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Bibliography on: Archaea

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ESP: PubMed Auto Bibliography 20 Jul 2019 at 01:30 Created: 

Archaea

In 1977, Carl Woese and George Fox applied molecular techniques to biodiversity and discovered that life on Earth consisted of three, not two (prokaryotes and eukaryotes), major lineages, tracing back nearly to the very origin of life on Earth. The third lineage has come to be known as the Archaea. Organisms now considered Archaea were originally thought to be a kind of prokaryote, but Woese and Fox showed that they were as different from prokaryotes as they were from eukaryotes. To understand life on Earth one must also understand the Archaea .

Created with PubMed® Query: archaea[TITLE] OR archaebacteria[TITLE] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-07-19

Eloe-Fadrosh EA (2019)

Genome gazing in ammonia-oxidizing archaea.

Nature reviews. Microbiology pii:10.1038/s41579-019-0248-8 [Epub ahead of print].

RevDate: 2019-07-17

Liu TT, H Yang (2019)

An RNA-based quantitative and compositional study of ammonium-oxidizing bacteria and archaea in Lake Taihu, a eutrophic freshwater lake.

FEMS microbiology ecology pii:5533317 [Epub ahead of print].

Ammonium-oxidizing archaea (AOA) and bacteria (AOB) play crucial roles in ammonium oxidation in freshwater lake sediment. However, previous reports on the predominance of AOA and AOB in the surface sediment of Lake Taihu have been based on DNA levels, detecting the total abundance of microbiota (including inactive cells), and have resulted in numerous contradictory conclusions. Existing RNA-level studies detecting active transcription are very limited. The current study using RNA-based real-time quantification and clone library analysis demonstrated that the amoA gene abundance of active AOB was higher than that of active AOA, despite conflicting results at the DNA level. Further exploration revealed a significant positive correlation between the potential nitrification rate (PNR) and the abundance of AOA and AOB at the RNA level, with irregular or contradictory correlation found at the DNA level. Ultimately, using quantitative analysis of RNA levels, we show AOB to be the active dominant contributor to ammonium oxidation. Our investigations also indicated that AOB were more diverse at high-ammonium lake regions, with Nitrosomonas being the active and dominating cluster, but that AOA had an advantage in the low-ammonium lake region.

RevDate: 2019-07-17

DeMott MS, PC Dedon (2019)

The road less traveled: A new phosphorothioate antiviral defense mechanism discovered in Archaea.

Synthetic and systems biotechnology, 4(3):132-133 pii:S2405-805X(19)30040-7.

RevDate: 2019-07-08

Schwarz TS, Wäber NB, Feyh R, et al (2019)

Homologs of aquifex aeolicus protein-only RNase P are not the major RNase P activities in the archaea haloferax volcanii and methanosarcina mazei.

IUBMB life [Epub ahead of print].

The mature 5'-ends of tRNAs are generated by RNase P in all domains of life. The ancient form of the enzyme is a ribonucleoprotein consisting of a catalytic RNA and one or more protein subunits. However, in the hyperthermophilic bacterium Aquifex aeolicus and close relatives, RNase P is a protein-only enzyme consisting of a single type of polypeptide (Aq_880, ~23 kDa). In many archaea, homologs of Aq_880 were identified (termed HARPs for Homologs of Aquifex RNase P) in addition to the RNA-based RNase P, raising the question about the functions of HARP and the classical RNase P in these archaea. Here we investigated HARPs from two euryarchaeotes, Haloferax volcanii and Methanosarcina mazei. Archaeal strains with HARP gene knockouts showed no growth phenotypes under standard conditions, temperature and salt stress (H. volcanii) or nitrogen deficiency (M. mazei). Recombinant H. volcanii and M. mazei HARPs were basically able to catalyse specific tRNA 5'-end maturation in vitro. Furthermore, M. mazei HARP was able to rescue growth of an Escherichia coli RNase P depletion strain with comparable efficiency as Aq_880, while H. volcanii HARP was unable to do so. In conclusion, both archaeal HARPs showed the capacity (in at least one functional assay) to act as RNases P. However, the ease to obtain knockouts of the singular HARP genes and the lack of growth phenotypes upon HARP gene deletion contrasts with the findings that the canonical RNase P RNA gene cannot be deleted in H. volcanii, and a knockdown of RNase P RNA in H. volcanii results in severe tRNA processing defects. We conclude that archaeal HARPs do not make a major contribution to global tRNA 5'-end maturation in archaea, but may well exert a specialised, yet unknown function in (t)RNA metabolism. © 2019 IUBMB Life, 2019.

RevDate: 2019-07-04

DasSarma S, Fomenkov A, DasSarma SL, et al (2019)

Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei.

Microbiology resource announcements, 8(27): pii:8/27/e00577-19.

The genomes of two extremely halophilic Archaea species, Haloarcula marismortui and Haloferax mediterranei, were sequenced using single-molecule real-time sequencing. The ∼4-Mbp genomes are GC rich with multiple large plasmids and two 4-methyl-cytosine patterns. Methyl transferases were incorporated into the Restriction Enzymes Database (REBASE), and gene annotation was incorporated into the Haloarchaeal Genomes Database (HaloWeb).

RevDate: 2019-07-02

Pereira O, Hochart C, Auguet JC, et al (2019)

Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.

MicrobiologyOpen [Epub ahead of print].

Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.

RevDate: 2019-06-28

Zhao X, Li X, Li Y, et al (2019)

Shifting interactions among bacteria, fungi and archaea enhance removal of antibiotics and antibiotic resistance genes in the soil bioelectrochemical remediation.

Biotechnology for biofuels, 12:160 pii:1500.

Background: Antibiotics and antibiotic resistance genes (ARGs) are two pollutants in soil, especially ARGs as one of the top three threats to human health. The performance of soil microbial fuel cells (MFCs) fuelled with antibiotics was investigated.

Results: In this study, soil MFCs spiked with tetracycline exhibited optimal bioelectricity generation, which was 25% and 733% higher than those of MFCs spiked with sulfadiazine and control, respectively. Compared with the non-electrode treatment, not only did functional micro-organisms change in open- and closed-circuit treatments, but also the microbial affinities, respectively, increased by 50% and 340% to adapt to higher removal of antibiotics. For the open-circuit treatment, the ineffective interspecific relation of micro-organisms was reduced to assist the removal efficiency of antibiotics by 7-27%. For the closed-circuit treatment, an intensive metabolic network capable of bioelectricity generation, degradation and nitrogen transformation was established, which led to 10-35% higher removal of antibiotics. Importantly, the abundances of ARGs and mobile genetic element (MGE) genes decreased after the introduction of electrodes; especially in the closed-circuit treatment, the highest reduction of 47% and 53% was observed, respectively.

Conclusions: Soil MFCs possess advantages for the elimination of antibiotics and ARGs with sevenfold to eightfold higher electricity generation than that of the control treatment. Compared with sulphonamides, the enhancement removal of tetracycline is higher, while both potential ARG propagation risk is reduced in soil MFCs. This study firstly synchronously reveals the relationships among bacteria, fungi and archaea and with ARGs and MGE genes in soil bioelectrochemical systems.

RevDate: 2019-06-28

Trivedi C, Reich PB, Maestre FT, et al (2019)

Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands.

The ISME journal pii:10.1038/s41396-019-0465-1 [Epub ahead of print].

Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.

RevDate: 2019-06-28

Zhang H, Sun H, Zhou S, et al (2019)

Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems.

Scientific reports, 9(1):9367 pii:10.1038/s41598-019-45877-7.

Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.

RevDate: 2019-06-26

Bayer B, Pelikan C, Bittner MJ, et al (2019)

Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium.

mSystems, 4(4): pii:4/4/e00181-19.

Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2 However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments.IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.

RevDate: 2019-06-25

Horai S, Yamauchi N, H Naraoka (2019)

Simultaneous total analysis of core and polar membrane lipids in archaea by HPLC/HRMS coupled with heated electrospray ionization.

Rapid communications in mass spectrometry : RCM [Epub ahead of print].

RATIONALE: Archaea have characteristic membrane lipids including diether and/or tetraether isoprenoidal core lipids with various polar head groups. Since the polar group is removed soon after the end of archaeal activity, the occurrence of core and polar lipids are regarded as dead and active signals, respectively. The core and polar lipids have generally been analyzed separately using atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI), respectively, coupled with mass spectrometry.

METHODS: In this study, simultaneous analysis of core and polar archaeal lipids have been examined using heated electrospray ionization (HESI) by high performance liquid chromatography/high resolution mass spectrometry (HPLC/HRMS).

RESULTS: Both core and intact polar lipids can be analyzed simultaneously by HESI with good sensitivity (sub ng to 100 ng) and separation using a semi-bore diol column by normal phase chromatography. The core lipids eluted firstly to separate archeaol, then GDGTs followed by the polar lipids with glycosides and glycophosphates. The relative GDGT composition is identical between HESI and APCI methods.

CONCLUSIONS: The simultaneous analysis has a benefit to minimize sample amount and elution solvent as well as preparation work. The method can also be applied to a compound class fractionation for compound-specific carbon and hydrogen isotope analysis.

RevDate: 2019-06-21

Vuillemin A, Wankel SD, Coskun ÖK, et al (2019)

Archaea dominate oxic subseafloor communities over multimillion-year time scales.

Science advances, 5(6):eaaw4108 pii:aaw4108.

Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.

RevDate: 2019-06-18

Zhang X, Duan P, Wu Z, et al (2019)

Aged biochar stimulated ammonia-oxidizing archaea and bacteria-derived N2O and NO production in an acidic vegetable soil.

The Science of the total environment, 687:433-440 pii:S0048-9697(19)32696-8 [Epub ahead of print].

Both nitrous oxide (N2O) and nitric oxide (NO) emissions are typically high in greenhouse-based high N input vegetable soils. Biochar amendment has been widely recommended for mitigating soil N2O emissions in agriculture. However, knowledge of the regulatory mechanisms of fresh and aged biochar for both N2O and NO production during ammonia oxidation is lacking. Two vegetable soils with different pH values were used in aerobic incubation experiments with 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), 1-octyne and acetylene. The relative importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to N2O and NO production was investigated as influenced by fresh and aged biochar amendments. The results showed that AOA dominated N2O production in acidic soil, while AOB dominated N2O production in alkaline soil. Aged biochar stimulated both AOA- and AOB-derived N2O and NO production by 84.8 and 340%, respectively, in acidic soil but only increased AOA-derived N2O and NO production in alkaline soil. Fresh biochar amendment increased AOA- and AOB-derived NO in acidic soil and AOA-derived NO in alkaline soil but had negligible effects on AOA- and AOB-derived N2O in both soils. Fresh biochar decreased AOA-amoA but increased AOB-amoA gene abundances in acidic soil, whereas aged biochar increased AOA- and AOB-amoA gene abundances in both soils. These findings improved our understanding of N2O and NO production mechanisms under different biochar amendments in alkaline and acidic vegetable soils.

RevDate: 2019-06-14

Kırtel O, Lescrinier E, Van den Ende W, et al (2019)

Discovery of fructans in Archaea.

Carbohydrate polymers, 220:149-156.

Fructans are fructose-based oligo- and polysaccharides derived from sucrose that occur in a plethora of Eubacteria and plants. While fructan-producing (fructanogenic) Eubacteria are abundant in hypersaline environments, fructan production by Archaea has never been reported before. Exopolysaccharides accumulated by various Archaea from the Halobacteria class (belonging to the genera of Halomicrobium, Haloferax and Natronococcus) originating from different locations on Earth were structurally characterized as either levans or inulins with varying branching degrees (10%-16%). Thus, we show for the first time in the literature that fructans are produced in all three domains of life, including Archaea. This proof of concept will not only provide insight into Archaeal glycans and evolution but it may also open new frontiers for innovative strategies to overcome the ever-increasing threat of excessive salinization.

RevDate: 2019-06-13

Lemmens L, Maklad HR, Bervoets I, et al (2019)

Transcription Regulators in Archaea: Homologies and Differences with Bacterial Regulators.

Journal of molecular biology pii:S0022-2836(19)30335-3 [Epub ahead of print].

The fitness and survival of prokaryotic microorganisms depends on their ability to adequately respond to environmental changes, sudden stress conditions and metabolic shifts. An important mechanism underlying this response is the regulation of gene expression mediated by transcription factors that are responsive to small-molecule ligands or other intracellular signals. Despite constituting a distinct domain of life from bacteria and harboring a eukaryotic-like basal transcription apparatus, it is well-established that archaea have similar transcription factors pointing to the existence of shared ancestral proteins and to the occurrence of inter-domain horizontal gene transfer events. However, while global structural features of bacterial and archaeal transcription factors are indeed similar, other characteristics imply that archaeal regulators have undergone independent evolution. Here, we discuss the characteristics of Lrp/AsnC, MarR, ArsR/SmtB and TrmB families of transcription factors, which are the dominant families that constitute the transcription factor repertoire in archaea. We exemplify the evolutionary expansion of these families in archaeal lineages by emphasizing homologies and differences with bacterial counterparts in terms of ligand or signal response, physiological functions and mechanistic principles of regulation. As such, we aim to define future research approaches that enable further characterization of the functions and mechanisms of archaeal transcription factors.

RevDate: 2019-06-13

Ludt K, J Soppa (2019)

Polyploidy in halophilic archaea: regulation, evolutionary advantages, and gene conversion.

Biochemical Society transactions pii:BST20190256 [Epub ahead of print].

