Simon, J}, title = {Sequence analysis and specificity of distinct types of menaquinone methyltransferases indicate the widespread potential of methylmenaquinone production in bacteria and archaea.}, journal = {Environmental microbiology}, volume = {23}, number = {3}, pages = {1407-1421}, doi = {10.1111/1462-2920.15344}, pmid = {33264482}, issn = {1462-2920}, mesh = {*Actinobacteria ; *Archaea/enzymology ; Gammaproteobacteria ; *Methyltransferases/genetics ; Phylogeny ; Sequence Analysis ; Vitamin K 2 ; }, abstract = {Menaquinone (MK) serves as an essential membranous redox mediator in various electron transport chains of aerobic and anaerobic respiration. In addition, the composition of the quinone/quinol pool has been widely used as a biomarker in microbial taxonomy. The HemN-like class C radical SAM methyltransferases (RSMTs) MqnK, MenK and MenK2 have recently been shown to facilitate specific menaquinone methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesize 8-methylmenaquinone, 7-methylmenaquinone and 7,8-dimethylmenaquinone. However, the vast majority of protein sequences from the MqnK/MenK/MenK2 family belong to organisms, whose capacity to produce methylated menaquinones has not been investigated biochemically. Here, representative putative menK and menK2 genes from Collinsella tanakaei and Ferrimonas marina were individually expressed in Escherichia coli (wild-type or ubiE deletion mutant) and the corresponding cells were found to produce methylated derivatives of the endogenous MK and 2-demethylmenaquinone. Cluster and phylogenetic analyses of 828 (methyl)menaquinone methyltransferase sequences revealed signature motifs that allowed to discriminate enzymes of the MqnK/MenK/MenK2 family from other radical SAM enzymes and to identify C-7-specific menaquinone methyltransferases of the MenK2 subfamily. This study will help to predict the methylation status of the quinone/quinol pool of a microbial species (or even a microbial community) from its (meta)genome and contribute to the future design of microbial quinone/quinol pools in a Synthetic Biology approach.}, }
@article {pmid33257309, year = {2021}, author = {Lahme, S and Mand, J and Longwell, J and Smith, R and Enning, D}, title = {Severe Corrosion of Carbon Steel in Oil Field Produced Water Can Be Linked to Methanogenic Archaea Containing a Special Type of [NiFe] Hydrogenase.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {3}, pages = {}, pmid = {33257309}, issn = {1098-5336}, mesh = {Archaea/genetics/metabolism ; Archaeal Proteins/*chemistry/genetics/metabolism ; Carbon ; Corrosion ; Hydrogenase/*chemistry/genetics/metabolism ; *Industrial Waste ; Methane/metabolism ; *Oil and Gas Fields ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Steel/*chemistry ; Wastewater/*microbiology ; }, abstract = {Methanogenic archaea have long been implicated in microbially influenced corrosion (MIC) of oil and gas infrastructure, yet a first understanding of the underlying molecular mechanisms has only recently emerged. We surveyed pipeline-associated microbiomes from geographically distinct oil field facilities and found methanogens to account for 0.2 to 9.3% of the 16S rRNA gene sequencing reads. Neither the type nor the abundance of the detected methanogens was correlated with the perceived severity of MIC in these pipelines. Using fluids from one pipeline, MIC was reproduced in the laboratory, both under stagnant conditions and in customized corrosion reactors simulating pipeline flow. High corrosion rates (up to 2.43 mm Fe[0] · yr[-1]) with macroscopic, localized corrosion features were attributed to lithotrophic, mesophilic microbial activity. Other laboratory tests with the same waters yielded negligible corrosion rates (<0.08 mm Fe[0] · yr[-1]). Recently, a novel [NiFe] hydrogenase from Methanococcus maripaludis strain OS7 was demonstrated to accelerate corrosion. We developed a specific quantitative PCR (qPCR) assay and detected the gene encoding the large subunit of this hydrogenase (labeled micH) in corrosive (>0.15 mm Fe[0] · yr[-1]) biofilms. The micH gene, on the other hand, was absent in noncorrosive biofilms, despite an abundance of methanogens. Reconstruction of a nearly complete Methanococcus maripaludis genome from a highly corrosive mixed biofilm revealed micH and associated genes in nearly identical genetic configuration to that in strain OS7, thereby supporting our hypothesis that the encoded molecular mechanism contributed to corrosion. Lastly, the proposed MIC biomarker was detected in multiple oil fields, indicating a geographically widespread involvement of this [NiFe] hydrogenase in MIC.IMPORTANCE Microorganisms can deteriorate built environments, which is particularly problematic in the case of pipelines transporting hydrocarbons to industrial end users. MIC is notoriously difficult to detect and monitor and, as a consequence, is a particularly difficult corrosion mechanism to manage. Despite the advent of molecular tools and improved microbial monitoring strategies for oil and gas operations, specific underlying MIC mechanisms in pipelines remain largely enigmatic. Emerging mechanistic understanding of methanogenic MIC derived from pure culture work allowed us to develop a qPCR assay that distinguishes technically problematic from benign methanogens in a West African oil field. Detection of the same gene in geographically diverse samples from North America hints at the widespread applicability of this assay. The research presented here offers a step toward a mechanistic understanding of biocorrosion in oil fields and introduces a binary marker for (methanogenic) MIC that can find application in corrosion management programs in industrial settings.}, }
@article {pmid33241850, year = {2021}, author = {Kasirajan, L and Maupin-Furlow, JA}, title = {Halophilic archaea and their potential to generate renewable fuels and chemicals.}, journal = {Biotechnology and bioengineering}, volume = {118}, number = {3}, pages = {1066-1090}, pmid = {33241850}, issn = {1097-0290}, support = {R01 GM057498/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biofuels ; Biological Products/*metabolism ; *Halobacteriales/genetics/growth &amp; development ; Hydrogen-Ion Concentration ; Salinity ; Sodium Chloride ; }, abstract = {Lignocellulosic biofuels and chemicals have great potential to reduce our dependence on fossil fuels and mitigate air pollution by cutting down on greenhouse gas emissions. Chemical, thermal, and enzymatic processes are used to release the sugars from the lignocellulosic biomass for conversion to biofuels. These processes often operate at extreme pH conditions, high salt concentrations, and/or high temperature. These harsh treatments add to the cost of the biofuels, as most known biocatalysts do not operate under these conditions. To increase the economic feasibility of biofuel production, microorganisms that thrive in extreme conditions are considered as ideal resources to generate biofuels and value-added products. Halophilic archaea (haloarchaea) are isolated from hypersaline ecosystems with high salt concentrations approaching saturation (1.5-5 M salt concentration) including environments with extremes in pH and/or temperature. The unique traits of haloarchaea and their enzymes that enable them to sustain catalytic activity in these environments make them attractive resources for use in bioconversion processes that must occur across a wide range of industrial conditions. Biocatalysts (enzymes) derived from haloarchaea occupy a unique niche in organic solvent, salt-based, and detergent industries. This review focuses on the use of haloarchaea and their enzymes to develop and improve biofuel production. The review also highlights how haloarchaea produce value-added products, such as antibiotics, carotenoids, and bioplastic precursors, and can do so using feedstocks considered "too salty" for most microbial processes including wastes from the olive-mill, shell fish, and biodiesel industries.}, }
@article {pmid33232349, year = {2020}, author = {Euler, S and Jeffrey, LC and Maher, DT and Mackenzie, D and Tait, DR}, title = {Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0242339}, pmid = {33232349}, issn = {1932-6203}, mesh = {Agriculture ; Ammonium Compounds/metabolism ; Animal Husbandry ; Archaea/*isolation &amp; purification/metabolism ; Carbon/metabolism ; Ecosystem ; *Estuaries ; Fresh Water/analysis/microbiology ; Greenhouse Gases/analysis ; Housing ; Industry ; Methane/*metabolism ; Methanococcales/*isolation &amp; purification/metabolism ; Methylocystaceae/*isolation &amp; purification/metabolism ; *Microbiota ; Nitrates/metabolism ; Oxidation-Reduction ; Queensland ; *Saline Waters/analysis ; Salinity ; Sulfates/metabolism ; Temperature ; Thermodynamics ; *Water Microbiology ; Water Purification ; }, abstract = {In coastal aquatic ecosystems, prokaryotic communities play an important role in regulating the cycling of nutrients and greenhouse gases. In the coastal zone, estuaries are complex and delicately balanced systems containing a multitude of specific ecological niches for resident microbes. Anthropogenic influences (i.e. urban, industrial and agricultural land uses) along the estuarine continuum can invoke physical and biochemical changes that impact these niches. In this study, we investigate the relative abundance of methanogenic archaea and other prokaryotic communities, distributed along a land use gradient in the subtropical Burnett River Estuary, situated within the Great Barrier Reef catchment, Australia. Microbiological assemblages were compared to physicochemical, nutrient and greenhouse gas distributions in both pore and surface water. Pore water samples from within the most urbanised site showed a high relative abundance of methanogenic Euryarchaeota (7.8% of all detected prokaryotes), which coincided with elevated methane concentrations in the water column, ranging from 0.51 to 0.68 μM at the urban and sewage treatment plant (STP) sites, respectively. These sites also featured elevated dissolved organic carbon (DOC) concentrations (0.66 to 1.16 mM), potentially fuelling methanogenesis. At the upstream freshwater site, both methane and DOC concentrations were considerably higher (2.68 μM and 1.8 mM respectively) than at the estuarine sites (0.02 to 0.66 μM and 0.39 to 1.16 mM respectively) and corresponded to the highest relative abundance of methanotrophic bacteria. The proportion of sulfate reducing bacteria in the prokaryotic community was elevated within the urban and STP sites (relative abundances of 8.0%- 10.5%), consistent with electron acceptors with higher redox potentials (e.g. O2, NO3-) being scarce. Overall, this study showed that ecological niches in anthropogenically altered environments appear to give an advantage to specialized prokaryotes invoking a potential change in the thermodynamic landscape of the ecosystem and in turn facilitating the generation of methane-a potent greenhouse gas.}, }
