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Integrating viruses into soil food web biogeochemistry

Nature Microbiology volume 9, pages 1918–1928 (2024)Cite this article

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Abstract

The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. We highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.

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Fig. 1: Inclusion of viruses in the soil microbial food web.
Fig. 2: Physicochemical conditions of soils.
Fig. 3: Viral–host interactions in soils.

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Acknowledgements

C.C. was supported by a research grant (36223) from Villum Fonden and by the Novo Nordisk Foundation (NNF21OC0072586) in the call ‘Conferences, Symposia and Workshops 2021–2’. C.L. received funding from the Independent Research Fund Denmark (grant number 1127-00033B). K.M.-J. acknowledges the Dutch Research Council for funding the Veni project VI.Veni.202.086. The work of G.T. was supported by a Lawrence Livermore National Laboratory (LLNL) Laboratory Directed Research and Development grant (21-LW-060) and by LLNL’s US Department of Energy, Office of Biological and Environmental Research Genomic Science Program “Microbes Persist” Scientific Focus Area (award SCW1632). Work at LLNL was conducted under the auspices of the US Department of Energy under contract DE-AC52-07NA27344. T.Z. was supported by a scholarship from the China Scholarship Council and University of Groningen scholarship programme. C.L.E. was funded by the Novo Nordisk Foundation (grant number NNF19SA0059360). R.S. and Z.B. were supported by the Novo Nordisk foundation (grant number NNF20OC0065183).

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Authors and Affiliations

  1. Department of Environmental Science, Aarhus University, Roskilde, Denmark

    Cátia Carreira, Zivile Buivydaite, Tingting Chen, Christine Lorenzen Elberg, Anne Winding & Rumakanta Sapkota

  2. Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal

    Cátia Carreira

  3. Department of Ecoscience, Aarhus University, Roskilde, Denmark

    Christian Lønborg

  4. Directorate of Agricultural Research, Nepal Agricultural Research Council, Khajura, Nepal

    Basistha Acharya

  5. Nepal Agricultural Research Council, National Wheat Research Program, Bhairahawa, Nepal

    Laxman Aryal

  6. Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany

    Felipe Borim Corrêa

  7. Department of Ecology, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China

    Tingting Chen

  8. Department of Plant Pathology, University of California, Davis, Davis, CA, USA

    Joanne B. Emerson & Luke Hillary

  9. National Plant Pathology Research Center, Nepal Agricultural Research Council, Lalitpur, Nepal

    Ram B. Khadka

  10. Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec City, Québec, Canada

    Valérie Langlois

  11. Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands

    Kyle Mason-Jones

  12. Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden

    Tarquin Netherway

  13. Natural Resources Institute Finland, Helsinki, Finland

    Suvi Sutela

  14. Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA

    Gareth Trubl

  15. Ature Nature, Wageningen, the Netherlands

    Arno wa Kang’eri

  16. Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, the Netherlands

    Ruiqi Wang

  17. Computational Intelligence to Predict Health and Environmental Risks, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA

    Richard Allen White III

  18. North Carolina Research Campus, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA

    Richard Allen White III

  19. Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands

    Tianci Zhao

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  1. Cátia Carreira
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Contributions

C.C. conceived of the idea and wrote the first draft of the manuscript. C.C., C.L. and K.M.-J. provided the calculations. C.L., B.A., L.A., Z.B., F.B.C., T.C., C.L.E., J.B.E., L.H., R.B.K., V.L., K.M.-J., T.N., S.S., G.T., A.w.K., R.W., R.A.W., A.W., T.Z. and R.S. read and corrected the manuscript. A.w.K. provided the figures.

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Correspondence to Cátia Carreira.

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Carreira, C., Lønborg, C., Acharya, B. et al. Integrating viruses into soil food web biogeochemistry. Nat Microbiol 9, 1918–1928 (2024). https://doi.org/10.1038/s41564-024-01767-x

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