@article {pmid38402727,
year = {2024},
author = {Wang, R and Li, X and Lv, F and He, J and Lv, R and Wei, L},
title = {Sesame bacterial wilt significantly alters rhizosphere soil bacterial community structure, function, and metabolites in continuous cropping systems.},
journal = {Microbiological research},
volume = {282},
number = {},
pages = {127649},
doi = {10.1016/j.micres.2024.127649},
pmid = {38402727},
issn = {1618-0623},
mesh = {*Soil/chemistry ; *Sesamum ; Rhizosphere ; Soil Microbiology ; Biodiversity ; Bacteria/genetics ; },
abstract = {Bacterial wilt is the leading disease of sesame and alters the bacterial community composition, function, and metabolism of sesame rhizosphere soil. However, its pattern of change is unclear. Here, the purpose of this study was to investigate how these communities respond to three differing severities of bacterial wilt in mature continuously cropped sesame plants by metagenomic and metabolomic techniques, namely, absence (WH), moderate (WD5), and severe (WD9) wilt. The results indicated that bacterial wilt could significantly change the bacterial community structure in the rhizosphere soil of continuously cropped sesame plants. The biomarker species with significant differences will also change with increasing disease severity. In particular, the gene expression levels of Ralstonia solanacearum in the WD9 and WD5 treatments increased by 25.29% and 33.61%, respectively, compared to those in the WH treatment (4.35 log10 copies g-1). The occurrence of bacterial wilt significantly altered the functions of the bacterial community in rhizosphere soil. KEEG and CAZy functional annotations revealed that the number of significantly different functions in WH was greater than that in WD5 and WD9. Bacterial wilt significantly affected the relative content of metabolites, especially acids, in the rhizosphere soil, and compared with those in the rhizosphere soil from WH, 10 acids (including S-adenosylmethionine, N-acetylleucine, and desaminotyrosine, etc.) in the rhizosphere soil from WD5 or WD9 significantly increased. In comparison, the changes in the other 10 acids (including hypotaurine, erucic acid, and 6-hydroxynicotinic acid, etc.) were reversed. The occurrence of bacterial wilt also significantly inhibited metabolic pathways such as ABC transporter and amino acid biosynthesis pathways in rhizosphere soil and had a significant impact on two key enzymes (1.1.1.11 and 2.6.1.44). In conclusion, sesame bacterial wilt significantly alters the rhizosphere soil bacterial community structure, function, and metabolites. This study enhances the understanding of sesame bacterial wilt mechanisms and lays the groundwork for future prevention and control strategies against this disease.},
}

*Soil/chemistry
*Sesamum
Rhizosphere
Soil Microbiology
Biodiversity
Bacteria/genetics

@article {pmid38403443,
year = {2024},
author = {Román-Camacho, JJ and Mauricio, JC and Santos-Dueñas, IM and García-Martínez, T and García-García, I},
title = {Recent advances in applying omic technologies for studying acetic acid bacteria in industrial vinegar production: A comprehensive review.},
journal = {Biotechnology journal},
volume = {19},
number = {2},
pages = {e2300566},
doi = {10.1002/biot.202300566},
pmid = {38403443},
issn = {1860-7314},
support = {//Universidad de Córdoba/ ; PID2021-127766OB-I00//Ministry of Science and Innovation/ ; PY20_00590//Junta de Andalucía/ ; },
mesh = {*Acetic Acid/metabolism ; Fermentation ; Biodiversity ; *Microbiota ; Asia ; },
abstract = {Vinegar and related bioproducts containing acetic acid as the main component are among the most appreciated fermented foodstuffs in numerous European and Asian countries because of their exceptional organoleptic and bio-healthy properties. Regarding the acetification process and obtaining of final products, there is still a lack of knowledge on fundamental aspects, especially those related to the study of biodiversity and metabolism of the present microbiota. In this context, omic technologies currently allow for the massive analysis of macromolecules and metabolites for the identification and characterization of these microorganisms working in their natural media without the need for isolation. This review approaches comprehensive research on the application of omic tools for the identification of vinegar microbiota, mainly acetic acid bacteria, with subsequent emphasis on the study of the microbial diversity, behavior, and key molecular strategies used by the predominant groups throughout acetification. The current omics tools are enabling both the finding of new vinegar microbiota members and exploring underlying strategies during the elaboration process. The species Komagataeibacter europaeus may be a model organism for present and future research in this industry; moreover, the development of integrated meta-omic analysis may facilitate the achievement of numerous of the proposed milestones. This work might provide useful guidance for the vinegar industry establishing the first steps towards the improvement of the acetification conditions and the development of new products with sensory and bio-healthy profiles adapted to the agri-food market.},
}

*Acetic Acid/metabolism
Fermentation
Biodiversity
*Microbiota
Asia

@article {pmid38410449,
year = {2024},
author = {Seitz, VA and McGivem, BB and Borton, MA and Chaparro, JM and Schipanski, ME and Prenni, JE and Wrighton, KC},
title = {Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {38410449},
issn = {2693-5015},
support = {P30 CA046934/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND: Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils.

RESULTS: Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs.

CONCLUSIONS: We highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.},
}

@article {pmid38415986,
year = {2024},
author = {Genitsaris, S and Stefanidou, N and Hatzinikolaou, D and Kourkoutmani, P and Michaloudi, E and Voutsa, D and Gros, M and García-Gómez, E and Petrović, M and Ntziachristos, L and Moustaka-Gouni, M},
title = {Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints.},
journal = {Environmental toxicology and chemistry},
volume = {43},
number = {5},
pages = {1012-1029},
doi = {10.1002/etc.5834},
pmid = {38415986},
issn = {1552-8618},
support = {874990//Horizon 2020 Framework Programme/ ; },
mesh = {*Microbiota/drug effects ; *Water Pollutants, Chemical/toxicity ; Polycyclic Aromatic Hydrocarbons ; Bacteria/genetics ; Biodegradation, Environmental ; Seawater/microbiology ; Petroleum ; Plankton/genetics ; },
abstract = {The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;43:1012-1029. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.},
}

*Microbiota/drug effects
*Water Pollutants, Chemical/toxicity
Polycyclic Aromatic Hydrocarbons
Bacteria/genetics
Biodegradation, Environmental
Seawater/microbiology
Petroleum
Plankton/genetics

@article {pmid38421596,
year = {2024},
author = {Anu, K and Kumari, S and Choudhary, G and Devi, S},
title = {Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {2},
pages = {1545-1555},
pmid = {38421596},
issn = {1678-4405},
mesh = {*Hot Springs/microbiology ; India ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; *Biodiversity ; *Soil Microbiology ; *Phylogeny ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Water Microbiology ; },
abstract = {In light of their unique and challenging environment, the high-altitude Chumathang geothermal springs in Ladakh, India, are undeniably intriguing for microbiological study. The purpose of this study was to employ a culture-independent sequencing approach to give a comprehensive characterization of the unknown bacterial and archaeal community structure, composition and networks in water and soil from the Chumathang geothermal spring. A total of 50%, and 42.86% bacterial phyla were found in the water, and soil samples respectively and this analysis also showed a total of 9.62% and 7.94% of archaeal phyla in both the samples, respectively. Further, the presence of unclassified (derived from other sequences, water: 17.31%, and soil: 19.05%) and unclassified (derived from bacteria, water: 13.46%, and soil: 12.70%) were also observed in the current metagenomics investigation. Firmicutes and Proteobacteria were the most abundant bacterial phyla in water, whereas Proteobacteria and Bacteroidetes were the most abundant bacterial phyla in geothermal soil. Crenarchaeota and Euryarchaeota dominated archeal communities in soil and water, respectively. This metagenomic study gave a detailed insight into the microbial diversity found in Chumathang geothermal spring and surrounding area, located in Ladakh, India. Surprisingly, this finding indicated the existence of geographically distinct microbial communities that were suited to various geothermal water habitats along the Himalayan Geothermal Belt. Future studies must take into account the metabolic pathways of these microbial communities that exist in these extreme environments. This will allow us to obtain a better knowledge of the microbial metabolisms that are common at these geothermal locations, which have a lot of potential for biotechnological applications. They will also enable us to establish links between the microbial community composition and the physicochemical environment of geothermal water and area.},
}

*Hot Springs/microbiology
India
*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification
*Biodiversity
*Soil Microbiology
*Phylogeny
*Metagenomics
RNA, Ribosomal, 16S/genetics
Microbiota
Water Microbiology

@article {pmid38428395,
year = {2024},
author = {Fogarty, EC and Schechter, MS and Lolans, K and Sheahan, ML and Veseli, I and Moore, RM and Kiefl, E and Moody, T and Rice, PA and Yu, MK and Mimee, M and Chang, EB and Ruscheweyh, HJ and Sunagawa, S and Mclellan, SL and Willis, AD and Comstock, LE and Eren, AM},
title = {A cryptic plasmid is among the most numerous genetic elements in the human gut.},
journal = {Cell},
volume = {187},
number = {5},
pages = {1206-1222.e16},
pmid = {38428395},
issn = {1097-4172},
support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 DK138072/DK/NIDDK NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Bacteria/genetics ; Bacteroidetes/genetics ; Feces/microbiology ; *Metagenome ; *Plasmids/genetics ; *Gastrointestinal Tract ; },
abstract = {Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.},
}

Humans
*Bacteria/genetics
Bacteroidetes/genetics
Feces/microbiology
*Metagenome
*Plasmids/genetics
*Gastrointestinal Tract

@article {pmid38433907,
year = {2024},
author = {Rampelli, S and Gallois, S and D'Amico, F and Turroni, S and Fabbrini, M and Scicchitano, D and Candela, M and Henry, A},
title = {The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods.},
journal = {iScience},
volume = {27},
number = {3},
pages = {109211},
pmid = {38433907},
issn = {2589-0042},
abstract = {The human gut microbiome is losing biodiversity, due to the "microbiome modernization process" that occurs with urbanization. To keep track of it, here we applied shotgun metagenomics to the gut microbiome of the Baka, a group of forager-horticulturalists from Cameroon, who combine hunting and gathering with growing a few crops and working for neighboring Bantu-speaking farmers. We analyzed the gut microbiome of individuals with different access to and use of wild plant and processed foods, to explore the variation of their gut microbiome along the cline from hunter-gatherer to agricultural subsistence patterns. We found that 26 species-level genome bins from our cohort were pivotal for the degradation of the wild plant food substrates. These microbes include Old Friend species and are encoded for genes that are no longer present in industrialized gut microbiome. Our results highlight the potential relevance of these genes to human biology and health, in relation to lifestyle.},
}

@article {pmid38433960,
year = {2024},
author = {Banchi, E and Corre, E and Del Negro, P and Celussi, M and Malfatti, F},
title = {Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment.},
journal = {Marine life science & technology},
volume = {6},
number = {1},
pages = {126-142},
pmid = {38433960},
issn = {2662-1746},
abstract = {UNLABELLED: Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-023-00192-z.},
}

@article {pmid38443576,
year = {2024},
author = {Yu, MK and Fogarty, EC and Eren, AM},
title = {Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess.},
journal = {Nature microbiology},
volume = {9},
number = {3},
pages = {830-847},
pmid = {38443576},
issn = {2058-5276},
support = {RC2 DK122394/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Metagenome ; *Algorithms ; Life Style ; Machine Learning ; Plasmids/genetics ; },
abstract = {Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive 'plasmid systems' using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems.},
}

Humans
*Metagenome
*Algorithms
Life Style
Machine Learning
Plasmids/genetics

@article {pmid38444804,
year = {2024},
author = {Suo, B and Castro, MP and Sreenivasa, MY},
title = {Editorial: Microbiota biodiversity of traditional fermented products.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1380205},
doi = {10.3389/fmicb.2024.1380205},
pmid = {38444804},
issn = {1664-302X},
}

@article {pmid38445567,
year = {2024},
author = {Gottscho, AD and Mulcahy, DG and Leaché, AD and de Queiroz, K and Lovich, RE},
title = {Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape.},
journal = {Molecular ecology},
volume = {33},
number = {7},
pages = {e17308},
doi = {10.1111/mec.17308},
pmid = {38445567},
issn = {1365-294X},
support = {//Smithsonian Institution, L.A.B./ ; //Smithsonian Institution, Peter Buck Postdoctoral Fellowship/ ; 16-824//Department of Defense Legacy Resource Management Program/ ; },
mesh = {Animals ; Phylogeny ; *Metagenomics ; Colorado ; Ecosystem ; *Lizards/genetics ; Genetic Variation/genetics ; DNA, Mitochondrial/genetics ; Phylogeography ; },
abstract = {Phrynosoma mcallii (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analysed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and the Salton Sea. We recommend additional lands in the United States and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy. We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change, and other long-term impacts.},
}

Animals
Phylogeny
*Metagenomics
Colorado
Ecosystem
*Lizards/genetics
Genetic Variation/genetics
DNA, Mitochondrial/genetics
Phylogeography

@article {pmid38447371,
year = {2024},
author = {Wang, Y and Zhang, Z and Kang, J and Chen, B and Hong, W and Lv, B and Wang, T and Qian, H},
title = {Phages in different habitats and their ability to carry antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {469},
number = {},
pages = {133941},
doi = {10.1016/j.jhazmat.2024.133941},
pmid = {38447371},
issn = {1873-3336},
mesh = {Humans ; *Bacteriophages/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Biodiversity ; Genes, Bacterial ; },
abstract = {As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.},
}

Humans
*Bacteriophages/genetics
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Ecosystem
Biodiversity
Genes, Bacterial

@article {pmid38451250,
year = {2024},
author = {Bustos-Diaz, ED and Cruz-Perez, A and Garfias-Gallegos, D and D'Agostino, PM and Gehringer, MM and Cibrian-Jaramillo, A and Barona-Gomez, F},
title = {Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals.},
journal = {Microbial genomics},
volume = {10},
number = {3},
pages = {},
pmid = {38451250},
issn = {2057-5858},
mesh = {Phylogeny ; *Symbiosis ; Australia ; Coculture Techniques ; *Genomics ; },
abstract = {Cycads are known to host symbiotic cyanobacteria, including Nostocales species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition to Nostoc spp., symbiotic cyanobacteria of the genus Aulosira were identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includes Aulosira spp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.},
}

Phylogeny
*Symbiosis
Australia
Coculture Techniques
*Genomics

@article {pmid38455081,
year = {2024},
author = {Renzi, S and Nenciarini, S and Bacci, G and Cavalieri, D},
title = {Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome.},
journal = {Microbiome research reports},
volume = {3},
number = {1},
pages = {2},
pmid = {38455081},
issn = {2771-5965},
abstract = {Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.},
}

@article {pmid38457496,
year = {2024},
author = {Pigani, E and Mele, BH and Campese, L and Ser-Giacomi, E and Ribera, M and Iudicone, D and Suweis, S},
title = {Deviation from neutral species abundance distributions unveils geographical differences in the structure of diatom communities.},
journal = {Science advances},
volume = {10},
number = {10},
pages = {eadh0477},
pmid = {38457496},
issn = {2375-2548},
mesh = {*Diatoms ; Plankton ; Biodiversity ; Oceans and Seas ; Ecosystem ; },
abstract = {In recent years, the application of metagenomics techniques has advanced our understanding of plankton communities and their global distribution. Despite this progress, the relationship between the abundance distribution of diatom species and varying marine environmental conditions remains poorly understood. This study, leveraging data from the Tara Oceans expedition, tests the hypothesis that diatoms in sampled stations display a consistent species abundance distribution structure, as though they were sampled from a single ocean-wide metacommunity. Using a neutral sampling theory, we thus develop a framework to estimate the structure and diversity of diatom communities at each sampling station given the shape of the species abundance distribution of the metacommunity and the information of a reference station. Our analysis reveals a substantial temperature gradient in the discrepancies between predicted and observed biodiversity across the sampled stations. These findings challenge the hypothesis of a single neutral metacommunity, indicating that environmental differences substantially influence both the composition and structure of diatom communities.},
}

*Diatoms
Plankton
Biodiversity
Oceans and Seas
Ecosystem

@article {pmid38458994,
year = {2024},
author = {Coelho, LP and Santos-Júnior, CD and de la Fuente-Nunez, C},
title = {Challenges in computational discovery of bioactive peptides in 'omics data.},
journal = {Proteomics},
volume = {24},
number = {12-13},
pages = {e2300105},
pmid = {38458994},
issn = {1615-9861},
support = {HDTRA1-23-1-0001//Defense Threat Reduction Agency/ ; R35 GM138201/GM/NIGMS NIH HHS/United States ; //Langer Prize (AIChE Foundation)/ ; //Procter & Gamble Company, United Therapeutics/ ; //BBRF Young Investigator Grant/ ; FT230100724//Australian Research Council/ ; //Penn Health-Tech Accelerator Award/ ; DTRA//Defense Threat Reduction Agency/ ; HDTRA1-21-1-0014//Defense Threat Reduction Agency/ ; //Dean's Innovation Fund from the Perelman School of Medicine at the University of Pennsylvania/ ; R35GM138201//National Institute of General Medical Sciences of the National Institutes of Health/ ; //Nemirovsky Prize/ ; HDTRA11810041//Defense Threat Reduction Agency/ ; },
mesh = {*Peptides ; *Proteomics ; Metagenome ; Prokaryotic Cells/chemistry ; *Computational Biology/methods ; },
abstract = {Peptides have a plethora of activities in biological systems that can potentially be exploited biotechnologically. Several peptides are used clinically, as well as in industry and agriculture. The increase in available 'omics data has recently provided a large opportunity for mining novel enzymes, biosynthetic gene clusters, and molecules. While these data primarily consist of DNA sequences, other types of data provide important complementary information. Due to their size, the approaches proven successful at discovering novel proteins of canonical size cannot be naïvely applied to the discovery of peptides. Peptides can be encoded directly in the genome as short open reading frames (smORFs), or they can be derived from larger proteins by proteolysis. Both of these peptide classes pose challenges as simple methods for their prediction result in large numbers of false positives. Similarly, functional annotation of larger proteins, traditionally based on sequence similarity to infer orthology and then transferring functions between characterized proteins and uncharacterized ones, cannot be applied for short sequences. The use of these techniques is much more limited and alternative approaches based on machine learning are used instead. Here, we review the limitations of traditional methods as well as the alternative methods that have recently been developed for discovering novel bioactive peptides with a focus on prokaryotic genomes and metagenomes.},
}

*Peptides
*Proteomics
Metagenome
Prokaryotic Cells/chemistry
*Computational Biology/methods