@article {pmid33229086, year = {2021}, author = {Amin, FR and Khalid, H and El-Mashad, HM and Chen, C and Liu, G and Zhang, R}, title = {Functions of bacteria and archaea participating in the bioconversion of organic waste for methane production.}, journal = {The Science of the total environment}, volume = {763}, number = {}, pages = {143007}, doi = {10.1016/j.scitotenv.2020.143007}, pmid = {33229086}, issn = {1879-1026}, mesh = {Anaerobiosis ; *Archaea ; Bacteria ; Biofuels ; *Bioreactors ; Methane ; }, abstract = {Anaerobic digestion (AD) is a widely applied technology for treating organic wastes to generate renewable energy in the form of biogas. The effectiveness of AD process depends on many factors, among which the most important is the presence of active and healthy microbial community in the anaerobic digesters, which needs to be explored. However, the deciphering of microbial populations and their functions during the AD process of different materials is still incomplete, which restricts the understanding of its long-term performance under different operational conditions. This review describes the type, morphology, functions, and specific growth conditions of commonly found hydrolytic, acidogenic, acetogenic bacteria, and archaea during the AD process. The effects of microbes on the performance and stability of the digestion process are also presented. Furthermore, the article offers a deep understanding of the AD management strategies for the enhancement of methane production and the efficiency of the energy conversion process of various organic wastes.}, }
@article {pmid33226731, year = {2021}, author = {Diaz, PI}, title = {Subgingival fungi, Archaea, and viruses under the omics loupe.}, journal = {Periodontology 2000}, volume = {85}, number = {1}, pages = {82-89}, doi = {10.1111/prd.12352}, pmid = {33226731}, issn = {1600-0757}, mesh = {Archaea/genetics ; Bacteria/genetics ; DNA ; Fungi ; *Gingiva/microbiology ; Humans ; *Microbiota ; *Viruses ; }, abstract = {The microbial communities that inhabit the gingival crevice are responsible for the pathological processes that affect the periodontium. The changes in composition and function of subgingival bacteria as disease develops have been extensively studied. Subgingival communities, however, also contain fungi, Archaea, and viruses, which could contribute to the dysbiotic processes associated with periodontal diseases. High-throughput DNA sequencing has facilitated a better understanding of the mycobiome, archaeome, and virome. However, the number of studies available on the nonbacterial components of the subgingival microbiome remains limited in comparison with publications focusing on bacteria. Difficulties in characterizing fungal, archaeal, and viral populations arise from the small portion of the total metagenome mass they occupy and lack of comprehensive reference genome databases. In addition, specialized approaches potentially introducing bias are required to enrich for viral particles, while harsh methods of cell lysis are needed to recover nuclei acids from certain fungi. While the characterization of the subgingival diversity of fungi, Archaea and viruses is incomplete, emerging evidence suggests that they could contribute in different ways to subgingival dysbiosis. Certain fungi, such as Candida albicans are suggested to facilitate colonization of bacterial pathogens. Methanogenic Archaea are associated with periodontitis severity and are thought to partner synergistically with bacterial fermenters, while viruses may affect immune responses or shape microbial communities in ways incompletely understood. This review describes the manner in which omics approaches have improved our understanding of the diversity of fungi, Archaea, and viruses within subgingival communities. Further characterization of these understudied components of the subgingival microbiome is required, together with mechanistic studies to unravel their ecological role and potential contributions to dysbiosis.}, }
@article {pmid33223169, year = {2021}, author = {Cai, M and Richter-Heitmann, T and Yin, X and Huang, WC and Yang, Y and Zhang, C and Duan, C and Pan, J and Liu, Y and Liu, Y and Friedrich, MW and Li, M}, title = {Ecological features and global distribution of Asgard archaea.}, journal = {The Science of the total environment}, volume = {758}, number = {}, pages = {143581}, doi = {10.1016/j.scitotenv.2020.143581}, pmid = {33223169}, issn = {1879-1026}, mesh = {*Archaea/genetics ; *Eukaryota ; Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; }, abstract = {Asgard is a newly proposed archaeal superphylum, which has been suggested to hold the key to decipher the origin of Eukaryotes. However, their ecology remains largely unknown. Here, we conducted a meta-analysis of publicly available Asgard-associated 16S rRNA gene fragments, and found that just three previously proposed clades (Lokiarchaeota, Thorarchaeota, and Asgard clade 4) are widely distributed, whereas the other seven clades (phylum or class level) are restricted to the sediment biosphere. Asgard archaea, especially Loki- and Thorarchaeota, seem to adapt to marine sediments, and water depth (the depth of the sediment below water surface) and salinity might be crucial factors for the proportion of these microorganisms as revealed by multivariate regression analyses. However, the abundance of Asgard archaea exhibited distinct environmental drivers at the clade-level; for instance, the proportion of Asgard clade 4 was higher in less saline environments (salinity <6.35 psu), while higher for Heimdallarchaeota-AAG and Asgard clade 2 in more saline environment (salinity ≥35 psu). Furthermore, co-occurrence analysis allowed us to find a significant non-random association of different Asgard clades with other groups (e.g., Lokiarchaeota with Deltaproteobacteria and Anaerolineae; Odinarchaeota with Bathyarchaeota), suggesting different interaction potentials among these clades. Overall, these findings reveal Asgard archaea as a ubiquitous group worldwide and provide initial insights into their ecological features on a global scale.}, }
@article {pmid33202677, year = {2020}, author = {Diene, SM and Pinault, L and Armstrong, N and Azza, S and Keshri, V and Khelaifia, S and Chabrière, E and Caetano-Anolles, G and Rolain, JM and Pontarotti, P and Raoult, D}, title = {Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea.}, journal = {Life (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {33202677}, issn = {2075-1729}, abstract = {β-lactam antibiotics have a well-known activity which disturbs the bacterial cell wall biosynthesis and may be cleaved by β-lactamases. However, these drugs are not active on archaea microorganisms, which are naturally resistant because of the lack of β-lactam target in their cell wall. Here, we describe that annotation of genes as β-lactamases in Archaea on the basis of homologous genes is a remnant of identification of the original activities of this group of enzymes, which in fact have multiple functions, including nuclease, ribonuclease, β-lactamase, or glyoxalase, which may specialized over time. We expressed class B β-lactamase enzyme from Methanosarcina barkeri that digest penicillin G. Moreover, while weak glyoxalase activity was detected, a significant ribonuclease activity on bacterial and synthetic RNAs was demonstrated. The β-lactamase activity was inhibited by β-lactamase inhibitor (sulbactam), but its RNAse activity was not. This gene appears to have been transferred to the Flavobacteriaceae group especially the Elizabethkingia genus, in which the expressed gene shows a more specialized activity on thienamycin, but no glyoxalase activity. The expressed class C-like β-lactamase gene, from Methanosarcina sp., also shows hydrolysis activity on nitrocefin and is more closely related to DD-peptidase enzymes. Our findings highlight the need to redefine the nomenclature of β-lactamase enzymes and the specification of multipotent enzymes in different ways in Archaea and bacteria over time.}, }
@article {pmid33193193, year = {2020}, author = {Wang, H and Bier, R and Zgleszewski, L and Peipoch, M and Omondi, E and Mukherjee, A and Chen, F and Zhang, C and Kan, J}, title = {Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {576661}, pmid = {33193193}, issn = {1664-302X}, abstract = {In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.}, }
@article {pmid33184503, year = {2021}, author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL}, title = {Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.}, journal = {Nature microbiology}, volume = {6}, number = {1}, pages = {136}, doi = {10.1038/s41564-020-00827-2}, pmid = {33184503}, issn = {2058-5276}, }
@article {pmid33172134, year = {2020}, author = {Zink, IA and Wimmer, E and Schleper, C}, title = {Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales.}, journal = {Biomolecules}, volume = {10}, number = {11}, pages = {}, pmid = {33172134}, issn = {2218-273X}, support = {695192/ERC_/European Research Council/International ; }, mesh = {Clustered Regularly Interspaced Short Palindromic Repeats/*immunology ; RNA/genetics ; Species Specificity ; Sulfolobales/*genetics/*immunology ; }, abstract = {Prokaryotes are constantly coping with attacks by viruses in their natural environments and therefore have evolved an impressive array of defense systems. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system found in the majority of archaea and about half of bacteria which stores pieces of infecting viral DNA as spacers in genomic CRISPR arrays to reuse them for specific virus destruction upon a second wave of infection. In detail, small CRISPR RNAs (crRNAs) are transcribed from CRISPR arrays and incorporated into type-specific CRISPR effector complexes which further degrade foreign nucleic acids complementary to the crRNA. This review gives an overview of CRISPR immunity to newcomers in the field and an update on CRISPR literature in archaea by comparing the functional mechanisms and abundances of the diverse CRISPR types. A bigger fraction is dedicated to the versatile and prevalent CRISPR type III systems, as tremendous progress has been made recently using archaeal models in discerning the controlled molecular mechanisms of their unique tripartite mode of action including RNA interference, DNA interference and the unique cyclic-oligoadenylate signaling that induces promiscuous RNA shredding by CARF-domain ribonucleases. The second half of the review spotlights CRISPR in archaea outlining seminal in vivo and in vitro studies in model organisms of the euryarchaeal and crenarchaeal phyla, including the application of CRISPR-Cas for genome editing and gene silencing. In the last section, a special focus is laid on members of the crenarchaeal hyperthermophilic order Sulfolobales by presenting a thorough comparative analysis about the distribution and abundance of CRISPR-Cas systems, including arrays and spacers as well as CRISPR-accessory proteins in all 53 genomes available to date. Interestingly, we find that CRISPR type III and the DNA-degrading CRISPR type I complexes co-exist in more than two thirds of these genomes. Furthermore, we identified ring nuclease candidates in all but two genomes and found that they generally co-exist with the above-mentioned CARF domain ribonucleases Csx1/Csm6. These observations, together with published literature allowed us to draft a working model of how CRISPR-Cas systems and accessory proteins cross talk to establish native CRISPR anti-virus immunity in a Sulfolobales cell.}, }
