Soil viral diversity, ecology and climate change

Helsley, K. R., Brown, T. M., Furlong, K. & Williamson, K. E. Applications and limitations of tea extract as a virucidal agent to assess the role of phage predation in soils. Biol. Fertil. Soils 50, 263–274 (2014).

Google Scholar 

Suttle, C. A. Marine viruses — major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801–812 (2007).

CAS 
PubMed 

Google Scholar 

Winter, C., Bouvier, T., Weinbauer, M. G. & Thingstad, T. F. Trade-offs between competition and defense specialists among unicellular planktonic organisms: the “killing the winner” hypothesis revisited. Microbiol. Mol. Biol. Rev. 74, 42–57 (2010).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Pratama, A. A. & van Elsas, J. D. The ‘neglected’ soil virome–potential role and impact. Trends Microbiol. 26, 649–662 (2018).

CAS 
PubMed 

Google Scholar 

Williamson, K. E., Fuhrmann, J. J., Wommack, K. E. & Radosevich, M. Viruses in soil ecosystems: an unknown quantity within an unexplored territory. Annu. Rev. Virol. 4, 201–219 (2017).

CAS 
PubMed 

Google Scholar 

Gonzalez-Martin, C., Teigell-Perez, N., Lyles, M., Valladares, B. & Griffin, D. W. Epifluorescent direct counts of bacteria and viruses from topsoil of various desert dust storm regions. Res. Microbiol. 164, 17–21 (2013).

PubMed 

Google Scholar 

Ashelford, K. E., Day, M. J. & Fry, J. C. Elevated abundance of bacteriophage infecting bacteria in soil. Appl. Environ. Microbiol. 69, 285–289 (2003).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Bowatte, S., Newton, P. C., Takahashi, R. & Kimura, M. High frequency of virus-infected bacterial cells in a sheep grazed pasture soil in New Zealand. Soil Biol. Biochem. 42, 708–712 (2010).

CAS 

Google Scholar 

Takahashi, R. et al. High frequency of phage-infected bacterial cells in a rice field soil in Japan. Soil Sci. Plant Nutr. 57, 35–39 (2011).

Google Scholar 

Williamson, K. E., Radosevich, M. & Wommack, K. E. Abundance and diversity of viruses in six Delaware soils. Appl. Environ. Microbiol. 71, 3119–3125 (2005).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Liang, X. et al. Lysogenic reproductive strategies of viral communities vary with soil depth and are correlated with bacterial diversity. Soil Biol. Biochem. 144, 107767 (2020).

CAS 

Google Scholar 

Emerson, J. B. et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat. Microbiol. 3, 870–880 (2018).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Jansson, J. K. & Hofmockel, K. S. Soil microbiomes and climate change. Nat. Rev. Microbiol. 18, 35–46 (2020).

CAS 
PubMed 

Google Scholar 

Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl Acad. Sci. USA 103, 626–631 (2006).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Bi, L. et al. Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils. Environ. Microbiol. 23, 588–599 (2021).

CAS 
PubMed 

Google Scholar 

Starr, E. P., Nuccio, E. E., Pett-Ridge, J., Banfield, J. F. & Firestone, M. K. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. Proc. Natl Acad. Sci. USA 116, 25900–25908 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Hurst, C. J., Gerba, C. P. & Cech, I. Effects of environmental variables and soil characteristics on virus survival in soil. Appl. Environ. Microbiol. 40, 1067–1079 (1980).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Williamson, K. E., Wommack, K. E. & Radosevich, M. Sampling natural viral communities from soil for culture-independent analyses. Appl. Environ. Microbiol. 69, 6628–6633 (2003).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Wu, R. et al. DNA viral diversity, abundance, and functional potential vary across grassland soils with a range of historical moisture regimes. mBio 12, e02595521 (2021).

Google Scholar 

Chen, L. et al. Effect of different long-term fertilization regimes on the viral community in an agricultural soil of southern China. Eur. J. Soil Biol. 62, 121–126 (2014).