@article {pmid38462069,
year = {2024},
author = {Rossi, A and Marroni, F and Renoldi, N and Di Filippo, G and Gover, E and Marino, M and Innocente, N},
title = {An integrated approach to explore the microbial biodiversity of natural milk cultures for cheesemaking.},
journal = {Journal of dairy science},
volume = {107},
number = {7},
pages = {4288-4297},
doi = {10.3168/jds.2024-24463},
pmid = {38462069},
issn = {1525-3198},
mesh = {*Milk/microbiology ; *Cheese/microbiology ; Animals ; *Biodiversity ; },
abstract = {The use of natural milk culture (NMC) represents a key factor in Protected Designation of Origin (PDO) Montasio cheese, contributing to its distinctive sensory profile. The complex microbial ecosystem of NMC is the result of heat treatment and incubation conditions, which can vary considerably among different production plants. In this study, the microbiota of NMC collected from 10 PDO Montasio cheese dairies was investigated by employing colony counts and metagenomic analysis. Furthermore, residual sugars, organic acids, and volatile profiles were quantitatively investigated. Results showed that Streptococcus thermophilus was the dominant species in all NMC, and a subdominant population made of other streptococci and Ligilactobacillus salivarius was also present. The incubation temperature appeared to be the main driver of biodiversity in NMC. Metagenomics allowed us to evidence the presence of minor species involving safety (e.g., Staphylococcus aureus) as well as possible functional aspects (Next Generation Probiotics). Statistical analysis based on residual sugars, organic acids, and volatiles' content allowed to correlate the presence of specific microbial groups with metabolites of great technological and sensory relevance, which can contribute to giving value to the artisanal production procedures of NMC and clarify their role in the creation of the characteristics of PDO Montasio cheese.},
}

*Milk/microbiology
*Cheese/microbiology
Animals
*Biodiversity

@article {pmid38466097,
year = {2024},
author = {Möller, L and Vainshtein, Y and Meyer, B and Neidhardt, J and Eren, AM and Sohn, K and Rabus, R},
title = {Rich microbial and depolymerising diversity in Antarctic krill gut.},
journal = {Microbiology spectrum},
volume = {12},
number = {4},
pages = {e0403523},
pmid = {38466097},
issn = {2165-0497},
support = {KiGuMi//Bundesministerium für Bildung und Forschung (BMBF)/ ; },
mesh = {Humans ; Animals ; *Euphausiacea/metabolism ; Ecosystem ; Seasons ; Hydrolases/genetics/metabolism ; Biopolymers/metabolism ; },
abstract = {With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter, also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire.IMPORTANCEThe Antarctic krill (Euphausia superba) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.},
}

Humans
Animals
*Euphausiacea/metabolism
Ecosystem
Seasons
Hydrolases/genetics/metabolism
Biopolymers/metabolism

@article {pmid38468006,
year = {2024},
author = {Ma, J and Yao, Z and Zhang, M and Gao, J and Li, W and Yang, W},
title = {Microbial and environmental medium-driven responses to phosphorus fraction changes in the sediments of different lake types during the freezing period.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {17},
pages = {25147-25162},
pmid = {38468006},
issn = {1614-7499},
support = {42167018//the National Natural Science Foundation of China/ ; 2023YXXS026//the Fundamental Research Funds for Inner Mongolia University of Science & Technology/ ; },
mesh = {*Lakes ; *Water Pollutants, Chemical/analysis ; Ecosystem ; Phosphorus/analysis ; Freezing ; Sodium Hydroxide ; Environmental Monitoring ; Geologic Sediments ; Eutrophication ; China ; },
abstract = {The comparative study of the transformation among sediment phosphorus (P) fractions in different lake types is a global issue in lake ecosystems. However, interactions between sediment P fractions, environmental factors, and microorganisms vary with the nutrient status of lakes. In this study, we combine sequential extraction and metagenomics sequencing to assess the characteristics of P fractions and transformation in sediments from different lake types in the Inner Mongolian section of the Yellow River Basin. We then further explore the response of relevant microbial and environmental drivers to P fraction transformation and bioavailability in sediments. The sediments of all three lakes exhibited strong exogenous pollution input characteristics, and higher nutritional conditions led to enhanced sediment P fraction transformation ability. The transformation capacity of the sediment P fractions also differed among the different lake types at the same latitudes, which is affected by many factors such as lake environmental factors and microorganisms. Different drivers reflected the mutual control of weakly adsorbed phosphorus (WA-P), potential active phosphorus (PA-P), Fe/Al-bound phosphorus (NaOH-P), and Ca-bound phosphorus (HCl-P) with the bio-directly available phosphorus (Bio-P). The transformation of NaOH-P in reducing environments can improve P bioavailability, while HCl-P is not easily bioavailable in weakly alkaline environments. There were significant differences in the bacterial community diversity and composition between the different lake types at the same latitude (p < 0.05), and the role of P fractions was stronger in the sediments of lakes with rich biodiversity than in poor biodiversity. Lake eutrophication recovery was somewhat hindered by the microbial interactions of P cycling and P fractions within the sediment. This study provides data and theoretical support for exploring the commonalities and differences among different lake types in the Inner Mongolian section of the Yellow River Basin. Besides, it is representative and typical for promoting the optimization of ecological security patterns in ecologically fragile watersheds.},
}

*Lakes
*Water Pollutants, Chemical/analysis
Ecosystem
Phosphorus/analysis
Freezing
Sodium Hydroxide
Environmental Monitoring
Geologic Sediments
Eutrophication
China

@article {pmid38489588,
year = {2024},
author = {David, G and Bertolotti, A and Layer, R and Scofield, D and Hayward, A and Baril, T and Burnett, HA and Gudmunds, E and Jensen, H and Husby, A},
title = {Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.},
journal = {Genome biology and evolution},
volume = {16},
number = {4},
pages = {},
pmid = {38489588},
issn = {1759-6653},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Genomics ; *Genome ; Metagenomics ; Polymorphism, Single Nucleotide ; },
abstract = {Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.},
}

*Genomics
*Genome
Metagenomics
Polymorphism, Single Nucleotide

@article {pmid38490631,
year = {2024},
author = {Hu, M and Sardans, J and Sun, D and Yan, R and Wu, H and Ni, R and Peñuelas, J},
title = {Microbial diversity and keystone species drive soil nutrient cycling and multifunctionality following mangrove restoration.},
journal = {Environmental research},
volume = {251},
number = {Pt 2},
pages = {118715},
doi = {10.1016/j.envres.2024.118715},
pmid = {38490631},
issn = {1096-0953},
mesh = {*Wetlands ; *Soil Microbiology ; Soil/chemistry ; Microbiota ; Nitrogen Cycle ; Phosphorus/metabolism ; Biodiversity ; Nitrogen/metabolism ; Environmental Restoration and Remediation/methods ; Bacteria/classification/metabolism/genetics ; },
abstract = {Vegetation restoration exerts transformative effects on nutrient cycling, microbial communities, and ecosystem functions. While extensive research has been conducted on the significance of mangroves and their restoration efforts, the effectiveness of mangrove restoration in enhancing soil multifunctionality in degraded coastal wetlands remains unclear. Herein, we carried out a field experiment to explore the impacts of mangrove restoration and its chronosequence on soil microbial communities, keystone species, and soil multifunctionality, using unrestored aquaculture ponds as controls. The results revealed that mangrove restoration enhanced soil multifunctionality, with these positive effects progressively amplifying over the restoration chronosequence. Furthermore, mangrove restoration led to a substantial increase in microbial diversity and a reshaping of microbial community composition, increasing the relative abundance of dominant phyla such as Nitrospirae, Deferribacteres, and Fusobacteria. Soil multifunctionality exhibited positive correlations with microbial diversity, suggesting a link between variations in microbial diversity and soil multifunctionality. Metagenomic screening demonstrated that mangrove restoration resulted in a simultaneous increase in the abundance of nitrogen (N) related genes, such as N fixation (nirD/H/K), nitrification (pmoA-amoA/B/C), and denitrification (nirK, norB/C, narG/H, napA/B), as well as phosphorus (P)-related genes, including organic P mineralization (phnX/W, phoA/D/G, phnJ/N/P), inorganic P solubilization (gcd, ppx-gppA), and transporters (phnC/D/E, pstA/B/C/S)). The relationship between the abundance of keystone species (such as phnC/D/E) and restoration-induced changes in soil multifunctionality indicates that mangrove restoration enhances soil multifunctionality through an increase in the abundance of keystone species associated with N and P cycles. Additionally, it was observed that changes in microbial community and multifunctionality were largely associated with shifts in soil salinity. These findings demonstrate that mangrove restoration positively influences soil multifunctionality and shapes nutrient dynamics, microbial communities, and overall ecosystem resilience. As global efforts continue to focus on ecosystem restoration, understanding the complexity of mangrove-soil interactions is critical for effective nutrient management and mangrove conservation.},
}

*Wetlands
*Soil Microbiology
Soil/chemistry
Microbiota
Nitrogen Cycle
Phosphorus/metabolism
Biodiversity
Nitrogen/metabolism
Environmental Restoration and Remediation/methods
Bacteria/classification/metabolism/genetics

@article {pmid38505550,
year = {2024},
author = {Yang, S and Zhang, W and Yang, B and Feng, X and Li, Y and Li, X and Liu, Q},
title = {Metagenomic evidence for antibiotic-associated actinomycetes in the Karamay Gobi region.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1330880},
pmid = {38505550},
issn = {1664-302X},
abstract = {Due to the misuse of antibiotics, there is an increasing emergence and spread of multidrug-resistant (MDR) bacteria, leading to a human health crisis. To address clinical antibiotic resistance and prevent/control pathogenic microorganisms, the development of novel antibiotics is essential. This also offers a new approach to discovering valuable actinobacterial flora capable of producing natural bioactive products. In this study, we employed bioinformatics and macro-genome sequencing to collect 15 soil samples from three different locations in the Karamay Gobi region. First, we assessed the diversity of microorganisms in soil samples from different locations, analyzing the content of bacteria, archaea, actinomycetes, and fungi. The biodiversity of soil samples from outside the Gobi was found to be higher than that of soil samples from within and in the center of the Gobi. Second, through microbial interaction network analysis, we identified actinomycetes as the dominant group in the system. We have identified the top four antibiotic genes, such as Ecol_fabG_TRC, Efac_liaR_DAP, tetA (58), and macB, by CARD. These genes are associated with peptide antibiotics, disinfecting agents and antiseptics, tetracycline antibiotics, and macrolide antibiotics. In addition, we also obtained 40 other antibiotic-related genes through CARD alignment. Through in-depth analysis of desert soil samples, we identified several unstudied microbial species belonging to different families, including Erythrobacteriaceae, Solirubrobacterales, Thermoleophilaceae, Gaiellaceae, Nocardioidaceae, Actinomycetia, Egibacteraceae, and Acidimicrobiales. These species have the capability to produce peptide antibiotics, macrolide antibiotics, and tetracycline antibiotics, as well as disinfectants and preservatives. This study provides valuable theoretical support for future in-depth research.},
}

@article {pmid38510442,
year = {2024},
author = {Mousa, WK and Abu-Izneid, T and Salah-Tantawy, A},
title = {High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1294173},
pmid = {38510442},
issn = {1664-462X},
abstract = {INTRODUCTION: Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change.

METHODS: This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region).

RESULTS: Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions.

DISCUSSION: Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.},
}

@article {pmid38519631,
year = {2024},
author = {Pan, YF and Zhao, H and Gou, QY and Shi, PB and Tian, JH and Feng, Y and Li, K and Yang, WH and Wu, D and Tang, G and Zhang, B and Ren, Z and Peng, S and Luo, GY and Le, SJ and Xin, GY and Wang, J and Hou, X and Peng, MW and Kong, JB and Chen, XX and Yang, CH and Mei, SQ and Liao, YQ and Cheng, JX and Wang, J and Chaolemen, and Wu, YH and Wang, JB and An, T and Huang, X and Eden, JS and Li, J and Guo, D and Liang, G and Jin, X and Holmes, EC and Li, B and Wang, D and Li, J and Wu, WC and Shi, M},
title = {Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity.},
journal = {Nature ecology & evolution},
volume = {8},
number = {5},
pages = {947-959},
pmid = {38519631},
issn = {2397-334X},
mesh = {Animals ; *Culicidae/virology ; China ; *Virome ; *Mosquito Vectors/virology ; Metagenomics ; Arboviruses/genetics/classification ; Phylogeny ; Biodiversity ; },
abstract = {Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Here, using a meta-transcriptomic approach, we determined the viromes of 2,438 individual mosquitoes (81 species), spanning ~4,000 km along latitudes and longitudes in China. From these data we identified 393 viral species associated with mosquitoes, including 7 (putative) species of arthropod-borne viruses (that is, arboviruses). We identified potential mosquito species and geographic hotspots of viral diversity and arbovirus occurrence, and demonstrated that the composition of individual mosquito viromes was strongly associated with host phylogeny. Our data revealed a large number of viruses shared among mosquito species or genera, enhancing our understanding of the host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, perhaps reflecting long-distance mosquito dispersal. Together, these results greatly expand the known mosquito virome, linked viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the biogeography and diversity of viruses in insect vectors.},
}

Animals
*Culicidae/virology
China
*Virome
*Mosquito Vectors/virology
Metagenomics
Arboviruses/genetics/classification
Phylogeny
Biodiversity

@article {pmid38540015,
year = {2024},
author = {Zuo, C and Ma, P and Ma, X and Zhu, Y and Yan, S and Zhang, Z},
title = {Integrated Metagenomic and Metabolomic Analysis on Two Competing Mussels, Mytella strigata and Perna viridis, in China.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {6},
pages = {},
pmid = {38540015},
issn = {2076-2615},
support = {2022YFD2401204//National Key R&D Program of China/ ; 42006080//National Natural Science Foundation of China/ ; },
abstract = {Biological invasion is a primary direct driver of biodiversity loss. Recently, owing to exploitation competition with an invasive mussel, Mytella strigata (Hanley, 1843), there has been a drastic decrease in the population of native Perna viridis (Linnaeus, 1758) in several western Pacific regions. In the present study, intestinal microbiota, metabolome, and key digestive enzyme activities were compared between the two competing mussels, M. strigata and P. viridis, to elucidate the differences in intestinal microbiota and metabolic points. We observed that Proteobacteria, Firmicutes, and Bacteroidota were the three predominant bacterial phyla in the two species. The relative abundance of Bacteroidota related to carbohydrate-degrading ability was significantly higher in M. strigata than in P. viridis. Compared to P. viridis, different metabolites including maltose and trehalose were enriched in M. strigata. Lastly, higher carbohydrases activities of alpha-amylase, cellulase, and xylanase were observed in M. strigata than in P. viridis. These differences might play an important role in the adaptation process of M. strigata to the new environment. This study provides important basic knowledge for investigating the competition between M. strigata and P. viridis in terms of food resources utilization.},
}

@article {pmid38543562,
year = {2024},
author = {Masenya, K and Manganyi, MC and Dikobe, TB},
title = {Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543562},
issn = {2076-2607},
abstract = {Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, the field of metagenomics has emerged as a powerful tool for studying the microbial communities associated with cereal crops and their impact on plant health and growth. This chapter aims to provide a comprehensive overview of cereal metagenomics and its role in enhancing food security through the exploration of beneficial and pathogenic microbial interactions. Furthermore, we will examine how the integration of metagenomics with other tools can effectively address the adverse effects on food security. For this purpose, we discuss the integration of metagenomic data and machine learning in providing novel insights into the dynamic interactions shaping plant-microbe relationships. We also shed light on the potential applications of leveraging microbial diversity and epigenetic modifications in improving crop resilience and yield sustainability. Ultimately, cereal metagenomics has revolutionized the field of food security by harnessing the potential of beneficial interactions between cereals and their microbiota, paving the way for sustainable agricultural practices.},
}

@article {pmid38543568,
year = {2024},
author = {Li, J and Cheng, H and Yin, F and Liu, J and Zhang, XH and Yu, M},
title = {Deciphering Microbial Communities and Distinct Metabolic Pathways in the Tangyin Hydrothermal Fields of Okinawa Trough through Metagenomic and Genomic Analyses.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543568},
issn = {2076-2607},
support = {42376145 and 41976137//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Deep-sea hydrothermal vents have been extensively explored around the globe in the past decades, and the diversity of microbial communities and their ecological functions related to hydrothermal vents have become hotspots in the study of microbial biogeochemistry. However, knowledge of dominant microbial communities and their unique metabolic characteristics adapting to hydrothermal vents is still limited. In our study, the sediment sample near the Tangyin hydrothermal vent in the southern part of the Okinawa Trough was collected, and the most abundant phyla are Proteobacteria and Desulfobacterota based on the 16S rRNA genes and metagenome sequencing. Metagenomic analysis revealed that methane metabolism, sulfur reduction, and Fe[2+] uptake were abundantly distributed in hydrothermal sediment. In addition, most of the metagenomic assembly genomes (MAGs), belonging to Chloroflexota, Desulfobacterota, and Gammaproteobacteria, were found to be involved in methanogenesis, sulfur oxidation/reduction, and ferrous/ferric iron metabolisms. Among these MAGs, the two representative groups (Bathyarchaeia and Thioglobaceae) also showed distinct metabolic characteristics related to carbon, sulfur, and iron to adapt to hydrothermal environments. Our results reveal the dominant microbial populations and their metabolic features in the sediment near the Tangyin hydrothermal fields, providing a better understanding of microbial survival strategies in the extreme environment.},
}

@article {pmid38553666,
year = {2024},
author = {Ma, ZS},
title = {Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {137},
pmid = {38553666},
issn = {1471-2105},
mesh = {Animals ; Humans ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome ; Biodiversity ; Sequence Analysis, DNA ; Metagenomics/methods ; },
abstract = {BACKGROUND: Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists' (Linnaeus & Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies-amplicon sequencing and whole-genome (shotgun sequencing)-respectively generate two contrastingly different categories of metagenomic reads (data)-OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.

RESULTS: The ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan's near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.