All analyzed haloarachea are polyploid. In addition, haloarchaea contain more than one type of chromosome, and thus the gene dosage can be regulated independently on different replicons. Haloarchaea and several additional archaea have more than one replication origin on their major chromosome, in stark contrast with bacteria, which have a single replication origin. Two of these replication origins of Haloferax volcanii have been studied in detail and turned out to have very different properties. The chromosome copy number appears to be regulated in response to growth phases and environmental factors. Archaea typically contain about two Origin Recognition Complex (ORC) proteins, which are homologous to eukaryotic ORC proteins. However, haloarchaea are the only archaeal group that contains a multitude of ORC proteins. All 16 ORC protein paralogs from H. volcanii are involved in chromosome copy number regulation. Polyploidy has many evolutionary advantages for haloarchaea, e.g. a high resistance to desiccation, survival over geological times, and the relaxation of cell cycle-specific replication control. A further advantage is the ability to grow in the absence of external phosphate while using the many genome copies as internal phosphate storage polymers. Very efficient gene conversion operates in haloarchaea and results in the unification of genome copies. Taken together, haloarchaea are excellent models to study many aspects of genome biology in prokaryotes, exhibiting properties that have not been found in bacteria.

RevDate: 2019-06-11

Killelea T, Palud A, Akcha F, et al (2019)

The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea.

eLife, 8: pii:45320.

8-oxodeoxyguanosine (8-oxodG), a major oxidised base modification, has been investigated to study its impact on DNA replication in hyperthermophilic Archaea. Here we show that 8-oxodG is formed in the genome of growing cells, with elevated levels following exposure to oxidative stress. Functional characterisation of cell-free extracts and the DNA polymerisation enzymes, PolB, PolD, and the p41/p46 complex, alone or in the presence of accessory factors (PCNA and RPA) indicates that translesion synthesis occurs under replicative conditions. One of the major polymerisation effects was stalling, but each of the individual proteins could insert and extend past 8-oxodG with differing efficiencies. The introduction of RPA and PCNA influenced PolB and PolD in similar ways, yet provided a cumulative enhancement to the polymerisation performance of p41/p46. Overall, 8-oxodG translesion synthesis was seen to be potentially mutagenic leading to errors that are reminiscent of dA:8-oxodG base pairing.

RevDate: 2019-06-10

Wang W, Su Y, Wang B, et al (2019)

Spatiotemporal shifts of ammonia-oxidizing archaea abundance and structure during the restoration of a multiple pond and plant-bed/ditch wetland.

The Science of the total environment, 684:629-640 pii:S0048-9697(19)31966-7 [Epub ahead of print].

Ammonia-oxidizing archaea (AOA) microorganisms have been increasingly found in aquatic and terrestrial environments. These microorganisms make vital contributions to ammonia oxidation in such systems. However, their community succession characteristics in man-made wetland ecosystems have scarcely been reported. We assessed the AOA's spatiotemporal shifts in the sediments of a constructed wetland (CW) - the Shijiuyang constructed wetland (SJY-CW) - in China from the third year (2011) to the fifth year (2013) of the CW operation. The SJY-CW is composed of a pretreatment pond, a multiple plant-bed/ditch system, and a post-treatment pond. Results showed that AOA abundance in the pre- and post-treatment ponds remained invariant through 2011-2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with wetland operation. The AOA abundance in 2013 was one order of magnitude lower than that through 2011-2012, and the AOA abundance in the plant-bed/ditch system was generally higher than that in the pre- and post-treatment ponds from 2011 to 2013. AOA diversity showed little temporal differentiation with a slightly decreasing trend for community richness index Chao1 and diversity index Shannon H' from 2011 to 2013. The AOA community was dominated by the Nitrososphaera cluster accompanied by an increasing Nitrosopumilus cluster and Nitrososphaera sister cluster within the wetland operation. Hierarchical clustering and redundancy analysis verified the horizontal shifts of AOA communities. The shifts occurred preferentially in the central plant-bed/ditch system. The operational duration of the wetland became a key factor influencing AOA abundance and community shift in SJY-CW sediments.

RevDate: 2019-06-10

Stachler AE, Schwarz TS, Schreiber S, et al (2019)

CRISPRi as an efficient tool for gene repression in archaea.

Methods (San Diego, Calif.) pii:S1046-2023(18)30472-9 [Epub ahead of print].

In the years following its discovery and characterization, the CRISPR-Cas system has been modified and converted into a multitude of applications for eukaryotes and bacteria, such as genome editing and gene regulation. Since no such method has been available for archaea, we developed a tool for gene repression in the haloarchaeon Haloferax volcanii by repurposing its endogenous type I-B CRISPR-Cas system. Here, we present the two possible approaches for gene repression as well as our workflow to achieve and assess gene knockdown, offer recommendations on protospacer selection and give some examples of genes we have successfully silenced.

RevDate: 2019-05-31

Kurth JM, Smit NT, Berger S, et al (2019)

Anaerobic methanotrophic archaea of the ANME-2d clade feature lipid composition that differs from other ANME archaea.

FEMS microbiology ecology pii:5509572 [Epub ahead of print].

The anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast, Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments little is known about their lipid composition or carbon sources. To close this gap, we analysed the lipid composition of ANME-2d archaea and found that they mainly synthesize archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup which is rare among microorganisms. Batch incubations with 13C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea which primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterization and analysis of the carbon source of Ca. Methanoperedens facilitates distinction between ANME-2d and other ANMEs.

RevDate: 2019-05-31

Ijichi M, Itoh H, K Hamasaki (2019)

Vertical distribution of particle-associated and free-living ammonia-oxidizing archaea in Suruga Bay, a deep coastal embayment of Japan.

Archives of microbiology pii:10.1007/s00203-019-01680-6 [Epub ahead of print].

We analyzed the vertical distributions of ammonia-oxidizing archaea (AOA) in terms of abundance in Suruga Bay, Japan. We distinguished particle-associated (PA) from free-living (FL) assemblages. According to quantitative PCR measurements of the ammonia monooxygenase subunit A gene (amoA), most marine AOA were in an FL state. The vertical distributions of PA AOA ecotypes differed from the general trend; the Shallow Marine clade was dominant in both the surface and deep layers. Thus, although PA AOA account for a small percentage of AOA abundance, they have a community structure distinct from that of FL AOA in planktonic environments. Marine particles should be investigated further as an unexplored niche of AOA in the ocean.

RevDate: 2019-05-28

Walsh JC, Angstmann CN, Bisson-Filho AW, et al (2019)

Division plane placement in pleomorphic archaea is dynamically coupled to cell shape.

Molecular microbiology [Epub ahead of print].

One mechanism for achieving accurate placement of the cell division machinery is via Turing patterns, where non-linear molecular interactions spontaneously produce spatiotemporal concentration gradients. The resulting patterns are dictated by cell shape. For example, the Min system of Escherichia coli shows spatiotemporal oscillation between cell poles, leaving a mid-cell zone for division. The universality of pattern-forming mechanisms in divisome placement is currently unclear. We examined the location of the division plane in two pleomorphic archaea, Haloferax volcanii and Haloarcula japonica, and show that it correlates with the predictions of Turing patterning. Time-lapse analysis of H. volcanii shows that divisome locations after successive rounds of division are dynamically determined by daughter cell shape. For H. volcanii, we show that the location of DNA does not influence division plane location, ruling out nucleoid occlusion. Triangular cells provide a stringent test for Turing patterning, where there is a bifurcation in division plane orientation. For the two archaea examined, most triangular cells divide as predicted by a Turing mechanism, however, in some cases multiple division planes are observed resulting in cells dividing into three viable progeny. Our results suggest that the division site placement is consistent with a Turing patterning system in these archaea. This article is protected by copyright. All rights reserved.

RevDate: 2019-06-10

Zhang R, Neu TR, Li Q, et al (2019)

Insight Into Interactions of Thermoacidophilic Archaea With Elemental Sulfur: Biofilm Dynamics and EPS Analysis.

Frontiers in microbiology, 10:896.

Biooxidation of reduced inorganic sulfur compounds (RISCs) by thermoacidophiles is of particular interest for the biomining industry and for environmental issues, e.g., formation of acid mine drainage (AMD). Up to now, interfacial interactions of acidophiles with elemental sulfur as well as the mechanisms of sulfur oxidation by acidophiles, especially thermoacidophiles, are not yet fully clear. This work focused on how a crenarchaeal isolate Acidianus sp. DSM 29099 interacts with elemental sulfur. Analysis by Confocal laser scanning microscopy (CLSM) and Atomic force microscopy (AFM) in combination with Epifluorescence microscopy (EFM) shows that biofilms on elemental sulfur are characterized by single colonies and a monolayer in first stage and later on 3-D structures with a diameter of up to 100 μm. The analysis of extracellular polymeric substances (EPS) by a non-destructive lectin approach (fluorescence lectin-barcoding analysis) using several fluorochromes shows that intial attachment was featured by footprints rich in biofilm cells that were embedded in an EPS matrix consisting of various glycoconjugates. Wet chemistry data indicate that carbohydrates, proteins, lipids and uronic acids are the main components. Attenuated reflectance (ATR)-Fourier transformation infrared spectroscopy (FTIR) and high-performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD) indicate glucose and mannose as the main monosaccharides in EPS polysaccharides. EPS composition as well as sugar types in EPS vary according to substrate (sulfur or tetrathionate) and lifestyle (biofilms and planktonic cells). This study provides information on the building blocks/make up as well as dynamics of biofilms of thermoacidophilic archaea in extremely acidic environments.

RevDate: 2019-06-03

Zhang L, Dong H, Zhang J, et al (2019)

Influence of FeONPs amendment on nitrogen conservation and microbial community succession during composting of agricultural waste: Relative contributions of ammonia-oxidizing bacteria and archaea to nitrogen conservation.

Bioresource technology, 287:121463.

Composting amended with iron oxide nanoparticles (FeONPs, α-Fe2O3 and Fe3O4 NPs) were conducted to study the impacts of FeONPs on nitrogen conservation and microbial community. It was found that amendment of FeONPs, especially α-Fe2O3 NPs, reduced total nitrogen (TN) loss, and reserved more NH4+-N and mineral N. Pearson correlation analysis revealed that decrease of ammonia-oxidizing bacteria (AOB) in FeONPs treatments played more important role than ammonia-oxidizing archaea (AOA) in reserving more NH4+-N and mineral N, and reducing TN loss. Bacterial community composition at phylum level did not shift with addition of FeONPs. Firmicutes, Actinobacteria, and Proteobacteria were the three most dominant phyla in all treatments. Overall, this study provides a method to reduce TN loss and improve mineral N reservation during composting, and gives a deep insight into the role of AOB and AOA in nitrogen transformation.

RevDate: 2019-05-17

Safarpour A, Ebrahimi M, Shahzadeh Fazeli SA, et al (2019)

Supernatant Metabolites from Halophilic Archaea to Reduce Tumorigenesis in Prostate Cancer In-vitro and In-vivo.

Iranian journal of pharmaceutical research : IJPR, 18(1):241-253.

Halophilic archaea are known as the novel producers of natural products and their supernatant metabolites could have cytotoxic effects on cancer cells. In the present study, we screened the anticancer potential of supernatant metabolites from eight native haloarchaeal strains obtained from a culture collection in Iran. Five human cancer cell lines including breast, lung, prostate and also human fibroblast cells as the normal control were used in the present study. Moreover, to evaluate the anti-tumor effect of the selected supernatant, inhibition of sphere formation and tumor development was assessed in-vitro and in-vivo, respectively. Among all strains, supernatant metabolites from Halobacterium salinarum IBRC M10715 had the most potent cytotoxic effect on prostate cancer cell lines (IC50 = 0.5 mg/mL) without any effects on normal cells. It significantly increased both early and late apoptosis (about 11% and 9%, respectively) in the androgen-dependent PC3 cell line, reduced sphere formation ability of DU145 and PC3 cells with down-regulation of SOX2 gene expression. Furthermore, our results revealed that tumors developed in nude mice significantly shrank post intratumor injection of metabolites of the haloarchaeal strain. In conclusion, we suggested here for the first time that supernatant metabolites from Halobacterium salinarum IBRC M10715 could be a novel component against prostate cancer in-vitro and in-vivo with remarkable reduction in stem-like properties of tumor.

RevDate: 2019-05-15

Hepowit NL, JA Maupin-Furlow (2019)

Rhodanese-like domain protein UbaC and its role in ubiquitin-like protein modification and sulfur mobilization in Archaea.

Journal of bacteriology pii:JB.00254-19 [Epub ahead of print].

Ubiquitin-like protein (Ubl) modification targets proteins for transient inactivation and/or proteasome-mediated degradation in Archaea. Here the rhodanese-like domain (RHD) protein UbaC (HVO_1947) was found to co-purify with the E1-like enzyme (UbaA) of the Ubl modification machinery in the archaeon Haloferax volcanii UbaC was shown to be important for Ubl ligation, particularly for the attachment of the Ubl SAMP2/3s to protein targets after exposure to oxidants [NaOCl, dimethylsulfoxide (DMSO) and methionine sulfoxide (MetO)] and the proteasome inhibitor bortezomib. While UbaC was needed for ligation of the Ubl SAMP1 to MoaE (the large subunit of molybdopterin synthase), it was not important in the formation of oxidant induced SAMP1 protein conjugates. Indicative of defects in sulfur relay, mutation of ubaC impaired molybdenum cofactor (Moco)-dependent DMSO reductase activity and cell survival at elevated temperature suggesting a correlation with defects in the 2-thiolated state of wobble uridine tRNA. Overall the archaeal standalone RHD UbaC has important function in Ubl ligation and is associated with sulfur relay processes.ImportanceCanonical E2 Ub/Ubl conjugating enzymes are not conserved in the dual function Ubl systems associated with protein modification and sulfur relay. Instead, the C-terminal RHDs of E1-RHD fusion proteins are the apparent E2-modules of these systems in eukaryotes. E1s that lack an RHD are common in archaea. Here we identified an RHD (UbaC) that serves as an apparent E2 analog with the E1-like UbaA in the dual function Ubl sampylation system of archaea. Unlike the eukaryotic E1-RHD fusion, the archaeal RHD is a standalone protein. This new insight suggests that E1 function in Ubl pathways could be influenced by shifts in RHD abundance and/or competition with other protein partners in the cell.