Google Scholar 

Williamson, K. E., Radosevich, M., Smith, D. W. & Wommack, K. E. Incidence of lysogeny within temperate and extreme soil environments. Environ. Microbiol. 9, 2563–2574 (2007).

CAS 
PubMed 

Google Scholar 

Narr, A., Nawaz, A., Wick, L. Y., Harms, H. & Chatzinotas, A. Soil viral communities vary temporally and along a land use transect as revealed by virus-like particle counting and a modified community fingerprinting approach (fRAPD). Front. Microbiol. 8, 1975 (2017).

PubMed 
PubMed Central 

Google Scholar 

Fierer, N. et al. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl. Environ. Microbiol. 73, 7059–7066 (2007).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Paez-Espino, D. et al. Uncovering Earth’s virome. Nature 536, 425–430 (2016).

CAS 
PubMed 

Google Scholar 

Santos-Medellin, C. et al. Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities. ISME J. 15, 1956–1970 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Roux, S. et al. IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. Nucleic Acids Res. 49, D764–D775 (2021).

CAS 
PubMed 

Google Scholar 

Brum, J. R. & Sullivan, M. B. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat. Rev. Microbiol. 13, 147–159 (2015).

CAS 
PubMed 

Google Scholar 

Coutinho, F. H., Gregoracci, G. B., Walter, J. M., Thompson, C. C. & Thompson, F. L. Metagenomics sheds light on the ecology of marine microbes and their viruses. Trends Microbiol. 26, 955–965 (2018).

CAS 
PubMed 

Google Scholar 

Guo, J. et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 1–13 (2021).

Google Scholar 

Ren, J., Ahlgren, N. A., Lu, Y. Y., Fuhrman, J. A. & Sun, F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome 5, 1–20 (2017).

Google Scholar 

Shaffer, M. et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 48, 8883–8900 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Kieft, K., Zhou, Z. & Anantharaman, K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8, 1–23 (2020).

Google Scholar 

Paez-Espino, D., Pavlopoulos, G. A., Ivanova, N. N. & Kyrpides, N. C. Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nat. Protoc. 12, 1673–1682 (2017).

CAS 
PubMed 

Google Scholar 

Swanson, M. et al. Viruses in soils: morphological diversity and abundance in the rhizosphere. Ann. Appl. Biol. 155, 51–60 (2009).

Google Scholar 

Wu, R. et al. Moisture modulates soil reservoirs of active DNA and RNA viruses. Commun. Biol. 4, 1–11 (2021).

Google Scholar 

Trubl, G. et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems 3, e00076-18 (2018).

PubMed 
PubMed Central 

Google Scholar 

Al-Shayeb, B. et al. Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Fischer, M. G. Giant viruses come of age. Curr. Opin. Microbiol. 31, 50–57 (2016).

PubMed 

Google Scholar 

Raoult, D. et al. The 1.2-megabase genome sequence of Mimivirus. Science 306, 1344–1350 (2004).

CAS 
PubMed 

Google Scholar 

Pagnier, I. et al. A decade of improvements in Mimiviridae and Marseilleviridae isolation from amoeba. Intervirology 56, 354–363 (2013).

PubMed 

Google Scholar 

Boughalmi, M. et al. High‐throughput isolation of giant viruses of the Mimiviridae and Marseilleviridae families in the Tunisian environment. Environ. Microbiol. 15, 2000–2007 (2013).

PubMed 

Google Scholar 

Legendre, M. et al. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc. Natl Acad. Sci. USA 111, 4274–4279 (2014).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Legendre, M. et al. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. Proc. Natl Acad. Sci. USA 112, E5327–E5335 (2015).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Yoosuf, N. et al. Draft genome sequences of Terra1 and Terra2 viruses, new members of the family Mimiviridae isolated from soil. Virology 452, 125–132 (2014).

PubMed 

Google Scholar 

Schulz, F. et al. Hidden diversity of soil giant viruses. Nat. Commun. 9, 4881 (2018).

PubMed 
PubMed Central 

Google Scholar 

Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Hulo, C. et al. ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res. 39, D576–D582 (2011).