@article {pmid33171029, year = {2022}, author = {Dong, L and Gao, Y and Jing, X and Guo, H and Zhang, H and Lai, Q and Diao, Q}, title = {Pretreatments of Broussonetia papyrifera: in vitro assessment on gas and methane production, fermentation characteristic, and methanogenic archaea profile.}, journal = {Animal bioscience}, volume = {35}, number = {9}, pages = {1367-1378}, pmid = {33171029}, issn = {2765-0189}, abstract = {OBJECTIVE: The present study was conducted to examine the gas production, fermentation characteristics, nutrient degradation, and methanogenic community composition of a rumen fluid culture with Broussonetia papyrifera (B. papyrifera) subjected to ensiling or steam explosion (SE) pretreatment.<br><br>METHODS: Fresh B. papyrifera was collected and pretreated by ensiling or SE, which was then fermented with ruminal fluids as ensiled B. papyrifera group, steam-exploded B. papyrifera group, and untreated B. papyrifera group. The gas and methane production, fermentation characteristics, nutrient degradation, and methanogenic community were determined during the fermentation.<br><br>RESULTS: Cumulative methane production was significantly improved with SE pretreatment compared with ensiled or untreated biomass accompanied with more volatile fatty acids production. After 72 h incubation, SE and ensiling pretreatments decreased the acid detergent fiber contents by 39.4% and 22.9%, and neutral detergent fiber contents by 10.6% and 47.2%, respectively. Changes of methanogenic diversity and abundance of methanogenic archaea corresponded to the variations in fermentation pattern and methane production.<br><br>CONCLUSION: Compared with ensiling pretreatment, SE can be a promising technique for the efficient utilization of B. papyrifera, which would contribute to sustainable livestock production systems.}, }
@article {pmid33161088, year = {2021}, author = {Kajale, S and Jani, K and Sharma, A}, title = {Contribution of archaea and bacteria in sustaining climate change by oxidizing ammonia and sulfur in an Arctic Fjord.}, journal = {Genomics}, volume = {113}, number = {1 Pt 2}, pages = {1272-1276}, doi = {10.1016/j.ygeno.2020.11.005}, pmid = {33161088}, issn = {1089-8646}, mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Arctic Regions ; Bacteria/genetics/*metabolism ; *Climate Change ; Microbiota ; Oxidation-Reduction ; Sulfur/*metabolism ; }, abstract = {The present study attempts to investigate the microbial communities and their potential to oxidize ammonia and sulfur at different sites of Arctic Fjord by targeted metagenomics. The high throughput sequencing revealed archaeal Thaumarchaeota (79.3%), Crenarchaeota (10.9%), Euryarchaeota (5.4%), and Woesearchaeota (2.9%) across different depths. In contrast, the bacterial communities depict predominance of Proteobacteria (52.6%), which comprises of dominant genera viz. Sulfurovum (11.2%) and Sulfurimonas (6.3%). Characterizing the metabolic potential of microbial communities with prime focus on the ammonia and sulfur cycling revealed the presence of amoABC and narGHYZ/ nxrAB genes encoding key enzymes. The ammonia cycling coupled with an augmentation of members of Nitrosopumilus belonging to the phylum Thaumarcheaota suggests the vital role of archaeal communities. Similarly, the persistence of chemolithoautotrophic members of Sulfurovum and Sulfurimonas along with the anaerobic genera Desulfocapsa and Desulfobulbus harboring SOX (sulfur-oxidation) system indicates the modulatory role of bacterial communities in sulfur cycling.}, }
@article {pmid33157448, year = {2021}, author = {Yang, S and Li, L and Peng, X and Song, L}, title = {Leachate microbiome profile reveals bacteria, archaea and eukaryote dynamics and methanogenic function during solid waste decomposition.}, journal = {Bioresource technology}, volume = {320}, number = {Pt A}, pages = {124359}, doi = {10.1016/j.biortech.2020.124359}, pmid = {33157448}, issn = {1873-2976}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Bioreactors ; Eukaryota ; Methane ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Solid Waste ; }, abstract = {Bacterial, archaeal, and eukaryotic community composition and dynamics in leachate during solid waste decomposition were investigated using Illumina MiSeq sequencing. The functional enzyme-encoding genes of methanogenic pathways were also predicted via PICRUSt. Succession of bacterial, archaeal, and eukaryotic community composition in aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) was observed. The main representatives of microbial phyla, genera, and species significantly (p < 0.05) differed at least two phases. Protist Ciliophora occurred at ACP and was prevalent in MP, suggesting a short food chain establishment in the methanogenesis. Bacterial, archaeal, fungi and eukaryotic community structure were all pH and biochemical oxygen demand (BOD5) dependent patter. Acetoclastic and hydrogenotrophic methanogenesis pathways with associated functional genes differed during solid waste decomposition and were inhibited in ACP.}, }
@article {pmid33125862, year = {2020}, author = {Nußbaum, P and Ithurbide, S and Walsh, JC and Patro, M and Delpech, F and Rodriguez-Franco, M and Curmi, PMG and Duggin, IG and Quax, TEF and Albers, SV}, title = {An Oscillating MinD Protein Determines the Cellular Positioning of the Motility Machinery in Archaea.}, journal = {Current biology : CB}, volume = {30}, number = {24}, pages = {4956-4972.e4}, doi = {10.1016/j.cub.2020.09.073}, pmid = {33125862}, issn = {1879-0445}, mesh = {Archaeal Proteins/genetics/*metabolism ; Cell Membrane/metabolism ; Chemotaxis/*physiology ; Haloferax volcanii/*physiology ; Intravital Microscopy ; Time-Lapse Imaging ; }, abstract = {MinD proteins are well studied in rod-shaped bacteria such as E. coli, where they display self-organized pole-to-pole oscillations that are important for correct positioning of the Z-ring at mid-cell for cell division. Archaea also encode proteins belonging to the MinD family, but their functions are unknown. MinD homologous proteins were found to be widespread in Euryarchaeota and form a sister group to the bacterial MinD family, distinct from the ParA and other related ATPase families. We aimed to identify the function of four archaeal MinD proteins in the model archaeon Haloferax volcanii. Deletion of the minD genes did not cause cell division or size defects, and the Z-ring was still correctly positioned. Instead, one of the deletions (ΔminD4) reduced swimming motility and hampered the correct formation of motility machinery at the cell poles. In ΔminD4 cells, there is reduced formation of the motility structure and chemosensory arrays, which are essential for signal transduction. In bacteria, several members of the ParA family can position the motility structure and chemosensory arrays via binding to a landmark protein, and consequently these proteins do not oscillate along the cell axis. However, GFP-MinD4 displayed pole-to-pole oscillation and formed polar patches or foci in H. volcanii. The MinD4 membrane-targeting sequence (MTS), homologous to the bacterial MinD MTS, was essential for the oscillation. Surprisingly, mutant MinD4 proteins failed to form polar patches. Thus, MinD4 from H. volcanii combines traits of different bacterial ParA/MinD proteins.}, }
@article {pmid33123879, year = {2021}, author = {Liu, X and Shao, Y and Dong, Y and Dong, M and Xu, Z and Hu, X and Liu, A}, title = {Response of ammonia-oxidizing archaea and bacteria to sulfadiazine and copper and their interaction in black soils.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {9}, pages = {11357-11368}, pmid = {33123879}, issn = {1614-7499}, mesh = {*Ammonia ; Animals ; *Archaea ; Bacteria ; Copper ; Nitrification ; Oxidation-Reduction ; Soil ; Soil Microbiology ; Sulfadiazine ; }, abstract = {The large-scale development of animal husbandry and the wide agricultural application of livestock manure lead to more and more serious co-pollution of heavy metals and antibiotics in soil. In this study, two common feed additives, copper (Cu) and sulfadiazine (SDZ), were selected as target pollutants to evaluate the toxicity and interaction of antibiotics and heavy metals on ammonia oxidizers diversity, potential nitrification rate (PNR), and enzymatic activity in black soils. The results showed that soil enzyme activity was significantly inhibited by single Cu pollution, but the toxicity could be reduced by introducing low-concentration SDZ (5 mg · kg[-1]), which showed an antagonistic effect between Cu and SDZ (5 mg · kg[-1]), while the combined toxicity of high-concentration SDZ (10 mg · kg[-1]) and Cu were strengthened compared with the single Cu contamination on soil enzymes. In contrast, soil PNR was more sensitive to single Cu pollution and its combined pollution with SDZ than the enzyme activity. Real-time fluorescence quota PCR and Illumina Hiseq/Miseq sequencing results showed that ammonia-oxidizing archaea (AOA) was decreased in C2 (200 mg · kg[-1] Cu treatment) and ammonia-oxidizing bacteria (AOB) was obviously stimulated in soil contaminated in C2, while in S5 (5 mg · kg[-1] SDZ treatment), AOB was decreased; both AOA and AOB were significantly decreased at gene level in soils with combined pollutants (C2S5, 200 mg · kg[-1] Cu combined with 5 mg · kg[-1] SDZ). So, it can be concluded that combined pollution can cause more serious toxicity on the enzymatic activity, PNR, and ammonia-oxidizing microorganisms in soil through the synergistic effect between heavy metals and antibiotics pollutants.}, }
@article {pmid33093799, year = {2020}, author = {Jha, P and Singh, J and Vidyarthi, AS and Prasad, R}, title = {Unveiling the Biodiversity of Hyperthermophilic Archaea in Jharia Coal Mines: Potential Threat to Methanogenesis?.}, journal = {Current genomics}, volume = {21}, number = {5}, pages = {363-371}, pmid = {33093799}, issn = {1389-2029}, abstract = {AIM: To examine the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.<br><br>OBJECTIVES: 1) Bioinformatical analysis of the metagenomic data related to a taxonomic analysis obtained from the coal to investigate complete archaeal taxonomic features of the coal bed methane (CBM) microbiome. 2) Bioinformatical analysis of the metagenomic data related to a functional analysis obtained from the coal to investigate functional features relating to taxonomic diversity of the CBM microbiome. 3) The functional attributes have been examined specifically for ORFs related to sulfite reduction and methanogenesis.The taxonomic and functional biodiversity related to euryarchaeota will help in a better understanding of the obstacles associated with methane production imposed by the sulfate reducers.<br><br>BACKGROUND: The microbial methanogenesis in the coal microbiome is a resultant of substrate utilization by primarily fermentative bacteria and methanogens. The present work reveals the biodiversity of archaeal sulfate reducers and methanogens present in the underground coal mines of Jharia using metagenomics and pyrosequencing.<br><br>METHODOLOGY: Bioinformatical analysis for structural and functional attributes was accomplished using MG-RAST. The structural analysis was accomplished using RefSeq database, whereas the functional analysis was done via CoG database with a cut off value, a sequence percent identity, and sequence alignment length cut off of 1e[-5], 60% and 45, respectively.<br><br>RESULTS: Attained communities revealed the dominance of hyperthermophilic archaea Pyrococcus furiosus along with Thermococcus kodakarensis in the coal metagenome.The obtained results also suggest the presence of dissimilatory sulfite reductase and formylmethanofuran dehydrogenase, formylmethanofuran: tetrahydromethanopterin formyltransferase involved in sulfite reduction and methanogenesis, respectively, in the microbiome.<br><br>CONCLUSION: This report is the first attempt to showcase the existence of specific euryarchaeal diversity and their related functional attributes from Jharia coal mines through high throughput sequencing. The study helps in developing a better understanding of the presence of indigenous microbes (archaea) and their functions in the coal microbiome, which can be utilized further to resolve the energy crisis.}, }
