Metagenome Pubs

All JGI Publications

2024

Aplakidou, Eleni et al. (2024) Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Computational and Structural Biotechnology Journal 23, 2011-2033. 10.1016/j.csbj.2024.04.060
Aplakidou, Eleni et al. (2024) Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Computational and Structural Biotechnology Journal 23, 2011-2033. 10.1016/j.csbj.2024.04.060
Barnes, Elle M. et al. (2024) Abiotic stress reorganizes rhizosphere and endosphere network structure of Sorghum bicolor. Phytobiomes Journal . 10.1094/pbiomes-02-24-0012-r
Barnes, Elle M. et al. (2024) Abiotic stress reorganizes rhizosphere and endosphere network structure of Sorghum bicolor. Phytobiomes Journal . 10.1094/pbiomes-02-24-0012-r
Bustos-Diaz, Edder D. et al. (2024) Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals. Microbial Genomics 10(3), 001207. 10.1099/mgen.0.001207
Charon, Justine et al. (2024) Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities. Frontiers in Virology 4, 1371958. 10.3389/fviro.2024.1371958
Charon, Justine et al. (2024) Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities. Frontiers in Virology 4, 1371958. 10.3389/fviro.2024.1371958
Chuckran, Peter F. et al. (2024) Metatranscriptomes of California grassland soil microbial communities in response to rewetting. Microbiology Resource Announcements 13(6), e00322-24. 10.1128/mra.00322-24
Chuckran, Peter F. et al. (2024) Metatranscriptomes of California grassland soil microbial communities in response to rewetting. Microbiology Resource Announcements 13(6), e00322-24. 10.1128/mra.00322-24
Coclet, Clément et al. (2024) MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.. mSystems . 10.1128/msystems.00888-24
Coclet, Clément et al. (2024) MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.. mSystems . 10.1128/msystems.00888-24
Coleine, Claudia et al. (2024) Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability. The Science of The Total Environment 917, 170290. 10.1016/j.scitotenv.2024.170290
Colman, Daniel R. et al. (2024) Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution. Nature Communications 15(1), 7506. 10.1038/s41467-024-51841-5
Colman, Daniel R. et al. (2024) Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution. Nature Communications 15(1), 7506. 10.1038/s41467-024-51841-5
Cook, Ryan et al. (2024) Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages. ISME Communications 4(1), ycae079. 10.1093/ismeco/ycae079
Cook, Ryan et al. (2024) Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages. ISME Communications 4(1), ycae079. 10.1093/ismeco/ycae079
Curry, Kristen D et al. (2024) Reference-free structural variant detection in microbiomes via long-read co-assembly graphs. Bioinformatics 40(Supplement_1), i58-i67. 10.1093/bioinformatics/btae224
Curry, Kristen D et al. (2024) Reference-free structural variant detection in microbiomes via long-read co-assembly graphs. Bioinformatics 40(Supplement_1), i58-i67. 10.1093/bioinformatics/btae224
de Mesquita, Clifton P Bueno et al. (2024) Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland. ISME Communications 4(1), ycae040. 10.1093/ismeco/ycae040
de Mesquita, Clifton P Bueno et al. (2024) Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland. ISME Communications 4(1), ycae040. 10.1093/ismeco/ycae040
de Mesquita, Clifton P. Bueno et al. (2024) Fungal diversity and function in metagenomes sequenced from extreme environments. Fungal Ecology 72, 101383. 10.1016/j.funeco.2024.101383
de Mesquita, Clifton P. Bueno et al. (2024) Microbial Ecology and Site Characteristics Underlie Differences in Salinity‐Methane Relationships in Coastal Wetlands. Journal of Geophysical Research Biogeosciences 129(6). 10.1029/2024jg008133
de Mesquita, Clifton P. Bueno et al. (2024) Microbial Ecology and Site Characteristics Underlie Differences in Salinity‐Methane Relationships in Coastal Wetlands. Journal of Geophysical Research Biogeosciences 129(6). 10.1029/2024jg008133