RevDate: 2019-05-09

Lu S, Zhang X, Chen K, et al (2019)

The small subunit of DNA polymerase D (DP1) associates with GINS-GAN complex of the thermophilic archaea in Thermococcus sp. 4557.

MicrobiologyOpen [Epub ahead of print].

The eukaryotic GINS, Cdc45, and minichromosome maintenance proteins form an essential complex that moves with the DNA replication fork. The GINS protein complex has also been reported to associate with DNA polymerase. In archaea, the third domain of life, DNA polymerase D (PolD) is essential for DNA replication, and the genes encoding PolDs exist only in the genomes of archaea. The archaeal GAN (GINS-associated nuclease) is believed to be a homolog of the eukaryotic Cdc45. In this study, we found that the Thermococcus sp. 4557 DP1 (small subunit of PolD) interacted with GINS15 in vitro, and the 3'-5' exonuclease activity of DP1 was inhibited by GINS15. We also demonstrated that the GAN, GINS15, and DP1 proteins interact to form a complex adapting a GAN-GINS15-DP1 order. The results of this study imply that the complex constitutes a core of the DNA replisome in archaea.

RevDate: 2019-05-17

Makarova KS, Wolf YI, Karamycheva S, et al (2019)

Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts.

mBio, 10(3): pii:mBio.00715-19.

Numerous, diverse, highly variable defense and offense genetic systems are encoded in most bacterial genomes and are involved in various forms of conflict among competing microbes or their eukaryotic hosts. Here we focus on the offense and self-versus-nonself discrimination systems encoded by archaeal genomes that so far have remained largely uncharacterized and unannotated. Specifically, we analyze archaeal genomic loci encoding polymorphic and related toxin systems and ribosomally synthesized antimicrobial peptides. Using sensitive methods for sequence comparison and the "guilt by association" approach, we identified such systems in 141 archaeal genomes. These toxins can be classified into four major groups based on the structure of the components involved in the toxin delivery. The toxin domains are often shared between and within each system. We revisit halocin families and substantially expand the halocin C8 family, which was identified in diverse archaeal genomes and also certain bacteria. Finally, we employ features of protein sequences and genomic locus organization characteristic of archaeocins and polymorphic toxins to identify candidates for analogous but not necessarily homologous systems among uncharacterized protein families. This work confidently predicts that more than 1,600 archaeal proteins, currently annotated as "hypothetical" in public databases, are components of conflict and self-versus-nonself discrimination systems.IMPORTANCE Diverse and highly variable systems involved in biological conflicts and self-versus-nonself discrimination are ubiquitous in bacteria but much less studied in archaea. We performed comprehensive comparative genomic analyses of the archaeal systems that share components with analogous bacterial systems and propose an approach to identify new systems that could be involved in these functions. We predict polymorphic toxin systems in 141 archaeal genomes and identify new, archaea-specific toxin and immunity protein families. These systems are widely represented in archaea and are predicted to play major roles in interactions between species and in intermicrobial conflicts. This work is expected to stimulate experimental research to advance the understanding of poorly characterized major aspects of archaeal biology.

RevDate: 2019-05-17

Li Z, Kinosita Y, Rodriguez-Franco M, et al (2019)

Positioning of the Motility Machinery in Halophilic Archaea.

mBio, 10(3): pii:mBio.00377-19.

Bacteria and archaea exhibit tactical behavior and can move up and down chemical gradients. This tactical behavior relies on a motility structure, which is guided by a chemosensory system. Environmental signals are sensed by membrane-inserted chemosensory receptors that are organized in large ordered arrays. While the cellular positioning of the chemotaxis machinery and that of the flagellum have been studied in detail in bacteria, we have little knowledge about the localization of such macromolecular assemblies in archaea. Although the archaeal motility structure, the archaellum, is fundamentally different from the flagellum, archaea have received the chemosensory machinery from bacteria and have connected this system with the archaellum. Here, we applied a combination of time-lapse imaging and fluorescence and electron microscopy using the model euryarchaeon Haloferax volcanii and found that archaella were specifically present at the cell poles of actively dividing rod-shaped cells. The chemosensory arrays also had a polar preference, but in addition, several smaller arrays moved freely in the lateral membranes. In the stationary phase, rod-shaped cells became round and chemosensory arrays were disassembled. The positioning of archaella and that of chemosensory arrays are not interdependent and likely require an independent form of positioning machinery. This work showed that, in the rod-shaped haloarchaeal cells, the positioning of the archaellum and of the chemosensory arrays is regulated in time and in space. These insights into the cellular organization of H. volcanii suggest the presence of an active mechanism responsible for the positioning of macromolecular protein complexes in archaea.IMPORTANCE Archaea are ubiquitous single cellular microorganisms that play important ecological roles in nature. The intracellular organization of archaeal cells is among the unresolved mysteries of archaeal biology. With this work, we show that cells of haloarchaea are polarized. The cellular positioning of proteins involved in chemotaxis and motility is spatially and temporally organized in these cells. This suggests the presence of a specific mechanism responsible for the positioning of macromolecular protein complexes in archaea.

RevDate: 2019-05-06

Isupov MN, Boyko KM, Sutter JM, et al (2019)

Corrigendum: Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization.

Frontiers in bioengineering and biotechnology, 7:79.

[This corrects the article DOI: 10.3389/fbioe.2019.00007.].

RevDate: 2019-05-15

Webster G, Mullins AJ, Watkins AJ, et al (2019)

Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments.

Microbiology resource announcements, 8(18): pii:8/18/e00342-19.

The genomes of two Methanococcoides spp. that were isolated from marine sediments and are capable of carrying out methanogenesis from choline and other methylotrophic substrates were sequenced. The average nucleotide identity and in silico DNA-DNA hybridization analyses demonstrate that they represent species different from those previously described.

RevDate: 2019-04-25

Gupta A, D Swati (2019)

Riboswitches in Archaea.

Combinatorial chemistry & high throughput screening pii:CCHTS-EPUB-98237 [Epub ahead of print].

AIM AND OBJECTIVE: Riboswitches are cis-acting, non-coding RNA elements found in the 5'UTR of bacterial mRNA and 3' UTR of eukaryotic mRNA, that fold in a complex manner to act as receptors for specific metabolites hence altering their conformation in response to the change in concentrations of a ligand or metabolite. Riboswitches function as gene regulators in numerous bacteria, archaea, fungi, algae and plants. This study identifies different classes of riboswitches in the Archaeal domain of life. Previous studies have suggested that Riboswitches carry a conserved aptameric domain in different domains of life. Since, Archaea are considered to be the most idiosyncratic organisms it was interesting to look for the conservation pattern of Riboswitches in these obviously strange microorganisms.

MATERIALS AND METHODS: Completely sequenced Archaeal Genomes present in the NCBI repository were used for studying riboswitches and other ncRNAs. The sequence files in FASTA format were downloaded from NCBI Genome database and information related to these genomes was retrieved from GenBank. Three bioinformatics approaches were used namely, ab initio, consensus structure prediction and statistical model-based prediction for identifying Riboswitches.

RESULTS: Archaeal genomes have a sporadic distribution of putative riboswitches like the TPP, FMN, Guanidine, Lysine and c-di-AMP riboswitches, which are known to occur in bacteria. Also, a class of riboswitch sensing c-di-GMP, a second messenger, has been identified in few Archaeal organisms.

CONCLUSION: This study clearly reveals that Bioinformatics methods are likely to play a major role in identifying conserved riboswitches and in establishing how widespread these classes are in all domains of life, even though the final confirmation may come from wet lab methods.

RevDate: 2019-05-02

Cândido ES, Cardoso MH, Chan LY, et al (2019)

Short Cationic Peptide Derived from Archaea with Dual Antibacterial Properties and Anti-Infective Potential.

ACS infectious diseases [Epub ahead of print].

Bacterial biofilms and associated infections represent one of the biggest challenges in the clinic, and as an alternative to counter bacterial infections, antimicrobial peptides have attracted great attention in the past decade. Here, ten short cationic antimicrobial peptides were generated through a sliding-window strategy on the basis of the 19-amino acid residue peptide, derived from a Pyrobaculum aerophilum ribosomal protein. PaDBS1R6F10 exhibited anti-infective potential as it decreased the bacterial burden in murine Pseudomonas aeruginosa cutaneous infections by more than 1000-fold. Adverse cytotoxic and hemolytic effects were not detected against mammalian cells. The peptide demonstrated structural plasticity in terms of its secondary structure in the different environments tested. PaDBS1R6F10 represents a promising antimicrobial agent against bacteria infections, without harming human cells.

RevDate: 2019-04-26

Wemheuer F, von Hoyningen-Huene AJE, Pohlner M, et al (2019)

Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean.

Archaea (Vancouver, B.C.), 2019:3717239.

Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by Candidatus Nitrosopumilus (Thaumarchaeota) and other members of the Nitrosopumilaceae (Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.

RevDate: 2019-05-28
CmpDate: 2019-05-28

Seitz KW, Dombrowski N, Eme L, et al (2019)

Asgard archaea capable of anaerobic hydrocarbon cycling.

Nature communications, 10(1):1822 pii:10.1038/s41467-019-09364-x.

Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.

RevDate: 2019-05-28
CmpDate: 2019-05-28

Dong X, Greening C, Rattray JE, et al (2019)

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.

Nature communications, 10(1):1816 pii:10.1038/s41467-019-09747-0.

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.

RevDate: 2019-04-21

Verma S, Kumar R, GK Meghwanshi (2019)

Identification of new members of alkaliphilic lipases in archaea and metagenome database using reconstruction of ancestral sequences.

3 Biotech, 9(5):165.

The application of bioinformatics in lipase research has the potential to discover robust members from different genomic/metagenomic databses. In this study, we explored the diversity and distribution of alkaliphilic lipases in archaea domain and metagenome data sets through phylogenetic survey. Reconstructed ancestral sequence of alkaphilic lipase was used to search the homologous alkaliphilic lipases among the archaea and metagenome public databases. Our investigation revealed a total 21 unique sequences of new alkaliphilic lipases in the archaeal and environmental metagenomic protein databases that shared significant sequence similarity to the bacterial alkaliphilic lipases. Most of the identified new members of alkaliphilic lipases belong to class Haloarchaea. The searched list of homologs also comprised of one characterized lipase from alkalohyperthermophilic Archaeoglobus fulgidus. All the newly identified alkaliphilic lipase members showed conserved pentapeptide [X-His-Ser-X-Gly] motif, a key feature of lipase family. Furthermore, detailed analysis of all these new sequences showed homology either with thermostable or alkalophilic lipases. The reconstructed ancestral sequence-based searches increased the sensitivity and efficacies to detect remotely homologous sequences. We hypothesize that this study can enrich our current knowledge on lipases in designing more potential thermo-alkaliphilic lipases for industrial applications.

RevDate: 2019-04-17

Langer SG, Gabris C, Einfalt D, et al (2019)

Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters.

Microbial biotechnology [Epub ahead of print].

Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.

RevDate: 2019-04-17

Gomes-Filho JV, L Randau (2019)

RNA stabilization in hyperthermophilic archaea.

Annals of the New York Academy of Sciences [Epub ahead of print].

Analyses of the RNA metabolism of hyperthermophilic archaea highlight the efficiency of regulatory RNAs and RNA-guided processes at extreme temperatures. These organisms must overcome the intrinsic thermolability of RNAs. Elevated levels of RNA modifications and structured GC-rich regions are observed for many universal noncoding RNA families. Guide RNAs are often protected from degradation by their presence within ribonucleoprotein complexes. Modification and ligation of RNA termini can be employed to impair exonucleolytic degradation. Finally, antisense strand transcription promotes the formation of RNA duplexes and can be used to stabilize RNA regions. In our review, we provide examples of these RNA stabilization mechanisms that have been observed in hyperthermophilic archaeal model organisms.

RevDate: 2019-04-26

Santos-Zavaleta A, Pérez-Rueda E, Sánchez-Pérez M, et al (2019)

Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.

BMC genomics, 20(1):299 pii:10.1186/s12864-019-5619-z.

BACKGROUND: Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms.

RESULTS: In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σS regulon in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69 bacterial taxonomical divisions and using E. coli K-12 as a framework, we suggest three main events that resulted in this regulon's actual form: (i) in a first step, rpoS, a gene widely distributed in bacteria and archaea cellular domains, was recruited to regulate genes involved in ancient metabolic processes, such as those associated with glycolysis and the tricarboxylic acid cycle; (ii) in a second step, the regulon recruited those genes involved in metabolic processes, which are mainly taxonomically constrained to Proteobacteria, with some secondary losses, such as those genes involved in responses to stress or starvation and cell adhesion, among others; and (iii) in a posterior step, Crl might have been recruited in Enterobacteriaceae; because its taxonomical pattern constrained to this bacterial order, however further analysis are necessary.

CONCLUSIONS: Therefore, we suggest that the regulon Crl is highly flexible for phenotypic adaptation, probably as consequence of the diverse growth environments associated with all organisms in which members of this regulatory network are present.

RevDate: 2019-05-16

Eggenberger OM, Leriche G, Koyanagi T, et al (2019)

Fluid surface coatings for solid-state nanopores: comparison of phospholipid bilayers and archaea-inspired lipid monolayers.

Nanotechnology, 30(32):325504 [Epub ahead of print].