CONCLUSIONS: All of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.},
}

Animals
Humans
Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome
Biodiversity
Sequence Analysis, DNA
Metagenomics/methods

@article {pmid38558277,
year = {2024},
author = {Ye, S and Lu, Y and Li, G and Li, D and Wu, Y and Yao, Y},
title = {Stenotrophomonas maltophilia Isolated from the Gut Symbiotic Community of the Plastic-Eating Tenebrio molitor.},
journal = {Applied biochemistry and biotechnology},
volume = {196},
number = {11},
pages = {7805-7815},
pmid = {38558277},
issn = {1559-0291},
support = {02020200-K02013008//Zhejiang University/ ; },
mesh = {Animals ; *Stenotrophomonas maltophilia/isolation & purification/genetics ; *Tenebrio/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; Plastics ; },
abstract = {Polyvinyl chloride (PVC) waste is a major environmental challenge. In this study, we found that a PVC-eating insect, Tenebrio molitor, could survive by consuming PVC as a dietary supplement. To understand the gut symbiotic community, metagenomic analysis was performed to reveal the biodiversity of a symbiotic community in the midgut of Tenebrio molitor. Among them, seven genera were enriched from the midgut of the insect under culture conditions with PVC as carbon source. A strain of Stenotrophomonas maltophilia was isolated from the midgut symbiotic community of the plastic-eating Tenebrio molitor. To unravel the functional gene for the biodegradation enzyme, we sequenced the whole genome of Stenotrophomonas maltophilia and found that orf00390, annotated as a hydrolase, was highly expressed in the PVC culture niche.},
}

Animals
*Stenotrophomonas maltophilia/isolation & purification/genetics
*Tenebrio/microbiology
*Symbiosis
Gastrointestinal Microbiome
Plastics

@article {pmid38562473,
year = {2024},
author = {Seth, N and Vats, S and Lakhanpaul, S and Arafat, Y and Mazumdar-Leighton, S and Bansal, M and Babu, CR},
title = {Microbial community diversity of an integrated constructed wetland used for treatment of sewage.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1355718},
pmid = {38562473},
issn = {1664-302X},
abstract = {The microbial community diversity in Constructed Wetland System (CWS) plays a key role in the removal of pollutants from waste water. An integrated functional CWS developed at Neela Hauz Biodiversity Park, Delhi was selected to assess the diversity in composition and structure of microbial community diversity of sludge and sediment of CWS, based on metagenomic approach using 16S rRNA genes. The sediment showed higher diversity than sludge and both formed distinct clusters. The taxonomic structure of the microbial community of CWS is represented by 6,731 OTUs distributed among 2 kingdoms, 103 phyla, 227 classes, 337 orders, 320 families, 295 identified genera, and 84 identified species. The relative abundance of top 5 dominant phyla of sludge and sediment varied from 3.77% (Acidobacteria) to 35.33% (Proteobacteria) and 4.07% (Firmicutes) to 28.20% (Proteobacteria), respectively. The range of variation in relative abundance of top 5 dominant genera of sludge and sediment was 2.58% (Hyphomicrobium) to 6.61% (Planctomyces) and 2.47% (Clostridium) to 4.22% (Syntrophobacter), respectively. The rich microbial diversity of CWS makes it perform better in pollutants removal (59.91-95.76%) than other CWs. Based on the abundance values of taxa, the taxa are grouped under four frequency distribution classes-abundant (>20), common (10-19), rare (5-9), and very rare (1-4). The unique structure of microbial communities of integrated CWS is that the number of abundant taxa decreases in descending order of taxonomic hierarchy, while the number of rare and very rare taxa increases. For example, the number of abundant phyla was 14 and 21 in sludge and sediment, respectively and both communities have only 3 abundant genera each. This is in contrast to 4 and 17 very rare phyla in sludge and sediment, respectively and both the communities have 114 and 91 very rare genera, respectively. The outcomes of the study is that the integrated CWS has much higher microbial community diversity than the diversity reported for other CWs, and the rich diversity can be used for optimizing the performance efficiency of CWS in the removal of pollutants from waste water. Such structural diversity might be an adaptation to heterogeneous environment of CWS.},
}

@article {pmid38565528,
year = {2024},
author = {Liang, JL and Feng, SW and Lu, JL and Wang, XN and Li, FL and Guo, YQ and Liu, SY and Zhuang, YY and Zhong, SJ and Zheng, J and Wen, P and Yi, X and Jia, P and Liao, B and Shu, WS and Li, JT},
title = {Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2827},
pmid = {38565528},
issn = {2041-1723},
support = {41622106//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177009//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Bacteriophages/genetics ; Ecosystem ; Phosphorus ; Metagenome/genetics ; Soil ; },
abstract = {Phosphorus (P) limitation of ecosystem processes is widespread in terrestrial habitats. While a few auxiliary metabolic genes (AMGs) in bacteriophages from aquatic habitats are reported to have the potential to enhance P-acquisition ability of their hosts, little is known about the diversity and potential ecological function of P-acquisition genes encoded by terrestrial bacteriophages. Here, we analyze 333 soil metagenomes from five terrestrial habitat types across China and identify 75 viral operational taxonomic units (vOTUs) that encode 105 P-acquisition AMGs. These AMGs span 17 distinct functional genes involved in four primary processes of microbial P-acquisition. Among them, over 60% (11/17) have not been reported previously. We experimentally verify in-vitro enzymatic activities of two pyrophosphatases and one alkaline phosphatase encoded by P-acquisition vOTUs. Thirty-six percent of the 75 P-acquisition vOTUs are detectable in a published global topsoil metagenome dataset. Further analyses reveal that, under certain circumstances, the identified P-acquisition AMGs have a greater influence on soil P availability and are more dominant in soil metatranscriptomes than their corresponding bacterial genes. Overall, our results reinforce the necessity of incorporating viral contributions into biogeochemical P cycling.},
}

*Bacteriophages/genetics
Ecosystem
Phosphorus
Metagenome/genetics
Soil

@article {pmid38566975,
year = {2024},
author = {Moubset, O and Filloux, D and Fontes, H and Julian, C and Fernandez, E and Galzi, S and Blondin, L and Chehida, SB and Lett, JM and Mesléard, F and Kraberger, S and Custer, JM and Salywon, A and Makings, E and Marais, A and Chiroleu, F and Lefeuvre, P and Martin, DP and Candresse, T and Varsani, A and Ravigné, V and Roumagnac, P},
title = {Virome release of an invasive exotic plant species in southern France.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae025},
pmid = {38566975},
issn = {2057-1577},
abstract = {The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.},
}

@article {pmid38579579,
year = {2024},
author = {Lavilla-Lerma, ML and Aibar-Almazán, A and Martínez-Amat, A and Jiménez-García, JD and Hita-Contreras, F},
title = {Moderate-intensity continuous training and high-intensity interval training modulate the composition of the oral microbiota of elderly adults: Randomized controlled trial.},
journal = {Maturitas},
volume = {185},
number = {},
pages = {107973},
doi = {10.1016/j.maturitas.2024.107973},
pmid = {38579579},
issn = {1873-4111},
mesh = {Humans ; Aged ; *High-Intensity Interval Training/methods ; Middle Aged ; Female ; Male ; *Saliva/microbiology ; *Mouth/microbiology ; *Microbiota ; Exercise/physiology ; Bacteroidetes ; },
abstract = {OBJECTIVE: We investigates the effects of 16-week high-intensity interval training and moderate-intensity continuous training on the composition of the oral microbiota. To the best of our knowledge, at the time of writing this paper no other scholars had described the oral metagenomic changes associated with prescribed exercise in older adults.

METHODS: Forty-three participants aged 60-74 years were randomized 1:1:1 to a control group, high-intensity interval training or moderate-intensity continuous training twice weekly for 16 weeks. Saliva samples were sequenced at baseline, week 8 and week 16 of intervention.

RESULTS: High-intensity interval training produced significant differences over time in Richness and a clear trend to decreased Simpson and Shannon diversity indices. In contrast, Simpson and Shannon indices showed an upward trend over time with moderate-intensity continuous training, which also decreased Firmicutes and increased Bacteroidetes levels. Significant differences in the abundance of pathogenic species were also observed after the participants completed the exercise interventions of either type.

CONCLUSIONS: Both types of exercise promoted subtle changes in the oral microbiota, confirming the modulatory effect of high-intensity interval training and moderate-intensity continuous training on the oral microbiome. Clinical trial registration NCT05220670.},
}

Humans
Aged
*High-Intensity Interval Training/methods
Middle Aged
Female
Male
*Saliva/microbiology
*Mouth/microbiology
*Microbiota
Exercise/physiology
Bacteroidetes

@article {pmid38599113,
year = {2024},
author = {Pilkington, LI and Kerner, W and Bertoldi, D and Larcher, R and Lee, SA and Goddard, MR and Albanese, D and Franceschi, P and Fedrizzi, B},
title = {Integration and holistic analysis of multiple multidimensional soil data sets.},
journal = {Talanta},
volume = {274},
number = {},
pages = {125954},
doi = {10.1016/j.talanta.2024.125954},
pmid = {38599113},
issn = {1873-3573},
mesh = {*Soil/chemistry ; Soil Microbiology ; Fungi ; Biodiversity ; New Zealand ; },
abstract = {Complex matrices such as soil have a range of measurable characteristics, and thus data to describe them can be considered multidimensional. These characteristics can be strongly influenced by factors that introduce confounding effects that hinder analyses. Traditional statistical approaches lack the flexibility and granularity required to adequately evaluate such matrices, particularly those with large dataset of varying data types (i.e. quantitative non-compositional, quantitative compositional). We present a statistical workflow designed to effectively analyse complex, multidimensional systems, even in the presence of confounding variables. The developed methodology involves exploratory analysis to identify the presence of confounding variables, followed by data decomposition (including strategies for both compositional and non-compositional quantitative data) to minimise the influence of these confounding factors such as sampling site/location. These data processing methods then allow for common patterns to be highlighted in the data, including the identification of biomarkers and determination of non-trivial associations between variables. We demonstrate the utility of this statistical workflow by jointly analysing the chemical composition and fungal biodiversity of New Zealand vineyard soils that have been managed with either organic low-input or conventional input approaches. By applying this pipeline, we were able to identify biomarkers that distinguish viticultural soil from both approaches and also unearth links and associations between the chemical and metagenomic profiles. While soil is an example of a system that can require this type of statistical methodology, there are a range of biological and ecological systems that are challenging to analyse due to the complex interplay of global and local effects. Utilising our developed pipeline will greatly enhance the way that these systems can be studied and the quality and impact of insight gained from their analysis.},
}

*Soil/chemistry
Soil Microbiology
Fungi
Biodiversity
New Zealand

@article {pmid38606341,
year = {2024},
author = {Eitel, M and Osigus, HJ and Brenzinger, B and Wörheide, G},
title = {Beauty in the beast - Placozoan biodiversity explored through molluscan predator genomics.},
journal = {Ecology and evolution},
volume = {14},
number = {4},
pages = {e11220},
pmid = {38606341},
issn = {2045-7758},
abstract = {The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell-less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator-prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole-body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study - the presence of placozoans in the sea floor sediment interstitium - in the context of their ecological, biological, and natural history implications.},
}

@article {pmid38611776,
year = {2024},
author = {Szulc, J and Okrasa, M and Nowak, A and Ryngajłło, M and Nizioł, J and Kuźniar, A and Ruman, T and Gutarowska, B},
title = {Uncontrolled Post-Industrial Landfill-Source of Metals, Potential Toxic Compounds, Dust, and Pathogens in Environment-A Case Study.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {7},
pages = {},
pmid = {38611776},
issn = {1420-3049},
support = {Phase IV of the National Program "Safety and working conditions improvement"//Ministry of Science and Higher Education and the National Centre for Research and Development/ ; 726/BN/D/2019-2021//Regional Found for Environmental Protection and Water Management in Lodz/ ; },
mesh = {Humans ; *Dust ; Caco-2 Cells ; Metals ; *Mercury ; Soil ; },
abstract = {The aim of this case study was the evaluation of the selected metals' concentration, potential toxic compound identification, cytotoxicity analysis, estimation of the airborne dust concentration, biodiversity, and number of microorganisms in the environment (leachate, soil, air) of the biggest uncontrolled post-industrial landfills in Poland. Based on the results obtained, preliminary solutions for the future management of post-industrial objects that have become an uncontrolled landfill were indicated. In the air, the PM1 fraction dominated, constituting 78.1-98.2% of the particulate matter. Bacterial counts were in the ranges of 9.33 × 10[1]-3.21 × 10[3] CFU m[-3] (air), 1.87 × 10[5]-2.30 × 10[6] CFU mL[-1] (leachates), and 8.33 × 10[4]-2.69 × 10[6] CFU g[-1] (soil). In the air, the predominant bacteria were Cellulosimicrobium and Stenotrophomonas. The predominant fungi were Mycosphaerella, Cladosporium, and Chalastospora. The main bacteria in the leachates and soils were Acinetobacter, Mortierella, Proteiniclasticum, Caloramator, and Shewanella. The main fungi in the leachates and soils were Lindtneria. Elevated concentrations of Pb, Zn, and Hg were detected. The soil showed the most pronounced cytotoxic potential, with rates of 36.55%, 63.08%, and 100% for the A-549, Caco-2, and A-549 cell lines. Nine compounds were identified which may be responsible for this cytotoxic effect, including 2,4,8-trimethylquinoline, benzo(f)quinoline, and 1-(m-tolyl)isoquinoline. The microbiome included bacteria and fungi potentially metabolizing toxic compounds and pathogenic species.},
}

Humans
*Dust
Caco-2 Cells
Metals
*Mercury
Soil

@article {pmid38622738,
year = {2024},
author = {Wu, LY and Wijesekara, Y and Piedade, GJ and Pappas, N and Brussaard, CPD and Dutilh, BE},
title = {Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {97},
pmid = {38622738},
issn = {1474-760X},
support = {Consolidator grant 865694//H2020 European Research Council/ ; Consolidator grant 865694//H2020 European Research Council/ ; 955974//H2020 Marie Skłodowska-Curie Actions/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; 865694/ERC_/European Research Council/International ; },
mesh = {Metagenome ; Ecosystem ; Metagenomics/methods ; Computational Biology/methods ; Databases, Genetic ; *Viruses/genetics ; },
abstract = {BACKGROUND: As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance.

RESULTS: We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered.

CONCLUSIONS: Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.},
}

Metagenome
Ecosystem
Metagenomics/methods
Computational Biology/methods
Databases, Genetic
*Viruses/genetics

@article {pmid38631646,
year = {2024},
author = {Muscarella, SM and Alduina, R and Badalucco, L and Capri, FC and Di Leto, Y and Gallo, G and Laudicina, VA and Paliaga, S and Mannina, G},
title = {Water reuse of treated domestic wastewater in agriculture: Effects on tomato plants, soil nutrient availability and microbial community structure.},
journal = {The Science of the total environment},
volume = {928},
number = {},
pages = {172259},
doi = {10.1016/j.scitotenv.2024.172259},
pmid = {38631646},
issn = {1879-1026},
mesh = {*Solanum lycopersicum ; *Wastewater ; *Soil Microbiology ; *Soil/chemistry ; *Agricultural Irrigation/methods ; *Microbiota ; *Waste Disposal, Fluid/methods ; Nitrogen/analysis ; Agriculture/methods ; },
abstract = {The reuse of treated wastewater (TWW) in agriculture for crop irrigation is desirable. Crop responses to irrigation with TWW depend on the characteristics of TWW and on intrinsic and extrinsic soil properties. The aim of this study was to assess the response of tomato (Solanum lycopersicum L.) cultivated in five different soils to irrigation with TWW, compared to tap water (TAP) and an inorganic NPK solution (IFW). In addition, since soil microbiota play many important roles in plant growth, a metataxonomic analysis was performed to reveal the prokaryotic community structures of TAP, TWW and IFW treated soil, respectively. A 56-days pot experiment was carried out. Plant biometric parameters, and chemical, biochemical and microbiological properties of different soils were investigated. Shoot and root dry and fresh weights, as well as plant height, were the highest in plants irrigated with IFW followed by those irrigated with TWW, and finally with TAP water. Plant biometric parameters were positively affected by soil total organic carbon (TOC) and nitrogen (TN). Electrical conductivity was increased by TWW and IFW, being such an increase proportional to clay and TOC. Soil available P was not affected by TWW, whereas mineral N increased following their application. Total microbial biomass, as well as, main microbial groups were positively affected by TOC and TN, and increased according to the following order: IFW > TWW > TAP. However, the fungi-to-bacteria ratio was lowered in soil irrigated with TWW because of its adverse effect on fungi. The germicidal effect of sodium hypochlorite on soil microorganisms was affected by soil pH. Nutrients supplied by TWW are not sufficient to meet the whole nutrients requirement of tomato, thus integration by fertilization is required. Bacteria were more stimulated than fungi by TWW, thus leading to a lower fungi-to-bacteria ratio. Interestingly, IFW and TWW treatment led to an increased abundance of Proteobacteria and Acidobacteria phyla and Balneimonas, Rubrobacter, and Steroidobacter genera. This soil microbiota structure modulation paralleled a general decrement of fungi versus bacteria abundance ratio, the increment of electrical conductivity and nitrogen content of soil and an improvement of tomato growth. Finally, the potential adverse effect of TWW added with sodium chloride on soil microorganisms depends on soil pH.},
}

*Solanum lycopersicum
*Wastewater
*Soil Microbiology
*Soil/chemistry
*Agricultural Irrigation/methods
*Microbiota
*Waste Disposal, Fluid/methods
Nitrogen/analysis
Agriculture/methods

@article {pmid38640749,
year = {2024},
author = {Gago, JF and Viver, T and Urdiain, M and Ferreira, E and Robledo, P and Rossello-Mora, R},
title = {Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode.},
journal = {Systematic and applied microbiology},
volume = {47},
number = {2-3},
pages = {126506},
doi = {10.1016/j.syapm.2024.126506},
pmid = {38640749},
issn = {1618-0984},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Groundwater/microbiology ; *Phylogeny ; *Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Islands ; Sequence Analysis, DNA ; Spain ; Metagenome ; Genome, Bacterial/genetics ; Temperature ; },
abstract = {Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.},
}

*RNA, Ribosomal, 16S/genetics
*Groundwater/microbiology
*Phylogeny
*Metagenomics
*Bacteria/classification/genetics/isolation & purification
DNA, Bacterial/genetics
Islands
Sequence Analysis, DNA
Spain
Metagenome
Genome, Bacterial/genetics
Temperature

@article {pmid38642657,
year = {2024},
author = {Vacca, M and Celano, G and Serale, N and Costantino, G and Calabrese, FM and Calasso, M and De Angelis, M},
title = {Dynamic microbial and metabolic changes during Apulian Caciocavallo cheesemaking and ripening produced according to a standardized protocol.},
journal = {Journal of dairy science},
volume = {107},
number = {9},
pages = {6541-6557},
doi = {10.3168/jds.2023-24049},
pmid = {38642657},
issn = {1525-3198},
mesh = {*Cheese/microbiology ; Animals ; Milk/microbiology/chemistry ; Food Microbiology ; },
abstract = {The microbiota of a cheese play a critical role in influencing its sensory and physicochemical properties. In this study, traditional Apulian Caciocavallo cheeses coming from 4 different dairies in the same area and produced following standardized procedures were examined, as well as the different bulk milks and natural whey starter (NWS) cultures used. Moreover, considering the cheese wheels as the blocks of Caciocavallo cheeses as whole, these were characterized at different layers (i.e., core, under-rind, and rind) of the block using a multi-omics approach. In addition to physical-chemical characterization, culturomics, quantitative PCR, metagenomics, and metabolomics analysis were carried out after salting and throughout the ripening time (2 mo) to investigate major shifts in the succession of the microbiota and flavor development. Culture-dependent and 16S rRNA metataxonomics results clearly clustered samples based on microbiota biodiversity related to the production dairy plant as a result of the use of different NWS or the intrinsic conditions of each production site. At the beginning of the ripening, cheeses were dominated by Lactobacillus, and in 2 dairies (Art and SdC), Streptococcus genera were associated with the NWS. The analysis allowed us to show that although the diversity of identified genera did not change significantly between the rind, under-rind, and core fractions of the same samples, there was an evolution in the relative abundance and absolute quantification, modifying and differentiating profiles during ripening. The real-time PCR, also known as quantitative or qPCR, mainly differentiated the temporal adaptation of those species originating from bulk milks and those provided by NWS. The primary starters detected in NWS and cheeses contributed to the high relative concentration of 1-butanol, 2-butanol, 2-heptanol, 2-butanone, acetoin, delta-dodecalactone, hexanoic acid ethyl ester, octanoic acid ethyl ester, and volatile free fatty acids during ripening, whereas cheeses displaying low abundances of Streptococcus and Lactococcus (dairy Del) had a lower total concentration of acetoin compared with Art and SdC. However, the subdominant strains and nonstarter lactic acid bacteria present in cheeses are responsible for the production of secondary metabolites belonging to the chemical classes of ketones, alcohols, and organic acids, reaffirming the importance and relevance of autochthonous strains of each dairy plant although only considering a delimited production area.},
}

