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 

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