@article {pmid33077635, year = {2020}, author = {Chávez, J and Devos, DP and Merino, E}, title = {Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea.}, journal = {Journal of bacteriology}, volume = {203}, number = {2}, pages = {}, pmid = {33077635}, issn = {1098-5530}, mesh = {Archaea/classification/genetics/*physiology ; Bacteria/classification/*genetics ; Genome, Archaeal/physiology ; Genome, Bacterial/physiology ; Phylogeny ; Riboswitch/*physiology ; Sigma Factor/*physiology ; Transcription Factors/*physiology ; }, abstract = {In prokaryotes, the key players in transcription initiation are sigma factors and transcription factors that bind to DNA to modulate the process, while premature transcription termination at the 5' end of the genes is regulated by attenuation and, in particular, by attenuation associated with riboswitches. In this study, we describe the distribution of these regulators across phylogenetic groups of bacteria and archaea and find that their abundance not only depends on the genome size, as previously described, but also varies according to the phylogeny of the organism. Furthermore, we observed a tendency for organisms to compensate for the low frequencies of a particular type of regulatory element (i.e., transcription factors) with a high frequency of other types of regulatory elements (i.e., sigma factors). This study provides a comprehensive description of the more abundant COG, KEGG, and Rfam families of transcriptional regulators present in prokaryotic genomes.IMPORTANCE In this study, we analyzed the relationship between the relative frequencies of the primary regulatory elements in bacteria and archaea, namely, transcription factors, sigma factors, and riboswitches. In bacteria, we reveal a compensatory behavior for transcription factors and sigma factors, meaning that in phylogenetic groups in which the relative number of transcription factors was low, we found a tendency for the number of sigma factors to be high and vice versa. For most of the phylogenetic groups analyzed here, except for Firmicutes and Tenericutes, a clear relationship with other mechanisms was not detected for transcriptional riboswitches, suggesting that their low frequency in most genomes does not constitute a significant impact on the global variety of transcriptional regulatory elements in prokaryotic organisms.}, }
@article {pmid33068423, year = {2020}, author = {L Bräuer, S and Basiliko, N and M P Siljanen, H and H Zinder, S}, title = {Methanogenic archaea in peatlands.}, journal = {FEMS microbiology letters}, volume = {367}, number = {20}, pages = {}, doi = {10.1093/femsle/fnaa172}, pmid = {33068423}, issn = {1574-6968}, mesh = {Archaea/*classification ; Methane/metabolism ; Microbiota/physiology ; *Soil ; *Soil Microbiology ; *Wetlands ; }, abstract = {Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.}, }
@article {pmid33051370, year = {2020}, author = {Abby, SS and Kerou, M and Schleper, C}, title = {Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments.}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {33051370}, issn = {2150-7511}, mesh = {Adaptation, Physiological/*genetics ; Ammonia/*metabolism ; Aquatic Organisms/*genetics ; Archaea/*genetics/metabolism ; Carbon Cycle ; Evolution, Molecular ; *Genome, Archaeal ; Oxidation-Reduction ; *Soil Microbiology ; }, abstract = {Unlike all other archaeal lineages, ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here, we reconstructed the genomic content and growth temperature of the ancestor of all AOA, as well as the ancestors of the marine and soil lineages, based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic, autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (i) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (ii) an expansion of regulatory capacities in transcription and central metabolic functions, and (iii) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.}, }
@article {pmid33045546, year = {2021}, author = {Park, JG and Lee, B and Heo, TY and Cheon, AI and Jun, HB}, title = {Metagenomics approach and canonical correspondence analysis of novel nitrifiers and ammonia-oxidizing archaea in full scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124205}, doi = {10.1016/j.biortech.2020.124205}, pmid = {33045546}, issn = {1873-2976}, mesh = {*Ammonia ; Anaerobiosis ; *Archaea/genetics ; Metagenomics ; Nitrification ; Nitrites ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Various microorganisms are involved in nitrogen removal, and their group compositions depend closely on operating parameters. The structures and functions of nitrification microorganisms in full-scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes were analyzed using metagenomics and canonical correspondence analysis. The community structure of ammonia-oxidizing archaea in the oxidation ditch was 3.8 (winter) - 6.3 (summer) times higher than in A2/O, and the complete ammonia oxidizer was only found in the oxidation ditch process. The canonical correspondence analysis of various environmental variables showed that Nitrosomonadales, Crenarchaeota, and Nitrospira inopinata correlate highly with nitrification, and Nitrospira was involved in NO2[-]-N oxidation rather than Nitrobacter. The longer solid and hydraulic retention times in the oxidation ditch were more effective in achieving a wider range of novel nitrification than A2/O. This result indicates that microbial communities of novel nitrifiers and ammonia-oxidizing archaea improved in the oxidation ditch process, significantly contributing to stable nitrogen removal.}, }
@article {pmid33040791, year = {2020}, author = {Song, W and Sun, C}, title = {Diversity and distribution of bacteria and archaea in Tuosu Lake in Qaidam Basin.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {66}, number = {6}, pages = {86-92}, pmid = {33040791}, issn = {1165-158X}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biodiversity ; Lakes ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; }, abstract = {Microbes in plateau lakes are important participants of material circulation and energy flow in plateau ecosystems. Knowledge of the microbiota, such as bacteria and archaea, community distribution and diversity in plateau lakes is the basis to understand the species succession, adaptation, maintenance and metabolic mechanisms of specific environmental microbial ecosystems. This work aimed to reveal the diversity and# succession of the microbiota in Tuosu Lake to provide a biological basis for the exploration and development of microbial resources in the plateau lakes. The distribution and diversity of microflora in Tuosu Lake, hypoxia, high altitude, alkaline, closed plateau lake with fresh water supply, was investigated. The total DNA was extracted from six samples with different salinity from different geographical locations of Tuosu Lake. The 16S rRNA gene of bacteria and archaea were determined by using high-throughput sequencing-based on an Illumina Miseq sequencing platform. The microbiota in Tuosu Lake has a high diversity and complexity and there are a large number of unclassified microbial species. The bacterial communities in Tuosu Lake are dominated by Proteobacteria (44.3%) and Actbacteria (17.2%). Among them, β-Proteobacteria is the dominant genus in the low-salt sample, while γ-Proteobacteria is more advantageous in the samples with higher salinity. The archaeal communities are dominated by Euryarchaeota (50%) and Woesearchaeota__DHVEG-6 (42.6%). The vast majority of the methanogenic archaea in Tuosu Lake samples belong to Methanomicrobia, and the methanogens in low-salinity samples are significantly more abundant than those in high-salt samples. Diversity and distribution appear to be highly influenced by water salinity and pH.}, }
@article {pmid33025566, year = {2021}, author = {Takamura, E and Taki, S and Sakamoto, H and Satomura, T and Sakuraba, H and Ohshima, T and Suye, SI}, title = {Site-Directed Mutagenesis of Multicopper Oxidase from Hyperthermophilic Archaea for High-Voltage Biofuel Cells.}, journal = {Applied biochemistry and biotechnology}, volume = {193}, number = {2}, pages = {492-501}, pmid = {33025566}, issn = {1559-0291}, mesh = {Amino Acid Substitution ; *Archaeal Proteins/chemistry/genetics ; *Bioelectric Energy Sources ; *Mutagenesis, Site-Directed ; *Mutation, Missense ; *Oxidoreductases/chemistry/genetics ; *Pyrobaculum/enzymology/genetics ; }, abstract = {Enzymes from hyperthermophilic archaea are potential candidates for industrial use because of their superior pH, thermal, and long-term stability, and are expected to improve the long-term stability of biofuel cells (BFCs). However, the reported multicopper oxidase (MCO) from hyperthermophilic archaea has lower redox potential than MCOs from other organisms, which leads to a decrease in the cell voltage of BFCs. In this study, we attempted to positively shift the redox potential of the MCO from hyperthermophilic archaeon Pyrobaculum aerophilum (McoP). Mutations (M470L and M470F) were introduced into the axial ligand of the T1 copper atom of McoP, and the enzymatic chemistry and redox potentials were compared with that of the parent (M470). The redox potentials of M470L and M470F shifted positively by about 0.07 V compared with that of M470. In addition, the catalytic activity of the mutants towards 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) increased 1.2-1.3-fold. The thermal stability of the mutants and the electrocatalytic performance for O2 reduction of M470F was slightly reduced compared with that of M470. This research provides useful enzymes for application as biocathode catalysts for high-voltage BFCs.}, }
@article {pmid33022088, year = {2021}, author = {Thiroux, S and Dupont, S and Nesbø, CL and Bienvenu, N and Krupovic, M and L'Haridon, S and Marie, D and Forterre, P and Godfroy, A and Geslin, C}, title = {The first head-tailed virus, MFTV1, infecting hyperthermophilic methanogenic deep-sea archaea.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3614-3626}, doi = {10.1111/1462-2920.15271}, pmid = {33022088}, issn = {1462-2920}, mesh = {Archaea/genetics ; *Archaeal Viruses/genetics ; Ecosystem ; Methanocaldococcus ; *Viruses ; }, abstract = {Deep-sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep-sea autotrophic archaea. Here, we provide the first evidence of an infection of hyperthermophilic methanogenic archaea by a head-tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm-long non-contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head-tailed virus described thus far. The viral genome is a double-stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here open a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea.}, }