*Cheese/microbiology
Animals
Milk/microbiology/chemistry
Food Microbiology

@article {pmid38643272,
year = {2024},
author = {Hauptfeld, E and Pappas, N and van Iwaarden, S and Snoek, BL and Aldas-Vargas, A and Dutilh, BE and von Meijenfeldt, FAB},
title = {Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3373},
pmid = {38643272},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; Software ; Algorithms ; *Microbiota/genetics ; Metagenomics ; },
abstract = {Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.},
}

*Metagenome/genetics
Software
Algorithms
*Microbiota/genetics
Metagenomics

@article {pmid38644048,
year = {2024},
author = {Wielkopolan, B and Szabelska-Beręsewicz, A and Gawor, J and Obrępalska-Stęplowska, A},
title = {Cereal leaf beetle-associated bacteria enhance the survival of their host upon insecticide treatments and respond differently to insecticides with different modes of action.},
journal = {Environmental microbiology reports},
volume = {16},
number = {2},
pages = {e13247},
pmid = {38644048},
issn = {1758-2229},
support = {UMO-2020/37/N/NZ9/02577//Polish National Science Centre/ ; },
mesh = {Animals ; *Insecticides/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Larva/microbiology/drug effects ; *Coleoptera/microbiology/drug effects ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects ; Metagenomics ; Pyrethrins/pharmacology ; Chlorpyrifos ; Pantoea/genetics/drug effects ; },
abstract = {The cereal leaf beetle (CLB, Oulema melanopus) is one of the major cereal pests. The effect of insecticides belonging to different chemical classes, with different mechanisms of action and the active substances' concentrations on the CLB bacterial microbiome, was investigated. Targeted metagenomic analysis of the V3-V4 regions of the 16S ribosomal gene was used to determine the composition of the CLB bacterial microbiome. Each of the insecticides caused a decrease in the abundance of bacteria of the genus Pantoea, and an increase in the abundance of bacteria of the genus Stenotrophomonas, Acinetobacter, compared to untreated insects. After cypermethrin application, a decrease in the relative abundance of bacteria of the genus Pseudomonas was noted. The dominant bacterial genera in cypermethrin-treated larvae were Lactococcus, Pantoea, while in insects exposed to chlorpyrifos or flonicamid it was Pseudomonas. Insecticide-treated larvae were characterized, on average, by higher biodiversity and richness of bacterial genera, compared to untreated insects. The depletion of CLB-associated bacteria resulted in a decrease in larval survival, especially after cypermethrin and chlorpyrifos treatments. The use of a metagenome-based functional prediction approach revealed a higher predicted function of bacterial acetyl-CoA C-acetyltransferase in flonicamid and chlorpyrifos-treated larvae and tRNA dimethyltransferase in cypermethrin-treated insects than in untreated insects.},
}

Animals
*Insecticides/pharmacology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Larva/microbiology/drug effects
*Coleoptera/microbiology/drug effects
RNA, Ribosomal, 16S/genetics
Microbiota/drug effects
Metagenomics
Pyrethrins/pharmacology
Chlorpyrifos
Pantoea/genetics/drug effects

@article {pmid38646932,
year = {2024},
author = {Saranholi, BH and França, FM and Vogler, AP and Barlow, J and Vaz de Mello, FZ and Maldaner, ME and Carvalho, E and Gestich, CC and Howes, B and Banks-Leite, C and Galetti, PM},
title = {Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics.},
journal = {Molecular ecology resources},
volume = {24},
number = {5},
pages = {e13961},
doi = {10.1111/1755-0998.13961},
pmid = {38646932},
issn = {1755-0998},
support = {1989427//University of Bristol (PolicyBristol, SYNPAM)/ ; ProjectBIOCLIMATE//BNP Paribas Foundation (Climate and Biodiversity Initiative)/ ; 2258319//Cabot Seedcorn 2023 (Voices of Amazonia)/ ; 303524/2019-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 406767/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 420254/2018-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441257/2023-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441573/2020-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441659/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 1777136//University of Bristol (Liv Sidse Jansen Memorial Foundation, FOR-TRAITS)/ ; NE/S011811/1//Natural Environment Research Council/ ; 170839//Climate and Net Zero Impact Awards (Scaling-up TAOCA)/ ; MR/X032949/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Coleoptera/genetics/classification ; *Mammals/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/methods ; Biodiversity ; Metagenomics/methods ; DNA/genetics ; Feces/chemistry ; },
abstract = {Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.},
}

Animals
*Coleoptera/genetics/classification
*Mammals/genetics/classification
*DNA Barcoding, Taxonomic/methods
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal/genetics
Sequence Analysis, DNA/methods
Biodiversity
Metagenomics/methods
DNA/genetics
Feces/chemistry

@article {pmid38647870,
year = {2024},
author = {Yang, F and Li, Q and Yin, X},
title = {Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {2},
pages = {1587-1599},
pmid = {38647870},
issn = {1678-4405},
support = {ZR2020KC036//Natural Science Foundation of Shandong Province/ ; },
mesh = {*Salinity ; *Estuaries ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Metagenomics ; Arctic Regions ; Microbiota ; Ice Cover/microbiology ; Genetic Variation ; Biodiversity ; Metagenome ; Sulfur/metabolism ; Nitrogen/metabolism ; Phylogeny ; },
abstract = {Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.},
}

*Salinity
*Estuaries
*Bacteria/genetics/classification/drug effects/isolation & purification
*Metagenomics
Arctic Regions
Microbiota
Ice Cover/microbiology
Genetic Variation
Biodiversity
Metagenome
Sulfur/metabolism
Nitrogen/metabolism
Phylogeny

@article {pmid38652444,
year = {2024},
author = {Li, D and Wang, H and Chen, N and Jiang, H and Chen, N},
title = {Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {3},
pages = {2423-2435},
pmid = {38652444},
issn = {1678-4405},
support = {WXBSH2021001//Postdoctoral Science Foundation of West Anhui University/ ; WGKQ2021021//The High-level Talent Project of West Anhui University/ ; GXYQ2020127//the Provincial Level Nature Science Foundation of Anhui Education Department/ ; 2022AH010090//Anhui Scientific Research and Innovation Team of Quality Evaluation and Improvement of Traditional Chinese Medicine/ ; KJ2021A0924//Natural Science Research Project of Anhui Provincial Colleges and Universities/ ; },
mesh = {*Soil Microbiology ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism/enzymology ; *Lakes/microbiology ; China ; *Rhizosphere ; Phylogeny ; Microbiota ; Biodiversity ; Metagenome ; },
abstract = {To investigate the impact of Poa alpigena Lindm on rhizosphere and bulk soil microorganisms in Haixin Mountain, Qinghai Lake, this study employed metagenomics technology to analyze the microbial communities of the samples. Results showed that 65 phyla, 139 classes, 278 orders, 596 families, 2376 genera, and 5545 species of soil microorganisms were identified from rhizosphere and bulk soil samples. Additionally, a microbial gene library specific to Poa alpigena Lindm was established for Qinghai Lake. Through α-diversity analysis, the richness and diversity of bulk microorganisms both significantly had a higher value than that in rhizosphere soil. The indicator microorganisms of rhizosphere and bulk soil at class level were Actinobacteria and Alphaproteobacteria, respectively. KEGG pathway analysis indicated that Carotenoid biosynthesis, Starch and sucrose metabolism, Bacterial chemotaxis, MAPK signaling pathway, Terpenoid backbone biosynthesis, and vancomycin resistance were the key differential metabolic pathways of rhizosphere soil microorganisms; in contrast, in bulk soil, the key differential metabolic were Benzoate degradation, Glycolysis gluconeogenesis, Aminobenzoate degradation, ABC transporters, Glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, Degradation of aromatic compounds, Methane metabolism, Pyruvate metabolism and Microbial metabolism diverse environments. Our results indicated that Poa alpigena Lindm rhizosphere soil possessed selectivity for microorganisms in Qinghai Lake Haixin Mountain, and the rhizosphere soil also provided a suitable survival environment for microorganisms.},
}

*Soil Microbiology
*Metagenomics
*Bacteria/genetics/classification/isolation & purification/metabolism/enzymology
*Lakes/microbiology
China
*Rhizosphere
Phylogeny
Microbiota
Biodiversity
Metagenome

@article {pmid38655082,
year = {2024},
author = {Thøgersen, MS and Zervas, A and Stougaard, P and Ellegaard-Jensen, L},
title = {Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1358787},
pmid = {38655082},
issn = {1664-302X},
abstract = {The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.},
}

@article {pmid38662153,
year = {2024},
author = {Choudhary, G and Kumari, S and Anu, K and Devi, S},
title = {Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {2},
pages = {1465-1476},
pmid = {38662153},
issn = {1678-4405},
mesh = {*Hot Springs/microbiology ; India ; *Bacteria/genetics/classification/isolation & purification ; *High-Throughput Nucleotide Sequencing ; *Microbiota ; *Archaea/genetics/classification/isolation & purification ; *Metagenomics ; Phylogeny ; Biodiversity ; },
abstract = {Due to their distinctive physicochemical characteristics, hot springs are extremely important. The whole genome metagenomic sequencing technology can be utilized to analyze the diverse microbial community that thrives in this habitat due to the particular selection pressure that prevails there. The current investigation emphasizes on culture-independent metagenomic study of the Panamik hot spring and its nearby areas from Ladakh, India. Based on different diversity indices, sequence analysis of the soil reservoir showed higher species richness and diversity in comparison to water and sediment samples. The mineral content and various physicochemical pameters like temperature, pH had an impact on the composition of the microbial community of the geothermal springs. The phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacter, Firmicutes, and Verrucomicrobia in bacterial domain dominate the thermos-alkaline spring at Panamik in different concentrations. Economically significant microbes from the genera Actinobacter, Thermosynechoccus, Candidatus Solibacter, Chthoniobacter, Synechoccus, Pseudomonas and Sphingomonas, were prevalent in hot spring. In the archaeal domain, the most dominant phylum and genera were Euryarchaeota and Thermococcus in all the samples. Further, the most abundant species were Methanosarcina barkeri, Nitrospumilus maritimus and Methanosarcina acetivorans. The present study which only examined one of the several thermal springs present in the Himalayan geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the hot springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Panamik hot spring, which serve as a repository for unidentified microbial lineages.},
}

*Hot Springs/microbiology
India
*Bacteria/genetics/classification/isolation & purification
*High-Throughput Nucleotide Sequencing
*Microbiota
*Archaea/genetics/classification/isolation & purification
*Metagenomics
Phylogeny
Biodiversity

@article {pmid38663298,
year = {2024},
author = {Rout, AK and Dixit, S and Tripathy, PS and Rout, SS and Parida, SN and Parida, PK and Sarkar, DJ and Kumar Das, B and Singh, AK and Behera, BK},
title = {Metagenomic landscape of sediments of river Ganga reveals microbial diversity, potential plastic and xenobiotic degradation enzymes.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134377},
doi = {10.1016/j.jhazmat.2024.134377},
pmid = {38663298},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology/chemistry ; *Biodegradation, Environmental ; *Bacteria/genetics/enzymology ; Biodiversity ; Xenobiotics/metabolism ; Water Pollutants, Chemical/analysis ; India ; Plastics ; Metagenome ; Metagenomics ; Benzhydryl Compounds ; },
abstract = {The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8-3.7 ppm), COD (23-29.2 ppm) and organic carbon (0.18-0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.},
}

*Geologic Sediments/microbiology
*Rivers/microbiology/chemistry
*Biodegradation, Environmental
*Bacteria/genetics/enzymology
Biodiversity
Xenobiotics/metabolism
Water Pollutants, Chemical/analysis
India
Plastics
Metagenome
Metagenomics
Benzhydryl Compounds

@article {pmid38668594,
year = {2024},
author = {Bishop, SL and Solonenka, JT and Giebelhaus, RT and Bakker, DTR and Li, ITS and Murch, SJ},
title = {Microbial Diversity Impacts Non-Protein Amino Acid Production in Cyanobacterial Bloom Cultures Collected from Lake Winnipeg.},
journal = {Toxins},
volume = {16},
number = {4},
pages = {},
pmid = {38668594},
issn = {2072-6651},
support = {Unknown//Natural Sciences and Engineering Research Council/ ; Unknown//Canadian Foundation for Innovation/ ; },
mesh = {*Lakes/microbiology ; *Cyanobacteria/metabolism/genetics/isolation & purification ; Manitoba ; Harmful Algal Bloom ; Amino Acids/analysis/metabolism ; Tandem Mass Spectrometry ; Biodiversity ; Microbiota ; Cyanobacteria Toxins ; },
abstract = {Lake Winnipeg in Manitoba, Canada is heavily impacted by harmful algal blooms that contain non-protein amino acids (NPAAs) produced by cyanobacteria: N-(2-aminoethyl)glycine (AEG), β-aminomethyl-L-alanine (BAMA), β-N-methylamino-L-alanine (BMAA), and 2,4-diaminobutyric acid (DAB). Our objective was to investigate the impact of microbial diversity on NPAA production by cyanobacteria using semi-purified crude cyanobacterial cultures established from field samples collected by the Lake Winnipeg Research Consortium between 2016 and 2021. NPAAs were detected and quantified by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) using validated analytical methods, while Shannon and Simpson alpha diversity scores were determined from 16S rRNA metagenomic sequences. Alpha diversity in isolate cultures was significantly decreased compared to crude cyanobacterial cultures (p < 0.001), indicating successful semi-purification. BMAA and AEG concentrations were higher in crude compared to isolate cultures (p < 0.0001), and AEG concentrations were correlated to the alpha diversity in cultures (r = 0.554; p < 0.0001). BAMA concentrations were increased in isolate cultures (p < 0.05), while DAB concentrations were similar in crude and isolate cultures. These results demonstrate that microbial community complexity impacts NPAA production by cyanobacteria and related organisms.},
}

*Lakes/microbiology
*Cyanobacteria/metabolism/genetics/isolation & purification
Manitoba
Harmful Algal Bloom
Amino Acids/analysis/metabolism
Tandem Mass Spectrometry
Biodiversity
Microbiota
Cyanobacteria Toxins

@article {pmid38672407,
year = {2024},
author = {Schiano-Lomoriello, D and Abicca, I and Contento, L and Gabrielli, F and Alfonsi, C and Di Pietro, F and Papa, FT and Ballesteros-Sánchez, A and Sánchez-González, JM and Rocha-De-Lossada, C and Mazzotta, C and Giannaccare, G and Bonzano, C and Borroni, D},
title = {Infectious Keratitis: Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index.},
journal = {Biomolecules},
volume = {14},
number = {4},
pages = {},
pmid = {38672407},
issn = {2218-273X},
mesh = {*Keratitis/microbiology ; Humans ; *Biodiversity ; Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Microbiota/genetics ; },
abstract = {Purpose: To characterize microbial keratitis diversity utilizing species richness and Shannon Diversity Index. Methods: Corneal impression membrane was used to collect samples. All swabs were processed and analyzed by Biolab Laboratory (level V-SSN Excellence: ISO 9001:2015), Biolab Srl (Ascoli Piceno, Italy). DNA extraction, library preparation, and sequencing were performed in all samples. After sequencing, low-quality and polyclonal sequences were filtered out by the Ion software. At this point, we employed Kraken2 for microbial community analysis in keratitis samples. Nuclease-free water and all the reagents included in the experiment were used as a negative control. The primary outcome was the reduction in bacterial DNA (microbial load) at T1, expressed as a percentage of the baseline value (T0). Richness and Shannon alpha diversity metrics, along with Bray-Curtis beta diversity values, were calculated using the phyloseq package in R. Principal coordinate analysis was also conducted to interpret these metrics. Results: 19 samples were included in the study. The results exhibited a motley species richness, with the highest recorded value surpassing 800 species. Most of the samples displayed richness values ranging broadly from under 200 to around 600, indicating considerable variability in species count among the keratitis samples. Conclusions: A significant presence of both typical and atypical bacterial phyla in keratitis infections, underlining the complexity of the disease's microbial etiology.},
}

*Keratitis/microbiology
Humans
*Biodiversity
Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics
Microbiota/genetics

@article {pmid38674632,
year = {2024},
author = {Couto, RDS and Abreu, WU and Rodrigues, LRR and Marinho, LF and Morais, VDS and Villanova, F and Pandey, RP and Deng, X and Delwart, E and da Costa, AC and Leal, E},
title = {Genomoviruses in Liver Samples of Molossus molossus Bats.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
pmid = {38674632},
issn = {2076-2607},
abstract = {CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.},
}

@article {pmid38674691,
year = {2024},
author = {Deryabin, D and Lazebnik, C and Vlasenko, L and Karimov, I and Kosyan, D and Zatevalov, A and Duskaev, G},
title = {Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
pmid = {38674691},
issn = {2076-2607},
support = {22-16-00036//Russian Science Foundation/ ; FNWZ-2022-0010//research project/ ; },
abstract = {The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community's variants in chickens' ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection.},
}

@article {pmid38674771,
year = {2024},
author = {Gómez, F and Rodríguez, N and Rodríguez-Manfredi, JA and Escudero, C and Carrasco-Ropero, I and Martínez, JM and Ferrari, M and De Angelis, S and Frigeri, A and Fernández-Sampedro, M and Amils, R},
title = {Association of Acidotolerant Cyanobacteria to Microbial Mats below pH 1 in Acidic Mineral Precipitates in Río Tinto River in Spain.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
pmid = {38674771},
issn = {2076-2607},
abstract = {This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining the extremely low pH and the high concentration of heavy metals, while maintaining a high level of microbial diversity. These multi-layered mineral deposits are stable all year round and are characterized by a succession of thick greenish-blue and brownish layers mainly composed of natrojarosite. The temperature and absorbance above and below the mineral precipitates were followed and stable conditions were detected inside the mineral precipitates. Different methodologies, scanning and transmission electron microscopy, immunological detection, fluorescence in situ hybridization, and metagenomic analysis were used to describe the biodiversity existing in these microbial mats, demonstrating, for the first time, the existence of acid-tolerant cyanobacteria in a hyperacidic environment of below pH 1. Up to 0.46% of the classified sequences belong to cyanobacterial microorganisms, and 1.47% of the aligned DNA reads belong to the Cyanobacteria clade.},
}

@article {pmid38679240,
year = {2024},
author = {Chen, C and Gong, H and Wei, Y and Xu, T and Li, J and Ding, GC},
title = {Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy.},
journal = {Bioresource technology},
volume = {401},
number = {},
pages = {130746},
doi = {10.1016/j.biortech.2024.130746},
pmid = {38679240},
issn = {1873-2976},
mesh = {*Nitrogen ; *Denitrification ; *Agriculture/methods ; *Soil/chemistry ; Nitrates ; Soil Microbiology ; Soil Pollutants/metabolism ; },
abstract = {Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.},
}

*Nitrogen
*Denitrification
*Agriculture/methods
*Soil/chemistry
Nitrates
Soil Microbiology
Soil Pollutants/metabolism