de Mesquita, Clifton P. Bueno et al. (2024) Fungal diversity and function in metagenomes sequenced from extreme environments. Fungal Ecology 72, 101383. 10.1016/j.funeco.2024.101383
Denison, Elizabeth R. et al. (2024) Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie. mSystems 9(7), e00753-24. 10.1128/msystems.00753-24
Denison, Elizabeth R. et al. (2024) Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie. mSystems 9(7), e00753-24. 10.1128/msystems.00753-24
Doré, Hugo et al. (2024) Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proceedings of the National Academy of Sciences of the United States of America 121(9), e2316469121. 10.1073/pnas.2316469121
Eloe-Fadrosh, Emiley A. et al. (2024) A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics. Methods in Molecular Biology 2802, 587-609. 10.1007/978-1-0716-3838-5_20
Eloe-Fadrosh, Emiley A. et al. (2024) A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics. Methods in Molecular Biology 2802, 587-609. 10.1007/978-1-0716-3838-5_20
Fadum, J. M. et al. (2024) Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics. mSystems 9(2), e01059-23. 10.1128/msystems.01059-23
Fong, Allison A. et al. (2024) Overview of the MOSAiC expedition: Ecosystem. Elementa: Science of the Anthropocene 12(1). 10.1525/elementa.2023.00135
Fong, Allison A. et al. (2024) Overview of the MOSAiC expedition: Ecosystem. Elementa: Science of the Anthropocene 12(1). 10.1525/elementa.2023.00135
Hartman, Wyatt H. et al. (2024) Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient. mSystems 9(1), e00936-23. 10.1128/msystems.00936-23
Kohtz, Anthony J. et al. (2024) Cultivation and visualization of a methanogen of the phylum Thermoproteota. Nature 632(8027), 1118-1123. 10.1038/s41586-024-07631-6
Kohtz, Anthony J. et al. (2024) Cultivation and visualization of a methanogen of the phylum Thermoproteota. Nature 632(8027), 1118-1123. 10.1038/s41586-024-07631-6
Krukenberg, Viola et al. (2024) Methyl-reducing methanogenesis by a thermophilic culture of Korarchaeia. Nature 632(8027), 1131-1136. 10.1038/s41586-024-07829-8
Krukenberg, Viola et al. (2024) Methyl-reducing methanogenesis by a thermophilic culture of Korarchaeia. Nature 632(8027), 1131-1136. 10.1038/s41586-024-07829-8
Li, Songjun et al. (2024) Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming. Frontiers in Microbiology 15, 1369102. 10.3389/fmicb.2024.1369102
Li, Songjun et al. (2024) Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming. Frontiers in Microbiology 15, 1369102. 10.3389/fmicb.2024.1369102
Li, Yaoming et al. (2024) Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost.. mSphere , e0025924. 10.1128/msphere.00259-24
Li, Yaoming et al. (2024) Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost.. mSphere , e0025924. 10.1128/msphere.00259-24
Liu, Xiao Jun A et al. (2024) Microbial responses to long-term warming differ across soil microenvironments. ISME Communications 4(1), ycae051. 10.1093/ismeco/ycae051
Liu, Xiao Jun A et al. (2024) Microbial responses to long-term warming differ across soil microenvironments. ISME Communications 4(1), ycae051. 10.1093/ismeco/ycae051
Lui, Lauren M. et al. (2024) Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses. mSystems 9(9), e00242-24. 10.1128/msystems.00242-24
Lui, Lauren M. et al. (2024) Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses. mSystems 9(9), e00242-24. 10.1128/msystems.00242-24
Lumian, Jessica et al. (2024) Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock. Frontiers in Microbiology 14, 1330602. 10.3389/fmicb.2023.1330602
McGivern, Bridget B. et al. (2024) Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature Microbiology 9(6), 1454-1466. 10.1038/s41564-024-01691-0
McGivern, Bridget B. et al. (2024) Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature Microbiology 9(6), 1454-1466. 10.1038/s41564-024-01691-0