In the context of sensing and characterizing single proteins with synthetic nanopores, lipid bilayer coatings provide at least four benefits: first, they minimize unwanted protein adhesion to the pore walls by exposing a zwitterionic, fluid surface. Second, they can slow down protein translocation and rotation by the opportunity to tether proteins with a lipid anchor to the fluid bilayer coating. Third, they provide the possibility to impart analyte specificity by including lipid anchors with a specific receptor or ligand in the coating. Fourth, they offer a method for tuning nanopore diameters by choice of the length of the lipid's acyl chains. The work presented here compares four properties of various lipid compositions with regard to their suitability as nanopore coatings for protein sensing experiments: (1) electrical noise during current recordings through solid-state nanopores before and after lipid coating, (2) long-term stability of the recorded current baseline and, by inference, of the coating, (3) viscosity of the coating as quantified by the lateral diffusion coefficient of lipids in the coating, and (4) the success rate of generating a suitable coating for quantitative nanopore-based resistive pulse recordings. We surveyed lipid coatings prepared from bolaamphiphilic, monolayer-forming lipids inspired by extremophile archaea and compared them to typical bilayer-forming phosphatidylcholine lipids containing various fractions of curvature-inducing lipids or cholesterol. We found that coatings from archaea-inspired lipids provide several advantages compared to conventional phospholipids; the stable, low noise baseline qualities and high viscosity make these membranes especially suitable for analysis that estimates physical protein parameters such as the net charge of proteins as they enable translocation events with sufficiently long duration to time-resolve dwell time distributions completely. The work presented here reveals that the ease or difficulty of coating a nanopore with lipid membranes did not depend significantly on the composition of the lipid mixture, but rather on the geometry and surface chemistry of the nanopore in the solid state substrate. In particular, annealing substrates containing the nanopore increased the success rate of generating stable lipid coatings.

RevDate: 2019-05-08
CmpDate: 2019-05-08

Xiong L, Liu S, Chen S, et al (2019)

A new type of DNA phosphorothioation-based antiviral system in archaea.

Nature communications, 10(1):1688 pii:10.1038/s41467-019-09390-9.

Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.

RevDate: 2019-04-02

Bayer B, Vojvoda J, Reinthaler T, et al (2019)

Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

Two mesophilic, neutrophilic and aerobic marine ammonia-oxidizing archaea, designated strains NF5T and D3CT, were isolated from coastal surface water of the Northern Adriatic Sea. Cells were straight small rods 0.20-0.25 µm wide and 0.49-2.00 µm long. Strain NF5T possessed archaella as cell appendages. Glycerol dibiphytanyl glycerol tetraethers with zero to four cyclopentane moieties (GDGT-0 to GDGT-4) and crenarchaeol were the major core lipids. Menaquinone MK6 : 0 was the major respiratory quinone. Both isolates gained energy by oxidizing ammonia (NH3) to nitrite (NO2-) and used bicarbonate as a carbon source. Strain D3CT was able use urea as a source of ammonia for energy production and growth. Addition of hydrogen peroxide (H2O2) scavengers (catalase or α-keto acids) was required to sustain growth. Optimal growth occurred between 30 and 32 °C, pH 7.1 and 7.3 and between 34 and 37‰ salinity. The cellular metal abundance ranking of both strains was Fe>Zn>Cu>Mn>Co. The genomes of strains NF5T and D3CT have a DNA G+C content of 33.4 and 33.8 mol%, respectively. Phylogenetic analyses of 16S rRNA gene sequences revealed that both strains are affiliated with the class Nitrososphaeria, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. The two isolates are separated by phenotypic and genotypic characteristics and are assigned to distinct species within the genus Nitrosopumilus gen. nov. according to average nucleotide identity thresholds of their closed genomes. Isolates NF5T (=JCM 32270T =NCIMB 15114T) and D3CT (=JCM 32271T =DSM 106147T =NCIMB 15115T) are type strains of the species Nitrosopumilusadriaticus sp. nov. and Nitrosopumiluspiranensis sp. nov., respectively.

RevDate: 2019-04-02

Straka LL, Meinhardt KA, Bollmann A, et al (2019)

Affinity informs environmental cooperation between ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (Anammox) bacteria.

The ISME journal pii:10.1038/s41396-019-0408-x [Epub ahead of print].

Anaerobic ammonia-oxidizing (Anammox) bacteria (AnAOB) rely on nitrite supplied by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Affinities for ammonia and oxygen play a crucial role in AOA/AOB competition and their association with AnAOB. In this work we measured the affinity constants for ammonia and oxygen (half-saturation; km) of two freshwater AOA enrichments, an AOA soil isolate (N. viennensis), and a freshwater AnAOB enrichment. The AOA enrichments had similar kinetics (μmax ≈ 0.36 d-1, km,NH4 ≈ 0.78 µM, and km,O2 ≈ 2.9 µM), whereas N. viennensis had similar km values but lower μmax (0.23 d-1). In agreement with the current paradigm, these AOA strains showed a higher affinity for ammonia (lower km,NH4; 0.34-1.27 µM) than published AOB measurements (>20 µM). The slower growing AnAOB (μmax ≈ 0.16 d-1) had much higher km values (km,NH4 ≈ 132 µM, km,NO2 ≈ 48 µM) and were inhibited by oxygen at low levels (half-oxygen inhibition; ki,O2 ≈ 0.092 µM). The higher affinity of AOA for ammonia relative to AnAOB, suggests AOA/AnAOB cooperation is only possible where AOA do not outcompete AnAOB for ammonia. Using a biofilm model, we show that environments of ammonia/oxygen counter diffusion, such as stratified lakes, favors this cooperation.

RevDate: 2019-04-15

Zou D, Li Y, Kao SJ, et al (2019)

Genomic adaptation to eutrophication of ammonia-oxidizing archaea in the Pearl River estuary.

Environmental microbiology [Epub ahead of print].

Ammonia-oxidizing archaea (AOA) are ubiquitous in natural ecosystems, and they are responsible for a significant fraction of ammonia oxidation globally. Since the first AOA isolate was established a decade ago, molecular surveys of their environmental distribution [based primarily on amplicon sequencing of the amoA, which codes for the alpha subunit of ammonia monooxygenase (AMO)], show that their habitats are believed to range from marine to terrestrial environments. However, the mechanisms of adaptation underpinning to their habitat expansion remain poorly understood. Here, we report that AOA accounts for almost all of the ammonia oxidizers in the shelf water adjacent to the Pearl River estuary (PRE), with the Nitrosopumilus maritimus SCM1-like (SCM1-like) being the main amoA genotype. Using a metagenomic approach, seven high-quality AOA genomes were reconstructed from the PRE. Phylogenetic analysis indicated that four of these genomes with high completeness were closely affiliated with the Nitrosomatrinus catalina strain SPOT01, which was originally isolated off the coast of California. Genomic comparison revealed that the PRE AOA genomes encoded genes functioning in amino acid synthesis, xenobiotic biodegradation metabolism and transportation of inorganic phosphate and heavy metals. This illustrates the different adaptations of AOA in one of the largest estuaries in China, which is strongly influenced by anthropogenic input. Overall, this study provides additional genomic information about estuarine AOA and highlights the importance of their contribution to nitrification in eutrophic coastal environments.

RevDate: 2019-04-27

Wu RN, Meng H, Wang YF, et al (2019)

Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests.

Applied microbiology and biotechnology, 103(10):4229-4240.

Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al3+, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.

RevDate: 2019-04-16

Chen SC, Musat N, Lechtenfeld OJ, et al (2019)

Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep.

Nature, 568(7750):108-111.

Ethane is the second most abundant component of natural gas in addition to methane, and-similar to methane-is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps1-3, and through ethane-dependent sulfate reduction in slurries4-7. Nevertheless, the microorganisms and reactions that catalyse this process have to date remained unknown8. Here we describe ethane-oxidizing archaea that were obtained by specific enrichment over ten years, and analyse these archaea using phylogeny-based fluorescence analyses, proteogenomics and metabolite studies. The co-culture, which oxidized ethane completely while reducing sulfate to sulfide, was dominated by an archaeon that we name 'Candidatus Argoarchaeum ethanivorans'; other members were sulfate-reducing Deltaproteobacteria. The genome of Ca. Argoarchaeum contains all of the genes that are necessary for a functional methyl-coenzyme M reductase, and all subunits were detected in protein extracts. Accordingly, ethyl-coenzyme M (ethyl-CoM) was identified as an intermediate by liquid chromatography-tandem mass spectrometry. This indicated that Ca. Argoarchaeum initiates ethane oxidation by ethyl-CoM formation, analogous to the recently described butane activation by 'Candidatus Syntrophoarchaeum'9. Proteogenomics further suggests that oxidation of intermediary acetyl-CoA to CO2 occurs through the oxidative Wood-Ljungdahl pathway. The identification of an archaeon that uses ethane (C2H6) fills a gap in our knowledge of microorganisms that specifically oxidize members of the homologous alkane series (CnH2n+2) without oxygen. Detection of phylogenetic and functional gene markers related to those of Ca. Argoarchaeum at deep-sea gas seeps10-12 suggests that archaea that are able to oxidize ethane through ethyl-CoM are widespread members of the local communities fostered by venting gaseous alkanes around these seeps.

RevDate: 2019-03-29

Qiu X, Yao Y, Wang H, et al (2019)

Halophilic Archaea Mediate the Formation of Proto-Dolomite in Solutions With Various Sulfate Concentrations and Salinities.

Frontiers in microbiology, 10:480.

In the past several decades, sulfate concentration and salinity have been considered to be the two essential hydrochemical factors in the formation of dolomite, yet arguments against this hypothesis have existed simultaneously. To clarify the effects of sulfate concentration and salinity in the mineralization of dolomite, we conducted experiments on dolomite precipitation mediated by a halophilic archaeon, Natrinema sp. J7-1 with various sulfate concentrations and salinities. This strain was cultured in a series of modified growth media (MGM) with salinities of 140, 200, and 280‰. Cells in the post-log phase were harvested and used to mediate the formation of dolomite in solutions with various sulfate concentrations of 0, 3, 29.8, and 100 mM and salinities of 140, 200, and 280‰. X-ray diffraction (XRD) spectra showed that proto-dolomite, monohydrocalcite, and aragonite formed in samples with cells, yet only aragonite was detected in samples without cells. Proto-dolomite was found in all biotic samples, regardless of the variation in salinity and sulfate concentration. Moreover, the relative abundances of proto-dolomite in the precipitates were positively correlated with the salinities of the media but were uncorrelated with the sulfate concentrations of the solutions. Scanning electronic microscopy (SEM) and energy dispersive spectroscopy (EDS) results showed that all the proto-dolomites were sphere or sphere aggregates with a mole ratio of Mg/Ca close to 1.0. No obvious variations in morphology and Mg/Ca were found among samples with various sulfate concentrations or salinities. This work reveals that a variation of sulfate concentration in solution (from 0 to 100 mM) does not affect the formation of dolomite mediated by halophilic archaea, but an increase of salinity (from 140 to 280‰) enhances this process. Our results indicate that under natural conditions, an increase in salinity may be more significant than the decrease of sulfates in microbe-mediated dolomite formation.

RevDate: 2019-03-26

Fu X, Adams Z, J Maupin-Furlow (2019)

Assays for ubiquitin-like protein ligation and proteasome function in archaea.

Methods in enzymology, 619:161-178.

Ubiquitin-like protein (Ubl) ligation is common to diverse archaea and targets many cellular pathways, including those associated with sulfur mobilization, and also tags proteins as substrates for degradation by the proteasome. Here we highlight protocols to assay proteasome function and Ubl ligation in archaea. A chase assay is described to monitor the impact of proteasome function on the stability of Ubl-modified proteins in the cell. A method to reconstitute Ubl ligation using a purified E1-like enzyme (UbaA), Ubl (SAMP2), methionine sulfoxide reductase A (MsrA), and cell lysate of an ΔmsrA ΔubaA Δsamp1-3 mutant is also described. MsrA is found to have the surprising ability to stimulate the formation of Ubl bonds. Haloferax volcanii, a halophilic archaeon originally isolated from the Dead Sea, serves as the model organism for these protocols.

RevDate: 2019-03-29

Sogodogo E, Fellag M, Loukil A, et al (2019)

Nine Cases of Methanogenic Archaea in Refractory Sinusitis, an Emerging Clinical Entity.

Frontiers in public health, 7:38.

The authors report the cases of 9 patients eventually diagnosed with methanogenic archaea refractory or recalcitrant chronic rhinosinusitis, a condition known to involve various anaerobic bacteria but in which the role of methanogenic archaea is unknown. The authors retrospectively searched these microorganisms by PCR in surgically-collected sinusal pus specimens from patients diagnosed with refractory sinusitis, defined by the persistance of sinus inflammation and related-symptoms for more than 12 weeks despite appropriate treatment. Of the 116 tested sinus surgical specimens, 12 (10.3%) from 9 patients (six females, three males; aged 20-71 years) were PCR-positive. These specimens were further investigated by fluorescence in-situ hybridization, PCR amplicon-sequencing and culture. Methanobrevibacter smithii was documented in four patients and Methanobrevibacter oralis in another four, one of whom was also culture-positive. They were associated with a mixed flora including Gram-positive and Gram-negative bacteria. In the latter patient, "Methanobrevibacter massiliense" was the sole microorganism detected. These results highlight methanogenic archaea as being part of a mixed anaerobic flora involved in refractory sinusitis, and suggest that the treatment of this condition should include an antibiotic active against methanogens, notably a nitroimidazole derivative.

RevDate: 2019-03-18

Braun F, Thomalla L, van der Does C, et al (2019)

Cyclic nucleotides in archaea: Cyclic di-AMP in the archaeon Haloferax volcanii and its putative role.

MicrobiologyOpen [Epub ahead of print].

The role of cyclic nucleotides as second messengers for intracellular signal transduction has been well described in bacteria. One recently discovered bacterial second messenger is cyclic di-adenylate monophosphate (c-di-AMP), which has been demonstrated to be essential in bacteria. Compared to bacteria, significantly less is known about second messengers in archaea. This study presents the first evidence of in vivo presence of c-di-AMP in an archaeon. The model organism Haloferax volcanii was demonstrated to produce c-di-AMP. Its genome encodes one diadenylate cyclase (DacZ) which was shown to produce c-di-AMP in vitro. Similar to bacteria, the dacZ gene is essential and homologous overexpression of DacZ leads to cell death, suggesting the need for tight regulation of c-di-AMP levels. Such tight regulation often indicates the control of important regulatory processes. A central target of c-di-AMP signaling in bacteria is cellular osmohomeostasis. The results presented here suggest a comparable function in H. volcanii. A strain with decreased c-di-AMP levels exhibited an increased cell area in hypo-salt medium, implying impaired osmoregulation. In summary, this study expands the field of research on c-di-AMP and its physiological function to archaea and indicates that osmoregulation is likely to be a common function of c-di-AMP in bacteria and archaea.