@article {pmid33021028, year = {2021}, author = {Wei, D and Zeng, S and Hou, D and Zhou, R and Xing, C and Deng, X and Yu, L and Wang, H and Deng, Z and Weng, S and Huang, Z and He, J}, title = {Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages.}, journal = {Journal of applied microbiology}, volume = {130}, number = {5}, pages = {1442-1455}, doi = {10.1111/jam.14846}, pmid = {33021028}, issn = {1365-2672}, mesh = {Ammonia/*metabolism ; Animals ; *Aquaculture ; Archaea/classification/genetics/growth &amp; development/*metabolism ; Bacteria/classification/genetics/growth &amp; development/*metabolism ; Ecosystem ; Geologic Sediments/chemistry/*microbiology ; Microbiota/*physiology ; Nitrogen Cycle ; Nitrosomonadaceae/classification/growth &amp; development/metabolism ; Oxidation-Reduction ; Penaeidae/*growth &amp; development ; Phylogeny ; Ponds/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {AIMS: Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages.<br><br>METHODS AND RESULTS: We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and &#x3b2;-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase.<br><br>CONCLUSIONS: AOA and AOB play the different ecological roles in SCP sediments at different culture stages.<br><br>Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.}, }
@article {pmid33013726, year = {2020}, author = {Mani, K and Taib, N and Hugoni, M and Bronner, G and Bragança, JM and Debroas, D}, title = {Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1891}, pmid = {33013726}, issn = {1664-302X}, abstract = {The microbial fluctuations along an increasing salinity gradient during two different salt production phases - initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes on Illumina MiSeq platform. Elemental analysis of the brine samples showed high concentration of sodium (Na[+]) and chloride (Cl[-]) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea transited from sediment to brine while Bacteria transited from brine to sediment with increasing salinity. Frequency of Archaea was found to be significantly enriched even in low and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum, Haloarcula, Halorhabdus, and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence frequency of Halorubrum, and Halorhabdus decreased while Haloarcula, Haloplanus, and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes, Proteobacteria, and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira, Desulfovermiculus, and Marinobacter were selectively present in sediments. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame.}, }
@article {pmid33005311, year = {2020}, author = {Jung, J and Kim, JS and Taffner, J and Berg, G and Ryu, CM}, title = {Archaea, tiny helpers of land plants.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {2494-2500}, pmid = {33005311}, issn = {2001-0370}, abstract = {Archaea are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome. Only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. This review discusses recent progress in identifying how archaea contribute to plant traits such as growth, adaptation to abiotic stresses, and immune activation. We synthesized the most recent functional and molecular data on archaea, including root colonization and the volatile emission to activate plant systemic immunity. These data represent a paradigm shift in our understanding of plant-microbiota interactions.}, }
@article {pmid33002447, year = {2021}, author = {Berger, S and Cabrera-Orefice, A and Jetten, MSM and Brandt, U and Welte, CU}, title = {Investigation of central energy metabolism-related protein complexes of ANME-2d methanotrophic archaea by complexome profiling.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1862}, number = {1}, pages = {148308}, doi = {10.1016/j.bbabio.2020.148308}, pmid = {33002447}, issn = {1879-2650}, support = {339880/ERC_/European Research Council/International ; }, mesh = {Archaea/*enzymology ; Archaeal Proteins/chemistry/*metabolism ; Electron Transport ; *Energy Metabolism ; }, abstract = {The anaerobic oxidation of methane is important for mitigating emissions of this potent greenhouse gas to the atmosphere and is mediated by anaerobic methanotrophic archaea. In a 'Candidatus Methanoperedens BLZ2' enrichment culture used in this study, methane is oxidized to CO2 with nitrate being the terminal electron acceptor of an anaerobic respiratory chain. Energy conservation mechanisms of anaerobic methanotrophs have mostly been studied at metagenomic level and hardly any protein data is available at this point. To close this gap, we used complexome profiling to investigate the presence and subunit composition of protein complexes involved in energy conservation processes. All enzyme complexes and their subunit composition involved in reverse methanogenesis were identified. The membrane-bound enzymes of the respiratory chain, such as F420H2:quinone oxidoreductase, membrane-bound heterodisulfide reductase, nitrate reductases and Rieske cytochrome bc1 complex were all detected. Additional or putative subunits such as an octaheme subunit as part of the Rieske cytochrome bc1 complex were discovered that will be interesting targets for future studies. Furthermore, several soluble proteins were identified, which are potentially involved in oxidation of reduced ferredoxin produced during reverse methanogenesis leading to formation of small organic molecules. Taken together these findings provide an updated, refined picture of the energy metabolism of the environmentally important group of anaerobic methanotrophic archaea.}, }
@article {pmid32994183, year = {2020}, author = {Wolff, P and Villette, C and Zumsteg, J and Heintz, D and Antoine, L and Chane-Woon-Ming, B and Droogmans, L and Grosjean, H and Westhof, E}, title = {Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea.}, journal = {RNA (New York, N.Y.)}, volume = {26}, number = {12}, pages = {1957-1975}, pmid = {32994183}, issn = {1469-9001}, mesh = {Base Sequence ; Methanococcus/*genetics ; Nucleic Acid Conformation ; Nucleotides/*chemistry ; Pyrococcus furiosus/*genetics ; RNA, Archaeal/chemistry/genetics ; RNA, Transfer/*chemistry/*genetics ; Sulfolobus acidocaldarius/*genetics ; }, abstract = {To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius Notable observations are the frequent occurrence of ac[4]C nucleotides in thermophilic archaeal tRNAs, the presence of m[7]G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.}, }
@article {pmid32991817, year = {2021}, author = {Chen, T and Hu, W and He, S and Zhang, X and Niu, Y}, title = {Diversity and community structure of ammonia-oxidizing archaea in rhizosphere soil of four plant groups in Ebinur Lake wetland.}, journal = {Canadian journal of microbiology}, volume = {67}, number = {4}, pages = {271-280}, doi = {10.1139/cjm-2020-0228}, pmid = {32991817}, issn = {1480-3275}, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Lakes ; *Microbiota ; Plants/classification ; *Rhizosphere ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Wetlands ; }, abstract = {The aim of this study was to reveal the differences in the community structure of ammonia-oxidizing archaea (AOA) between rhizosphere and non-rhizosphere soil, to provide a theoretical basis for further study on the relationship between halophyte rhizosphere soil microorganisms and salt tolerance. The results of diversity and community structure showed that the diversity of the AOA community in rhizosphere soil of Reeds was higher than that in non-rhizosphere soil in spring and lower than that in non-rhizosphere soil in summer and autumn. In summer, the diversity of rhizosphere soil of Karelinia caspica was higher than that of non-rhizosphere soil and lower than that of non-rhizosphere soil in spring and autumn. The diversity of rhizosphere soil of Halocnemum strobilaceum in 3 seasons was lower than that in non-rhizosphere soil. The diversity of rhizosphere soil of Salicornia was higher than that in non-rhizosphere soil in 3 seasons. In addition, the relative abundance of AOA in rhizosphere soil of 4 plants was higher than that in non-rhizosphere soil. The AOA community in all soil samples was mainly concentrated in Crenarchaeota and Thaumarchaeota. Redundancy analysis results showed salinity, soil water moisture, pH, and soil organic matter were important factors affecting the differentiation of AOA communities.}, }
@article {pmid32983044, year = {2020}, author = {Zou, D and Liu, H and Li, M}, title = {Community, Distribution, and Ecological Roles of Estuarine Archaea.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {2060}, pmid = {32983044}, issn = {1664-302X}, abstract = {Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.}, }
@article {pmid32967357, year = {2020}, author = {Brázda, V and Luo, Y and Bartas, M and Kaura, P and Porubiaková, O and Šťastný, J and Pečinka, P and Verga, D and Da Cunha, V and Takahashi, TS and Forterre, P and Myllykallio, H and Fojta, M and Mergny, JL}, title = {G-Quadruplexes in the Archaea Domain.}, journal = {Biomolecules}, volume = {10}, number = {9}, pages = {}, pmid = {32967357}, issn = {2218-273X}, support = {CZ.02.1.01/0.0/0.0/15_003/0000477//ERDF/International ; 18-15548S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; }, mesh = {Archaea/classification/*genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Circular Dichroism ; DNA/*chemistry/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; *G-Quadruplexes ; Genome, Archaeal/*genetics ; Genomics/methods ; Nucleic Acid Conformation ; Phylogeny ; RNA/*chemistry/genetics/metabolism ; Species Specificity ; }, abstract = {The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.}, }
@article {pmid32955155, year = {2020}, author = {Stahl, DA}, title = {The path leading to the discovery of the ammoniaoxidizing archaea.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4507-4519}, doi = {10.1111/1462-2920.15239}, pmid = {32955155}, issn = {1462-2920}, support = {/EPA/EPA/United States ; /NASA/NASA/United States ; /DE/NIDCR NIH HHS/United States ; /EPA/EPA/United States ; /NASA/NASA/United States ; /DE/NIDCR NIH HHS/United States ; }, }
@article {pmid32936753, year = {2020}, author = {Yin, XM and Yang, XY and Hou, J and Zhu, L and Cui, HL}, title = {Natronomonas halophila sp. nov. and Natronomonas salina sp. nov., two novel halophilic archaea.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {11}, pages = {5686-5692}, doi = {10.1099/ijsem.0.004463}, pmid = {32936753}, issn = {1466-5034}, mesh = {China ; DNA, Archaeal/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; Halobacteriaceae/*classification/isolation &amp; purification ; Lakes/*microbiology ; *Mining ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saline Waters ; Sequence Analysis, DNA ; }, abstract = {Two halophilic archaeal strains, C90[T] and YPL13[T], were isolated from a salt lake and a salt mine in PR China. The two strains were found to form two clusters (97.5 and 89.5 % similarity between them, respectively) separating them from the three current members of the genus Natronomonas (95.4-97.0 % and 86.6-89.3 % similarity, respectively) on the basis of the 16S rRNA and rpoB' gene sequence similarities and phylogenetic analysis. Diverse phenotypic characteristics differentiate strains C90[T] and YPL13[T] from current Natronomonas members. The polar lipids of strain C90[T] were phosphatidic acid, phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulphate, two unidentified glycolipids, a major glycolipid and a minor glycolipid, while those of strain YPL13[T] were PG, PGP-Me, two unidentified phospholipids and a glycolipid. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between the two strains were 79.8 and 27.1 %, respectively, which were much lower than the threshold values proposed as a species boundaries (ANI 95-96 % and isDDH 70 %), which revealed that the two strains represent two novel species; these values (ANI 76.6-80.0 % and isDDH 21.6-27.0 %) of the strains examined in this study and the current members of Natronomonas are much lower than the recommended threshold values, suggesting that strains C90[T] and YPL13[T] represent two genomically different species of Natronomonas. These results showed that strains C90[T] (=CGMCC 1.13738[T]=JCM 32961[T]) and YPL13[T] (=CGMCC 1.13884[T]=JCM 31111[T]) represent two novel species of Natronomonas, for which the names Natronomonas halophila sp. nov. and Natronomonas salina sp. nov. are proposed.}, }