Mills, Daniel B. et al. (2024) Constraining the oxygen requirements for modern microbial eukaryote diversity. Proceedings of the National Academy of Sciences of the United States of America 121(2), e2303754120. 10.1073/pnas.2303754120
Murali, Ranjani et al. (2024) Diversity and evolution of nitric oxide reduction in bacteria and archaea. Proceedings of the National Academy of Sciences of the United States of America 121(26), e2316422121. 10.1073/pnas.2316422121
Murali, Ranjani et al. (2024) Diversity and evolution of nitric oxide reduction in bacteria and archaea. Proceedings of the National Academy of Sciences of the United States of America 121(26), e2316422121. 10.1073/pnas.2316422121
Nelson, Amelia R et al. (2024) Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrae047. 10.1093/ismejo/wrae047
Nguyen, Thuy M. et al. (2024) Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert. Microbiology Resource Announcements 13(3), e00980-23. 10.1128/mra.00980-23
Nguyen, Thuy M. et al. (2024) Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting. Microbiology Resource Announcements 13(2), e01080-23. 10.1128/mra.01080-23
Powell, Tyler et al. (2024) Metagenome-assembled bacterial genomes from benthic microbial mats in ice-covered Lake Vanda, Antarctica. Microbiology Resource Announcements 13(5), e01250-23. 10.1128/mra.01250-23
Powell, Tyler et al. (2024) Metagenome-assembled bacterial genomes from benthic microbial mats in ice-covered Lake Vanda, Antarctica. Microbiology Resource Announcements 13(5), e01250-23. 10.1128/mra.01250-23
Rasmussen, Anna N et al. (2024) Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrae148. 10.1093/ismejo/wrae148
Rasmussen, Anna N et al. (2024) Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrae148. 10.1093/ismejo/wrae148
Rasmussen, Anna N. et al. (2024) Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA. mSystems 9(7), e00314-24. 10.1128/msystems.00314-24
Rasmussen, Anna N. et al. (2024) Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA. mSystems 9(7), e00314-24. 10.1128/msystems.00314-24
Robinson, David et al. (2024) Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes. Frontiers in Microbiology 15, 1422941. 10.3389/fmicb.2024.1422941
Robinson, David et al. (2024) Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes. Frontiers in Microbiology 15, 1422941. 10.3389/fmicb.2024.1422941
Rodríguez-Ramos, Josué et al. (2024) Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments. Microbiology Resource Announcements 13(6), e00033-24. 10.1128/mra.00033-24
Rodríguez-Ramos, Josué et al. (2024) Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments. Microbiology Resource Announcements 13(6), e00033-24. 10.1128/mra.00033-24
Sanz-Sáez, Isabel et al. (2024) Microorganisms Involved in Methylmercury Demethylation and Mercury Reduction are Widely Distributed and Active in the Bathypelagic Deep Ocean Waters. Environmental Science and Technology 58(31), 13795-13807. 10.1021/acs.est.4c00663
Sanz-Sáez, Isabel et al. (2024) Microorganisms Involved in Methylmercury Demethylation and Mercury Reduction are Widely Distributed and Active in the Bathypelagic Deep Ocean Waters. Environmental Science and Technology 58(31), 13795-13807. 10.1021/acs.est.4c00663
Sebastián, Marta et al. (2024) Water aging and the quality of organic carbon sources drive niche partitioning of the active bathypelagic prokaryotic microbiome. Limnology and Oceanography 69(3), 562-575. 10.1002/lno.12505
St John, Emily et al. (2024) Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae. Systematic and Applied Microbiology 47(2-3), 126507. 10.1016/j.syapm.2024.126507
St John, Emily et al. (2024) Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae. Systematic and Applied Microbiology 47(2-3), 126507. 10.1016/j.syapm.2024.126507
Stewart, Rachel D. et al. (2024) Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration. mSystems 9(3), e01188-23. 10.1128/msystems.01188-23