RevDate: 2019-04-11

Du Y, Shu K, Guo X, et al (2019)

Moderate Grazing Promotes Grassland Nitrous Oxide Emission by Increasing Ammonia-Oxidizing Archaea Abundance on the Tibetan Plateau.

Current microbiology, 76(5):620-625.

Grasslands are suffering from long-term overgrazing because of the population inflation. Furthermore, nitrous oxide (N2O) is a major greenhouse gas that also depletes stratospheric ozone. However, the emission rate of grassland N2O and underlying mechanisms remained unclear under different grazing intensities. We conducted a field manipulation under four grazing intensities to compare its N2O fluxes and main affected factors. It was indicated that alpine meadow N2O emission rates increased from 39.7 ± 3.1 to 47.8 ± 2.3 μg m-2 h-1 (p < 0.05), then decreased to 43.4 ± 4.1 and 32.9 ± 1.4 μg m-2 h-1 with grazing intensity increasing from 4 to 8, 12 and 16 sheep ha-1, respectively. Multiple-stepwise regression analysis indicated that the predominant affected soil factors were separately TN and BD, pH and BD, also pH and BD, SOC and BD. Simple linear regression models revealed that ammonia-oxidizing archaea (AOA) contributed much to N2O emission (R2 = 0.77). Additionally, the R2 coefficient of linear regression was 0.87 between nosZ genes and N2O emission rates in alpine meadow. Much attention should be paid to protecting alpine meadow from degradation to mitigate N2O emission source on the Tibetan Plateau.

RevDate: 2019-03-23

He D, Piergentili C, Ross J, et al (2019)

Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea.

The Biochemical journal, 476(6):975-989 pii:BCJ20180922.

Ferritins are a large family of intracellular proteins that protect the cell from oxidative stress by catalytically converting Fe(II) into less toxic Fe(III) and storing iron minerals within their core. Encapsulated ferritins (EncFtn) are a sub-family of ferritin-like proteins, which are widely distributed in all bacterial and archaeal phyla. The recently characterized Rhodospirillum rubrum EncFtn displays an unusual structure when compared with classical ferritins, with an open decameric structure that is enzymatically active, but unable to store iron. This EncFtn must be associated with an encapsulin nanocage in order to act as an iron store. Given the wide distribution of the EncFtn family in organisms with diverse environmental niches, a question arises as to whether this unusual structure is conserved across the family. Here, we characterize EncFtn proteins from the halophile Haliangium ochraceum and the thermophile Pyrococcus furiosus, which show the conserved annular pentamer of dimers topology. Key structural differences are apparent between the homologues, particularly in the centre of the ring and the secondary metal-binding site, which is not conserved across the homologues. Solution and native mass spectrometry analyses highlight that the stability of the protein quaternary structure differs between EncFtn proteins from different species. The ferroxidase activity of EncFtn proteins was confirmed, and we show that while the quaternary structure around the ferroxidase centre is distinct from classical ferritins, the ferroxidase activity is still inhibited by Zn(II). Our results highlight the common structural organization and activity of EncFtn proteins, despite diverse host environments and contexts within encapsulins.

RevDate: 2019-04-30

Borrel G, Adam PS, McKay LJ, et al (2019)

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.

Nature microbiology, 4(4):603-613.

Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea ('Candidatus Methanoliparia'). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.

RevDate: 2019-04-30

Wang Y, Wegener G, Hou J, et al (2019)

Expanding anaerobic alkane metabolism in the domain of Archaea.

Nature microbiology, 4(4):595-602.

Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea1. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global survey of MCR-encoding genomes based on metagenomic data from various environments. Eleven high-quality mcr-containing metagenomic-assembled genomes were obtained belonging to the Archaeoglobi in the Euryarchaeota, Hadesarchaeota and different TACK superphylum archaea, including the Nezhaarchaeota, Korarchaeota and Verstraetearchaeota. Archaeoglobi WYZ-LMO1 and WYZ-LMO3 and Korarchaeota WYZ-LMO9 encode both the (reverse) methanogenesis and the dissimilatory sulfate reduction pathway, suggesting that they have the genomic potential to couple both pathways in individual organisms. The Hadesarchaeota WYZ-LMO4-6 and Archaeoglobi JdFR-42 encode highly divergent MCRs, enzymes that may enable them to thrive on non-methane alkanes. The occurrence of mcr genes in different archaeal phyla indicates that MCR-based alkane metabolism is common in the domain of Archaea.

RevDate: 2019-04-11

Lopes-Dos-Santos RMA, De Troch M, Bossier P, et al (2019)

Labelling halophilic Archaea using 13C and 15N stable isotopes: a potential tool to investigate haloarchaea consumption by metazoans.

Extremophiles : life under extreme conditions, 23(3):359-365.

The use of stable isotope (SI) labelling and tracing of live diets is currently considered one of the most comprehensive tools to detect their uptake and assimilation by aquatic organisms. These techniques are indeed widely used in nutritional studies to follow the fate of specific microbial dietary components, unraveling trophic interactions. Nevertheless, to the current date our understanding of aquatic trophic relationships has yet to include a whole domain of life, the Archaea. The aim of the present research was, therefore, to describe a halophilic Archaea (haloarchaea) labelling procedure, using the SI 13C and 15N, to enable the application of SI tracing in future studies of haloarchaea consumption by aquatic metazoans. To this end, three 13C enriched carbon sources and two 15N enriched nitrogen sources were tested as potential labels to enrich cells of three haloarchaea strains when supplemented to the culture medium. Our overall results indicate 13C-glycerol as the most effective carbon source to achieve an efficient 13C enrichment in haloarchaea cells, with Δδ13C values above 5000‰ in all tested haloarchaea strains. As for 15N enriched nitrogen sources, both (15NH4)2SO4 and 15NH4Cl seem to be readily assimilated, also resulting in efficient 15N enrichment in haloarchaea cells, with Δδ15N values higher than 20,000‰. We believe that the proposed methodology will allow for the use of SI labelled haloarchaea biomass in feeding tests, potentially providing unambiguous confirmation of the assimilation of haloarchaea biomass by aquatic metazoans.

RevDate: 2019-04-12

Díaz-Perales A, Quesada V, Peinado JR, et al (2019)

Withdrawal: Identification and characterization of human archaemetzincin-1 and -2, two novel members of a family of metalloproteases widely distributed in Archaea.

The Journal of biological chemistry, 294(4):1434.

RevDate: 2019-05-20

Rissanen AJ, Peura S, Mpamah PA, et al (2019)

Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake.

FEMS microbiology letters, 366(5):.

Although sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA) in sediment cores collected from a typical small boreal lake. While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles. The vertical stratification patterns of the bacterial and archaeal communities resembled those in marine sediments with well-characterized groups (e.g. Methanomicrobia, Proteobacteria, Cyanobacteria, Bacteroidetes) dominating in the surface sediment and being replaced by poorly-known groups (e.g. Bathyarchaeota, Aminicenantes and Caldiserica) in the deeper layers. The results also suggested that, similar to marine systems, the deep bacterial and archaeal communities were predominantly assembled by selective survival of taxa able to persist in the low energy conditions. Methanotrophs were rare, further corroborating the role of these methanogen-rich sediments as important methane emitters. Based on their taxonomy, the deep-dwelling groups were putatively organo-heterotrophic, organo-autotrophic and/or acetogenic and thus may contribute to changes in the lake sediment carbon storage.

RevDate: 2019-06-09

Barnett DJM, Mommers M, Penders J, et al (2019)

Intestinal archaea inversely associated with childhood asthma.

The Journal of allergy and clinical immunology, 143(6):2305-2307.

RevDate: 2019-02-27

Wang L, Li K, Sheng R, et al (2019)

Remarkable N2O emissions by draining fallow paddy soil and close link to the ammonium-oxidizing archaea communities.

Scientific reports, 9(1):2550 pii:10.1038/s41598-019-39465-y.

Fallow paddies experience natural flooding and draining water status due to rainfall and evaporation, which could induce considerable nitrous oxide (N2O) emissions and need to be studied specially. In this study, intact soil columns were collected from a fallow paddy field and the flooding-draining process was simulated in a microcosm experiment. The results showed that both N2O concentrations in the soil and N2O emission rates were negligible during flooding period, which were greatly elevated by draining the fallow paddy soil. The remarkable N2O concentrations in the soil and N2O emission/h during draining both had significant relationships with the Arch-amoA gene (P < 0.01) but not the Bac-amoA, narG, nirK, nirS, and nosZ genes, indicating that the ammonium-oxidizing archaea (AOA) might be the important players in soil N2O net production and emissions after draining. Moreover, we observed that N2O concentrations in the upper soil layers (0-10 cm) were not significantly different from that in the 10-20 cm layer under draining condition (P > 0.05). However, the number of AOA and the nitrification substrate (NH4+-N) in the 0-10 cm layer were significantly higher than in the 10-20 cm layer (P < 0.01), indicating N2O production in the 0-10 cm layer might be higher than the measured concentration and would contribute considerably to N2O emissions as shorter distance of gas diffusion to the soil surface.

RevDate: 2019-04-08

Wang Y, Feng X, Natarajan VP, et al (2019)

Diverse anaerobic methane- and multi-carbon alkane-metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment.

Environmental microbiology, 21(4):1344-1355.

Anaerobic oxidation of methane greatly contributes to global carbon cycling, yet the anaerobic oxidation of non-methane alkanes by archaea was only recently detected in lab enrichments. The distribution and activity of these archaea in natural environments are not yet reported and understood. Here, a combination of metagenomic and metatranscriptomic approaches was utilized to understand the ecological roles and metabolic potentials of methyl-coenzyme M reductase (MCR)-based alkane oxidizing (MAO) archaea in Guaymas Basin sediments. Diverse MAO archaea, including multi-carbon alkane oxidizer Ca. Syntrophoarchaeum spp., anaerobic methane oxidizing archaea ANME-1 and ANME-2c as well as sulfate-reducing bacteria HotSeep-1 and Seep-SRB2 that potentially involved in MAO processes, coexisted and showed activity in Guaymas Basin sediments. High-quality genomic bins of Ca. Syntrophoarchaeum spp., ANME-1 and ANME-2c were retrieved. They all contain and expressed mcr genes and genes in Wood-Ljungdahl pathway for the complete oxidation from alkane to CO2 in local environment, while Ca. Syntrophoarchaeum spp. also possess beta-oxidation genes for multi-carbon alkane degradation. A global survey of potential multi-carbon alkane metabolism archaea shows that they are usually present in organic rich environments but are not limit to hydrothermal or marine ecosystems. Our study provided new insights into ecological and metabolic potentials of MAO archaea in natural environments.

RevDate: 2019-04-30
CmpDate: 2019-04-30

Maier LK, A Marchfelder (2019)

It's all about the T: transcription termination in archaea.

Biochemical Society transactions, 47(1):461-468.

One of the most fundamental biological processes driving all life on earth is transcription. The, at first glance, relatively simple cycle is divided into three stages: initiation at the promoter site, elongation throughout the open reading frame, and finally termination and product release at the terminator. In all three processes, motifs of the template DNA and protein factors of the transcription machinery including the multisubunit polymerase itself as well as a broad range of associated transcription factors work together and mutually influence each other. Despite several decades of research, this interplay holds delicate mechanistic and structural details as well as interconnections yet to be explored. One of the surprising characteristics of archaeal biology is the use of eukaryotic-like information processing systems against a backdrop of a bacterial-like genome. Archaeal genomes usually comprise main chromosomes alongside chromosomal plasmids, and the genetic information is encoded in single transcriptional units as well as in multicistronic operons alike their bacterial counterparts. Moreover, archaeal genomes are densely packed and this necessitates a tight regulation of transcription and especially assured termination events in order to prevent read-through into downstream coding regions and the accumulation of antisense transcripts.

RevDate: 2019-03-03

Ul-Hasan S, Bowers RM, Figueroa-Montiel A, et al (2019)

Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California.

PloS one, 14(2):e0212355 pii:PONE-D-18-28583.

Microbial communities control numerous biogeochemical processes critical for ecosystem function and health. Most analyses of coastal microbial communities focus on the characterization of bacteria present in either sediment or seawater, with fewer studies characterizing both sediment and seawater together at a given site, and even fewer studies including information about non-bacterial microbial communities. As a result, knowledge about the ecological patterns of microbial biodiversity across domains and habitats in coastal communities is limited-despite the fact that archaea, bacteria, and microbial eukaryotes are present and known to interact in coastal habitats. To better understand microbial biodiversity patterns in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites along the coastline of Puerto Nuevo, Baja California, Mexico using both 16S and 18S rRNA gene amplicon sequencing. We found that sediment hosted approximately 500-fold more operational taxonomic units (OTUs) for bacteria, archaea, and microbial eukaryotes than seawater (p < 0.001). Distinct phyla were found in sediment versus seawater samples. Of the top ten most abundant classes, Cytophagia (bacterial) and Chromadorea (eukaryal) were specific to the sediment environment, whereas Cyanobacteria and Bacteroidia (bacterial) and Chlorophyceae (eukaryal) were specific to the seawater environment. A total of 47 unique genera were observed to comprise the core taxa community across environment types and sites. No archaeal taxa were observed as part of either the abundant or core taxa. No significant differences were observed for sediment community composition across domains or between sites. For seawater, the bacterial and archaeal community composition was statistically different for the Major Outlet site (p < 0.05), the site closest to a residential area, and the eukaryal community composition was statistically different between all sites (p < 0.05). Our findings highlight the distinct patterns and spatial heterogeneity in microbial communities of a coastal region in Baja California, Mexico.

