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

the Soil Virosphere Consortium

doi:10.1038/s41564-024-01686-x

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

the Soil Virosphere Consortium

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

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.

Original language	English
Pages (from-to)	1873-1883
Number of pages	11
Journal	Nature Microbiology
Volume	9
Issue number	7
DOIs	https://doi.org/10.1038/s41564-024-01686-x
State	Published - Jul 2024

Funding

This work was supported by the US DOE, Office of Biological and Environmental Research (BER) as part of BER\u2019s Genomic Sciences Program (GSP) under FWP 70880. A portion of this work was conducted by the US DOE JGI (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US DOE operated under contract no. DE-AC02-05CH11231. We thank Y. Song for his help in data visualization. We also thank the National Ecological Observatory Network for providing publicly available soil metagenomes.

Funders	Funder number
Biological and Environmental Research
Thelma Doelger Trust for Animals
Bertolino	FWP 70880
Bertolino
Office of Science	DE-AC02-05CH11231
Office of Science

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10.1038/s41564-024-01686-x

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title = "A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts",

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.",

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

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year = "2024",

month = jul,

doi = "10.1038/s41564-024-01686-x",

language = "English",

volume = "9",

pages = "1873--1883",

journal = "Nature Microbiology",

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AU - Nolan, Matt

AU - Paez-Espino, David

AU - Kyrpides, Nikos C.

AU - Jansson, Janet K.

AU - McDermott, Jason E.

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AU - Blanchard, Jeffrey L.

AU - Liu, Xiao Jun A.

AU - Rodrigues, Jorge L.Mazza

AU - Freedman, Zachary B.

AU - Baldrian, Petr

AU - Stursova, Martina

AU - DeAngelis, Kristen M.

AU - Lee, Sungeun

AU - Godoy-Vitorino, Filipa

AU - Yeoh, Yun Kit

AU - Cadillo-Quiroz, Hinsby

AU - Tringe, Susannah G.

AU - Chauhan, Archana

AU - Cowan, Don A.

AU - Van Goethem, Marc W.

AU - Woyke, Tanja

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AU - Konstantinidis, Konstantinos T.

AU - Juenger, Thomas E.

AU - Hart, Stephen C.

AU - Myrold, David D.

AU - Onstott, Tullis C.

AU - Bohannan, Brendan J.M.

AU - Schmer, Marty R.

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AU - Nüsslein, Klaus

AU - Makhalanyane, Thulani P.

AU - Dynarski, Katherine A.

AU - Taş, Neslihan

AU - Nicol, Graeme W.

AU - Hazard, Christina

AU - Scully, Erin D.

AU - Jain, Kunal R.

AU - Madamwar, Datta

AU - Bissett, Andrew

AU - Constant, Philippe

AU - Oliveira, Rafael S.

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AB - 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.

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

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