CAS 
PubMed 

Google Scholar 

Adriaenssens, E. M. et al. Environmental drivers of viral community composition in Antarctic soils identified by viromics. Microbiome 5, 1–14 (2017).

Google Scholar 

Liang, X. et al. Viral abundance and diversity vary with depth in a southeastern United States agricultural ultisol. Soil Biol. Biochem. 137, 107546 (2019).

CAS 

Google Scholar 

International Committee on Taxonomy of Viruses Executive Committee. The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nat. Microbiol. 5, 668–674 (2020).

CAS 

Google Scholar 

Adriaenssens, E. M. et al. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV bacterial and archaeal viruses subcommittee. Arch. Virol. 165, 1253–1260 (2020).

CAS 
PubMed 

Google Scholar 

Roux, S. et al. Minimum information about an uncultivated virus genome (MIUViG). Nat. Biotechnol. 37, 29–37 (2019).

CAS 
PubMed 

Google Scholar 

Kim, K.-H. et al. Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl. Environ. Microbiol. 74, 5975–5985 (2008).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Han, L.-L., Yu, D.-T., Zhang, L.-M., Shen, J.-P. & He, J.-Z. Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils. Sci. Rep. 7, 1–10 (2017).

Google Scholar 

Reavy, B. et al. Distinct circular single-stranded DNA viruses exist in different soil types. Appl. Environ. Microbiol. 81, 3934–3945 (2015).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Trubl, G. et al. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ 7, e7265 (2019).

PubMed 
PubMed Central 

Google Scholar 

Marine, R. et al. Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome. Microbiome 2, 3 (2014).

PubMed 
PubMed Central 

Google Scholar 

Han, L.-L. et al. Distribution of soil viruses across China and their potential role in phosphorous metabolism. Environ. Microbiome 17, 6 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Peck, K. M. & Lauring, A. S. Complexities of viral mutation rates. J. Virol. 92, e01031-17 (2018).

PubMed 
PubMed Central 

Google Scholar 

Malathi, V. & Renuka Devi, P. ssDNA viruses: key players in global virome. Virusdisease 30, 3–12 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Steward, G. F. et al. Are we missing half of the viruses in the ocean? ISME J. 7, 672–679 (2013).

CAS 
PubMed 

Google Scholar 

Hillary, L. S., Adriaenssens, E. M., Jones, D. L. & McDonald, J. E. RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels. ISME Commun. 2, 1–10 (2022).

Google Scholar 

Schroeder, J. W., Dobson, A., Mangan, S. A., Petticord, D. F. & Herre, E. A. Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model. Nat. Commun. 11, 1–10 (2020).

Google Scholar 

Chen, I.-M. A. et al. The IMG/M data management and analysis system v. 6.0: new tools and advanced capabilities. Nucleic Acids Res. 49, D751–D763 (2021).

CAS 
PubMed 

Google Scholar 

Neri, U. et al. A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages. Zenodo https://doi.org/10.5281/zenodo.6553771 (2022).

Article 

Google Scholar 

Koonin, E. V. et al. Global organization and proposed megataxonomy of the virus world. Microbiol. Mol. Biol. Rev. 84, e00061-19 (2020).

PubMed 
PubMed Central 

Google Scholar 

Neri, U. et al. A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages. Preprint at bioRxiv https://doi.org/10.1101/2022.02.15.480533 (2022).

Article 

Google Scholar 

Albright, M. B. et al. Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition. ISME Commun. 2, 24 (2022).

Google Scholar 

Braga, L. P. et al. Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. Microbiome 8, 52 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Wang, Y. et al. Heterogeneity of soil bacterial and bacteriophage communities in three rice agroecosystems and potential impacts of bacteriophage on nutrient cycling. Environ. Microbiome 17, 17 (2022).

PubMed 
PubMed Central 

Google Scholar 

Williamson, K. E., Schnitker, J. B., Radosevich, M., Smith, D. W. & Wommack, K. E. Cultivation-based assessment of lysogeny among soil bacteria. Microb. Ecol. 56, 437–447 (2008).