@article {pmid32935184, year = {2021}, author = {He, Y and Zhou, Y and Weng, R and Wang, J and Chen, J and Huang, M}, title = {Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {314-322}, pmid = {32935184}, issn = {1432-184X}, mesh = {Ammonia/analysis/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Calcium Compounds/analysis ; Environmental Restoration and Remediation/*methods ; Geologic Sediments/chemistry/*microbiology ; Nitrates/analysis ; Oxidation-Reduction ; Oxygen/analysis ; Rivers/chemistry/*microbiology ; Species Specificity ; Water Pollutants, Chemical/metabolism ; }, abstract = {In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO3)2 injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO3)2 injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO3)2 injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO3)2 runs. Taken together, Ca(NO3)2 was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.}, }
@article {pmid32925997, year = {2020}, author = {Aleksandrowicz, P and Brzezińska-Błaszczyk, E and Dudko, A and Agier, J}, title = {Archaea Occurrence in the Subgingival Biofilm in Patients with Peri-implantitis and Periodontitis.}, journal = {The International journal of periodontics &amp; restorative dentistry}, volume = {40}, number = {5}, pages = {677-683}, doi = {10.11607/prd.4670}, pmid = {32925997}, issn = {1945-3388}, mesh = {Archaea ; Biofilms ; *Dental Implants ; Humans ; *Peri-Implantitis ; *Periodontitis ; RNA, Ribosomal, 16S ; }, abstract = {This study aimed to determine the prevalence and diversity of archaea and select bacteria in the subgingival biofilm of patients with peri-implantitis in comparison to patients with unaffected implants and patients with periodontitis. Samples of subgingival biofilm from oral sites were collected for DNA extraction (n = 139). A 16S rRNA gene-based polymerase chain reaction assay was used to determine the presence of archaea and select bacteria. Seven samples were selected for direct sequencing. Archaea were detected in 10% of samples from peri-implantitis sites, but not in samples from the unaffected dental implant. Archaea were present in 53% and 64% of samples from mild and moderate/advanced periodontitis sites, respectively. The main representative of the Archaea domain found in biofilm from periodontitis and peri-implantitis sites was Methanobrevibacter oralis. The present results revealed that archaea are present in diseased but not healthy implants. It was also found that archaea were more abundant in periodontitis than in peri-implantitis sites. Hence, the potential role of archaea in peri-implantitis and periodontitis should be taken into consideration.}, }
@article {pmid32919036, year = {2020}, author = {Di Giulio, M}, title = {LUCA as well as the ancestors of archaea, bacteria and eukaryotes were progenotes: Inference from the distribution and diversity of the reading mechanism of the AUA and AUG codons in the domains of life.}, journal = {Bio Systems}, volume = {198}, number = {}, pages = {104239}, doi = {10.1016/j.biosystems.2020.104239}, pmid = {32919036}, issn = {1872-8324}, mesh = {Anticodon/genetics ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Codon/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; *Genetic Code ; Genetic Variation ; Open Reading Frames/genetics ; Origin of Life ; Phylogeny ; RNA, Transfer/genetics ; }, abstract = {Here I use the rationale assuming that if of a certain trait that exerts its function in some aspect of the genetic code or, more generally, in protein synthesis, it is possible to identify the evolutionary stage of its origin then it would imply that this evolutionary moment would be characterized by a high translational noise because this trait would originate for the first time during that evolutionary stage. That is to say, if this trait had a non-marginal role in the realization of the genetic code, or in protein synthesis, then the origin of this trait would imply that, more generally, it was the genetic code itself that was still originating. But if the genetic code were still originating - at that precise evolutionary stage - then this would imply that there was a high translational noise which in turn would imply that it was in the presence of a protocell, i.e. a progenote that was by definition characterized by high translational noise. I apply this rationale to the mechanism of modification of the base 34 of the anticodon of an isoleucine tRNA that leads to the reading of AUA and AUG codons in archaea, bacteria and eukaryotes. The phylogenetic distribution of this mechanism in these phyletic lineages indicates that this mechanism originated only after the evolutionary stage of the last universal common ancestor (LUCA), namely, during the formation of cellular domains, i.e., at the stage of ancestors of these main phyletic lineages. Furthermore, given that this mechanism of modification of the base 34 of the anticodon of the isoleucine tRNA would result to emerge at a stage of the origin of the genetic code - despite in its terminal phases - then all this would imply that the ancestors of bacteria, archaea and eukaryotes were progenotes. If so, all the more so, the LUCA would also be a progenote since it preceded these ancestors temporally. A consequence of all this reasoning might be that since these three ancestors were of the progenotes that were different from each other, if at least one of them had evolved into at least two real and different cells - basically different from each other - then the number of cellular domains would not be three but it would be greater than three.}, }
@article {pmid32892054, year = {2021}, author = {Qi, L and Ma, Z and Chang, SX and Zhou, P and Huang, R and Wang, Y and Wang, Z and Gao, M}, title = {Biochar decreases methanogenic archaea abundance and methane emissions in a flooded paddy soil.}, journal = {The Science of the total environment}, volume = {752}, number = {}, pages = {141958}, doi = {10.1016/j.scitotenv.2020.141958}, pmid = {32892054}, issn = {1879-1026}, mesh = {Archaea/genetics ; Charcoal ; Methane ; *Oryza ; *Soil ; Soil Microbiology ; }, abstract = {Biochar addition can reduce methane (CH4) emissions from paddy soils while the mechanisms involved are not entirely clear. Here, we studied the effect of biochar addition on CH4 emissions, and the abundance and community composition of methanogens and methanotrophs over two rice cultivation seasons. The experiment had the following five treatments: control (CK), chemical fertilizer application only (BC0), and 0.5% (w/w) (BC1), 1% (BC2), and 2% of biochar applied with chemical fertilizers (BC3). The season-wide CH4 emissions were decreased (P < 0.05) by 22.2-95.7% in biochar application compared with BC0 in the two rice seasons (2017 and 2018). In 2017, biochar application decreased methanogenic archaea (mcrA) but increased methanotrophic bacteria (pmoA) abundances, and decreased the ratio of mcrA/pmoA, as compared with BC0 (P < 0.05). In 2018, the abundance of mcrA was lower in BC2 and BC3 than in BC0 (P < 0.05) but was not different between BC0 and BC1, and the abundance of pmoA was lower in BC1, BC2 and BC3 than in BC0 (P < 0.05). The CH4 emissions were positively related to abundances of the mcrA gene (P < 0.01) but not to that of the pmoA gene in two rice seasons. Rice grain yield was increased by 62.2-94.1% in biochar addition treatments compared with BC0 in the first year (P < 0.01) and by 29.9-37.6% in BC2 and BC3 compared with BC0 in the second year (P < 0.05). Biochar application decreased CH4 emissions by reducing methanogenic archaea abundance in the studied flooded paddy soil.}, }
@article {pmid32892037, year = {2021}, author = {Niu, M and Zhou, F and Yang, Y and Sun, Y and Zhu, T and Shen, F}, title = {Abundance and composition of airborne archaea during springtime mixed dust and haze periods in Beijing, China.}, journal = {The Science of the total environment}, volume = {752}, number = {}, pages = {141641}, doi = {10.1016/j.scitotenv.2020.141641}, pmid = {32892037}, issn = {1879-1026}, mesh = {*Air Pollution ; Archaea/genetics ; Beijing ; China ; *Dust/analysis ; Humans ; Phylogeny ; }, abstract = {Archaea have an important role in the elemental biogeochemical cycle and human health. However, characteristics of airborne archaea affected by anthropogenic and natural processes are unclear. In this study, we investigated the abundance, structures, influencing factors and assembly processes of the archaeal communities in the air samples collected from Beijing in springtime using quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology and statistical analysis. The concentrations of airborne archaea ranged from 10[1] to 10[3] copies m[-3] (455 ± 211 copies m[-3]), accounting for 0.67% of the total prokaryote (sum of archaea and bacteria). An increase in airborne archaea was seen when the air quality shifted from clean to slightly polluted conditions. Sandstorm dust imported a large number of archaea to the local atmosphere. Euryarchaeota, Thaumarchaeota and Crenarchaeota were the dominant phyla, revealing the primary role of soil in releasing archaea to the ambient environment. Dispersal-related neutral processes play an important role in shaping the structure of airborne archaeal assembly. Of all phyla, methanogenic Euryarchaeota were most abundant in the air parcels come from the south of Beijing. Air masses from the west of Beijing, which brought sandstorm to Beijing, carried large amounts of ammonia oxidizing archaea Nitrososphaera. The results demonstrate the importance of air mass sources and local weather conditions in shaping the local airborne archaea community.}, }