@article {pmid38680886,
year = {2024},
author = {Nimnoi, P and Pirankham, P and Srimuang, K and Ruanpanun, P},
title = {Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17289},
pmid = {38680886},
issn = {2167-8359},
mesh = {Animals ; Bacteria/classification/isolation & purification/genetics ; Biodiversity ; Microbiota ; *Nematoda/microbiology ; *Oryza/microbiology/parasitology ; *Rhizosphere ; Soil/parasitology/chemistry ; *Soil Microbiology ; Thailand ; },
abstract = {Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.},
}

Animals
Bacteria/classification/isolation & purification/genetics
Biodiversity
Microbiota
*Nematoda/microbiology
*Oryza/microbiology/parasitology
*Rhizosphere
Soil/parasitology/chemistry
*Soil Microbiology
Thailand

@article {pmid38683843,
year = {2024},
author = {Hernández, AM and Alcaraz, LD and Hernández-Álvarez, C and Romero, MF and Jara-Servín, A and Barajas, H and Ramírez, CM and Peimbert, M},
title = {Revealing the microbiome diversity and biocontrol potential of field Aedes ssp.: Implications for disease vector management.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0302328},
pmid = {38683843},
issn = {1932-6203},
mesh = {*Aedes/microbiology ; Animals ; *Microbiota ; *Mosquito Vectors/microbiology ; *RNA, Ribosomal, 16S/genetics ; Wolbachia/genetics/physiology/isolation & purification ; Larva/microbiology ; Metagenomics/methods ; Mexico ; Mosquito Control/methods ; },
abstract = {The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome's impact on its host's health and fitness is well known. However, most studies on mosquito microbiomes have been conducted in laboratory settings. We explored the mixed microbial communities within Aedes spp., utilizing the 16S rRNA gene for diversity analysis and shotgun metagenomics for functional genomics. Our samples, which included Ae. aegypti and Ae. albopictus, spanned various developmental stages-eggs, larvae, and adults-gathered from five semiurban areas in Mexico. Our findings revealed a substantial diversity of 8,346 operational taxonomic units (OTUs), representing 967 bacterial genera and 126,366 annotated proteins. The host developmental stage was identified as the primary factor associated with variations in the microbiome composition. Subsequently, we searched for genes and species involved in mosquito biocontrol. Wolbachia accounted for 9.6% of the 16S gene sequences. We observed a high diversity (203 OTUs) of Wolbachia strains commonly associated with mosquitoes, such as wAlb, with a noticeable increase in abundance during the adult stages. Notably, we detected the presence of the cifA and cifB genes, which are associated with Wolbachia's cytoplasmic incompatibility, a biocontrol mechanism. Additionally, we identified 221 OTUs related to Bacillus, including strains linked to B. thuringiensis. Furthermore, we discovered multiple genes encoding insecticidal toxins, such as Cry, Mcf, Vip, and Vpp. Overall, our study contributes to the understanding of mosquito microbiome biodiversity and metabolic capabilities, which are essential for developing effective biocontrol strategies against this disease vector.},
}

*Aedes/microbiology
Animals
*Microbiota
*Mosquito Vectors/microbiology
*RNA, Ribosomal, 16S/genetics
Wolbachia/genetics/physiology/isolation & purification
Larva/microbiology
Metagenomics/methods
Mexico
Mosquito Control/methods

@article {pmid38691556,
year = {2024},
author = {Kawser, AQMR and Hoque, MN and Rahman, MS and Sakif, TI and Coffey, TJ and Islam, T},
title = {Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0303047},
pmid = {38691556},
issn = {1932-6203},
mesh = {Animals ; Bangladesh ; *Gastrointestinal Microbiome/genetics ; *Fishes/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; },
abstract = {The field of fish microbiome research has rapidly been advancing, primarily focusing on farmed or laboratory fish species rather than natural or marine fish populations. This study sought to reveal the distinctive gut bacteriome composition and diversity within the anadromous fish species Tenualosa ilisha (hilsa), which holds the status of being the national fish of Bangladesh. We conducted an analysis on 15 gut samples obtained from 15 individual hilsa fishes collected from three primary habitats (e.g., freshwater = 5, brackish water = 5 and marine water = 5) in Bangladesh. The analysis utilized metagenomics based on 16S rRNA gene sequencing targeting the V3-V4 regions. Our comprehensive identification revealed a total of 258 operational taxonomic units (OTUs). The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our analysis unveiled considerable taxonomic differences among the habitats (freshwater, brackish water, and marine water) of hilsa fishes, as denoted by a higher level of shared microbiota (p = 0.007, Kruskal-Wallis test). Among the identified genera in the gut of hilsa fishes, including Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, and Hafnia, several are recognized as fish probiotics. Importantly, some bacterial genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella identified in the gut of hilsa identified in this study have not been reported in any aquatic or marine fish species. Significantly, we observed that 67.50% (27/40) of bacterial genera were found to be common among hilsa fishes across all three habitats. Our findings offer compelling evidence for the presence of both exclusive and communal bacteriomes within the gut of hilsa fishes, exhibiting potential probiotic properties. These observations could be crucial for guiding future microbiome investigations in this economically significant fish species.},
}

Animals
Bangladesh
*Gastrointestinal Microbiome/genetics
*Fishes/microbiology
*RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification/isolation & purification
Biodiversity
Phylogeny

@article {pmid38714759,
year = {2024},
author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R},
title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.},
journal = {Nature microbiology},
volume = {9},
number = {5},
pages = {1152-1156},
pmid = {38714759},
issn = {2058-5276},
support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; },
mesh = {*Spectrum Analysis, Raman/methods ; *Internet ; Humans ; Databases, Factual ; },
}

*Spectrum Analysis, Raman/methods
*Internet
Humans
Databases, Factual

@article {pmid38720057,
year = {2024},
author = {Hirpara, KR and Hinsu, AT and Kothari, RK},
title = {Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10525},
pmid = {38720057},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Arachis/microbiology ; India ; *Soil Microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Farms ; Plant Roots/microbiology ; Phylogeny ; Metagenome ; Biodiversity ; },
abstract = {The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.},
}

*Rhizosphere
*Arachis/microbiology
India
*Soil Microbiology
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Farms
Plant Roots/microbiology
Phylogeny
Metagenome
Biodiversity

@article {pmid38720071,
year = {2024},
author = {Wienhausen, G and Moraru, C and Bruns, S and Tran, DQ and Sultana, S and Wilkes, H and Dlugosch, L and Azam, F and Simon, M},
title = {Ligand cross-feeding resolves bacterial vitamin B12 auxotrophies.},
journal = {Nature},
volume = {629},
number = {8013},
pages = {886-892},
pmid = {38720071},
issn = {1476-4687},
mesh = {Atlantic Ocean ; Coculture Techniques ; *Ligands ; Microbial Interactions ; Prophages/genetics/growth & development/metabolism ; *Vitamin B 12/biosynthesis/chemistry/metabolism ; *Alteromonadaceae/growth & development/metabolism ; *Rhodobacteraceae/cytology/metabolism/virology ; Ribonucleosides/metabolism ; Cobamides/metabolism ; Ecosystem ; },
abstract = {Cobalamin (vitamin B12, herein referred to as B12) is an essential cofactor for most marine prokaryotes and eukaryotes[1,2]. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics[2-4]. Here we show that two bacterial B12 auxotrophs can salvage different B12 building blocks and cooperate to synthesize B12. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B12. Release of B12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B12. These complex microbial interactions of ligand cross-feeding and joint B12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B12 producers. These findings add new players to our understanding of B12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.},
}

Atlantic Ocean
Coculture Techniques
*Ligands
Microbial Interactions
Prophages/genetics/growth & development/metabolism
*Vitamin B 12/biosynthesis/chemistry/metabolism
*Alteromonadaceae/growth & development/metabolism
*Rhodobacteraceae/cytology/metabolism/virology
Ribonucleosides/metabolism
Cobamides/metabolism
Ecosystem

@article {pmid38723976,
year = {2024},
author = {Bute, TF and Wyness, A and Wasserman, RJ and Dondofema, F and Keates, C and Dalu, T},
title = {Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems.},
journal = {The Science of the total environment},
volume = {932},
number = {},
pages = {173059},
doi = {10.1016/j.scitotenv.2024.173059},
pmid = {38723976},
issn = {1879-1026},
mesh = {*Extracellular Polymeric Substance Matrix ; *Microbiota ; *Ecosystem ; Geologic Sediments/microbiology/chemistry ; Bacteria/classification/genetics ; Seasons ; Environmental Monitoring ; },
abstract = {Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g[-1]; Protein mean 65 μg g[-1]) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g[-1]; Protein mean 26 μg g[-1]). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.},
}

*Extracellular Polymeric Substance Matrix
*Microbiota
*Ecosystem
Geologic Sediments/microbiology/chemistry
Bacteria/classification/genetics
Seasons
Environmental Monitoring

@article {pmid38730339,
year = {2024},
author = {Rekadwad, BN and Shouche, YS and Jangid, K},
title = {A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {162},
pmid = {38730339},
issn = {1471-2180},
support = {PDFSS-2013-14-ST-MAH-4350//University Grants Commission/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; *Seawater/microbiology ; India ; *Phylogeny ; *Supervised Machine Learning ; *Bays/microbiology ; Biodiversity ; DNA, Bacterial/genetics ; Salinity ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris.

RESULTS: The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study.

CONCLUSION: Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Microbiota/genetics
*Seawater/microbiology
India
*Phylogeny
*Supervised Machine Learning
*Bays/microbiology
Biodiversity
DNA, Bacterial/genetics
Salinity
Sequence Analysis, DNA/methods

@article {pmid38731876,
year = {2024},
author = {Park, G and Kim, S and Lee, W and Kim, G and Shin, H},
title = {Deciphering the Impact of Defecation Frequency on Gut Microbiome Composition and Diversity.},
journal = {International journal of molecular sciences},
volume = {25},
number = {9},
pages = {},
pmid = {38731876},
issn = {1422-0067},
support = {2021R1A2C1095215//Korea Basic Science Institute/ ; 2023R1A6C101A045//Korea Basic Science Institute/ ; OTTOGI Corporation through Research and Publication Projects//OTTOGI Corporation/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Male ; Adult ; *Defecation ; Female ; Metabolome ; Biodiversity ; Amino Acids, Branched-Chain/metabolism ; Metabolomics/methods ; Bacteria/classification/genetics/metabolism ; Bacteroides/genetics ; Metagenome ; },
abstract = {This study explores the impact of defecation frequency on the gut microbiome structure by analyzing fecal samples from individuals categorized by defecation frequency: infrequent (1-3 times/week, n = 4), mid-frequent (4-6 times/week, n = 7), and frequent (daily, n = 9). Utilizing 16S rRNA gene-based sequencing and LC-MS/MS metabolome profiling, significant differences in microbial diversity and community structures among the groups were observed. The infrequent group showed higher microbial diversity, with community structures significantly varying with defecation frequency, a pattern consistent across all sampling time points. The Ruminococcus genus was predominant in the infrequent group, but decreased with more frequent defecation, while the Bacteroides genus was more common in the frequent group, decreasing as defecation frequency lessened. The infrequent group demonstrated enriched biosynthesis genes for aromatic amino acids and branched-chain amino acids (BCAAs), in contrast to the frequent group, which had a higher prevalence of genes for BCAA catabolism. Metabolome analysis revealed higher levels of metabolites derived from aromatic amino acids and BCAA metabolism in the infrequent group, and lower levels of BCAA-derived metabolites in the frequent group, consistent with their predicted metagenomic functions. These findings underscore the importance of considering stool consistency/frequency in understanding the factors influencing the gut microbiome.},
}

*Gastrointestinal Microbiome/genetics
Humans
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
Male
Adult
*Defecation
Female
Metabolome
Biodiversity
Amino Acids, Branched-Chain/metabolism
Metabolomics/methods
Bacteria/classification/genetics/metabolism
Bacteroides/genetics
Metagenome

@article {pmid38734682,
year = {2024},
author = {Buysse, M and Koual, R and Binetruy, F and de Thoisy, B and Baudrimont, X and Garnier, S and Douine, M and Chevillon, C and Delsuc, F and Catzeflis, F and Bouchon, D and Duron, O},
title = {Detection of Anaplasma and Ehrlichia bacteria in humans, wildlife, and ticks in the Amazon rainforest.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3988},
pmid = {38734682},
issn = {2041-1723},
support = {ANR-21-CE02-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-25-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {*Anaplasma/genetics/isolation & purification/pathogenicity/classification ; *Ehrlichia/genetics/isolation & purification/classification ; Humans ; Animals ; *Rainforest ; *Ticks/microbiology ; *Animals, Wild/microbiology ; *Phylogeny ; Anaplasmosis/microbiology/epidemiology/transmission ; French Guiana ; Ehrlichiosis/microbiology/epidemiology/veterinary/transmission ; Metagenomics/methods ; Genome, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Tick-borne bacteria of the genera Ehrlichia and Anaplasma cause several emerging human infectious diseases worldwide. In this study, we conduct an extensive survey for Ehrlichia and Anaplasma infections in the rainforests of the Amazon biome of French Guiana. Through molecular genetics and metagenomics reconstruction, we observe a high indigenous biodiversity of infections circulating among humans, wildlife, and ticks inhabiting these ecosystems. Molecular typing identifies these infections as highly endemic, with a majority of new strains and putative species specific to French Guiana. They are detected in unusual rainforest wild animals, suggesting they have distinctive sylvatic transmission cycles. They also present potential health hazards, as revealed by the detection of Candidatus Anaplasma sparouinense in human red blood cells and that of a new close relative of the human pathogen Ehrlichia ewingii, Candidatus Ehrlichia cajennense, in the tick species that most frequently bite humans in South America. The genome assembly of three new putative species obtained from human, sloth, and tick metagenomes further reveals the presence of major homologs of Ehrlichia and Anaplasma virulence factors. These observations converge to classify health hazards associated with Ehrlichia and Anaplasma infections in the Amazon biome as distinct from those in the Northern Hemisphere.},
}

*Anaplasma/genetics/isolation & purification/pathogenicity/classification
*Ehrlichia/genetics/isolation & purification/classification
Humans
Animals
*Rainforest
*Ticks/microbiology
*Animals, Wild/microbiology
*Phylogeny
Anaplasmosis/microbiology/epidemiology/transmission
French Guiana
Ehrlichiosis/microbiology/epidemiology/veterinary/transmission
Metagenomics/methods
Genome, Bacterial/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid38742714,
year = {2024},
author = {Bei, Q and Reitz, T and Schädler, M and Hodgskiss, LH and Peng, J and Schnabel, B and Buscot, F and Eisenhauer, N and Schleper, C and Heintz-Buschart, A},
title = {Metabolic potential of Nitrososphaera-associated clades.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38742714},
issn = {1751-7370},
support = {//German Centre for Integrative Biodiversity Research/ ; FZT 118//Halle-Jena-Leipzig of the German Research Foundation/ ; HE 8266/4-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Soil Microbiology ; *Archaea/metabolism/genetics/classification ; *Ammonia/metabolism ; *Oxidation-Reduction ; Germany ; Metagenome ; Phylogeny ; Genome, Archaeal ; Soil/chemistry ; },
abstract = {Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.},
}

*Soil Microbiology
*Archaea/metabolism/genetics/classification
*Ammonia/metabolism
*Oxidation-Reduction
Germany
Metagenome
Phylogeny
Genome, Archaeal
Soil/chemistry

@article {pmid38743050,
year = {2024},
author = {Aguilar, C and Alwali, A and Mair, M and Rodriguez-Orduña, L and Contreras-Peruyero, H and Modi, R and Roberts, C and Sélem-Mojica, N and Licona-Cassani, C and Parkinson, EI},
title = {Actinomycetota bioprospecting from ore-forming environments.},
journal = {Microbial genomics},
volume = {10},
number = {5},
pages = {},
pmid = {38743050},
issn = {2057-5858},
support = {R35 GM138002/GM/NIGMS NIH HHS/United States ; },
mesh = {*Actinobacteria/genetics/metabolism ; Metagenomics ; Fluorides/metabolism ; Biological Products/metabolism ; Bioprospecting ; Metabolomics ; Biodiversity ; Genome, Bacterial ; Phylogeny ; Hydrogen-Ion Concentration ; Salinity ; },
abstract = {Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.},
}

*Actinobacteria/genetics/metabolism
Metagenomics
Fluorides/metabolism
Biological Products/metabolism
Bioprospecting
Metabolomics
Biodiversity
Genome, Bacterial
Phylogeny
Hydrogen-Ion Concentration
Salinity

@article {pmid38743658,
year = {2024},
author = {Yue, J and Zhang, D and Cao, M and Li, Y and Liang, Q and Liu, F and Dong, Y},
title = {Response of microbial community composition and function to land use in mining soils of Xikuang Mountain in Hunan.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0299550},
pmid = {38743658},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Mining ; China ; *Bacteria/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Soil/chemistry ; Ecosystem ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Nine land types in the northern mining area (BKQ) (mining land, smelting land, living area), the old mining area (LKQ) (whole-ore heap, wasteland, grassland), and southern mining area (NKQ) (grassland, shrubs, farmland) of Xikuang Mountain were chosen to explore the composition and functions of soil bacterial communities under different habitats around mining areas. The composition and functions of soil bacterial communities were compared among the sampling sites using 16S rRNA high-throughput sequencing and metagenomic sequencing. α diversity analysis showed the soil bacterial diversity and abundance in the old mining area were significantly higher than those in the northern mining area. β diversity analysis demonstrated that the soil bacterial community composition was highly similar among different vegetation coverages in the southern mining area. Microbial community function analysis showed the annotated KEGG function pathways and eggNOG function composition were consistent between the grassland of the old mining area and the grassland of the southern mining area. This study uncovers the soil bacterial community composition and functions among different habitats in the mining areas of Xikuang Mountain and will underlie soil ecosystem restoration in different habitats under heavy metal pollution around the mining areas there.},
}

*Soil Microbiology
*Mining
China
*Bacteria/genetics/classification
*RNA, Ribosomal, 16S/genetics
*Microbiota
*Soil/chemistry
Ecosystem
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid38744390,
year = {2024},
author = {Hu, W and Zheng, N and Zhang, Y and Li, S and Bartlam, M and Wang, Y},
title = {Metagenomics analysis reveals effects of salinity fluctuation on diversity and ecological functions of high and low nucleic acid content bacteria.},
journal = {The Science of the total environment},
volume = {933},
number = {},
pages = {173186},
doi = {10.1016/j.scitotenv.2024.173186},
pmid = {38744390},
issn = {1879-1026},
mesh = {*Salinity ; *Bacteria/genetics/classification ; *Metagenomics ; *RNA, Ribosomal, 16S ; Nucleic Acids ; Seawater/microbiology ; Biodiversity ; Microbiota ; Ecosystem ; },
abstract = {Salinity is a critical environmental factor in marine ecosystems and has complex and wide-ranging biological effects. However, the effects of changing salinity on diversity and ecological functions of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria are not well understood. In this study, we used 16S rRNA sequencing and metagenomic sequencing analysis to reveal the response of HNA and LNA bacterial communities and their ecological functions to salinity, which was decreased from 26 ‰ to 16 ‰. The results showed that salinity changes had significant effects on the community composition of HNA and LNA bacteria. Among LNA bacteria, 14 classes showed a significant correlation between relative abundance and salinity. Salinity changes can lead to the transfer of some bacteria from HNA bacteria to LNA bacteria. In the network topology relationship, the complexity of the network between HNA and LNA bacterial communities gradually decreased with decreased salinity. The abundance of some carbon and nitrogen cycling genes in HNA and LNA bacteria varied with salinity. Overall, this study demonstrates the effects of salinity on diversity and ecological functions and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions.},
}