Stewart, Rachel D. et al. (2024) Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration. mSystems 9(3), e01188-23. 10.1128/msystems.01188-23
Sun, Christine L. et al. (2024) Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient. Environmental Microbiology 26(8), e16665. 10.1111/1462-2920.16665
Sun, Christine L. et al. (2024) Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient. Environmental Microbiology 26(8), e16665. 10.1111/1462-2920.16665
Timmis, Kenneth et al. (2024) A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society. Microbial Biotechnology 17(5), e14456. 10.1111/1751-7915.14456
Timmis, Kenneth et al. (2024) A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society. Microbial Biotechnology 17(5), e14456. 10.1111/1751-7915.14456
Tothero, Gracee K. et al. (2024) Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon. Applied and Environmental Microbiology 90(9), e00599-24. 10.1128/aem.00599-24
Tothero, Gracee K. et al. (2024) Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon. Applied and Environmental Microbiology 90(9), e00599-24. 10.1128/aem.00599-24
Tsola, S. L. et al. (2024) Methanolobus use unspecific methyltransferases to produce methane from dimethylsulphide in Baltic Sea sediments. Microbiome 12(1), 3. 10.1186/s40168-023-01720-w
Tsola, S. L. et al. (2024) Methanomethylovorans are the dominant dimethylsulfide-degrading methanogens in gravel and sandy river sediment microcosms. Environmental Microbiome 19(1), 51. 10.1186/s40793-024-00591-4
Tsola, S. L. et al. (2024) Methanomethylovorans are the dominant dimethylsulfide-degrading methanogens in gravel and sandy river sediment microcosms. Environmental Microbiome 19(1), 51. 10.1186/s40793-024-00591-4
Tsuji, J. M. et al. (2024) Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre. Nature 627(8005), 915-922. 10.1038/s41586-024-07180-y
Tsuji, J. M. et al. (2024) Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre. Nature 627(8005), 915-922. 10.1038/s41586-024-07180-y
Walters, Kevin A. et al. (2024) Metagenome-assembled genomes from microbiomes fermenting dairy coproducts. Microbiology Resource Announcements 13(7), e00173-24. 10.1128/mra.00173-24
Walters, Kevin A. et al. (2024) Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture. Fermentation 10(8), 422. 10.3390/fermentation10080422
Walters, Kevin A. et al. (2024) Metagenome-assembled genomes from microbiomes fermenting dairy coproducts. Microbiology Resource Announcements 13(7), e00173-24. 10.1128/mra.00173-24
Walters, Kevin A. et al. (2024) Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture. Fermentation 10(8), 422. 10.3390/fermentation10080422
Zepernick, Brittany N et al. (2024) Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrad015. 10.1093/ismejo/wrad015
Zepernick, Brittany N et al. (2024) Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrad015. 10.1093/ismejo/wrad015
Zhang, Zihao et al. (2024) Orthophosphate uptake onto woodchips in denitrifying bioreactors is enhanced by anoxic-(anaerobic-)oxic cycling. The Science of The Total Environment 951, 175515. 10.1016/j.scitotenv.2024.175515
Zhang, Zihao et al. (2024) Orthophosphate uptake onto woodchips in denitrifying bioreactors is enhanced by anoxic-(anaerobic-)oxic cycling. The Science of The Total Environment 951, 175515. 10.1016/j.scitotenv.2024.175515
Zhong, Zhi-Ping et al. (2024) Viral potential to modulate microbial methane metabolism varies by habitat. Nature Communications 15(1), 1857. 10.1038/s41467-024-46109-x
Zhong, Zhi-Ping et al. (2024) Glacier-preserved Tibetan Plateau viral community probably linked to warm–cold climate variations. Nature Geoscience 17(9), 912-919. 10.1038/s41561-024-01508-z
Zhong, Zhi-Ping et al. (2024) Glacier-preserved Tibetan Plateau viral community probably linked to warm–cold climate variations. Nature Geoscience 17(9), 912-919. 10.1038/s41561-024-01508-z

