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ARS Home » Plains Area » Lincoln, Nebraska » Agroecosystem Management Research » Research » Publications at this Location » Publication #414822
Research Project: Integrated Agricultural Systems for a Resilient Circular Bioeconomy in the Central Plains

Location: Agroecosystem Management Research

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

Author
item GRAHAM, EMILY - Pacific Northwest National Laboratory
item CARMARGO, ANTONIO - Lawrence Berkeley National Laboratory
item WU, RUONAN - Pacific Northwest National Laboratory
item NECHES, RUSSELL - Lawrence Berkeley National Laboratory
item NOLAN, MATT - Lawrence Berkeley National Laboratory
item PAEZ-ESPINO, DAVID - Lawrence Berkeley National Laboratory
item KYRPIDES, NIKOS - Lawrence Berkeley National Laboratory
item JANSSON, JANET - Pacific Northwest National Laboratory
item MCDERMOTT, JASON - Pacific Northwest National Laboratory
item HOFMOCKEL, KIRSTEN - Pacific Northwest National Laboratory
item LIU, XIAO - University Of Oklahoma
item RODRIGUES, JORGE - University Of California, Davis
item FREEDMAN, ZACH - University Of Wisconsin
item BALDRIAN, PETR - Academy Of Sciences Of The Czech Republic (ASCR)
item STURSOVA, MARTINA - Academy Of Sciences Of The Czech Republic (ASCR)
item DEANGELIS, KRISTEN - University Of Massachusetts, Amherst
item LEE, SUNGEUN - Ecole Normale Superieure (ENS) De Lyon
item GODOY-VITORINO, FILIPA - University Of Puerto Rico
item YEOH, YUN - Australian Inst Of Marine Sciences
item CADILLO-QUIROZ, HINSBY - Arizona State University
item TRINGE, SUSANNAH - Lawrence Berkeley National Laboratory
item CHAUHAN, ARCHANA - Chandigarh University
item COWAN, DON - University Of Pretoria
item VAN GOETHEM, MARC - University Of Pretoria
item WOYKE, TANJA - Lawrence Berkeley National Laboratory
item DOVE, NICHOLAS - University Of California
item KONSTANTINIDIS, KONSTANTINOS - Georgia Institute Of Technology
item JUENGER, THOMAS - University Of Texas
item HART, STEPHEN - University Of California
item MYROLD, DAVID - Oregon State University
item ONSTOTT, TULLIS - Princeton University
item BOHANNAN, BRENDAN - University Of Oregon
item Schmer, Marty
item Palmer, Nathan - Nate
item NUSSLEIN, KLAUS - University Of Massachusetts
item MAKHALANYANE, THULANI - University Of Pretoria
item DYNARSKI, KATHERINE - University Of California, Davis
item TAS, NESLIHAN - Lawrence Berkeley National Laboratory
item NICOL, GRAEME - Ecole Normale Superieure (ENS) De Lyon
item HAZARD, CHRISTINA - Ecole Normale Superieure (ENS) De Lyon
item Scully, Erin
item JAIN, KUNAL - Sardar Patel University
item MADAMWAR, DATTA - Sardar Patel University
item BISSETT, ANDREW - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item CONSTANT, PHILIPPE - Institut National De La Recherche Scientifique (INRS)
item OLIVERIA, RAFAEL - Universidade De Campinas (UNICAMP)
item TEKACS-VESBACH, CHRISTINA - University Of New Mexico
item CREGGER, MELISSA - Oak Ridge National Laboratory
item CARRELL, ALYSSA - Oak Ridge National Laboratory
item KLINGEMAN, DAWN - Oak Ridge National Laboratory
item PIETRASIAK, NICOLE - University Of Nevada Las Vegas, Las Vegas, Nv

Submitted to: Nature Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2024
Publication Date: 6/20/2024
Citation: Graham, E., Carmargo, A., Wu, R., Neches, R., Nolan, M., Paez-Espino, D., Kyrpides, N., Jansson, J., McDermott, J., Hofmockel, K., Liu, X., Rodrigues, J., Freedman, Z., Baldrian, P., Stursova, M., Deangelis, K., Lee, S., Godoy-Vitorino, F., Yeoh, Y., Cadillo-Quiroz, H., Tringe, S., Chauhan, A., Cowan, D., Van Goethem, M., Woyke, T., Dove, N., Konstantinidis, K., Juenger, T., Hart, S., Myrold, D., Onstott, T., Bohannan, B., Schmer, M.R., Palmer, N.A., Nusslein, K., Makhalanyane, T., Dynarski, K., Tas, N., Nicol, G., Hazard, C., Scully, E.D., Jain, K., Madamwar, D., Bissett, A., Constant, P., Oliveria, R., Tekacs-Vesbach, C., Cregger, M., Carrell, A., Klingeman, D., Pietrasiak, N. 2024. A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts. Nature Microbiology. 9:1873-1883. https://doi.org/10.1038/s41564-024-01686-x.
DOI: https://doi.org/10.1038/s41564-024-01686-x

Interpretive Summary: Soil virus contributions to soil ecology are largely unknown due to the extreme diversity of soil components but are now thought to be important in global biogeochemical cycles. Our current understanding of soil viral global contributions, activities, and interactions with the soil microbiome and soil processes remains limited. To address this current limitation, a global soil virus database was developed from soils sampled across the world. The global soil virus database will serve as a basis for tool, theory, and model development to further advance soil ecology, biogeochemistry, ecology, and evolution.

Technical 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 (GSV) Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and comprised of 616,935 uncultivated viral genomes (UViGs) and 38,508 unique viral operational taxonomic units (vOTUs). Rarefaction curves from the GSV Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared vOTUs 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.