PubMed 

Google Scholar 

Huang, D. et al. Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress. Microbiome 9, 150 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Ghosh, D. et al. Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction. Appl. Environ. Microbiol. 75, 7142–7152 (2009).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Silveira, C. B. & Rohwer, F. L. Piggyback-the-winner in host-associated microbial communities. NPJ Biofilms Microbiomes 2, 16010 (2016).

PubMed 
PubMed Central 

Google Scholar 

Knowles, B. et al. Lytic to temperate switching of viral communities. Nature 531, 466–470 (2016).

CAS 
PubMed 

Google Scholar 

Thingstad, T. F. & Lignell, R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat. Microb. Ecol. 13, 19–27 (1997).

Google Scholar 

Thingstad, T. F. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol. Oceanogr. 45, 1320–1328 (2000).

Google Scholar 

Stewart, F. M. & Levin, B. R. The population biology of bacterial viruses: why be temperate. Theor. Popul. Biol. 26, 93–117 (1984).

CAS 
PubMed 

Google Scholar 

Obeng, N., Pratama, A. A. & van Elsas, J. D. The significance of mutualistic phages for bacterial ecology and evolution. Trends Microbiol. 24, 440–449 (2016).

CAS 
PubMed 

Google Scholar 

Liang, X. & Radosevich, M. Commentary: a host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Front. Microbiol. 10, 1201 (2019).

PubMed 
PubMed Central 

Google Scholar 

Parikka, K. J., Le Romancer, M., Wauters, N. & Jacquet, S. Deciphering the virus‐to‐prokaryote ratio (VPR): insights into virus–host relationships in a variety of ecosystems. Biol. Rev. 92, 1081–1100 (2017).

PubMed 

Google Scholar 

Roy, K. et al. Temporal dynamics of soil virus and bacterial populations in agricultural and early plant successional soils. Front. Microbiol. 11, 1494 (2020).

PubMed 
PubMed Central 

Google Scholar 

Dedrick, R. M. et al. Prophage-mediated defence against viral attack and viral counter-defence. Nat. Microbiol. 2, 16251 (2017).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Boyd, E. F. Bacteriophage-encoded bacterial virulence factors and phage–pathogenicity island interactions. Adv. Virus Res. 82, 91–118 (2012).

CAS 
PubMed 

Google Scholar 

Bondy-Denomy, J. et al. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 10, 2854–2866 (2016).

PubMed 
PubMed Central 

Google Scholar 

Schuch, R. & Fischetti, V. A. The secret life of the anthrax agent Bacillus anthracis: bacteriophage-mediated ecological adaptations. PLoS ONE 4, e6532 (2009).

PubMed 
PubMed Central 

Google Scholar 

Koskella, B. & Brockhurst, M. A. Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol. Rev. 38, 916–931 (2014).

CAS 
PubMed 

Google Scholar 

Levin, B. R. & Bull, J. J. Population and evolutionary dynamics of phage therapy. Nat. Rev. Microbiol. 2, 166–173 (2004).

CAS 
PubMed 

Google Scholar 

Paterson, S. et al. Antagonistic coevolution accelerates molecular evolution. Nature 464, 275–278 (2010).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Labrie, S. J., Samson, J. E. & Moineau, S. Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 8, 317–327 (2010).

CAS 
PubMed 

Google Scholar 

Nuñez, J. K., Lee, A. S., Engelman, A. & Doudna, J. A. Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity. Nature 519, 193–198 (2015).

PubMed 
PubMed Central 

Google Scholar 

Sant, D. G., Woods, L. C., Barr, J. J. & McDonald, M. J. Host diversity slows bacteriophage adaptation by selecting generalists over specialists. Nat. Ecol. Evol. 5, 350–359 (2021).

PubMed 

Google Scholar 

Poisot, T., Lounnas, M. & Hochberg, M. E. The structure of natural microbial enemy-victim networks. Ecol. Process. 2, 13 (2013).

Google Scholar 

Trubl, G. et al. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 9, 1–15 (2021).