RevDate: 2019-03-15

Flemming HC, S Wuertz (2019)

Bacteria and archaea on Earth and their abundance in biofilms.

Nature reviews. Microbiology, 17(4):247-260.

Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 1030 cells) exist in the 'big five' habitats: deep oceanic subsurface (4 × 1029), upper oceanic sediment (5 × 1028), deep continental subsurface (3 × 1029), soil (3 × 1029) and oceans (1 × 1029). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20-80% of cells in the subsurface exist as biofilms. Hence, overall, 40-80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life.

RevDate: 2019-02-11

Serrano P, Alawi M, de Vera JP, et al (2019)

Response of Methanogenic Archaea from Siberian Permafrost and Non-permafrost Environments to Simulated Mars-like Desiccation and the Presence of Perchlorate.

Astrobiology, 19(2):197-208.

Numerous preflight investigations were necessary prior to the exposure experiment BIOMEX on the International Space Station to test the basic potential of selected microorganisms to resist or even to be active under Mars-like conditions. In this study, methanogenic archaea, which are anaerobic chemolithotrophic microorganisms whose lifestyle would allow metabolism under the conditions on early and recent Mars, were analyzed. Some strains from Siberian permafrost environments have shown a particular resistance. In this investigation, we analyzed the response of three permafrost strains (Methanosarcina soligelidi SMA-21, Candidatus Methanosarcina SMA-17, Candidatus Methanobacterium SMA-27) and two related strains from non-permafrost environments (Methanosarcina mazei, Methanosarcina barkeri) to desiccation conditions (-80°C for 315 days, martian regolith analog simulants S-MRS and P-MRS, a 128-day period of simulated Mars-like atmosphere). Exposure of the different methanogenic strains to increasing concentrations of magnesium perchlorate allowed for the study of their metabolic shutdown in a Mars-relevant perchlorate environment. Survival and metabolic recovery were analyzed by quantitative PCR, gas chromatography, and a new DNA-extraction method from viable cells embedded in S-MRS and P-MRS. All strains survived the two Mars-like desiccating scenarios and recovered to different extents. The permafrost strain SMA-27 showed an increased methanogenic activity by at least 10-fold after deep-freezing conditions. The methanogenic rates of all strains did not decrease significantly after 128 days S-MRS exposure, except for SMA-27, which decreased 10-fold. The activity of strains SMA-17 and SMA-27 decreased after 16 and 60 days P-MRS exposure. Non-permafrost strains showed constant survival and methane production when exposed to both desiccating scenarios. All strains showed unaltered methane production when exposed to the perchlorate concentration reported at the Phoenix landing site (2.4 mM) or even higher concentrations. We conclude that methanogens from (non-)permafrost environments are suitable candidates for potential life in the martian subsurface and therefore are worthy of study after space exposure experiments that approach Mars-like surface conditions.

RevDate: 2019-05-07

Isupov MN, Boyko KM, Sutter JM, et al (2019)

Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization.

Frontiers in bioengineering and biotechnology, 7:7.

Two new thermophilic branched chain amino acid transaminases have been identified within the genomes of different hyper-thermophilic archaea, Geoglobus acetivorans, and Archaeoglobus fulgidus. These enzymes belong to the class IV of transaminases as defined by their structural fold. The enzymes have been cloned and over-expressed in Escherichia coli and the recombinant enzymes have been characterized both biochemically and structurally. Both enzymes showed high thermostability with optimal temperature for activity at 80 and 85°C, respectively. They retain good activity after exposure to 50% of the organic solvents, ethanol, methanol, DMSO and acetonitrile. The enzymes show a low activity to (R)-methylbenzylamine but no activity to (S)-methylbenzylamine. Both enzymes have been crystallized and their structures solved in the internal aldimine form, to 1.9 Å resolution for the Geoglobus enzyme and 2.0 Å for the Archaeoglobus enzyme. Also the Geoglobus enzyme structure has been determined in complex with the amino acceptor α-ketoglutarate and the Archaeoglobus enzyme in complex with the inhibitor gabaculine. These two complexes have helped to determine the conformation of the enzymes during enzymatic turnover and have increased understanding of their substrate specificity. A comparison has been made with another (R) selective class IV transaminase from the fungus Nectria haematococca which was previously studied in complex with gabaculine. The subtle structural differences between these enzymes has provided insight regarding their different substrate specificities.

RevDate: 2019-04-02

Portugal R, Shao N, Whitman WB, et al (2019)

Identification and biosynthesis of 2-(1H-imidazol-5-yl) ethan-1-ol (histaminol) in methanogenic archaea.

Microbiology (Reading, England), 165(4):455-462.

Histaminol is a relatively rare metabolite most commonly resulting from histidine metabolism. Here we describe histaminol production and secretion into the culture broth by the methanogen Methanococcus maripaludis S2 as well as a number of other methanogens. This work is the first identification of this compound as a natural product in methanogens. Its biosynthesis from histidine was confirmed by the incorporation of 2H3-histidine into histaminol by growing cells of M. maripaludis S2. Possible functions of this molecule could be cell signaling as observed with histamine in eukaryotes or uptake of metal ions.

RevDate: 2019-05-03
CmpDate: 2019-05-03

Jiao S, Xu Y, Zhang J, et al (2019)

Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems.

Microbiome, 7(1):15 pii:10.1186/s40168-019-0630-9.

BACKGROUND: Understanding the spatial distributions and ecological diversity of soil archaeal communities in agricultural ecosystems is crucial for improvements in crop productivity. Here, we conducted a comprehensive, continental-scale survey of soil archaeal communities in adjacent pairs of maize (dryland) and rice (wetland) fields in eastern China.

RESULTS: We revealed the consequential roles of environmental filtering in driving archaeal community assembly for both maize and rice fields. Rice fields, abundant with Euryarchaeota, had higher archaeal diversity and steeper distance-decay slopes than maize fields dominated by Thaumarchaeota. Dominant soil archaea showed distinct continental atlases and niche differentiation between dryland and wetland habitats, where they were associated with soil pH and mean annual temperature, respectively. After identifying their environmental preferences, we grouped the dominant archaeal taxa into different ecological clusters and determined the unique co-occurrence patterns within each cluster. Using this empirical dataset, we built a continental atlas of soil archaeal communities to provide reliable estimates of their spatial distributions in agricultural ecosystems.

CONCLUSIONS: Environmental filtering plays a crucial role in driving the distinct continental atlases of dominant soil archaeal communities between dryland and wetland, with contrasting strategies of archaeal-driven nutrient cycling within these two agricultural ecosystems. These findings improve our ability to predict how soil archaeal communities respond to environmental changes and to manage soil archaeal communities for provisioning of agricultural ecosystem services.

RevDate: 2019-04-10

Reinhardt A, Johnsen U, P Schönheit (2019)

l-Rhamnose catabolism in archaea.

Molecular microbiology, 111(4):1093-1108.

The halophilic archaeon Haloferax volcanii utilizes l-rhamnose as a sole carbon and energy source. It is shown that l-rhamnose is taken up by an ABC transporter and is oxidatively degraded to pyruvate and l-lactate via the diketo-hydrolase pathway. The genes involved in l-rhamnose uptake and degradation form a l-rhamnose catabolism (rhc) gene cluster. The rhc cluster also contains a gene, rhcR, that encodes the transcriptional regulator RhcR which was characterized as an activator of all rhc genes. 2-keto-3-deoxy-l-rhamnonate, a metabolic intermediate of l-rhamnose degradation, was identified as inducer molecule of RhcR. The essential function of rhc genes for uptake and degradation of l-rhamnose was proven by the respective knockout mutants. Enzymes of the diketo-hydrolase pathway, including l-rhamnose dehydrogenase, l-rhamnonolactonase, l-rhamnonate dehydratase, 2-keto-3-deoxy-l-rhamnonate dehydrogenase and 2,4-diketo-3-deoxy-l-rhamnonate hydrolase, were characterized. Further, genes of the diketo-hydrolase pathway were also identified in the hyperthermophilic crenarchaeota Vulcanisaeta distributa and Sulfolobus solfataricus and selected enzymes were characterized, indicating the presence of the diketo-hydrolase pathway in these archaea. Together, this is the first comprehensive description of l-rhamnose catabolism in the domain of archaea.

RevDate: 2019-05-03
CmpDate: 2019-05-03

Korzhenkov AA, Toshchakov SV, Bargiela R, et al (2019)

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity.

Microbiome, 7(1):11 pii:10.1186/s40168-019-0623-8.

BACKGROUND: The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8-18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations.

RESULTS: Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being "E-plasma", alongside low-abundant Cuniculiplasmataceae, 'Ca. Micrarchaeota' and 'Terrestrial Miscellaneous Euryarchaeal Group' (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, 'Ca. Mancarchaeum acidiphilum Mia14', 'Ca. Micrarchaeota'-related and diverse minor (< 2%) bacterial metagenomic reads.

CONCLUSION: Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem.

RevDate: 2019-03-15

Evans PN, Boyd JA, Leu AO, et al (2019)

An evolving view of methane metabolism in the Archaea.

Nature reviews. Microbiology, 17(4):219-232.

Methane is a key compound in the global carbon cycle that influences both nutrient cycling and the Earth's climate. A limited number of microorganisms control the flux of biologically generated methane, including methane-metabolizing archaea that either produce or consume methane. Methanogenic and methanotrophic archaea belonging to the phylum Euryarchaeota share a genetically similar, interrelated pathway for methane metabolism. The key enzyme in this pathway, the methyl-coenzyme M reductase (Mcr) complex, catalyses the last step in methanogenesis and the first step in methanotrophy. The discovery of mcr and divergent mcr-like genes in new euryarchaeotal lineages and novel archaeal phyla challenges long-held views of the evolutionary origin of this metabolism within the Euryarchaeota. Divergent mcr-like genes have recently been shown to oxidize short-chain alkanes, indicating that these complexes have evolved to metabolize substrates other than methane. In this Review, we examine the diversity, metabolism and evolutionary history of mcr-containing archaea in light of these recent discoveries.

RevDate: 2019-03-20
CmpDate: 2019-02-19

Díez-Villaseñor C, F Rodriguez-Valera (2019)

CRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans.

Nature communications, 10(1):294 pii:10.1038/s41467-018-08167-w.

Smacoviridae is a family of small (~2.5 Kb) CRESS-DNA (Circular Rep Encoding Single-Stranded (ss) DNA) viruses. These viruses have been found in faeces, were thought to infect eukaryotes and are suspected to cause gastrointestinal disease in humans. CRISPR-Cas systems are adaptive immune systems in prokaryotes, wherein snippets of genomes from invaders are stored as spacers that are interspersed between a repeated CRISPR sequence. Here we report several spacer sequences in the faecal archaeon Candidatus Methanomassiliicoccus intestinalis matching smacoviruses, implicating the archaeon as a firm candidate for a host. This finding may be relevant to understanding the potential origin of smacovirus-associated human diseases. Our results support that CRESS-DNA viruses can infect non-eukaryotes, which would mean that smacoviruses are the viruses with the smallest genomes to infect prokaryotes known to date. A probable target strand bias suggests that, in addition to double-stranded DNA, the CRISPR-Cas system can target ssDNA.

RevDate: 2019-02-22

Jeter VL, Mattes TA, Beattie NR, et al (2019)

A New Class of Phosphoribosyltransferases Involved in Cobamide Biosynthesis Is Found in Methanogenic Archaea and Cyanobacteria.

Biochemistry, 58(7):951-964.

Cobamides are coenzymes used by cells from all domains of life but made de novo by only some bacteria and archaea. The last steps of the cobamide biosynthetic pathway activate the corrin ring and the lower ligand base, condense the activated intermediates, and dephosphorylate the product prior to the release of the biologically active coenzyme. In bacteria, a phosphoribosyltransferase (PRTase) enyzme activates the base into its α-mononucleotide. The enzyme from Salmonella enterica (SeCobT) has been extensively biochemically and structurally characterized. The crystal structure of the putative PRTase from the archaeum Methanocaldococcus jannaschii (MjCobT) is known, but its function has not been validated. Here we report the in vivo and in vitro characterization of MjCobT. In vivo, in vitro, and phylogenetic data reported here show that MjCobT belongs to a new class of NaMN-dependent PRTases. We also show that the Synechococcus sp. WH7803 CobT protein has PRTase activity in vivo. Lastly, results of isothermal titration calorimetry and analytical ultracentrifugation analysis show that the biologically active form of MjCobT is a dimer, not a trimer, as suggested by its crystal structure.

RevDate: 2019-03-02

Dombrowski N, Lee JH, Williams TA, et al (2019)

Genomic diversity, lifestyles and evolutionary origins of DPANN archaea.

FEMS microbiology letters, 366(2):.

Archaea-a primary domain of life besides Bacteria-have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.

RevDate: 2019-02-15
CmpDate: 2019-02-07

Morgado SM, ACP Vicente (2019)

Exploring tRNA gene cluster in archaea.

Memorias do Instituto Oswaldo Cruz, 114:e180348 pii:S0074-02762019000100303.

BACKGROUND: Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain.

OBJECTIVE: Explore the occurrence of tRNA gene clusters in archaea.

METHODS: In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements.

FINDINGS: We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer.

MAIN CONCLUSIONS: tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.

RevDate: 2019-01-24
CmpDate: 2019-01-24

Xue F, Nan X, Li Y, et al (2019)

Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows.

BMC veterinary research, 15(1):7 pii:10.1186/s12917-018-1745-0.

BACKGROUND: Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows' production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows.

RESULTS: HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH3-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment.

CONCLUSIONS: HC feeding significantly decreased ruminal pH and increased the content of NH3-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH3 content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine's function in dairy cows and provided new strategies to improve dairy cows' health under high-concentrate feeding regime.