*Salinity
*Bacteria/genetics/classification
*Metagenomics
*RNA, Ribosomal, 16S
Nucleic Acids
Seawater/microbiology
Biodiversity
Microbiota
Ecosystem

@article {pmid38744885,
year = {2024},
author = {Qi, YL and Chen, YT and Xie, YG and Li, YX and Rao, YZ and Li, MM and Xie, QJ and Cao, XR and Chen, L and Qu, YN and Yuan, ZX and Xiao, ZC and Lu, L and Jiao, JY and Shu, WS and Li, WJ and Hedlund, BP and Hua, ZS},
title = {Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4066},
pmid = {38744885},
issn = {2041-1723},
support = {32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Hot Springs/microbiology ; *Archaea/genetics/classification ; *Genome, Archaeal ; China ; *Metagenome ; *Phylogeny ; *Metagenomics/methods ; Biodiversity ; Hydrogen-Ion Concentration ; Sulfur/metabolism ; Temperature ; Ecosystem ; },
abstract = {Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.},
}

*Hot Springs/microbiology
*Archaea/genetics/classification
*Genome, Archaeal
China
*Metagenome
*Phylogeny
*Metagenomics/methods
Biodiversity
Hydrogen-Ion Concentration
Sulfur/metabolism
Temperature
Ecosystem

@article {pmid38748395,
year = {2024},
author = {Jiya, N and Ghosh, R and Shede, P and Sharma, A},
title = {Comparative analysis of bacterial diversity in accumulated snow and exposed sediments across Antarctic Islands.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {3},
pages = {2355-2362},
pmid = {38748395},
issn = {1678-4405},
support = {SRG/2022/000126//Science and Engineering Research Board (SERB), Department of Science and Technology, India/ ; },
mesh = {Antarctic Regions ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Snow/microbiology ; *Biodiversity ; Phylogeny ; Islands ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Microbiota ; },
abstract = {The Antarctic continent hosts exceptional niches, making it an ideal environment for studying polyextremophilic microorganisms. These organisms are uniquely shaped by the geographic niches and variations in soil types. Here we present, a culture-independent approach using DNA metabarcoding to assess the bacterial communities associated with accumulated snow and exposed sediments across different Antarctic islands situated in the Larsemann Hills, Antarctica. The exposed sediments (ES) were found to be more diverse than the accumulated snow (AS) sediments as represented by the alpha diversity metrics. Out of the total 303 amplicon sequence variants (ASVs) found at the genus level, 93 were unique to accumulated snow sediments and 97 were unique to exposed sediments. The bacterial community composition in accumulated snow was dominated by the phylum Actinobacteriota (24.7%). However, Pseudonocardia (11.9%), Crossiella (11%), and Rhodanobacter (9.1%) were the predominant genera. In contrast, in the exposed sediments, Bacteroidota (24.6%) was the most prevalent phylum, with Crossiella (17.1%), Rhodanobacter (11.1%), and Blastocatella (10%) as the most abundant genera. Metagenomic imputations revealed the abundance of gene families responsible for carbon metabolism, coping with environmental stresses through DNA repair mechanisms, and carbon fixation.},
}

Antarctic Regions
*Geologic Sediments/microbiology
*Bacteria/classification/genetics/isolation & purification
*Snow/microbiology
*Biodiversity
Phylogeny
Islands
DNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Soil Microbiology
Microbiota

@article {pmid38750737,
year = {2024},
author = {Kaijser, W and Lorenz, AW and Brauer, VS and Burfeid-Castellanos, A and David, GM and Nuy, JK and Baikova, D and Beszteri, B and Gillmann, SM and Kiesel, J and Mayombo, NAS and Peters, K and Rettig, K and Rolauffs, P and Haase, P and Hering, D},
title = {Differential associations of five riverine organism groups with multiple stressors.},
journal = {The Science of the total environment},
volume = {934},
number = {},
pages = {173105},
doi = {10.1016/j.scitotenv.2024.173105},
pmid = {38750737},
issn = {1879-1026},
mesh = {*Rivers/microbiology ; *Environmental Monitoring ; Animals ; *Biodiversity ; Fungi ; Diatoms/physiology ; Invertebrates/physiology ; Fishes ; Bacteria/classification ; Water Pollutants, Chemical/analysis ; },
abstract = {The decline of river and stream biodiversity results from multiple simultaneous occuring stressors, yet few studies explore responses explore responses across various taxonomic groups at the same locations. In this study, we address this shortcoming by using a coherent data set to study the association of nine commonly occurring stressors (five chemical, one morphological and three hydraulic) with five taxonomic groups (bacteria, fungi, diatoms, macro-invertebrates and fish). According to studies on single taxonomic groups, we hypothesise that gradients of chemical stressors structure community composition of all taxonomic groups, while gradients of hydraulic and morphological stressors are mainly related to larger organisms such as benthic macro-invertebrates and fish. Organisms were sampled over two years at 20 sites in two catchments: a recently restored urban lowland catchment (Boye) and a moderately disturbed rural mountainous catchment (Kinzig). Dissimilarity matrices were computed for each taxonomic group within a catchment. Taxonomic dissimilarities between sites were linked to stressor dissimilarities using multivariable Generalized Linear Mixed Models. Stressor gradients were longer in the Boye, but did in contrast to the Kinzig not cover low stress intensities. Accordingly, responses of the taxonomic groups were stronger in the Kinzig catchment than in the recently restored Boye catchment. The discrepancy between catchments underlines that associations to stressors strongly depend on which part of the stressor gradient is covered in a catchment. All taxonomic groups were related to conductivity. Bacteria, fungi and macro-invertebrates change with dissolved oxygen, and bacteria and fungi with total nitrogen. Morphological and hydraulic stressors had minor correlations with bacteria, fungi and diatoms, while macro-invertebrates were strongly related to fine sediment and discharge, and fish to high flow peaks. The results partly support our hypotheses about the differential associations of the different taxonomic groups with the stressors.},
}

*Rivers/microbiology
*Environmental Monitoring
Animals
*Biodiversity
Fungi
Diatoms/physiology
Invertebrates/physiology
Fishes
Bacteria/classification
Water Pollutants, Chemical/analysis

@article {pmid38751720,
year = {2024},
author = {Singh, P and Singh, SM and Segawa, T and Singh, PK},
title = {Bacterial diversity and biopotentials of Hamtah glacier cryoconites, Himalaya.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1362678},
pmid = {38751720},
issn = {1664-302X},
abstract = {Cryoconite is a granular structure present on the glaciers and ice sheets found in polar regions including the Himalayas. It is composed of organic and inorganic matter which absorb solar radiations and reduce ice surface albedo, therefore impacting the melting and retreat of glaciers. Though climate warming has a serious impact on Himalayan glaciers, the biodiversity of sub-glacier ecosystems is poorly understood. Moreover, cryoconite holes are unique habitats for psychrophile biodiversity hotspots in the NW Himalayas, but unfortunately, studies on the microbial diversity of such habitats remain elusive. Therefore, the current study was designed to explore the bacterial diversity of the Hamtah Glacier Himalaya using both culturable and non-culturable approaches. The culturable bacterial count ranged from 2.0 × 10[3] to 8.8 × 10[5] colony-forming units (CFUs)/g at the different locations of the glacier. A total of 88 bacterial isolates were isolated using the culturable approach. Based on the 16S ribosomal RNA gene (16S rRNA), the identified species belong to seven genera, namely, Cryobacterium, Duganella, Janthinobacterium, Pseudomonas, Peribacillus, Psychrobacter, and Sphingomonas. In the non-culturable approach, high-throughput sequencing of 16S rRNA genes (using MiSeq) showed unique bacterial community profiles and represented 440 genera belonging to 20 phyla, namely, Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Acidobacteria, Planctomycetes, Cyanobacteria, Verrucomicrobia, Spirochaetes, Elusimicrobia, Armatimonadetes, Gemmatimonadetes, Deinococcus-Thermus, Nitrospirae, Chlamydiae, Chlorobi, Deferribacteres, Fusobacteria, Lentisphaerae, and others. High relative abundances of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were observed in the samples. Phototrophic (Cyanobacteria and Chloroflexi) and nitrifier (Nitrospirae) in bacterial populations indicated sustenance of the micro-ecosystem in the oligotrophic glacier environment. The isolates varied in their phenotypic characteristics, enzyme activities, and antibiotic sensitivity. Furthermore, the fatty acid profiles of bacterial isolates indicate the predominance of branched fatty acids. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a major proportion of the total fatty acid composition. High cold-adapted enzyme activities such as lipase and cellulase expressed by Cryobacterium arcticum (KY783365) and protease and cellulase activities by Pseudomonas sp. strains (KY783373, KY783377-79, KY783382) provide evidence of the possible applications of these organisms. Additionally, antibiotic tests indicated that most isolates were sensitive to antibiotics. In conclusion, the present study contributed for the first time to bacterial diversity and biopotentials of cryoconites of Hamtah Glacier, Himalayas. Furthermore, the cold-adapted enzymes and polyunsaturated fatty acids (PUFAs) may provide an opportunity for biotechnology in the Himalayas. Inductively coupled plasma mass spectrometry (ICPMS) analyses showed the presence of several elements in cryoconites, providing a clue for the accelerating melting and retreating of the Hamtah glacier.},
}

@article {pmid38755302,
year = {2024},
author = {Elbakary, M and Hammad, SF and Youseif, SH and Soliman, HSM},
title = {Revealing the diversity of Jojoba-associated fungi using amplicon metagenome approach and assessing the in vitro biocontrol activity of its cultivable community.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {7},
pages = {205},
pmid = {38755302},
issn = {1573-0972},
mesh = {*Fungi/genetics/classification/isolation & purification ; *Alternaria/genetics/growth & development ; *Soil Microbiology ; Metagenome ; Rhizoctonia/growth & development ; Phylogeny ; Plant Diseases/microbiology/prevention & control ; Fusarium/genetics/growth & development ; Antibiosis ; Plant Roots/microbiology ; Biodiversity ; Biological Control Agents ; Ascomycota/growth & development/genetics ; Plant Development ; },
abstract = {Jojoba shrubs are wild plants cultivated in arid and semiarid lands and characterized by tolerance to drought, salinity, and high temperatures. Fungi associated with such plants may be attributed to the tolerance of host plants against biotic stress in addition to the promotion of plant growth. Previous studies showed the importance of jojoba as jojoba oil in the agricultural field; however, no prior study discussed the role of jojoba-associated fungi (JAF) in reflecting plant health and the possibility of using JAF in biocontrol. Here, the culture-independent and culture-dependent approaches were performed to study the diversity of the jojoba-associated fungi. Then, the cultivable fungi were evaluated for in-vitro antagonistic activity and in vitro plant growth promotion assays. The metagenome analysis revealed the existence of four fungal phyla: Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota. The phylum Ascomycota was the most common and had the highest relative abundance in soil, root, branch, and fruit samples (59.7%, 50.7%, 49.8%, and 52.4%, respectively). Alternaria was the most abundant genus in aboveground tissues: branch (43.7%) and fruit (32.1%), while the genus Discosia had the highest abundance in the underground samples: soil (24%) and root (30.7%). For the culture-dependent method, a total of 14 fungi were isolated, identified, and screened for their chitinolytic and antagonist activity against three phytopathogenic fungi (Fusarium oxysporum, Alternaria alternata and Rhizoctonia solani) as well as their in vitro plant growth promotion (PGP) activity. Based on ITS sequence analysis, the selected potent isolates were identified as Aspergillus stellatusEJ-JFF3, Aspergillus flavus EJ-JFF4, Stilbocrea sp. EJ-JLF1, Fusarium solani EJ-JRF3, and Amesia atrobrunneaEJ-JSF4. The endophyte strain A. flavus EJ-JFF4 exhibited the highest chitinolytic activity (9 Enzyme Index) and antagonistic potential against Fusarium oxysporum, Alternaria alternata, and Rhizoctonia solani phytopathogens with inhibitory percentages of 72, 70, and 80 respectively. Also, A. flavus EJ-JFF4 had significant multiple PGP properties, including siderophore production (69.3%), phosphate solubilization (95.4 µg ml[-1]). The greatest production of Indol-3-Acetic Acid was belonged to A. atrobrunnea EJ-JSF4 (114.5 µg ml[-1]). The analysis of FUNGuild revealed the abundance of symbiotrophs over other trophic modes, and the guild of endophytes was commonly assigned in all samples. For the first time, this study uncovered fungal diversity associated with jojoba plants using a culture-independent approach and in-vitro assessed the roles of cultivable fungal strains in promoting plant growth and biocontrol. The present study indicated the significance of jojoba shrubs as a potential source of diverse fungi with high biocontrol and PGP activities.},
}

*Fungi/genetics/classification/isolation & purification
*Alternaria/genetics/growth & development
*Soil Microbiology
Metagenome
Rhizoctonia/growth & development
Phylogeny
Plant Diseases/microbiology/prevention & control
Fusarium/genetics/growth & development
Antibiosis
Plant Roots/microbiology
Biodiversity
Biological Control Agents
Ascomycota/growth & development/genetics
Plant Development

@article {pmid38764451,
year = {2024},
author = {Ameer, A and Saleem, F and Keating, C and Gundogdu, O and Ijaz, UZ and Javed, S},
title = {Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110487},
pmid = {38764451},
issn = {2352-3409},
abstract = {This article presents metagenomic-assembled genomes (MAGs) of prokaryotic organisms originating from chicken caeca. The samples originate from broiler chickens, one group was infected with Newcastle Disease Virus (NDV) and one uninfected control group. There were four birds per group. Both groups were raised on commercially available antibiotic free feed under a semi-controlled setup. The binning step of the samples identified 130 MAGs with ≥50 % completion, and ≤10 % contamination. The data presented includes sequences in FASTA format, tables of functional annotation of genes, and data from two different approaches for phylogenetic tree construction using these MAGs. Major geochemical cycles at community level including carbon, sulfur, and nitrogen cycles are also presented.},
}

@article {pmid38765606,
year = {2024},
author = {Aplakidou, E and Vergoulidis, N and Chasapi, M and Venetsianou, NK and Kokoli, M and Panagiotopoulou, E and Iliopoulos, I and Karatzas, E and Pafilis, E and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA and Baltoumas, FA},
title = {Visualizing metagenomic and metatranscriptomic data: A comprehensive review.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {2011-2033},
pmid = {38765606},
issn = {2001-0370},
abstract = {The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.},
}

@article {pmid38773202,
year = {2024},
author = {Pfingstl, T and Hiruta, SF and Shimano, S},
title = {Mitochondrial metagenomics reveal the independent colonization of the world's coasts by intertidal oribatid mites (Acari, Oribatida, Ameronothroidea).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11634},
pmid = {38773202},
issn = {2045-2322},
support = {I 3815//Austrian Science Fund/ ; },
mesh = {Animals ; *Mites/genetics/classification ; *Phylogeny ; *Metagenomics/methods ; Genome, Mitochondrial ; Mitochondria/genetics ; Metagenome ; Evolution, Molecular ; Ecosystem ; },
abstract = {Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225-146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses.},
}

Animals
*Mites/genetics/classification
*Phylogeny
*Metagenomics/methods
Genome, Mitochondrial
Mitochondria/genetics
Metagenome
Evolution, Molecular
Ecosystem

@article {pmid38789907,
year = {2024},
author = {Vishal, V and Das, T and Lal, S and Rahaman, S},
title = {Endophytic bacterial diversity in the latex-bearing caulosphere of Hevea brasiliensis Müll. Arg.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {3},
pages = {2473-2481},
pmid = {38789907},
issn = {1678-4405},
mesh = {*Hevea/microbiology ; *Latex/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Endophytes/genetics/classification/isolation & purification/metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; India ; },
abstract = {Rubber trees are a commercial cash crop, and the milky latex or polyisoprene they produce is the natural source of rubber. Little is known about the bacterial populations found in active zone of latex-bearing caulosphere. We employed a tailored cloud microbial bioinformatic approach for the identification and potential hypothetical ecological roles of an uncultured endophytic hidden bacterial community in the active zone of the latex-bearing caulosphere of Hevea brasiliensis. Small pieces of slivers were collected from healthy plant from the village: Belonia, South Tripura, rubber plantation in Northeastern India. These uncultured bacteria were identified using the V3-V4 hypervariable amplicon region of the 16 S rDNA gene. A total of 209,586 contigs have been generated. EasyMAP Version 1.0, a cloud-based microbial bioinformatics tool with an integrated QIIME2 pipeline, was used to analyze contigs. We detected 15 phyla and 91 OTUs (operational taxonomic units). Proteobacteria (73.5%) was the most enriched phylum, followed by Firmicutes (13.8%), Bacteroidetes (5.2%), and Actinobacteria (3.2%). Ammonia oxidizers, sulfate reducers, dehalogenation, chitin degradation, nitrite reducers, and aromatic hydrocarbon degraders were the most prevalent functional categories in the active zones of caulosphere. Furthermore, Gammaproteobacteria (49.2%) and Erwinia (29.19%) were the most abundant classes and genera of endophytic bacterial communities. Thus, the presence of a substantial amount of phosphate-solubilizing Gammaproteobacteria (PSB) may stimulate growth, increase plant resilience, suppress disease, and aid in the rubber and sugar breakdown. This is the first report of microbial endophytes associated with Hevea caulosphere.},
}

*Hevea/microbiology
*Latex/metabolism
*Bacteria/classification/genetics/isolation & purification/metabolism
*Endophytes/genetics/classification/isolation & purification/metabolism
*Phylogeny
RNA, Ribosomal, 16S/genetics
Biodiversity
India

@article {pmid38790063,
year = {2024},
author = {Zhang, B and Xiao, L and Lyu, L and Zhao, F and Miao, M},
title = {Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {96},
pmid = {38790063},
issn = {2049-2618},
mesh = {*Symbiosis ; *Ciliophora/genetics/classification/physiology ; *Bacteria/genetics/classification ; Archaea/genetics/classification ; Phylogeny ; Metagenome ; Biodiversity ; },
abstract = {BACKGROUND: The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates.

RESULTS: To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range.