Google Scholar 

Poullain, V., Gandon, S., Brockhurst, M. A., Buckling, A. & Hochberg, M. E. The evolution of specificity in evolving and coevolving antagonistic interactions between a bacteria and its phage. Evolution 62, 1–11 (2008).

PubMed 

Google Scholar 

McGee, L. W. et al. Synergistic pleiotropy overrides the costs of complexity in viral adaptation. Genetics 202, 285–295 (2016).

CAS 
PubMed 

Google Scholar 

Wommack, K. E. & Colwell, R. R. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64, 69–114 (2000).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Starr, E. P. et al. Stable-isotope-informed, genome-resolved metagenomics uncovers potential cross-kingdom interactions in Rhizosphere soil. mSphere 6, e00085-21 (2021).

PubMed Central 

Google Scholar 

Osterhout, R. E., Figueroa, I. A., Keasling, J. D. & Arkin, A. P. Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol. 7, 82 (2007).

PubMed 
PubMed Central 

Google Scholar 

Quesada, J. M., Soriano, Ma. I. & Espinosa-Urgel, M. Stability of a Pseudomonas putida KT2440 bacteriophage-carried genomic island and its impact on rhizosphere fitness. Appl. Environ. Microbiol. 78, 6963–6974 (2012).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Li, G., Cortez, M. H., Dushoff, J. & Weitz, J. S. When to be temperate: on the fitness benefits of lysis vs. lysogeny. Virus Evol. 6, veaa042 (2020).

PubMed 
PubMed Central 

Google Scholar 

Jin, M. et al. Diversities and potential biogeochemical impacts of mangrove soil viruses. Microbiome 7, 58 (2019).

PubMed 
PubMed Central 

Google Scholar 

Zheng, X. et al. Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. ISME J. 16, 1397–1408 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Wu, R. et al. Structural characterization of a soil viral auxiliary metabolic gene product–a functional chitosanase. Nat. Commun. 13, 5485 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Pedersen, J. S. T. et al. An assessment of the performance of scenarios against historical global emissions for IPCC reports. Glob. Environ. Change 66, 102199 (2021).

Google Scholar 

Girardin, G. et al. Viruses carried to soil by irrigation can be aerosolized later during windy spells. Agron. Sustain. Dev. 36, 59 (2016).

Google Scholar 

Chen, P.-S. et al. Ambient influenza and avian influenza virus during dust storm days and background days. Environ. Health Perspect. 118, 1211–1216 (2010).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Zablocki, O., Adriaenssens, E. M. & Cowan, D. Diversity and ecology of viruses in hyperarid desert soils. Appl. Environ. Microbiol. 82, 770–777 (2016).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Kimura, M., Jia, Z.-J., Nakayama, N. & Asakawa, S. Ecology of viruses in soils: past, present and future perspectives. Soil Sci. Plant Nutr. 54, 1–32 (2008).

Google Scholar 

Yeager, J. & O’Brien, R. Enterovirus inactivation in soil. Appl. Environ. Microbiol. 38, 694–701 (1979).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Reanney, D. & Marsh, S. The ecology of viruses attacking Bacillus stearothermophilus in soil. Soil Biol. Biochem. 5, 399–408 (1973).

Google Scholar 

Wu, R. et al. Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming. ISME J. 14, 1651–1662 (2020).

PubMed 
PubMed Central 

Google Scholar 

Hugelius, G. et al. Estimated stocks of circumpolar permafrost carbon with quantified uncertainty ranges and identified data gaps. Biogeosciences 11, 6573–6593 (2014).

Google Scholar 

Graham, D. E. et al. Microbes in thawing permafrost: the unknown variable in the climate change equation. ISME J. 6, 709–712 (2012).

CAS 
PubMed 

Google Scholar 

Jansson, J. K. & Taş, N. The microbial ecology of permafrost. Nat. Rev. Microbiol. 12, 414–425 (2014).

CAS 
PubMed 

Google Scholar 

Taş, N. et al. Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. ISME J. 8, 1904–1919 (2014).

PubMed 
PubMed Central 

Google Scholar 

Taş, N. et al. Landscape topography structures the soil microbiome in arctic polygonal tundra. Nat. Commun. 9, 777 (2018).