@article {pmid32889138, year = {2020}, author = {Nikolayev, S and Cohen-Rosenzweig, C and Eichler, J}, title = {Evolutionary considerations of the oligosaccharyltransferase AglB and other aspects of N-glycosylation across Archaea.}, journal = {Molecular phylogenetics and evolution}, volume = {153}, number = {}, pages = {106951}, doi = {10.1016/j.ympev.2020.106951}, pmid = {32889138}, issn = {1095-9513}, mesh = {Archaea/*classification/*enzymology/genetics ; Archaeal Proteins/*genetics ; Glycosylation ; Hexosyltransferases/*genetics ; Membrane Proteins/*genetics ; *Phylogeny ; }, abstract = {Various biological markers in members of the TACK and Asgard archaeal super-phyla show Eukarya-like traits. These include the oligosaccharyltransferase, responsible for transferring glycans from the lipid carrier upon which they are assembled onto selected asparagine residues of target proteins during N-glycosylation. In Archaea, oligosaccharyltransferase activity is catalyzed by AglB. To gain deeper insight into AglB and N-glycosylation across archaeal phylogeny, bioinformatics approaches were employed to address variability in AglB sequence motifs involved in enzyme activity, construct a phylogenetic tree based on AglB sequences, search for archaeal homologues of non-catalytic subunits of the multimeric eukaryal oligosaccharyltransferase complex and predict the presence of aglB-based clusters of glycosylation-related genes in the Euryarchaeota and the DPANN, TACK and Asgard super-phyla. In addition, site-directed mutagenesis and mass spectrometry were employed to study the natural variability in the WWDXG motif central to oligosaccharyltransferase activity seen in archaeal AglB. The results clearly distinguish AglB from members of the DPANN super-phylum and the Euryarchaeota from the same enzyme in members of the TACK and Asgard super-phyla, which showed considerable similarity to its eukaryal homologue Stt3. The results thus support the evolutionary proximity of Eukarya and the TACK and Asgard archaea.}, }
@article {pmid32887961, year = {2020}, author = {Parks, DH and Chuvochina, M and Chaumeil, PA and Rinke, C and Mussig, AJ and Hugenholtz, P}, title = {Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea.}, journal = {Nature biotechnology}, volume = {38}, number = {9}, pages = {1098}, doi = {10.1038/s41587-020-0539-7}, pmid = {32887961}, issn = {1546-1696}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32887944, year = {2020}, author = {Reichart, NJ and Jay, ZJ and Krukenberg, V and Parker, AE and Spietz, RL and Hatzenpichler, R}, title = {Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment.}, journal = {The ISME journal}, volume = {14}, number = {11}, pages = {2851-2861}, pmid = {32887944}, issn = {1751-7370}, support = {80NSSC19K0449/ImNASA/Intramural NASA/United States ; 80NSSC19K1633/ImNASA/Intramural NASA/United States ; }, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Hot Springs ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Wyoming ; }, abstract = {Metagenomic studies have revolutionized our understanding of the metabolic potential of uncultured microorganisms in various ecosystems. However, many of these genomic predictions have yet to be experimentally tested, and the functional expression of genomic potential often remains unaddressed. In order to obtain a more thorough understanding of cell physiology, novel techniques capable of testing microbial metabolism under close to in situ conditions must be developed. Here, we provide a benchmark study to demonstrate that bioorthogonal non-canonical amino acid tagging (BONCAT) in combination with fluorescence-activated cell sorting (FACS) and 16S rRNA gene sequencing can be used to identify anabolically active members of a microbial community incubated in the presence of various growth substrates or under changing physicochemical conditions. We applied this approach to a hot spring sediment microbiome from Yellowstone National Park (Wyoming, USA) and identified several microbes that changed their activity levels in response to substrate addition, including uncultured members of the phyla Thaumarchaeota, Acidobacteria, and Fervidibacteria. Because shifts in activity in response to substrate amendment or headspace changes are indicative of microbial preferences for particular growth conditions, results from this and future BONCAT-FACS studies could inform the development of cultivation media to specifically enrich uncultured microbes. Most importantly, BONCAT-FACS is capable of providing information on the physiology of uncultured organisms at as close to in situ conditions as experimentally possible.}, }
@article {pmid32857850, year = {2020}, author = {Yue, L and Li, J and Zhang, B and Qi, L and Li, Z and Zhao, F and Li, L and Zheng, X and Dong, X}, title = {The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.}, journal = {Nucleic acids research}, volume = {48}, number = {17}, pages = {9589-9605}, pmid = {32857850}, issn = {1362-4962}, mesh = {Archaeal Proteins/*genetics/metabolism ; DNA, Complementary/genetics ; DNA-Directed RNA Polymerases/genetics/metabolism ; Genome, Archaeal ; Methanococcus/*genetics ; Mutation ; Phylogeny ; Ribonucleases/*genetics/metabolism ; Transcription, Genetic ; Uridine ; }, abstract = {Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination factor of Archaea, the ribonuclease aCPSF1, and elucidated its 3'-end cleavage triggered termination mechanism. The depletion of Mmp-aCPSF1 in Methanococcus maripaludis caused a genome-wide transcription termination defect and disordered transcriptome. Transcript-3'end-sequencing revealed that transcriptions primarily terminate downstream of a uridine-rich motif where Mmp-aCPSF1 performed an endoribonucleolytic cleavage, and the endoribonuclease activity was determined to be essential to the in vivo transcription termination. Co-immunoprecipitation and chromatin-immunoprecipitation detected interactions of Mmp-aCPSF1 with RNA polymerase and chromosome. Phylogenetic analysis revealed that the aCPSF1 orthologs are ubiquitously distributed among the archaeal phyla, and two aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to terminate transcription of M. maripaludis. Therefore, the aCPSF1 dependent termination mechanism could be widely employed in Archaea, including Lokiarchaeota belonging to Asgard Archaea, the postulated archaeal ancestor of Eukaryotes. Strikingly, aCPSF1-dependent archaeal transcription termination reported here exposes a similar 3'-cleavage mode as the eukaryotic RNA polymerase II termination, thus would shed lights on understanding the evolutionary linking between archaeal and eukaryotic termination machineries.}, }
@article {pmid32852144, year = {2021}, author = {Tang, HM and Xiao, XP and Li, C and Shi, LH and Cheng, KK and Wen, L and Li, WY and Wang, K}, title = {Influences of different manure N input on soil ammonia-oxidizing archaea and bacterial activity and community structure in a double-cropping rice field.}, journal = {Journal of applied microbiology}, volume = {130}, number = {3}, pages = {937-947}, doi = {10.1111/jam.14830}, pmid = {32852144}, issn = {1365-2672}, mesh = {Ammonia/metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; China ; Fertilizers/analysis ; Manure/*analysis ; *Microbiota ; Nitrogen/analysis/*metabolism ; Oryza/growth &amp; development/microbiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {AIMS: The short-term effects of different organic manure nitrogen (N) input on soil ammonia-oxidizing archaea (AOA) and bacterial (AOB) activity and community structure at maturity stages of early rice and late rice were investigated in the present paper, in a double-cropping rice system in southern China.<br><br>METHODS AND RESULTS: A field experiment was done by applying five different organic and inorganic N input treatments: (i) 100% N of chemical fertilizer (M0), (ii) 30% N of organic manure and 70% N of chemical fertilizer (M30), (iii) 50% N of organic manure and 50% N of chemical fertilizer (M50), (iv) 100% N of organic manure (M100) and (v) without N fertilizer input as control (CK). Microbial community changes were assessed using fatty acid methyl esters, and ammonia oxidizer (AO) changes were followed using quantitative PCR. The results showed that AOA were higher than that of AOB based upon amoA gene copy at maturity stages of early rice and late rice. Also, the abundance of AOB and AOA with M30, M50 and M100 treatments was significantly higher than that of CK treatment. Manure N input treatments had significant effect on AOB and AOA abundance, and a higher correlation between AOB and manure N input was observed. AOB correlated moderately with soil organic carbon content, and AOA correlated moderately with water-filled pore space.<br><br>CONCLUSIONS: This study found that abundance of AOB and AOA was increased under the given organic N conditions, and the soil AOB and AOA community and diversity were changed by different short-term organic manure N input treatments.<br><br>Soil microbial community and specific N-utilizing microbial groups were affected by organic manure N input practices.}, }
@article {pmid32851593, year = {2020}, author = {Cendron, F and Niero, G and Carlino, G and Penasa, M and Cassandro, M}, title = {Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing.}, journal = {Journal of applied genetics}, volume = {61}, number = {4}, pages = {593-605}, pmid = {32851593}, issn = {2190-3883}, mesh = {Animals ; Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Breeding ; Cattle ; Feces/microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Lactation/*genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups.}, }
@article {pmid32849470, year = {2020}, author = {Nagler, M and Podmirseg, SM and Mayr, M and Ascher-Jenull, J and Insam, H}, title = {Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1894}, pmid = {32849470}, issn = {1664-302X}, abstract = {Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.}, }
@article {pmid32829441, year = {2021}, author = {Silveira, R and Silva, MRSS and de Roure Bandeira de Mello, T and Alvim, EACC and Marques, NCS and Kruger, RH and da Cunha Bustamante, MM}, title = {Bacteria and Archaea Communities in Cerrado Natural Pond Sediments.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {563-578}, pmid = {32829441}, issn = {1432-184X}, mesh = {*Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Geologic Sediments ; Phylogeny ; *Ponds ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Natural ponds in the Brazilian Cerrado harbor high biodiversity but are still poorly studied, especially their microbial assemblage. The characterization of the microbial community in aquatic environments is fundamental for understanding its functioning, particularly under the increasing pressure posed by land conversion and climate change. Here, we aim to characterize the structure (abundance, richness, and diversity) and composition of the Bacteria and Archaea in the sediment of two natural ponds belonging to different basins that primarily differ in size and depth in the Cerrado. Sediment samples were collected in the dry and rainy seasons and the transition periods between both. The structure and composition of Bacteria and Archaea were assessed by 16S rRNA gene pyrosequencing. We identified 45 bacterial and four archaeal groups. Proteobacteria and Acidobacteria dominated the bacterial community, while Euryarchaeota and Thaumarchaeota dominated the archaeal community. Seasonal fluctuations in the relative abundance of microbial taxa were observed, but pond characteristics were more determinant to community composition differences. Microbial communities are highly diverse, and local variability could partially explain the microbial structure's main differences. Functional predictions based in 16S rRNA gene accessed with Tax4Fun indicated an enriched abundance of predicted methane metabolism in the deeper pond, where higher abundance of methanogenic archaea Methanocella, Methanosaeta, and Methanomicrobiaceae was detected. Our dataset encompasses the more comprehensive survey of prokaryotic microbes in Cerrado's aquatic environments. Here, we present basic and essential information about composition and diversity, for initial insights into the ecology of Bacteria and Archaea in these environments.}, }