RevDate: 2019-02-20

Wang Y, Huang JM, Cui GJ, et al (2019)

Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean.

Environmental microbiology, 21(2):716-729.

Various lineages of ammonia-oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high-quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B (polB) and methyladenine DNA glycosylase (tag) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin-like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B12 -independent MetE and B12 -dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co-occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans.

RevDate: 2019-03-26

Li J, Liu R, Tao Y, et al (2018)

Archaea in Wastewater Treatment: Current Research and Emerging Technology.

Archaea (Vancouver, B.C.), 2018:6973294.

RevDate: 2019-01-11
CmpDate: 2019-01-11

Li N, Chen Y, Zhang Z, et al (2019)

Response of ammonia-oxidizing archaea to heavy metal contamination in freshwater sediment.

Journal of environmental sciences (China), 77:392-399.

It has been well-documented that the distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soils can be affected by heavy metal contamination, whereas information about the impact of heavy metal on these ammonia-oxidizing microorganisms in freshwater sediment is still lacking. The present study explored the change of sediment ammonia-oxidizing microorganisms in a freshwater reservoir after being accidentally contaminated by industrial discharge containing high levels of metals. Bacterial amoA gene was found to be below the quantitative PCR detection and was not successfully amplified by conventional PCR. The number of archaeal amoA gene in reservoir sediments were 9.62 × 102-1.35 × 107 copies per gram dry sediment. AOA abundance continuously decreased, and AOA richness, diversity and community structure also considerably varied with time. Therefore, heavy metal pollution could have a profound impact on freshwater sediment AOA community. This work could expand our knowledge of the effect of heavy metal contamination on nitrification in natural ecosystems.

RevDate: 2018-12-20

Yu H, Susanti D, McGlynn SE, et al (2018)

Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea.

Frontiers in microbiology, 9:2917.

Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F420-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.

RevDate: 2019-04-28

Lvov DK, Sizikova TE, Lebedev VN, et al (2018)

[Plasmids of archaea as possible ancestors of DNA-containing viruses].

Voprosy virusologii, 63(5):197-201.

Тhе kingdom Archaea, as well as Bacteria, belongs to the overkingdom Prokaryota. Halophilic archaea (Halorubrum lacusprofundi) isolated from Antarctic saline lakes contain plasmids (pR1SE) that code proteins taking part in the formation of membranes of archaea vesicles. The molecular and biological properties of pR1SE and the peculiarity of its interaction with sensitive cells are considered in this article. The role of structural proteins coded by pR1S in the process of formation of vesicle membrane complex is paid special attention. Plasmid-containing archaea vesicles model some properties of viruses. Archaea plasmids can be viewed as possible ancestors of DNA-containing viruses.

RevDate: 2019-05-17

Jaffe AL, Castelle CJ, Dupont CL, et al (2019)

Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea.

Molecular biology and evolution, 36(3):435-446.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for carboxylase activity. Genome-level metabolic analyses supported the inference that these RuBisCO function in a CO2-incorporating pathway that consumes nucleotides. Importantly, some Gottesmanbacteria (CPR) also encode a phosphoribulokinase that may augment carbon metabolism through a partial Calvin-Benson-Bassham cycle. Based on the scattered distribution of RuBisCO and its discordant evolutionary history, we conclude that this enzyme has been extensively laterally transferred across the CPR bacteria and DPANN archaea. We also report RuBisCO-like proteins in phage genomes from diverse environments. These sequences cluster with proteins in the Beckwithbacteria (CPR), implicating phage as a possible mechanism of RuBisCO transfer. Finally, we synthesize our metabolic and evolutionary analyses to suggest that lateral gene transfer of RuBisCO may have facilitated major shifts in carbon metabolism in several important bacterial and archaeal lineages.

RevDate: 2019-04-08
CmpDate: 2019-04-08

Wang S, Zheng Z, Zou H, et al (2019)

Characterization of the secondary metabolite biosynthetic gene clusters in archaea.

Computational biology and chemistry, 78:165-169.

Secondary metabolites are a range of bioactive compounds yielded by bacteria, fungi and plants, etc. The published archaea genomic data provide the opportunity for efficient identification of secondary metabolite biosynthetic gene clusters (BGCs) by genome mining. However, the study of secondary metabolites in archaea is still rare. By using the antiSMASH, we found two main putative secondary metabolite BGCs, bacteriocin and terpene in 203 Archaea genomes. Compared with the genomes of Euryarchaeota that usually lives in less complexity of environment, the genomes of Crenarchaeota usually contained more abundant bacteriocin. In these archaea genomes, we also found the positive correlation between the abundance of bacteriocin and the abundance of CRISPR spacer, suggesting the bacteriocin might be a crucial component of the innate immune system that defense the microbe living in the common environment. The structure analysis of the bacteriocin gene clusters gave a clue that the assisted genes located at the edge of clusters evolved faster than the core biosynthetic genes. To the best of our knowledge, we are the first to systematically explore the distribution of secondary metabolites in archaea, and the investigation of the relationship between BGC and CRISPR spacer expands our understanding of the evolutionary dynamic of these functional molecules.

RevDate: 2018-12-06

Alva V, AN Lupas (2018)

Histones Predate the Split Between Bacteria and Archaea.

Bioinformatics (Oxford, England) pii:5232221 [Epub ahead of print].

Motivation: Histones form octameric complexes called nucleosomes, which organize the genomic DNA of eukaryotes into chromatin. Each nucleosome comprises two copies each of the histones H2A, H2B, H3, and H4, which share a common ancestry. Although histones were initially thought to be a eukaryotic innovation, the subsequent identification of archaeal homologs led to the notion that histones emerged before the divergence of archaea and eukaryotes.

Results: Here, we report the detection and classification of two new groups of histone homologs, which are present in both archaea and bacteria. Proteins in one group consist of two histone subunits welded into single-chain pseudodimers, whereas in the other they resemble eukaryotic core histone subunits and show sequence patterns characteristic of DNA binding. The sequences come from a broad spectrum of deeply-branching lineages, excluding their genesis by horizontal gene transfer. Our results extend the origin of histones to the Last Universal Common Ancestor.

Supplementary information: Supplementary data are available at Bioinformatics online.

RevDate: 2019-05-27

Higuchi ML, Kawakami JT, Ikegami RN, et al (2018)

Archaea Symbiont of T. cruzi Infection May Explain Heart Failure in Chagas Disease.

Frontiers in cellular and infection microbiology, 8:412.

Background: Archaeal genes present in Trypanosoma cruzi may represent symbionts that would explain development of heart failure in 30% of Chagas disease patients. Extracellular vesicles in peripheral blood, called exosomes (< 0.1 μm) or microvesicles (>0.1 μm), present in larger numbers in heart failure, were analyzed to determine whether they are derived from archaea in heart failure Chagas disease. Methods: Exosomes and microvesicles in serum supernatant from 3 groups were analyzed: heart failure Chagas disease (N = 26), asymptomatic indeterminate form (N = 21) and healthy non-chagasic control (N = 16). Samples were quantified with transmission electron microscopy, flow cytometer immunolabeled with anti-archaemetzincin-1 antibody (AMZ 1, archaea collagenase) and probe anti-archaeal DNA and zymography to determine AMZ1 (Archaeal metalloproteinase) activity. Results: Indeterminate form patients had higher median numbers of exosomes/case vs. heart failure patients (58.5 vs. 25.5, P < 0.001), higher exosome content of AMZ1 antigens (2.0 vs. 0.0; P < 0.001), and lower archaeal DNA content (0.2 vs. 1.5, P = 0.02). A positive correlation between exosomes and AMZ1 content was seen in indeterminate form (r = 0.5, P < 0.001), but not in heart failure patients (r = 0.002, P = 0.98). Higher free archaeal DNA (63.0 vs. 11.1, P < 0.001) in correlation with exosome numbers (r = 0.66, P = 0.01) was seen in heart failure but not in indeterminate form (r = 0.29, P = 0.10). Flow cytometer showed higher numbers of AMZ1 microvesicles in indeterminate form (64 vs. 36, P = 0.02) and higher archaeal DNA microvesicles in heart failure (8.1 vs. 0.9, P < 0.001). Zymography showed strong% collagenase activity in HF group, mild activity in IF compared to non-chagasic healthy group (121 ± 14, 106 ± 13 and 100; P < 0.001). Conclusions: Numerous exosomes, possibly removing and degrading abnormal AMZ1 collagenase, are associated with indeterminate form. Archaeal microvesicles and their exosomes, possibly associated with release of archaeal AMZ1 in heart failure, are future candidates of heart failure biomarkers if confirmed in larger series, and the therapeutic focus in the treatment of Chagas disease.

RevDate: 2019-04-08

Buddeweg A, Daume M, Randau L, et al (2018)

Noncoding RNAs in Archaea: Genome-Wide Identification and Functional Classification.

Methods in enzymology, 612:413-442.

Noncoding RNAs (ncRNAs) fulfill essential functions in eukaryotes and bacteria, but also in the third domain of life, the Archaea. Many archaeal organisms live in hostile environments that provide unique challenges for their transcriptional and translational regulatory pathways. Computational analyses and RNA-sequencing methodologies allowed for the genome-wide detection of ncRNA molecules in archaea. Several new classes of ncRNAs have been discovered and are expected to enable life in these extreme habitats. Here, we provide an overview of the current knowledge on archaeal ncRNAs and their deduced or biochemically verified functions. In addition, details of applying RNA-seq methodology for the detection of ncRNAs in Sulfolobus acidocaldarius are provided. Identified ncRNAs include small RNAs (sRNAs) that regulate gene expression and C/D box sRNAs that guide 2'-O methylation of target RNAs.

RevDate: 2019-03-29

Zhou Z, Liu Y, Lloyd KG, et al (2019)

Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea).

The ISME journal, 13(4):885-901.

Marine Benthic Group D (MBG-D) archaea, discovered by 16S rRNA gene survey decades ago, are ecologically important, yet understudied and uncultured sedimentary archaea. In this study, a comprehensive meta-analysis based on the 16S rRNA genes of MBG-D archaea showed that MBG-D archaea are one of the most frequently found archaeal lineages in global sediment with widespread distribution and high abundance, including 16 subgroups in total. Interestingly, some subgroups show significant segregations toward salinity and methane seeps. Co-occurrence analyses indicate significant non-random association of MBG-D archaea with Lokiarchaeota (in both saline and freshwater sediments) and Hadesarchaea, suggesting potential interactions among these archaeal groups. Meanwhile, based on four nearly complete metagenome-assembled genomes (MAGs) and corresponding metatranscriptomes reconstructed from mangrove and intertidal mudflat sediments, we provide insights on metabolic potentials and ecological functions of MBG-D archaea. MBG-D archaea appear to be capable of transporting and assimilating peptides and generating acetate and ethanol through fermentation. Metatranscriptomic analysis suggests high expression of genes for acetate and amino acid utilization and for peptidases, especially the M09B-type extracellular peptidase (collagenase) showing high expression levels in all four mangrove MAGs. Beyond heterotrophic central carbon metabolism, the MBG-D genomes include genes that might encode two autotrophic pathways: Wood-Ljundahl (WL) pathways using both H4MPT and H4folate as C1 carriers, and an incomplete dicarboxylate/4-hydroxybutyrate cycle with alternative bypasses from pyruvate to malate/oxaloacetate during dicarboxylation. These findings reveal MBG-D archaea as an important ubiquitous benthic sedimentary archaeal group with specific mixotrophic metabolisms, so we proposed the name Thermoprofundales as a new Order within the Class Thermoplasmata. Globally, Thermoprofundales and other benthic archaea might synergistically transform benthic organic matter, possibly playing a vital role in sedimentary carbon cycle.

RevDate: 2019-01-02
CmpDate: 2019-01-02

Vipindas PV, Jabir T, Jasmin C, et al (2018)

Diversity and seasonal distribution of ammonia-oxidizing archaea in the water column of a tropical estuary along the southeast Arabian Sea.

World journal of microbiology & biotechnology, 34(12):188.

Diversity and distribution pattern of ammonia-oxidizing archaea (AOA) were studied across a salinity gradient in the water column of Cochin Estuary (CE), a tropical monsoonal estuary along the southeast Arabian Sea. The water column of CE was found to be nutrient rich with high bacterial (3.7-6.7 × 108 cells L-1) and archaeal abundance (1.9-4.5 × 108 cells L-1). Diversity and seasonal variation in the distribution pattern of AOA were studied using clone library analysis and Denaturing gradient gel electrophoresis (DGGE). Clone library analysis of both the amoA and 16S rRNA gene sequences showed similar diversity pattern, however the diversity was more clear when the 16S rRNA gene sequences were analyzed. More than 70% of the sequences retrieved were clustered under uncultured Thaumarchaeota group 1 lineage and the major fractions of the remaining sequences were grouped into the Nitrosopumilus lineage and Nitrosopelagicus lineage. The AOA community in the CE was less adaptable to changing environmental conditions and its distribution showed seasonal variations within the DGGE banding pattern with higher diversity during the pre-monsoon period. The distribution of AOA also showed its preference to intermediate salinity for their higher diversity. Summer monsoon associated runoff and flushing played a critical role in regulating the seasonality of AOA distribution.

RevDate: 2019-04-08
CmpDate: 2019-04-08

Woodall LC, Jungblut AD, Hopkins K, et al (2018)

Deep-sea anthropogenic macrodebris harbours rich and diverse communities of bacteria and archaea.

PloS one, 13(11):e0206220 pii:PONE-D-18-11942.

The deep sea is the largest biome on earth, and microbes dominate in biomass and abundance. Anthropogenic litter is now almost ubiquitous in this biome, and its deposition creates new habitats and environments, including for microbial assemblages. With the ever increasing accumulation of this debris, it is timely to identify and describe the bacterial and archaeal communities that are able to form biofilms on macrodebris in the deep sea. Using 16S rRNA gene high throughput sequencing, we show for the first time the composition of bacteria and archaea on macrodebris collected from the deep sea. Our data suggest differences in the microbial assemblage composition across litter of different materials including metal, rubber, glass, fabric and plastic. These results imply that anthropogenic macrodebris provide diverse habitats for bacterial and archaeal biofilms and each may harbour distinct microbial communities.