PubMed 
PubMed Central 

Google Scholar 

Mackelprang, R. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480, 368–371 (2011).

CAS 
PubMed 

Google Scholar 

Mondav, R. et al. Discovery of a novel methanogen prevalent in thawing permafrost. Nat. Commun. 5, 3212 (2014).

PubMed 

Google Scholar 

Rivkina, E., Gilichinsky, D., Wagener, S., Tiedje, J. & McGrath, J. Biogeochemical activity of anaerobic microorganisms from buried permafrost sediments. Geomicrobiol. J. 15, 187–193 (1998).

Google Scholar 

Hultman, J. et al. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521, 208–212 (2015).

CAS 
PubMed 

Google Scholar 

Woodcroft, B. J. et al. Genome-centric view of carbon processing in thawing permafrost. Nature 560, 49–54 (2018).

CAS 
PubMed 

Google Scholar 

Guglielmin, M., Dalle Fratte, M. & Cannone, N. Permafrost warming and vegetation changes in continental Antarctica. Environ. Res. Lett. 9, 045001 (2014).

Google Scholar 

Goordial, J. et al. Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper‐arid polar desert. Environ. Microbiol. 19, 443–458 (2017).

CAS 
PubMed 

Google Scholar 

Cook, B. I., Smerdon, J. E., Seager, R. & Coats, S. Global warming and 21st century drying. Clim. Dyn. 43, 2607–2627 (2014).

Google Scholar 

Šťovíček, A., Kim, M., Or, D. & Gillor, O. Microbial community response to hydration-desiccation cycles in desert soil. Sci. Rep. 7, 45735 (2017).

PubMed 
PubMed Central 

Google Scholar 

Srinivasiah, S. et al. Direct assessment of viral diversity in soils by random PCR amplification of polymorphic DNA. Appl. Environ. Microbiol. 79, 5450–5457 (2013).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Zablocki, O. et al. High-level diversity of tailed phages, eukaryote-associated viruses, and virophage-like elements in the metaviromes of antarctic soils. Appl. Environ. Microbiol. 80, 6888–6897 (2014).

PubMed 
PubMed Central 

Google Scholar 

Roy Chowdhury, T. et al. Metaphenomic responses of a native prairie soil microbiome to moisture perturbations. mSystems 4, e00061-19 (2019).

PubMed 
PubMed Central 

Google Scholar 

Michen, B. & Graule, T. Isoelectric points of viruses. J. Appl. Microbiol. 109, 388–397 (2010).

CAS 
PubMed 

Google Scholar 

Nelson, A. R. et al. Playing with FiRE: a genome resolved view of the soil microbiome responses to high severity forest wildfire. Preprint at bioRxiv https://doi.org/10.1101/2021.08.17.456416 (2021).

Article 
PubMed 
PubMed Central 

Google Scholar 

Braga, L. P. et al. Novel virocell metabolic potential revealed in agricultural soils by virus‐enriched soil metagenome analysis. Environ. Microbiol. Rep. 13, 348–354 (2021).

CAS 
PubMed 

Google Scholar 

Hwang, Y., Rahlff, J., Schulze-Makuch, D., Schloter, M. & Probst, A. J. Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil. mSystems 6, e00385-21 (2021).

PubMed 
PubMed Central 

Google Scholar 

Ter Horst, A. M. et al. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. Microbiome 9, 233 (2021).

PubMed 
PubMed Central 

Google Scholar 

Van Goethem, M. W., Swenson, T. L., Trubl, G., Roux, S. & Northen, T. R. Characteristics of wetting-induced bacteriophage blooms in biological soil crust. mBio 10, e02287-19 (2019).

PubMed 
PubMed Central 

Google Scholar 

Kieft, K. et al. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nat. Commun. 12, 1–16 (2021).

Google Scholar 

Nayfach, S. et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat. Biotechnol. 39, 578–585 (2021).

CAS 
PubMed 

Google Scholar 

Lefkowitz, E. J. et al. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res. 46, D708–D717 (2018).

