Soil viral diversity, ecology and climate change

ABSTRACT Soil viruses are highly abundant and have important roles in the regulation of host dynamics and soil ecology. Climate change is resulting in unprecedented changes to soil

ecosystems and the life forms that reside there, including viruses. In this Review, we explore our current understanding of soil viral diversity and ecology, and we discuss how climate

change (such as extended and extreme drought events or more flooding and altered precipitation patterns) is influencing soil viruses. Finally, we provide our perspective on future research

needs to better understand how climate change will impact soil viral ecology. Access through your institution Buy or subscribe This is a preview of subscription content, access via your

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subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS BIOGEOGRAPHIC PATTERNS AND DRIVERS OF SOIL VIROMES Article 21 February 2024 A GLOBAL ATLAS OF

SOIL VIRUSES REVEALS UNEXPLORED BIODIVERSITY AND POTENTIAL BIOGEOCHEMICAL IMPACTS Article Open access 20 June 2024 INTEGRATING VIRUSES INTO SOIL FOOD WEB BIOGEOCHEMISTRY Article 02 August

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the laboratory of J.K.J. was supported by the US Department of Energy’s Office of Biological and Environmental Research and is a contribution of the Scientific Focus Area ‘Phenotypic

response of the soil microbiome to environmental perturbations’ (FWP 70880). Pacific Northwest National Laboratory is operated for the US Department of Energy by Battelle Memorial Institute

under contract DE-AC05-76RLO1830. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA Janet K. Jansson & 

Ruonan Wu Authors * Janet K. Jansson View author publications You can also search for this author inPubMed Google Scholar * Ruonan Wu View author publications You can also search for this

author inPubMed Google Scholar CONTRIBUTIONS The authors contributed equally to all aspects of the article. CORRESPONDING AUTHOR Correspondence to Janet K. Jansson. ETHICS DECLARATIONS

COMPETING INTERESTS The authors declare no competing interests. PEER REVIEW PEER REVIEW INFORMATION _Nature Reviews Microbiology_ thanks Li-Li Han; Mark Radosevich, who co-reviewed with

Xiaolong Liang; and K. Eric Wommack, who co-reviewed with Hannah Locke, for their contribution to the peer review of this work. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature

remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. RELATED LINKS GLOBAL RNA VIRAL DATA: https://zenodo.org/record/6553771#.YyDwfezML0p

IMG/VR METADATA: https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=IMG_VR (JGI GENOME POTAL LOG-IN IS NEEDED) RIBOV1.4_INFO.TSV:

https://portal.nersc.gov/dna/microbial/prokpubs/Riboviria/RiboV1.4/RiboV1.4_Info.tsv RNA VIRUSES IN METATRANSCRIPTOMES DATABASE: https://riboviria.org VIRUS-HOST DB:

https://www.genome.jp/virushostdb SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION GLOSSARY * Auxiliary metabolic genes (AMGs) Genes carried on soil viruses that are not directly required

for viral replication and/or reproduction. * Bacteriophages Viruses that have a bacterial host. * CRISPR–Cas An adaptive immunity against foreign elements in many bacteria and most archaea.

DNA from the invasive elements (for example viruses) is first taken up and integrated into CRISPR loci as spacers with repeat sequences flanked on both sides. The CRISPR locus is

transcribed and modified into mature CRISPR RNA. CRISPR RNA guides the Cas nuclease complex to cleave the sequences after targeted recognition of the invading mobile genetic elements. *

Giant viruses Very large double-stranded DNA viruses with genomes as large as or larger than those of some bacteria. * Kill-the-winner hypothesis A hypothesis that the temperate phage

lifestyle is favoured when host densities are high. Thus, viruses have an opportunity to exploit their hosts via lysogeny instead of lysing them. * Metagenome Community DNA sequence data

that are derived by DNA sequencing. * Metatranscriptome Community RNA sequence data that are derived by RNA sequencing. * Piggyback-the-winner hypothesis A hypothesis that the dominant

bacterial hosts in a system are selectively lysed by phages. * Stable-isotope probing A method used to incorporate stable isotopes into biomolecules and thus to distinguish active cell

populations from inactive cell populations (for example, when 18O-labelled H2O is used) or to determine cells that perform a specific metabolic step (for example, when 13C-labelled

substrates are used). * Temperate phages Viruses (bacteriophages) that are incorporated into the genome of the bacterial host and display a lysogenic lifestyle. * Viral ‘dark matter’ A term

used to describe the largely unknown identities and functions of soil viruses. * Viral shunt Virus-mediated lysis of microbial cells that results in a bypass of the flow of nutrients from

microbial cells to higher trophic levels in the soil microbial food web. * Viromes Viruses that are extracted from the environment before sequencing. RIGHTS AND PERMISSIONS Springer Nature

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Jansson, J.K., Wu, R. Soil viral diversity, ecology and climate change. _Nat Rev Microbiol_ 21, 296–311 (2023). https://doi.org/10.1038/s41579-022-00811-z Download citation * Accepted: 29

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