A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Graham, Emily B.; Camargo, Antonio Pedro; Wu, Ruonan; Neches, Russell Y.; Nolan, Matt; Paez-Espino, David; Kyrpides, Nikos C.; Jansson, Janet K.; McDermott, Jason E.; Hofmockel, Kirsten S.; Blanchard, Jeffrey L.; Liu, Xiao Jun A.; Rodrigues, Jorge L. Mazza; Freedman, Zachary B.; Baldrian, Petr; Stursova, Martina; DeAngelis, Kristen M.; Lee, Sungeun; Godoy-Vitorino, Filipa; Yeoh, Yun Kit; Cadillo-Quiroz, Hinsby; Tringe, Susannah G.; Chauhan, Archana; Cowan, Don A.; Van Goethem, Marc W.; Woyke, Tanja; Dove, Nicholas C.; Konstantinidis, Konstantinos T.; Juenger, Thomas E.; Hart, Stephen C.; Myrold, David D.; Onstott, Tullis C.; Bohannan, Brendan J. M.; Schmer, Marty R.; Palmer, Nathan A.; Nüsslein, Klaus; Makhalanyane, Thulani P.; Dynarski, Katherine A.; Taş, Neslihan; Nicol, Graeme W.; Hazard, Christina; Scully, Erin D.; Jain, Kunal R.; Madamwar, Datta; Bissett, Andrew; Constant, Philippe; Oliveira, Rafael S.; Takacs-Vesbach, Cristina; Cregger, Melissa A.; Carrell, Alyssa A.; Klingeman, Dawn M.; Pietrasiak, Nicole

doi:10.1038/s41564-024-01686-x

Title: A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Journal Article · 20 June 2024 · Nature Microbiology

DOI: https://doi.org/10.1038/s41564-024-01686-x · OSTI ID:2328615

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Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Washington State Univ., Pullman, WA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Kyoto Univ. (Japan)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Oregon Health & Science Univ., Portland, OR (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Iowa State Univ., Ames, IA (United States)
Univ. of Massachusetts, Amherst, MA (United States)
Univ. of Oklahoma, Norman, OK (United States)
Univ. of California, Davis, CA (United States)
Univ. of Wisconsin, Madison, WI (United States)
Czech Academy of Sciences (CAS), Prague (Czech Republic)
Ecole Centrale de Lyon (France)
Univ. of Puerto Rico, San Juan, PR (United States)
Australian Institute of Marine Science (Australia)
Arizona State Univ., Tempe, AZ (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Panjab University (India)
Univ. of Pretoria (South Africa)
Univ. of California, Merced, CA (United States)
Georgia Institute of Technology, Atlanta, GA (United States)
Univ. of Texas, Austin, TX (United States)
Oregon State Univ., Corvallis, OR (United States)
Princeton Univ., NJ (United States)
Univ. of Oregon, Eugene, OR (United States)
US Dept. of Agriculture (USDA), Lincoln, NE (United States). Agricultural Research Service (ARS)
Stellenbosch University (South Africa)
US Dept. of Agriculture (USDA), Manhattan, KS (United States). Agricultural Research Service (ARS)
Sardar Patel University (India)
Charotar University of Science and Technology (India)
Commonwealth Scientific and Industrial Research Organisation (Australia)
Institut National de la Recherche Scientifique (INRS)(Canada)
Univ. of Campinas (UNICAMP) (Brazil)
Univ. of New Mexico, Albuquerque, NM (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Univ. of Nevada, Las Vegas, NV (United States)

AbstractHistorically 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.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE

Contributing Organization:: The Soil Virosphere Consortium

Grant/Contract Number:: AC05-76RL01830; AC02-05CH11231; AC05-00OR22725

OSTI ID:: 2328615

Alternate ID(s):: OSTI ID: 2397425; OSTI ID: 2479670

Report Number(s):: PNNL-SA-192887

Journal Information:: Nature Microbiology, Vol. 9, Issue 7; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands Santos-Medellín, Christian; Estera-Molina, Katerina; Yuan, Mengting Proceedings of the National Academy of Sciences, Vol. 119, Issue 45 https://doi.org/10.1073/pnas.2209132119	journal	November 2022
An intracellular compass spatially coordinates cell cycle modules in Caulobacter crescentus Lasker, Keren; Mann, Thomas H.; Shapiro, Lucy Current Opinion in Microbiology, Vol. 33 https://doi.org/10.1016/j.mib.2016.06.007	journal	October 2016
A genomic catalog of Earth’s microbiomes Nayfach, Stephen; Roux, Simon; Seshadri, Rekha Nature Biotechnology, Vol. 39, Issue 4, p. 499-509 https://doi.org/10.1038/s41587-020-0718-6	journal	November 2020
Blind spots in global soil biodiversity and ecosystem function research Guerra, Carlos A.; Heintz-Buschart, Anna; Sikorski, Johannes Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-17688-2	journal	August 2020
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
Identification of mobile genetic elements with geNomad Camargo, Antonio Pedro; Roux, Simon; Schulz, Frederik Nature Biotechnology https://doi.org/10.1038/s41587-023-01953-y	journal	September 2023
Elucidation of roles for vitamin B ₁₂ in regulation of folate, ubiquinone, and methionine metabolism Romine, Margaret F.; Rodionov, Dmitry A.; Maezato, Yukari Proceedings of the National Academy of Sciences, Vol. 114, Issue 7 https://doi.org/10.1073/pnas.1612360114	journal	January 2017

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