2023

Adriaenssens, Evelien M. et al. (2023) Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification. Nature Biotechnology 41(7), 898-902. 10.1038/s41587-023-01844-2
AminiTabrizi, Roya et al. (2023) Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils. Global Change Biology 29(7), 1951-1970. 10.1111/gcb.16614
Amundson, Kaela K et al. (2023) Long-term CRISPR locus dynamics and stable host-virus co-existence in subsurface fractured shales. Current Biology . 10.1016/j.cub.2023.06.033
Barnett, Samuel E. et al. (2023) Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing. mBio 14(2), e03584-22. 10.1128/mbio.03584-22
Barnett, Samuel E. et al. (2023) Metagenomic stable isotope probing reveals bacteriophage participation in soil carbon cycling. Environmental Microbiology . 10.1111/1462-2920.16395
Bieniada, Aneta et al. (2023) Methane Cycling Microbial Community Characteristics: Comparing Natural, Actively Extracted, Restored and Unrestored Boreal Peatlands. Wetlands 43(7), 83. 10.1007/s13157-023-01726-y
Blum, Laura N. et al. (2023) Distribution and abundance of tetraether lipid cyclization genes in terrestrial hot springs reflect pH. Environmental Microbiology . 10.1111/1462-2920.16375
Booker, Anne E. et al. (2023) Life strategies for Aminicenantia in subseafloor oceanic crust. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-10. 10.1038/s41396-023-01454-5
Bowen, Jennifer L. et al. (2023) Microbial Ecology in a Changing Climate. , 289-314. 10.1201/9781003126096-18
Buessecker, Steffen et al. (2023) Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(10), 1649-1659. 10.1038/s41396-023-01472-3
Chai, Yen Ning et al. (2023) Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum. mSystems 9(1), e01190-23. 10.1128/msystems.01190-23
Chan, Clara S. et al. (2023) Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions. Applied and Environmental Microbiology 89(12), e00570-23. 10.1128/aem.00570-23
Coclet, Clement et al. (2023) Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. Microbiome 11(1), 237. 10.1186/s40168-023-01666-z
Coclet, Clement et al. (2023) Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. Microbiome 11(1), 237. 10.1186/s40168-023-01666-z
Coclet, Clement et al. (2023) Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. Microbiome 11(1), 237. 10.1186/s40168-023-01666-z
Coutinho, Felipe H. et al. (2023) Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities. Microbiome 11(1), 118. 10.1186/s40168-023-01547-5
de Mesquita, Clifton P. Bueno et al. (2023) Methyl-Based Methanogenesis: an Ecological and Genomic Review. Microbiology and Molecular Biology Reviews 87(1), e00024-22. 10.1128/mmbr.00024-22
Ellenbogen, Jared B. et al. (2023) Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems 9(1), e00698-23. 10.1128/msystems.00698-23
Eme, Laura et al. (2023) Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 618(7967), 992-999. 10.1038/s41586-023-06186-2
Ettinger, Cassandra L. et al. (2023) Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability. Microbiome 11(1), 103. 10.1186/s40168-023-01554-6
Fernandes‐Martins, Maria C. et al. (2023) Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs. Environmental Microbiology 25(5), 1022-1040. 10.1111/1462-2920.16340
Fernández-González, Antonio J. et al. (2023) Long-Term Persistence of Three Microbial Wildfire Biomarkers in Forest Soils. Forests 14(7), 1383. 10.3390/f14071383
Fremin, Brayon J. et al. (2023) Identification of over ten thousand candidate structured RNAs in viruses and phages. Computational and Structural Biotechnology Journal 21, 5630-5639. 10.1016/j.csbj.2023.11.010
Fremin, Brayon J. et al. (2023) Identification of over ten thousand candidate structured RNAs in viruses and phages. Computational and Structural Biotechnology Journal 21, 5630-5639. 10.1016/j.csbj.2023.11.010
Fremin, Brayon J. et al. (2023) Identification of over ten thousand candidate structured RNAs in viruses and phages. Computational and Structural Biotechnology Journal 21, 5630-5639. 10.1016/j.csbj.2023.11.010
George, Nikhil A. et al. (2023) CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts. Scientific Reports 13(1), 5611. 10.1038/s41598-023-32078-6
Gilbert, Naomi E. et al. (2023) Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean. mSystems 8(2), e01260-22. 10.1128/msystems.01260-22
Green, Stefan J. et al. (2023) Metagenomic Methods for Addressing NASA’s Planetary Protection Policy Requirements on Future Missions: A Workshop Report. Astrobiology . 10.1089/ast.2022.0044
He, Shaomei et al. (2023) Diversity, distribution, and expression of opsin genes in freshwater lakes. Molecular Ecology 32(11), 2798-2817. 10.1111/mec.16891
Hildebrand, Gina A et al. (2023) Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants. The Science of The Total Environment 899, 165689. 10.1016/j.scitotenv.2023.165689
Hill, Thomas C. J. et al. (2023) Resolving the controls over the production and emission of ice-nucleating particles in sea spray. Environmental Science Atmospheres 3(6), 970-990. 10.1039/d2ea00154c
Honeker, Linnea K. et al. (2023) Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest. Nature Microbiology 8(8), 1480-1494. 10.1038/s41564-023-01432-9
Howe, Adina et al. (2023) Seasonal activities of the phyllosphere microbiome of perennial crops. Nature Communications 14(1), 1039. 10.1038/s41467-023-36515-y
Hwang, Yunha et al. (2023) Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats. Nature Microbiology 8(5), 946-957. 10.1038/s41564-023-01347-5
Kieft, Brandon et al. (2023) Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater. Nature Communications 14(1), 5380. 10.1038/s41467-023-40907-5
Koedooder, Coco et al. (2023) Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia. mSystems 8(6), e00742-23. 10.1128/msystems.00742-23
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2022