CONCLUSIONS: As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.},
}

*Symbiosis
*Ciliophora/genetics/classification/physiology
*Bacteria/genetics/classification
Archaea/genetics/classification
Phylogeny
Metagenome
Biodiversity

@article {pmid38796259,
year = {2024},
author = {Shenoy, BD and Khandeparker, RDS and Fernandes, P and Amberkar, U},
title = {Fungal diversity associated with Goa's tarballs: Insights from ITS region amplicon sequencing.},
journal = {Fungal biology},
volume = {128},
number = {3},
pages = {1751-1757},
doi = {10.1016/j.funbio.2024.03.001},
pmid = {38796259},
issn = {1878-6146},
mesh = {India ; *DNA, Fungal/genetics ; *Fungi/genetics/classification/isolation & purification ; *Biodiversity ; Sequence Analysis, DNA ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; Petroleum/microbiology ; },
abstract = {This study explores the fungal diversity associated with tarballs, weathered crude oil deposits, on Goa's tourist beaches. Despite tarball pollution being a longstanding issue in Goa state in India, comprehensive studies on associated fungi are scarce. Our research based on amplicon sequence analysis of fungal ITS region fills this gap, revealing a dominance of Aspergillus, particularly Aspergillus penicillioides, associated with tarballs from Vagator and Morjim beaches. Other notable species, including Aspergillus sydowii, Aspergillus carbonarius, and Trichoderma species, were identified, all with potential public health and ecosystem implications. A FUNGuild analysis was conducted to investigate the potential ecological roles of these fungi, revealing a diverse range of roles, including nutrient cycling, disease propagation, and symbiotic relationships. The study underscores the need for further research and monitoring, given the potential health risks and contribution of tarball-associated fungi to the bioremediation of crude oil-contaminated beaches.},
}

India
*DNA, Fungal/genetics
*Fungi/genetics/classification/isolation & purification
*Biodiversity
Sequence Analysis, DNA
DNA, Ribosomal Spacer/genetics
Phylogeny
Petroleum/microbiology

@article {pmid38800117,
year = {2023},
author = {Ryan, MJ and Mauchline, TH and Malone, JG and Jones, S and Thompson, CMA and Bonnin, JM and Stewart, H and Yau, PTO and Taketani, RG and Clark, IM and Holden, N},
title = {The UK Crop Microbiome Cryobank: a utility and model for supporting Phytobiomes research.},
journal = {CABI agriculture and bioscience},
volume = {4},
number = {1},
pages = {53},
pmid = {38800117},
issn = {2662-4044},
abstract = {Plant microbiomes are the microbial communities essential to the functioning of the phytobiome-the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critical to crop health, improved yields and quality food. However, crop microbiomes are relatively under-researched, and this is associated with a fundamental need to underpin phytobiome research through the provision of a supporting infrastructure. The UK Crop Microbiome Cryobank (UKCMC) project is developing a unique, integrated and open-access resource to enable the development of solutions to improve soil and crop health. Six economically important crops (Barley, Fava Bean, Oats, Oil Seed Rape, Sugar Beet and Wheat) are targeted, and the methods as well as data outputs will underpin research activity both in the UK and internationally. This manuscript describes the approaches being taken, from characterisation, cryopreservation and analysis of the crop microbiome through to potential applications. We believe that the model research framework proposed is transferable to different crop and soil systems, acting not only as a mechanism to conserve biodiversity, but as a potential facilitator of sustainable agriculture systems.},
}

@article {pmid38804464,
year = {2024},
author = {Lappan, R and Thakar, J and Molares Moncayo, L and Besser, A and Bradley, JA and Goordial, J and Trembath-Reichert, E and Greening, C},
title = {The atmosphere: a transport medium or an active microbial ecosystem?.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38804464},
issn = {1751-7370},
support = {RGY0058/2022//Human Frontier Science Program/ ; },
mesh = {*Atmosphere ; *Ecosystem ; Microbiota ; Air Microbiology ; Biodiversity ; Bacteria/metabolism/classification/growth & development ; },
abstract = {The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.},
}

*Atmosphere
*Ecosystem
Microbiota
Air Microbiology
Biodiversity
Bacteria/metabolism/classification/growth & development

@article {pmid38817668,
year = {2024},
author = {Gupta, P and Hiller, A and Chowdhury, J and Lim, D and Lim, DY and Saeij, JPJ and Babaian, A and Rodriguez, F and Pereira, L and Morales-Tapia, A},
title = {A parasite odyssey: An RNA virus concealed in Toxoplasma gondii.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae040},
pmid = {38817668},
issn = {2057-1577},
abstract = {We are entering a 'Platinum Age of Virus Discovery', an era marked by exponential growth in the discovery of virus biodiversity, and driven by advances in metagenomics and computational analysis. In the ecosystem of a human (or any animal) there are more species of viruses than simply those directly infecting the animal cells. Viruses can infect all organisms constituting the microbiome, including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this interaction network we must employ computationally assisted virology as a means of analyzing and interpreting the millions of available samples to make inferences about the ways in which viruses may intersect human health. From a computational viral screen of human neuronal datasets, we identified a novel narnavirus Apocryptovirus odysseus (Ao) which likely infects the neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we present in silico evidence that Ao is a plausible pro-inflammatory factor in human and mouse cells infected by T. gondii. T. gondii infects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. In a broader screen of over 7.6 million samples, we explored phylogenetically proximal viruses to Ao and discovered nineteen Apocryptovirus species, all found in libraries annotated as vertebrate transcriptome or metatranscriptomes. While samples containing this genus of narnaviruses are derived from sheep, goat, bat, rabbit, chicken, and pigeon samples, the presence of virus is strongly predictive of parasitic Apicomplexa nucleic acid co-occurrence, supporting the fact that Apocryptovirus is a genus of parasite-infecting viruses. This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict that this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.},
}

@article {pmid38821286,
year = {2024},
author = {Liddicoat, C and Edwards, RA and Roach, M and Robinson, JM and Wallace, KJ and Barnes, AD and Brame, J and Heintz-Buschart, A and Cavagnaro, TR and Dinsdale, EA and Doane, MP and Eisenhauer, N and Mitchell, G and Rai, B and Ramesh, SA and Breed, MF},
title = {Bioenergetic mapping of 'healthy microbiomes' via compound processing potential imprinted in gut and soil metagenomes.},
journal = {The Science of the total environment},
volume = {940},
number = {},
pages = {173543},
doi = {10.1016/j.scitotenv.2024.173543},
pmid = {38821286},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Gastrointestinal Microbiome ; *Metagenome ; Humans ; Microbiota ; Energy Metabolism ; Soil/chemistry ; },
abstract = {Despite mounting evidence of their importance in human health and ecosystem functioning, the definition and measurement of 'healthy microbiomes' remain unclear. More advanced knowledge exists on health associations for compounds used or produced by microbes. Environmental microbiome exposures (especially via soils) also help shape, and may supplement, the functional capacity of human microbiomes. Given the synchronous interaction between microbes, their feedstocks, and micro-environments, with functional genes facilitating chemical transformations, our objective was to examine microbiomes in terms of their capacity to process compounds relevant to human health. Here we integrate functional genomics and biochemistry frameworks to derive new quantitative measures of in silico potential for human gut and environmental soil metagenomes to process a panel of major compound classes (e.g., lipids, carbohydrates) and selected biomolecules (e.g., vitamins, short-chain fatty acids) linked to human health. Metagenome functional potential profile data were translated into a universal compound mapping 'landscape' based on bioenergetic van Krevelen mapping of function-level meta-compounds and corresponding functional relative abundances, reflecting imprinted genetic capacity of microbiomes to metabolize an array of different compounds. We show that measures of 'compound processing potential' associated with human health and disease (examining atherosclerotic cardiovascular disease, colorectal cancer, type 2 diabetes and anxious-depressive behavior case studies), and displayed seemingly predictable shifts along gradients of ecological disturbance in plant-soil ecosystems (three case studies). Ecosystem quality explained 60-92 % of variation in soil metagenome compound processing potential measures in a post-mining restoration case study dataset. With growing knowledge of the varying proficiency of environmental microbiota to process human health associated compounds, we might design environmental interventions or nature prescriptions to modulate our exposures, thereby advancing microbiota-oriented approaches to human health. Compound processing potential offers a simplified, integrative approach for applying metagenomics in ongoing efforts to understand and quantify the role of microbiota in environmental- and human-health.},
}

*Soil Microbiology
*Gastrointestinal Microbiome
*Metagenome
Humans
Microbiota
Energy Metabolism
Soil/chemistry

@article {pmid38843834,
year = {2024},
author = {Santos-Júnior, CD and Torres, MDT and Duan, Y and Rodríguez Del Río, Á and Schmidt, TSB and Chong, H and Fullam, A and Kuhn, M and Zhu, C and Houseman, A and Somborski, J and Vines, A and Zhao, XM and Bork, P and Huerta-Cepas, J and de la Fuente-Nunez, C and Coelho, LP},
title = {Discovery of antimicrobial peptides in the global microbiome with machine learning.},
journal = {Cell},
volume = {187},
number = {14},
pages = {3761-3778.e16},
pmid = {38843834},
issn = {1097-4172},
support = {R35 GM138201/GM/NIGMS NIH HHS/United States ; },
mesh = {*Machine Learning ; *Antimicrobial Peptides/pharmacology/chemistry/genetics ; Humans ; *Microbiota ; Animals ; Anti-Bacterial Agents/pharmacology ; Mice ; Metagenome ; Bacteria/drug effects/genetics ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and 87,920 prokaryotic genomes from environmental and host-associated habitats to create the AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, few of which match existing databases. AMPSphere provides insights into the evolutionary origins of peptides, including by duplication or gene truncation of longer sequences, and we observed that AMP production varies by habitat. To validate our predictions, we synthesized and tested 100 AMPs against clinically relevant drug-resistant pathogens and human gut commensals both in vitro and in vivo. A total of 79 peptides were active, with 63 targeting pathogens. These active AMPs exhibited antibacterial activity by disrupting bacterial membranes. In conclusion, our approach identified nearly one million prokaryotic AMP sequences, an open-access resource for antibiotic discovery.},
}

*Machine Learning
*Antimicrobial Peptides/pharmacology/chemistry/genetics
Humans
*Microbiota
Animals
Anti-Bacterial Agents/pharmacology
Mice
Metagenome
Bacteria/drug effects/genetics
Gastrointestinal Microbiome/drug effects

@article {pmid38852299,
year = {2024},
author = {Herruzo-Ruiz, AM and Trombini, C and Moreno-Garrido, I and Blasco, J and Alhama, J and Michán, C},
title = {Ions and nanoparticles of Ag and/or Cd metals in a model aquatic microcosm: Effects on the abundance, diversity and functionality of the sediment bacteriome.},
journal = {Marine pollution bulletin},
volume = {204},
number = {},
pages = {116525},
doi = {10.1016/j.marpolbul.2024.116525},
pmid = {38852299},
issn = {1879-3363},
mesh = {*Silver/toxicity ; *Geologic Sediments/chemistry/microbiology ; *Water Pollutants, Chemical/analysis ; *Cadmium/analysis ; *Microbiota/drug effects ; *Metal Nanoparticles/toxicity ; Bacteria ; Ions ; RNA, Ribosomal, 16S ; Biodiversity ; },
abstract = {Metals can be adsorbed on particulate matter, settle in sediments and cause alterations in aquatic environments. This study assesses the effect of Ag and/or Cd, both in ionic and nanoparticle (NP) forms, on the microbiome of sediments. For that purpose, aquatic controlled-microcosm experiments were exposed to an environmentally relevant and at tenfold higher doses of each form of the metals. Changes in the bacteriome were inferred by 16S rDNA sequencing. Ionic Ag caused a significant decrease of several bacterial families, whereas the effect was opposite when mixed with Cd, e.g., Desulfuromonadaceae family; in both cases, the bacteriome functionalities were greatly affected, particularly the nitrogen and sulfur metabolism. Compared to ionic forms, metallic NPs produced hardly any change in the abundance of microbial families, although the α-biodiversity of the bacteriome was reduced, and the functionality altered, when exposed to the NPs´ mixture. Our goal is to understand how metals, in different forms and combinations, released into the environment may endanger the health of aquatic ecosystems. This work may help to understand how aquatic metal pollution alters the structure and functionality of the microbiome and biogeochemical cycles, and how these changes can be addressed.},
}

*Silver/toxicity
*Geologic Sediments/chemistry/microbiology
*Water Pollutants, Chemical/analysis
*Cadmium/analysis
*Microbiota/drug effects
*Metal Nanoparticles/toxicity
Bacteria
Ions
RNA, Ribosomal, 16S
Biodiversity

@article {pmid38854849,
year = {2024},
author = {Mahar, JE and Wille, M and Harvey, E and Moritz, CC and Holmes, EC},
title = {The diverse liver viromes of Australian geckos and skinks are dominated by hepaciviruses and picornaviruses and reflect host taxonomy and habitat.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae044},
pmid = {38854849},
issn = {2057-1577},
abstract = {Lizards have diverse ecologies and evolutionary histories, and represent a promising group to explore how hosts shape virome structure and virus evolution. Yet, little is known about the viromes of these animals. In Australia, squamates (lizards and snakes) comprise the most diverse order of vertebrates, and Australia hosts the highest diversity of lizards globally, with the greatest breadth of habitat use. We used meta-transcriptomic sequencing to determine the virome of nine co-distributed, tropical lizard species from three taxonomic families in Australia and analyzed these data to identify host traits associated with viral abundance and diversity. We show that lizards carry a large diversity of viruses, identifying more than thirty novel, highly divergent vertebrate-associated viruses. These viruses were from nine viral families, including several that contain well known pathogens, such as the Flaviviridae, Picornaviridae, Bornaviridae, Iridoviridae, and Rhabdoviridae. Members of the Flaviviridae were particularly abundant across species sampled here, largely belonging to the genus Hepacivirus: fourteen novel hepaciviruses were identified, broadening the known diversity of this group and better defining its evolution by uncovering new reptilian clades. The evolutionary histories of the viruses studied here frequently aligned with the biogeographic and phylogenetic histories of the hosts, indicating that exogenous viruses may help infer host evolutionary history if sampling is strategic and sampling density high enough. Notably, analysis of alpha and beta diversity revealed that virome composition and richness in the animals sampled here was shaped by host taxonomy and habitat. In sum, we identified a diverse range of reptile viruses that broadly contributes to our understanding of virus-host ecology and evolution.},
}

@article {pmid38856205,
year = {2024},
author = {Krausfeldt, LE and Shmakova, E and Lee, HW and Mazzei, V and Loftin, KA and Smith, RP and Karwacki, E and Fortman, PE and Rosen, BH and Urakawa, H and Dadlani, M and Colwell, RR and Lopez, JV},
title = {Microbial diversity, genomics, and phage-host interactions of cyanobacterial harmful algal blooms.},
journal = {mSystems},
volume = {9},
number = {7},
pages = {e0070923},
pmid = {38856205},
issn = {2379-5077},
support = {W912HZ-19-2-0014//DOD | USA | U.S. Army Corps of Engineers (USACE)/ ; //USGS Environmental Health Program/ ; },
mesh = {*Cyanobacteria/virology/genetics ; *Harmful Algal Bloom ; *Bacteriophages/genetics ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Metagenome ; Lakes/microbiology/virology ; Genomics ; Biodiversity ; },
abstract = {UNLABELLED: The occurrence of cyanobacterial harmful algal blooms (cyanoHABs) is related to their physical and chemical environment. However, less is known about their associated microbial interactions and processes. In this study, cyanoHABs were analyzed as a microbial ecosystem, using 1 year of 16S rRNA sequencing and 70 metagenomes collected during the bloom season from Lake Okeechobee (Florida, USA). Biogeographical patterns observed in microbial community composition and function reflected ecological zones distinct in their physical and chemical parameters that resulted in bloom "hotspots" near major lake inflows. Changes in relative abundances of taxa within multiple phyla followed increasing bloom severity. Functional pathways that correlated with increasing bloom severity encoded organic nitrogen and phosphorus utilization, storage of nutrients, exchange of genetic material, phage defense, and protection against oxidative stress, suggesting that microbial interactions may promote cyanoHAB resilience. Cyanobacterial communities were highly diverse, with picocyanobacteria ubiquitous and oftentimes most abundant, especially in the absence of blooms. The identification of novel bloom-forming cyanobacteria and genomic comparisons indicated a functionally diverse cyanobacterial community with differences in its capability to store nitrogen using cyanophycin and to defend against phage using CRISPR and restriction-modification systems. Considering blooms in the context of a microbial ecosystem and their interactions in nature, physiologies and interactions supporting the proliferation and stability of cyanoHABs are proposed, including a role for phage infection of picocyanobacteria. This study displayed the power of "-omics" to reveal important biological processes that could support the effective management and prediction of cyanoHABs.

IMPORTANCE: Cyanobacterial harmful algal blooms pose a significant threat to aquatic ecosystems and human health. Although physical and chemical conditions in aquatic systems that facilitate bloom development are well studied, there are fundamental gaps in the biological understanding of the microbial ecosystem that makes a cyanobacterial bloom. High-throughput sequencing was used to determine the drivers of cyanobacteria blooms in nature. Multiple functions and interactions important to consider in cyanobacterial bloom ecology were identified. The microbial biodiversity of blooms revealed microbial functions, genomic characteristics, and interactions between cyanobacterial populations that could be involved in bloom stability and more coherently define cyanobacteria blooms. Our results highlight the importance of considering cyanobacterial blooms as a microbial ecosystem to predict, prevent, and mitigate them.},
}

*Cyanobacteria/virology/genetics
*Harmful Algal Bloom
*Bacteriophages/genetics
RNA, Ribosomal, 16S/genetics
Microbiota/genetics
Metagenome
Lakes/microbiology/virology
Genomics
Biodiversity

@article {pmid38862509,
year = {2024},
author = {Overbey, EG and Ryon, K and Kim, J and Tierney, BT and Klotz, R and Ortiz, V and Mullane, S and Schmidt, JC and MacKay, M and Damle, N and Najjar, D and Matei, I and Patras, L and Garcia Medina, JS and Kleinman, AS and Wain Hirschberg, J and Proszynski, J and Narayanan, SA and Schmidt, CM and Afshin, EE and Innes, L and Saldarriaga, MM and Schmidt, MA and Granstein, RD and Shirah, B and Yu, M and Lyden, D and Mateus, J and Mason, CE},
title = {Collection of biospecimens from the inspiration4 mission establishes the standards for the space omics and medical atlas (SOMA).},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4964},
pmid = {38862509},
issn = {2041-1723},
support = {R01 ES032638/ES/NIEHS NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; },
mesh = {*Specimen Handling/standards ; Humans ; *Space Flight ; *Biological Specimen Banks/standards ; Exobiology ; *Preservation, Biological/standards ; Metagenomics/standards ; },
abstract = {The SpaceX Inspiration4 mission provided a unique opportunity to study the impact of spaceflight on the human body. Biospecimen samples were collected from four crew members longitudinally before (Launch: L-92, L-44, L-3 days), during (Flight Day: FD1, FD2, FD3), and after (Return: R + 1, R + 45, R + 82, R + 194 days) spaceflight, spanning a total of 289 days across 2021-2022. The collection process included venous whole blood, capillary dried blood spot cards, saliva, urine, stool, body swabs, capsule swabs, SpaceX Dragon capsule HEPA filter, and skin biopsies. Venous whole blood was further processed to obtain aliquots of serum, plasma, extracellular vesicles and particles, and peripheral blood mononuclear cells. In total, 2,911 sample aliquots were shipped to our central lab at Weill Cornell Medicine for downstream assays and biobanking. This paper provides an overview of the extensive biospecimen collection and highlights their processing procedures and long-term biobanking techniques, facilitating future molecular tests and evaluations.As such, this study details a robust framework for obtaining and preserving high-quality human, microbial, and environmental samples for aerospace medicine in the Space Omics and Medical Atlas (SOMA) initiative, which can aid future human spaceflight and space biology experiments.},
}