@article {pmid32826220, year = {2020}, author = {Dhamad, AE and Lessner, DJ}, title = {A CRISPRi-dCas9 System for Archaea and Its Use To Examine Gene Function during Nitrogen Fixation by Methanosarcina acetivorans.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {21}, pages = {}, pmid = {32826220}, issn = {1098-5336}, mesh = {Archaeal Proteins/*genetics/metabolism ; *CRISPR-Cas Systems ; Gene Expression ; Genes, Archaeal/*genetics ; Methanosarcina/*genetics/metabolism ; Nitrogen Fixation/*genetics ; }, abstract = {CRISPR-based systems are emerging as the premier method to manipulate many cellular processes. In this study, a simple and efficient CRISPR interference (CRISPRi) system for targeted gene repression in archaea was developed. The Methanosarcina acetivorans CRISPR-Cas9 system was repurposed by replacing Cas9 with the catalytically dead Cas9 (dCas9) to generate a CRISPRi-dCas9 system for targeted gene repression. To test the utility of the system, genes involved in nitrogen (N2) fixation were targeted for dCas9-mediated repression. First, the nif operon (nifHI1I2DKEN) that encodes molybdenum nitrogenase was targeted by separate guide RNAs (gRNAs), one targeting the promoter and the other targeting nifD Remarkably, growth of M. acetivorans with N2 was abolished by dCas9-mediated repression of the nif operon with each gRNA. The abundance of nif transcripts was >90% reduced in both strains expressing the gRNAs, and NifD was not detected in cell lysate. Next, we targeted NifB, which is required for nitrogenase cofactor biogenesis. Expression of a gRNA targeting the coding sequence of NifB decreased nifB transcript abundance >85% and impaired but did not abolish growth of M. acetivorans with N2 Finally, to ascertain the ability to study gene regulation using CRISPRi-dCas9, nrpR1, encoding a subunit of the repressor of the nif operon, was targeted. The nrpR1 repression strain grew normally with N2 but had increased nif operon transcript abundance, consistent with NrpR1 acting as a repressor. These results highlight the utility of the system, whereby a single gRNA when expressed with dCas9 can block transcription of targeted genes and operons in M. acetivoransIMPORTANCE Genetic tools are needed to understand and manipulate the biology of archaea, which serve critical roles in the biosphere. Methanogenic archaea (methanogens) are essential for the biological production of methane, an intermediate in the global carbon cycle, an important greenhouse gas, and a biofuel. The CRISPRi-dCas9 system in the model methanogen Methanosarcina acetivorans is, to our knowledge, the first Cas9-based CRISPR interference system in archaea. Results demonstrate that the system is remarkably efficient in targeted gene repression and provide new insight into nitrogen fixation by methanogens, the only archaea with nitrogenase. Overall, the CRISPRi-dCas9 system provides a simple, yet powerful, genetic tool to control the expression of target genes and operons in methanogens.}, }
@article {pmid32822422, year = {2020}, author = {Flores-Bautista, E and Hernandez-Guerrero, R and Huerta-Saquero, A and Tenorio-Salgado, S and Rivera-Gomez, N and Romero, A and Ibarra, JA and Perez-Rueda, E}, title = {Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0237135}, pmid = {32822422}, issn = {1932-6203}, mesh = {Archaea/*genetics/pathogenicity ; Archaeal Proteins/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Binding Sites ; DNA, Archaeal/metabolism ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Escherichia coli K12/*genetics/pathogenicity ; Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Protein Binding ; Transcription Factors/*genetics/metabolism ; Virulence/genetics ; }, abstract = {DNA-binding Transcription Factors (TFs) play a central role in regulation of gene expression in prokaryotic organisms, and similarities at the sequence level have been reported. These proteins are predicted with different abundances as a consequence of genome size, where small organisms contain a low proportion of TFs and large genomes contain a high proportion of TFs. In this work, we analyzed a collection of 668 experimentally validated TFs across 30 different species from diverse taxonomical classes, including Escherichia coli K-12, Bacillus subtilis 168, Corynebacterium glutamicum, and Streptomyces coelicolor, among others. This collection of TFs, together with 111 hidden Markov model profiles associated with DNA-binding TFs collected from diverse databases such as PFAM and DBD, was used to identify the repertoire of proteins putatively devoted to gene regulation in 1321 representative genomes of Archaea and Bacteria. The predicted regulatory proteins were posteriorly analyzed in terms of their genomic context, allowing the prediction of functions for TFs and their neighbor genes, such as genes involved in virulence, enzymatic functions, phosphorylation mechanisms, and antibiotic resistance. The functional analysis associated with PFAM groups showed diverse functional categories were significantly enriched in the collection of TFs and the proteins encoded by the neighbor genes, in particular, small-molecule binding and amino acid transmembrane transporter activities associated with the LysR family and proteins devoted to cellular aromatic compound metabolic processes or responses to drugs, stress, or abiotic stimuli in the MarR family. We consider that with the increasing data derived from new technologies, novel TFs can be identified and help improve the predictions for this class of proteins in complete genomes. The complete collection of experimentally characterized and predicted TFs is available at http://web.pcyt.unam.mx/EntrafDB/.}, }
@article {pmid32817089, year = {2020}, author = {Fonseca, DR and Halim, MFA and Holten, MP and Costa, KC}, title = {Type IV-Like Pili Facilitate Transformation in Naturally Competent Archaea.}, journal = {Journal of bacteriology}, volume = {202}, number = {21}, pages = {}, pmid = {32817089}, issn = {1098-5530}, mesh = {Archaeal Proteins/*metabolism ; *DNA, Archaeal ; *Gene Transfer, Horizontal ; Methanococcus/*genetics ; Methanomicrobiaceae/*genetics ; }, abstract = {Naturally competent organisms are capable of DNA uptake directly from the environment through the process of transformation. Despite the importance of transformation to microbial evolution, DNA uptake remains poorly characterized outside of the bacterial domain. Here, we identify the pilus as a necessary component of the transformation machinery in archaea. We describe two naturally competent organisms, Methanococcus maripaludis and Methanoculleus thermophilus In M. maripaludis, replicative vectors were transferred with an average efficiency of 2.4 × 10[3] transformants μg[-1] DNA. In M. thermophilus, integrative vectors were transferred with an average efficiency of 2.7 × 10[3] transformants μg[-1] DNA. Additionally, natural transformation of M. thermophilus could be used to introduce chromosomal mutations. To our knowledge, this is the first demonstration of a method to introduce targeted mutations in a member of the order Methanomicrobiales For both organisms, mutants lacking structural components of the type IV-like pilus filament were defective for DNA uptake, demonstrating the importance of pili for natural transformation. Interestingly, competence could be induced in a noncompetent strain of M. maripaludis by expressing pilin genes from a replicative vector. These results expand the known natural competence pili to include examples from the archaeal domain and highlight the importance of pili for DNA uptake in diverse microbial organisms.IMPORTANCE Microbial organisms adapt and evolve by acquiring new genetic material through horizontal gene transfer. One way that this occurs is natural transformation, the direct uptake and genomic incorporation of environmental DNA by competent organisms. Archaea represent up to a third of the biodiversity on Earth, yet little is known about transformation in these organisms. Here, we provide the first characterization of a component of the archaeal DNA uptake machinery. We show that the type IV-like pilus is essential for natural transformation in two archaeal species. This suggests that pili are important for transformation across the tree of life and further expands our understanding of gene flow in archaea.}, }
@article {pmid32812678, year = {2020}, author = {Wang, K and Yan, H and Peng, X and Hu, H and Zhang, H and Hou, D and Chen, W and Qian, P and Liu, J and Cai, J and Chai, X and Zhang, D}, title = {Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective.}, journal = {Molecular ecology}, volume = {29}, number = {19}, pages = {3762-3776}, doi = {10.1111/mec.15600}, pmid = {32812678}, issn = {1365-294X}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; China ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between-domain differences in underlying mechanism are largely unassessed. Using a high-coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism-dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism-stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism-vs.-stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.}, }
@article {pmid32788376, year = {2020}, author = {Darnell, CL and Zheng, J and Wilson, S and Bertoli, RM and Bisson-Filho, AW and Garner, EC and Schmid, AK}, title = {The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea.}, journal = {mBio}, volume = {11}, number = {4}, pages = {}, pmid = {32788376}, issn = {2150-7511}, support = {203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; DP2 AI117923/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/*genetics/growth &amp; development ; Archaeal Proteins/*genetics ; Cell Division/*genetics ; *Gene Expression Regulation, Archaeal ; Protein Domains ; Transcription Factors/*genetics ; Transcription, Genetic ; }, abstract = {Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. Here, we use genetics, functional genomics, and quantitative imaging to identify and characterize the novel CdrSL gene regulatory network in a model species of archaea. We demonstrate the central role of these ribbon-helix-helix family transcription factors in the regulation of cell division through specific transcriptional control of the gene encoding FtsZ2, a putative tubulin homolog. Using time-lapse fluorescence microscopy in live cells cultivated in microfluidics devices, we further demonstrate that FtsZ2 is required for cell division but not elongation. The cdrS-ftsZ2 locus is highly conserved throughout the archaeal domain, and the central function of CdrS in regulating cell division is conserved across hypersaline adapted archaea. We propose that the CdrSL-FtsZ2 transcriptional network coordinates cell division timing with cell growth in archaea.IMPORTANCE Healthy cell growth and division are critical for individual organism survival and species long-term viability. However, it remains unknown how cells of the domain Archaea maintain a healthy cell cycle. Understanding the archaeal cell cycle is of paramount evolutionary importance given that an archaeal cell was the host of the endosymbiotic event that gave rise to eukaryotes. Here, we identify and characterize novel molecular players needed for regulating cell division in archaea. These molecules dictate the timing of cell septation but are dispensable for growth between divisions. Timing is accomplished through transcriptional control of the cell division ring. Our results shed light on mechanisms underlying the archaeal cell cycle, which has thus far remain