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2021

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2018

Anantharaman, K. et al. (2018) Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J . 10.1038/s41396-018-0078-0
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2017

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2016

Beall, B. F. et al. (2016) Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate. Environ Microbiol 18(6), 1704-19. 10.1111/1462-2920.12819
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2015

Abdul Rahman, N. et al. (2015) A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome 3, 5. 10.1186/s40168-015-0067-8
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2014

Aylward, F. O. et al. (2014) Convergent bacterial microbiotas in the fungal agricultural systems of insects. MBio 5(6). 10.1128/mBio.02077-14
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2013

Allers, E. et al. (2013) Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean. ISME J 7(2), 256-68. 10.1038/ismej.2012.108
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2012

Aylward, F. O. et al. (2012) Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. ISME J 6(9), 1688-701. 10.1038/ismej.2012.10
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2011

Adams, A. S. et al. (2011) Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio. ISME J 5(8), 1323-31. 10.1038/ismej.2011.14
Burnum, K. E. et al. (2011) Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. Isme Journal 5(1), 161-164. DOI 10.1038/ismej.2010.97
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2010

Allgaier, M. et al. (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One 5(1), e8812. 10.1371/journal.pone.0008812
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2008

Blow, M. J. et al. (2008) Identification of ancient remains through genomic sequencing. Genome Research 18(8), 1347-1353. DOI 10.1101/gr.076091.108
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2006

Markowitz, V. M. et al. (2006) An experimental metagenome data management and analysis system. Bioinformatics 22(14), e359-67. 10.1093/bioinformatics/btl217