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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.

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Fig. 1: Taxonomic composition of soil DNA and RNA viruses and their known hosts.
Fig. 2: Different aspects of soil viral ecology and lifestyles.
Fig. 3: Impacts of permafrost thaw on soil viruses.
Fig. 4: Impacts of changes in soil moisture on soil viruses.

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Acknowledgements

Research in 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.

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Correspondence to Janet K. Jansson.

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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.

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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

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.

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Jansson, J.K., Wu, R. Soil viral diversity, ecology and climate change. Nat Rev Microbiol (2022). https://doi.org/10.1038/s41579-022-00811-z

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