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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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.
The authors declare no competing interests.
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.
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Global RNA viral data: https://zenodo.org/record/6553771#.YyDwfezML0p
(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
- Auxiliary metabolic genes (AMGs)
Genes carried on soil viruses that are not directly required for viral replication and/or reproduction.
Viruses that have a bacterial host.
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.
Community DNA sequence data that are derived by DNA sequencing.
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.
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