RevDate: 2019-03-22

Lim S, Glover DJ, DS Clark (2018)

Prefoldins in Archaea.

Advances in experimental medicine and biology, 1106:11-23.

Molecular chaperones promote the correct folding of proteins in aggregation-prone cellular environments by stabilizing nascent polypeptide chains and providing appropriate folding conditions. Prefoldins (PFDs) are molecular chaperones found in archaea and eukaryotes, generally characterized by a unique jellyfish-like hexameric structure consisting of a rigid beta-barrel backbone with protruding flexible coiled-coils. Unlike eukaryotic PFDs that mainly interact with cytoskeletal components, archaeal PFDs can stabilize a wide range of substrates; such versatility reflects PFD's role as a key element in archaeal chaperone systems, which often lack general nascent-chain binding chaperone components such as Hsp70. While archaeal PFDs mainly exist as hexameric complexes, their structural diversity ranges from tetramers to filamentous oligomers. PFDs bind and stabilize nonnative proteins using varying numbers of coiled-coils, and subsequently transfer the substrate to a group II chaperonin (CPN) for refolding. The distinct structure and specific function of archaeal PFDs have been exploited for a broad range of applications in biotechnology; furthermore, a filament-forming variant of PFD has been used to fabricate nanoscale architectures of defined shapes, demonstrating archaeal PFDs' potential applicability in nanotechnology.

RevDate: 2019-06-10

Turgeman-Grott I, Joseph S, Marton S, et al (2019)

Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation.

Nature microbiology, 4(1):177-186.

CRISPR-Cas systems provide prokaryotes with sequence-specific immunity against viruses and plasmids based on DNA acquired from these invaders, known as spacers. Surprisingly, many archaea possess spacers that match chromosomal genes of related species, including those encoding core housekeeping genes. By sequencing genomes of environmental archaea isolated from a single site, we demonstrate that inter-species spacers are common. We show experimentally, by mating Haloferax volcanii and Haloferax mediterranei, that spacers are indeed acquired chromosome-wide, although a preference for integrated mobile elements and nearby regions of the chromosome exists. Inter-species mating induces increased spacer acquisition and may result in interactions between the acquisition machinery of the two species. Surprisingly, many of the spacers acquired following inter-species mating target self-replicons along with those originating from the mating partner, indicating that the acquisition machinery cannot distinguish self from non-self under these conditions. Engineering the chromosome of one species to be targeted by the other's CRISPR-Cas reduces gene exchange between them substantially. Thus, spacers acquired during inter-species mating could limit future gene transfer, resulting in a role for CRISPR-Cas systems in microbial speciation.

RevDate: 2019-03-14

Song GC, Im H, Jung J, et al (2019)

Plant growth-promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae.

Environmental microbiology, 21(3):940-948.

Archaea have inhabited the earth for a long period of time and are ubiquitously distributed in diverse environments. However, few studies have focused on the interactions of archaea with other organisms, including eukaryotes such as plants, since it is difficult to cultivate sufficient numbers of archaeal cells for analysis. In this study, we investigated the interaction between soil archaea and Arabidopsis thaliana. We demonstrate for the first time that soil archaea promote plant growth and trigger induced systemic resistance (ISR) against the necrotrophic bacterium Pectobacterium carotovorum subsp. carotovorum SCC1 and biotrophic bacterium Pseudomonas syringae pv. tomato DC3000. Ammonia-oxidizing archaeon Nitrosocosmicus oleophilus MY3 cells clearly colonized the root surface of Arabidopsis plants, and increased resistance against both pathogenic species via the salicylic acid-independent signalling pathway. This mechanism of bacterial resistance resembles that underlying soil bacteria- and fungi-mediated ISR signalling. Additionally, volatile emissions from N. oleophilus MY3 were identified as major archaeal determinants that elicit ISR. Our results lay a foundation for archaea-plant interactions as a new field of research.

RevDate: 2018-12-07

Najafi A, Moradinasab M, Seyedabadi M, et al (2018)

First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran.

The open microbiology journal, 12:323-332.

Background: Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran.

Methods: Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy identification of sponge sample. Also, symbiotic archaea were identified using the culture-independent analysis of the 16S rRNA gene and PCR- cloning.

Results: In this study, analysis of multilocus DNA marker and morphological characteristics revealed that the sponge species belonged to Chondrilla australiensis isolate PG_BU4. PCR cloning and sequencing showed that all of the sequences of archaeal 16S rRNA gene libraries clustered into the uncultured archaeal group.

Conclusion: The present study is the first report of the presence of the genus of Chondrilla in the Persian Gulf. Traditional taxonomy methods, when used along with molecular techniques, could play a significant role in the accurate taxonomy of sponges. Also, the uncultured archaea may promise a potential source for bioactive compounds. Further functional studies are needed to explore the role of the sponge-associated uncultured archaea as a part of the marine symbiosis.

RevDate: 2019-06-10

Peck RF, Graham SM, AM Gregory (2019)

Species Widely Distributed in Halophilic Archaea Exhibit Opsin-Mediated Inhibition of Bacterioruberin Biosynthesis.

Journal of bacteriology, 201(2): pii:JB.00576-18.

Halophilic Archaea are a distinctive pink color due to a carotenoid pigment called bacterioruberin. To sense or utilize light, many halophilic Archaea also produce rhodopsins, complexes of opsin proteins with a retinal prosthetic group. Both bacterioruberin and retinal are synthesized from isoprenoid precursors, with lycopene as the last shared intermediate. We previously described a regulatory mechanism by which Halobacterium salinarum bacterioopsin and Haloarcula vallismortis cruxopsin inhibit bacterioruberin synthesis catalyzed by lycopene elongase. In this work, we found that opsins in all three major Halobacteria clades inhibit bacterioruberin synthesis, suggesting that this regulatory mechanism existed in the common Halobacteria ancestor. Halophilic Archaea, which are generally heterotrophic and aerobic, likely evolved from an autotrophic, anaerobic methanogenic ancestor by acquiring many genes from Bacteria via lateral gene transfer. These bacterial "imports" include genes encoding opsins and lycopene elongases. To determine if opsins from Bacteria inhibit bacterioruberin synthesis, we tested bacterial opsins and found that an opsin from Curtobacterium, in the Actinobacteria phylum, inhibits bacterioruberin synthesis catalyzed by its own lycopene elongase, as well as that catalyzed by several archaeal enzymes. We also determined that the lycopene elongase from Halococcus salifodinae, a species from a family of Halobacteria lacking opsin homologs, retained the capacity to be inhibited by opsins. Together, our results indicate that opsin-mediated inhibition of bacterioruberin biosynthesis is a widely distributed mechanism found in both Archaea and Bacteria, possibly predating the divergence of the two domains. Further analysis may provide insight into the acquisition and evolution of the genes and their host species.IMPORTANCE All organisms use a variety of mechanisms to allocate limited resources to match their needs in their current environment. Here, we explore how halophilic microbes use a novel mechanism to allow efficient production of rhodopsin, a complex of an opsin protein and a retinal prosthetic group. We previously demonstrated that Halobacterium salinarum bacterioopsin directs available resources toward retinal by inhibiting synthesis of bacterioruberin, a molecule that shares precursors with retinal. In this work, we show that this mechanism can be carried out by proteins from halophilic Archaea that are not closely related to H. salinarum and those in at least one species of Bacteria Therefore, opsin-mediated inhibition of bacterioruberin synthesis may be a highly conserved, ancient regulatory mechanism.

RevDate: 2019-01-16

Seth-Pasricha M, Senn S, Sanman LE, et al (2019)

Catalytic linkage between caspase activity and proteostasis in Archaea.

Environmental microbiology, 21(1):286-298.

The model haloarchaeon, Haloferax volcanii possess an extremely high, and highly specific, basal caspase activity in exponentially growing cells that closely resembles caspase-4. This activity is specifically inhibited by the pan-caspase inhibitor, z-VAD-FMK, and has no cross-reactivity with other known protease families. Although it is one of the dominant cellular proteolytic activities in exponentially growing H. volcanii cells, the interactive cellular roles remain unknown and the protein(s) responsible for this activity remain elusive. Here, biochemical purification and in situ trapping with caspase targeted covalent inhibitors combined with genome-enabled proteomics, structural analysis, targeted gene knockouts and treatment with canavanine demonstrated a catalytic linkage between caspase activity and thermosomes, proteasomes and cdc48b, a cell division protein and proteasomal degradation facilitating ATPase, as part of an 'interactase' of stress-related protein complexes with an established link to the unfolded protein response (UPR). Our findings provide novel cellular and biochemical context for the observed caspase activity in Archaea and add new insight to understanding the role of this activity, implicating their possible role in the establishment of protein stress and ER associated degradation pathways in Eukarya.

RevDate: 2018-11-14

Harish A (2018)

What is an archaeon and are the Archaea really unique?.

PeerJ, 6:e5770.

The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the ToL. To explore the causes for this persistent ambiguity, I examine multiple datasets and different phylogenetic approaches that support contradicting conclusions. I find that the uncertainty is primarily due to a scarcity of information in standard datasets-universal core-genes datasets-to reliably resolve the conflicts. These conflicts can be resolved efficiently by comparing patterns of variation in the distribution of functional genomic signatures, which are less diffused unlike patterns of primary sequence variation. Relatively lower heterogeneity in distribution patterns minimizes uncertainties and supports statistically robust phylogenetic inferences, especially of the earliest divergences of life. This case study further highlights the limitations of primary sequence data in resolving difficult phylogenetic problems, and raises questions about evolutionary inferences drawn from the analyses of sequence alignments of a small set of core genes. In particular, the findings of this study corroborate the growing consensus that reversible substitution mutations may not be optimal phylogenetic markers for resolving early divergences in the ToL, nor for determining the polarity of evolutionary transitions across the ToL.

RevDate: 2019-03-07
CmpDate: 2019-03-07

Pornkulwat P, Kurisu F, Soonglerdsongpha S, et al (2018)

Incorporation of 13C-HCO3- by ammonia-oxidizing archaea and bacteria during ammonia oxidation of sludge from a municipal wastewater treatment plant.

Applied microbiology and biotechnology, 102(24):10767-10777.

Ammonia-oxidizing archaea (AOA) have recently been proposed as potential players for ammonia removal in wastewater treatment plants (WWTPs). However, there is little evidence directly showing the contribution of AOA to ammonia oxidation in these engineered systems. In this study, DNA-stable isotope probing (DNA-SIP) with labeled 13C-HCO3- was introduced to sludge from a municipal WWTP. Quantitative PCR demonstrated that AOA amoA genes outnumbered AOB amoA genes in this WWTP sludge. AOA amoA gene sequence analysis revealed that AOA present in this WWTP were specific to one subcluster within the group 1.1b Thaumarchaeota. When ammonia was supplied to DNA-SIP incubation, the DNA-SIP profiles demonstrated the incorporation of the 13C into AOA and AOB. However, the 13C was not found to be assimilated into both microorganisms in the incubation without ammonia. Specific primers were designed to target amoA genes of AOA belonging to the subcluster found in this WWTP. Applying the primers to DNA-SIP experiment revealed that AOA of this subcluter most likely utilized inorganic carbon during ammonia oxidation under the studied conditions.

RevDate: 2018-12-11

Lemor M, Kong Z, Henry E, et al (2018)

Differential Activities of DNA Polymerases in Processing Ribonucleotides during DNA Synthesis in Archaea.

Journal of molecular biology, 430(24):4908-4924.

Consistent with the fact that ribonucleotides (rNTPs) are in excess over deoxyribonucleotides (dNTPs) in vivo, recent findings indicate that replicative DNA polymerases (DNA Pols) are able to insert ribonucleotides (rNMPs) during DNA synthesis, raising crucial questions about the fidelity of DNA replication in both Bacteria and Eukarya. Here, we report that the level of rNTPs is 20-fold higher than that of dNTPs in Pyrococcus abyssi cells. Using dNTP and rNTP concentrations present in vivo, we recorded rNMP incorporation in a template-specific manner during in vitro synthesis, with the family-D DNA Pol (PolD) having the highest propensity compared with the family-B DNA Pol and the p41/p46 complex. We also showed that ribonucleotides accumulate at a relatively high frequency in the genome of wild-type Thermococcales cells, and this frequency significantly increases upon deletion of RNase HII, the major enzyme responsible for the removal of RNA from DNA. Because ribonucleotides remain in genomic DNA, we then analyzed the effects on polymerization activities by the three DNA Pols. Depending on the identity of the base and the sequence context, all three DNA Pols bypass rNMP-containing DNA templates with variable efficiency and nucleotide (mis)incorporation ability. Unexpectedly, we found that PolD correctly base-paired a single ribonucleotide opposite rNMP-containing DNA templates. An evolutionary scenario is discussed concerning rNMP incorporation into DNA and genome stability.

RevDate: 2019-04-09
CmpDate: 2019-04-09

Huang L, Ashraf S, DMJ Lilley (2019)

The role of RNA structure in translational regulation by L7Ae protein in archaea.

RNA (New York, N.Y.), 25(1):60-69.

A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5'-leader of the mRNA of its structural gene to regulate translation. To function as a regulator, the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem-loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archaeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation that is specifically recognized by the L7Ae protein, so stabilizing the stem-loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus, L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.

RevDate: 2019-05-28

Rinke C, Rubino F, Messer LF, et al (2019)

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).

The ISME journal, 13(3):663-675.

Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca. Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca. Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca. Poseidoniales to occupy a variety of ecological niches and to become the most successful archaeal lineage in ocean surface waters.

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ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

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In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

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Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

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In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

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Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

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When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

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