*Specimen Handling/standards
Humans
*Space Flight
*Biological Specimen Banks/standards
Exobiology
*Preservation, Biological/standards
Metagenomics/standards

@article {pmid38865431,
year = {2024},
author = {Tedersoo, L and Hosseyni Moghaddam, MS and Mikryukov, V and Hakimzadeh, A and Bahram, M and Nilsson, RH and Yatsiuk, I and Geisen, S and Schwelm, A and Piwosz, K and Prous, M and Sildever, S and Chmolowska, D and Rueckert, S and Skaloud, P and Laas, P and Tines, M and Jung, JH and Choi, JH and Alkahtani, S and Anslan, S},
title = {EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {38865431},
issn = {1758-0463},
support = {Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; },
mesh = {*Eukaryota/genetics ; RNA, Ribosomal, 18S/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Animals ; Genes, rRNA/genetics ; Phylogeny ; },
abstract = {Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.},
}

*Eukaryota/genetics
RNA, Ribosomal, 18S/genetics
Databases, Genetic
Databases, Nucleic Acid
Animals
Genes, rRNA/genetics
Phylogeny

@article {pmid38870892,
year = {2024},
author = {Dubois, L and Valles-Colomer, M and Ponsero, A and Helve, O and Andersson, S and Kolho, KL and Asnicar, F and Korpela, K and Salonen, A and Segata, N and de Vos, WM},
title = {Paternal and induced gut microbiota seeding complement mother-to-infant transmission.},
journal = {Cell host & microbe},
volume = {32},
number = {6},
pages = {1011-1024.e4},
doi = {10.1016/j.chom.2024.05.004},
pmid = {38870892},
issn = {1934-6069},
mesh = {Humans ; Male ; Female ; *Infant, Newborn/growth & development ; *Gastrointestinal Microbiome ; Cesarean Section ; Antibiotic Prophylaxis ; Fecal Microbiota Transplantation ; Biodiversity ; Parturition ; Metagenomics ; Feces/microbiology ; },
abstract = {Microbial colonization of the neonatal gut involves maternal seeding, which is partially disrupted in cesarean-born infants and after intrapartum antibiotic prophylaxis. However, other physically close individuals could complement such seeding. To assess the role of both parents and of induced seeding, we analyzed two longitudinal metagenomic datasets (health and early life microbiota [HELMi]: N = 74 infants, 398 samples, and SECFLOR: N = 7 infants, 35 samples) with cesarean-born infants who received maternal fecal microbiota transplantation (FMT). We found that the father constitutes a stable source of strains for the infant independently of the delivery mode, with the cumulative contribution becoming comparable to that of the mother after 1 year. Maternal FMT increased mother-infant strain sharing in cesarean-born infants, raising the average bacterial empirical growth rate while reducing pathogen colonization. Overall, our results indicate that maternal seeding is partly complemented by that of the father and support the potential of induced seeding to restore potential deviations in this process.},
}

Humans
Male
Female
*Infant, Newborn/growth & development
*Gastrointestinal Microbiome
Cesarean Section
Antibiotic Prophylaxis
Fecal Microbiota Transplantation
Biodiversity
Parturition
Metagenomics
Feces/microbiology

@article {pmid38876022,
year = {2024},
author = {Sivalingam, P and Sabatino, R and Sbaffi, T and Corno, G and Fontaneto, D and Borgomaneiro, G and Rogora, M and Crotti, E and Mapelli, F and Borin, S and Pilar, AL and Eckert, EM and Di Cesare, A},
title = {Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {475},
number = {},
pages = {134885},
doi = {10.1016/j.jhazmat.2024.134885},
pmid = {38876022},
issn = {1873-3336},
mesh = {*Wastewater/microbiology ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Genes, Bacterial/drug effects ; Water Pollution ; Water Microbiology ; Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics/classification ; },
abstract = {Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.},
}

*Wastewater/microbiology
Drug Resistance, Microbial/genetics
Lakes/microbiology
Genes, Bacterial/drug effects
Water Pollution
Water Microbiology
Microbiota/drug effects
Anti-Bacterial Agents/pharmacology
Plasmids/genetics
Drug Resistance, Bacterial/genetics
Bacteria/drug effects/genetics/classification

@article {pmid38881221,
year = {2024},
author = {Greco, C and Andersen, DT and Yallop, ML and Barker, G and Jungblut, AD},
title = {Genome-resolved metagenomics reveals diverse taxa and metabolic complexity in Antarctic lake microbial structures.},
journal = {Environmental microbiology},
volume = {26},
number = {6},
pages = {e16663},
doi = {10.1111/1462-2920.16663},
pmid = {38881221},
issn = {1462-2920},
support = {//The Arctic and Antarctic Research Institute/ ; //The Trottier Family Foundation/ ; 80NSSC18K1094/NASA/NASA/United States ; NE/L002434/1//UK Research and Innovation/ ; //TAWANI Foundation of Chicago/ ; },
mesh = {Antarctic Regions ; *Lakes/microbiology ; *Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Cyanobacteria/genetics/classification/metabolism ; Microbiota/genetics ; Phylogeny ; Geologic Sediments/microbiology ; Metagenome ; Genome, Bacterial ; Archaea/genetics/classification/metabolism ; },
abstract = {Lake Untersee, a lake in Antarctica that is perennially covered with ice, is home to unique microbial structures that are not lithified. We have evaluated the structure of the community and its metabolic potential across the pigmented upper layers and the sediment-enriched deeper layers in these pinnacle and cone-shaped microbial structures using metagenomics. These microbial structures are inhabited by distinct communities. The upper layers of the cone-shaped structures have a higher abundance of the cyanobacterial MAG Microcoleus, while the pinnacle-shaped structures have a higher abundance of Elainellacea MAG. This suggests that cyanobacteria influence the morphologies of the mats. We identified stark contrasts in the composition of the community and its metabolic potential between the upper and lower layers of the mat. The upper layers of the mat, which receive light, have an increased abundance of photosynthetic pathways. In contrast, the lower layer has an increased abundance of heterotrophic pathways. Our results also showed that Lake Untersee is the first Antarctic lake with a substantial presence of ammonia-oxidizing Nitrospiracea and amoA genes. The genomic capacity for recycling biological molecules was prevalent across metagenome-assembled genomes (MAGs) that cover 19 phyla. This highlights the importance of nutrient scavenging in ultra-oligotrophic environments. Overall, our study provides new insights into the formation of microbial structures and the potential metabolic complexity of Antarctic laminated microbial mats. These mats are important environments for biodiversity that drives biogeochemical cycling in polar deserts.},
}

Antarctic Regions
*Lakes/microbiology
*Metagenomics
*Bacteria/genetics/classification/metabolism
*Cyanobacteria/genetics/classification/metabolism
Microbiota/genetics
Phylogeny
Geologic Sediments/microbiology
Metagenome
Genome, Bacterial
Archaea/genetics/classification/metabolism

@article {pmid38881319,
year = {2024},
author = {Shah, M and Bornemann, TLV and Nuy, JK and Hahn, MW and Probst, AJ and Beisser, D and Boenigk, J},
title = {Genome-resolved metagenomics reveals the effect of nutrient availability on bacterial genomic properties across 44 European freshwater lakes.},
journal = {Environmental microbiology},
volume = {26},
number = {6},
pages = {e16634},
doi = {10.1111/1462-2920.16634},
pmid = {38881319},
issn = {1462-2920},
support = {//Stemmler-Stiftung/ ; //Bauer-Stiftung zur Förderung von Wissenschaft und Forschung/ ; },
mesh = {*Bacteria/genetics/classification/metabolism ; *Genome, Bacterial ; *Metagenomics/methods ; *Phosphorus/metabolism ; *Nutrients/metabolism ; *Nitrogen/metabolism ; *Lakes/microbiology ; Europe ; Base Composition ; Carbon/metabolism ; Genome Size ; Microbiota/genetics ; Phylogeny ; },
abstract = {Understanding intricate microbial interactions in the environment is crucial. This is especially true for the relationships between nutrients and bacteria, as phosphorus, nitrogen and organic carbon availability are known to influence bacterial population dynamics. It has been suggested that low nutrient conditions prompt the evolutionary process of genome streamlining. This process helps conserve scarce nutrients and allows for proliferation. Genome streamlining is associated with genomic properties such as %GC content, genes encoding sigma factors, percent coding regions, gene redundancy, and functional shifts in processes like cell motility and ATP binding cassette transporters, among others. The current study aims to unveil the impact of nutrition on the genome size, %GC content, and functional properties of pelagic freshwater bacteria. We do this at finer taxonomic resolutions for many metagenomically characterized communities. Our study confirms the interplay of trophic level and genomic properties. It also highlights that different nutrient types, particularly phosphorus and nitrogen, impact these properties differently. We observed a covariation of functional traits with genome size. Larger genomes exhibit enriched pathways for motility, environmental interaction, and regulatory genes. ABC transporter genes reflect the availability of nutrients in the environment, with small genomes presumably relying more on metabolites from other organisms. We also discuss the distinct strategies different phyla adopt to adapt to oligotrophic environments. The findings contribute to our understanding of genomic adaptations within complex microbial communities.},
}

*Bacteria/genetics/classification/metabolism
*Genome, Bacterial
*Metagenomics/methods
*Phosphorus/metabolism
*Nutrients/metabolism
*Nitrogen/metabolism
*Lakes/microbiology
Europe
Base Composition
Carbon/metabolism
Genome Size
Microbiota/genetics
Phylogeny

@article {pmid38881655,
year = {2024},
author = {Xu, Y and Feng, T and Ding, Z and Li, L and Li, Z and Cui, K and Chen, W and Pan, H and Zhu, P and Liu, Q},
title = {Age-related compositional and functional changes in the adult and breastfed buffalo rumen microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1342804},
pmid = {38881655},
issn = {1664-302X},
abstract = {INTRODUCTION: The buffalo is an important domestic animal globally, providing milk, meat, and labor to more than 2 billion people in 67 countries. The rumen microorganisms of buffaloes play an indispensable role in enabling the healthy functionality and digestive function of buffalo organisms. Currently, there is a lack of clarity regarding the differences in the composition and function of rumen microorganisms among buffaloes at different growth stages.

METHODS: In this study, metagenomics sequencing technology was applied to examine the compositional and functional differences of rumen microorganisms in adult and breastfed buffaloes.

RESULTS: The results revealed that the rumen of adult buffaloes had significantly higher levels of the following dominant genera: Prevotella, UBA1711, RF16, Saccharofermentans, F23-D06, UBA1777, RUG472, and Methanobrevibacter_A. Interestingly, the dominant genera specific to the rumen of adult buffaloes showed a significant positive correlation (correlation>0.5, p-value<0.05) with both lignocellulose degradation-related carbohydrate-active enzymes (CAZymes) and immune signaling pathways activated by antigenic stimulation. The rumen of breastfed buffaloes had significantly higher levels of the following dominant genera: UBA629, CAG- 791, Selenomonas_C, Treponema_D, Succinivibrio, and RC9. Simultaneously, the rumen-dominant genera specific to breastfed buffaloes were significantly positively correlated (correlation>0.5, p-value<0.05) with CAZymes associated with lactose degradation, amino acid synthesis pathways, and antibiotic-producing pathways.

DISCUSSION: This indicates that rumen microorganisms in adult buffaloes are more engaged in lignocellulose degradation, whereas rumen microorganisms in breastfed buffaloes are more involved in lactose and amino acid degradation, as well as antibiotic production. In conclusion, these findings suggest a close relationship between differences in rumen microbes and the survival needs of buffaloes at different growth stages.},
}

@article {pmid38882194,
year = {2024},
author = {Saleem, F and Ameer, A and Star-Shirko, B and Keating, C and Gundogdu, O and Ijaz, UZ and Javed, S},
title = {Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110552},
pmid = {38882194},
issn = {2352-3409},
abstract = {This article focuses the recovery of prokaryotic organisms including bacteria and archaea from 9 different groups of chicken raised in different farm setups in Pakistan. The groups comprise of three different breeds (Broilers, White Layers, and Black Australorp) of chicken raised in different farming setups that include antibiotic-free control, commercial (open and controlled shed), and backyard farms. We have recovered 569 Metagenomics-Assembled Genomes (MAGs) with a completeness of ≥50 % and contamination of ≤10 %. For each MAG, functional annotations were obtained that include KEGG modules, carbohydrate active enzymes (CAZymes), peptidases, geochemical cycles, antibiotic resistance genes, stress genes, and virulence genes. Furthermore, two different sets of Single Copy Genes (SCGs) were used to construct the phylogenetic trees. Based on the reconstructed phylogeny, phylogenetic gain of each MAG is calculated to give an account of novelty.},
}

@article {pmid38898104,
year = {2024},
author = {Ji, M and Li, Y and Zhou, J and Song, W and Zhou, Y and Ma, K and Wang, M and Liu, X and Li, Y and Gong, X and Tu, Q},
title = {Temporal turnover of viral biodiversity and functional potential in intertidal wetlands.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {48},
pmid = {38898104},
issn = {2055-5008},
support = {32371598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92051110//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Wetlands ; *Biodiversity ; *Viruses/genetics/classification/isolation & purification ; *Metagenome ; Seasons ; Microbiota ; Genome, Viral ; Metagenomics/methods ; Virome/genetics ; Phylogeny ; },
abstract = {As the central members of the microbiome networks, viruses regulate the composition of microbial communities and drive the nutrient cycles of ecosystems by lysing host cells. Therefore, uncovering the dynamic patterns and the underlying ecological mechanisms mediating the tiniest viral communities across space and through time in natural ecosystems is of crucial importance for better understanding the complex microbial world. Here, the temporal dynamics of intertidal viral communities were investigated via a time-series sampling effort. A total of 1911 viral operational taxonomic units were recovered from 36 bimonthly collected shotgun metagenomes. Functionally important auxiliary metabolic genes involved in carbohydrate, sulfur, and phosphorus metabolism were detected, some of which (e.g., cysH gene) were stably present within viral genomes over time. Over the sampling period, strong and comparable temporal turnovers were observed for intertidal viromes and their host microbes. Winter was determined as the pivotal point for the shifts in viral diversity patterns. Notably, the viral micro-diversity covaried with the macro-diversity, following similar temporal patterns. The relative abundances of viral taxa also covaried with their host prokaryotes. Meanwhile, the virus-host relationships at the whole community level were relatively stable. Further statistical analyses demonstrated that the dynamic patterns of viral communities were highly deterministic, for which temperature was the major driver. This study provided valuable mechanistic insights into the temporal turnover of viral communities in complex ecosystems such as intertidal wetlands.},
}

*Wetlands
*Biodiversity
*Viruses/genetics/classification/isolation & purification
*Metagenome
Seasons
Microbiota
Genome, Viral
Metagenomics/methods
Virome/genetics
Phylogeny

@article {pmid38898980,
year = {2024},
author = {Zhang, J and Tang, A and Jin, T and Sun, D and Guo, F and Lei, H and Lin, L and Shu, W and Yu, P and Li, X and Li, B},
title = {A panoramic view of the virosphere in three wastewater treatment plants by integrating viral-like particle-concentrated and traditional non-concentrated metagenomic approaches.},
journal = {iMeta},
volume = {3},
number = {3},
pages = {e188},
pmid = {38898980},
issn = {2770-596X},
abstract = {Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral-like particle-concentrated (VPC, representing free viral-like particles) and non-concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage-derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus-carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems.},
}

@article {pmid38902374,
year = {2024},
author = {Graham, EB and Camargo, AP and Wu, R and Neches, RY and Nolan, M and Paez-Espino, D and Kyrpides, NC and Jansson, JK and McDermott, JE and Hofmockel, KS and , },
title = {A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts.},
journal = {Nature microbiology},
volume = {9},
number = {7},
pages = {1873-1883},
pmid = {38902374},
issn = {2058-5276},
mesh = {*Soil Microbiology ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; *Metagenome ; *Soil/chemistry ; *Genome, Viral/genetics ; *Microbiota/genetics ; Carbon/metabolism ; Metagenomics ; Phylogeny ; Virome/genetics ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.},
}

*Soil Microbiology
*Viruses/genetics/classification/isolation & purification
*Biodiversity
*Metagenome
*Soil/chemistry
*Genome, Viral/genetics
*Microbiota/genetics
Carbon/metabolism
Metagenomics
Phylogeny
Virome/genetics
Bacteria/genetics/classification/isolation & purification

@article {pmid38902796,
year = {2024},
author = {Chaudhari, NM and Pérez-Carrascal, OM and Overholt, WA and Totsche, KU and Küsel, K},
title = {Genome streamlining in Parcubacteria transitioning from soil to groundwater.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {41},
pmid = {38902796},
issn = {2524-6372},
abstract = {BACKGROUND: To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.

RESULTS: Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.

CONCLUSIONS: Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.},
}

@article {pmid38909792,
year = {2024},
author = {Zhu, J and Chen, G and Tang, S and Cheng, K and Wu, K and Cai, Z and Zhou, J},
title = {The micro-ecological feature of colonies is a potential strategy for Phaeocystis globosa bloom formation.},
journal = {The Science of the total environment},
volume = {946},
number = {},
pages = {174134},
doi = {10.1016/j.scitotenv.2024.174134},
pmid = {38909792},
issn = {1879-1026},
mesh = {*Haptophyta/growth & development ; *Harmful Algal Bloom ; *Microbiota ; Microalgae ; Bacteria/classification ; Biodiversity ; },
abstract = {Phaeocystis globosa is among the dominant microalgae associated with harmful algal blooms. P. globosa has a polymorphic life cycle and its ecological success has been attributed to algal colony formation, however, few studies have assessed differences in microbial communities and their functional profiles between intra- and extra-colonies during P. globosa blooms. To address this, environmental and metagenomics tools were used to conduct a time-series analysis of the bacterial composition and metabolic characteristics of intra- and extra-colonies during a natural P. globosa bloom. The results show that bacterial composition, biodiversity, and network interactions differed significantly between intra- and extra-colonies. Dominant extra-colonial bacteria were Bacteroidia and Saccharimonadis, while dominant intra-colonial bacteria included Alphaproteobacteria and Gammaproteobacteria. Despite the lower richness and diversity observed in the intra-colonial bacterial community, relative to extra-colonies, the complexity and interconnectedness of the intra-colonial networks were higher. Regarding bacterial function, more functional genes were enriched in substance metabolism (polysaccharides, iron element and dimethylsulfoniopropionate) and signal communication (quorum sensing, indoleacetic acid-IAA) pathways in intra- than in extra-colonies. Conceptual model construction showed that microbial cooperative synthesis of ammonium, vitamin B12, IAA, and siderophores were strongly related to the P. globosa bloom, particularly in the intra-colonial environment. Overall, our data highlight the differences in bacterial structure and functions within and outside the colony during P. globosa blooms. These findings represent fundamental information indicating that phenotypic heterogeneity is a selective strategy that improves microbial population competitiveness and environmental adaptation, benefiting P. globosa bloom formation and persistence.},
}

*Haptophyta/growth & development
*Harmful Algal Bloom
*Microbiota
Microalgae
Bacteria/classification
Biodiversity