CAS 
PubMed 

Google Scholar 

Hough, M. et al. Biotic and environmental drivers of plant microbiomes across a permafrost thaw gradient. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.00796 (2020).

Article 
PubMed 
PubMed Central 

Google Scholar 

Naylor, D. et al. Soil microbiomes under climate change and implications for carbon cycling. Annu. Rev. Environ. Resour. 45, 29–59 (2020).

Google Scholar 

Williamson, K. E. et al. Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods. Biol. Fertil. Soils 49, 857–869 (2013).

Google Scholar 

Graham, E. B. et al. Untapped viral diversity in global soil metagenomes. Preprint at bioRxiv https://doi.org/10.1101/583997 (2019).

Article 

Google Scholar 

Shakya, M., Lo, C.-C. & Chain, P. S. Advances and challenges in metatranscriptomic analysis. Front. Genet. 10, 904 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Steffan, J. J., Derby, J. A. & Brevik, E. C. Soil pathogens that may potentially cause pandemics, including severe acute respiratory syndrome (SARS) coronaviruses. Curr. Opin. Environ. Sci. Health 17, 35–40 (2020).

PubMed 
PubMed Central 

Google Scholar 

Fortier, L.-C. & Sekulovic, O. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence 4, 354–365 (2013).

PubMed 
PubMed Central 

Google Scholar 

Breitbart, M., Miyake, J. H. & Rohwer, F. Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol. Lett. 236, 249–256 (2004).

CAS 
PubMed 

Google Scholar 

Hassard, F. et al. Abundance and distribution of enteric bacteria and viruses in coastal and estuarine sediments — a review. Front. Microbiol. 7, 1692 (2016).

PubMed 
PubMed Central 

Google Scholar 

Shade, A. et al. Fundamentals of microbial community resistance and resilience. Front. Microbiol. 3, 417 (2012).

PubMed 
PubMed Central 

Google Scholar 

Sano, E., Carlson, S., Wegley, L. & Rohwer, F. Movement of viruses between biomes. Appl. Environ. Microbiol. 70, 5842–5846 (2004).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Casteel, M. J., Sobsey, M. D. & Mueller, J. P. Fecal contamination of agricultural soils before and after hurricane-associated flooding in North Carolina. J. Environ. Sci. Health A 41, 173–184 (2006).

CAS 

Google Scholar 

Wu, R., Trubl, G., Taş, N. & Jansson, J. K. Permafrost as a potential pathogen reservoir. One Earth 5, 351–360 (2022).

Google Scholar 

Trebicki, P. Climate change and plant virus epidemiology. Virus Res. 286, 198059 (2020).

CAS 
PubMed 

Google Scholar 

Whitfield, A. E., Falk, B. W. & Rotenberg, D. Insect vector-mediated transmission of plant viruses. Virology 479, 278–289 (2015).

PubMed 

Google Scholar 

Velásquez, A. C., Castroverde, C. D. M. & He, S. Y. Plant–pathogen warfare under changing climate conditions. Curr. Biol. 28, R619–R634 (2018).

PubMed 
PubMed Central 

Google Scholar 

Prasch, C. M. & Sonnewald, U. Simultaneous application of heat, drought, and virus to Arabidopsis plants reveals significant shifts in signaling networks. Plant Physiol. 162, 1849–1866 (2013).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Sutela, S., Poimala, A. & Vainio, E. J. Viruses of fungi and oomycetes in the soil environment. FEMS Microbiol. Ecol. 95, fiz119 (2019).

CAS 
PubMed 

Google Scholar 

Wang, L. et al. Evidence for a novel negative-stranded RNA mycovirus isolated from the plant pathogenic fungus Fusarium graminearum. Virology 518, 232–240 (2018).

CAS 
PubMed 

Google Scholar 

Abdoulaye, A. H., Foda, M. F. & Kotta-Loizou, I. Viruses infecting the plant pathogenic fungus Rhizoctonia solani. Viruses 11, 1113 (2019).

CAS 
PubMed Central 

Google Scholar 

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