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Defending Earth’s terrestrial microbiome

Nature Microbiology volume 7, pages 1717–1725 (2022)Cite this article

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Abstract

Microbial life represents the majority of Earth’s biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth’s microbial biodiversity is under threat. Here we advocate for the conservation and restoration of soil microbial life, as well as active incorporation of microbial biodiversity into managed food and forest landscapes, with an emphasis on soil fungi. We analyse 80 experiments to show that native soil microbiome restoration can accelerate plant biomass production by 64% on average, across ecosystems. Enormous potential also exists within managed landscapes, as agriculture and forestry are the dominant uses of land on Earth. Along with improving and stabilizing yields, enhancing microbial biodiversity in managed landscapes is a critical and underappreciated opportunity to build reservoirs, rather than deserts, of microbial life across our planet. As markets emerge to engineer the ecosystem microbiome, we can avert the mistakes of aboveground ecosystem management and avoid microbial monocultures of single high-performing microbial strains, which can exacerbate ecosystem vulnerability to pathogens and extreme events. Harnessing the planet’s breadth of microbial life has the potential to transform ecosystem management, but it requires that we understand how to monitor and conserve the Earth’s microbiome.

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Fig. 1: Three strategies to protect microbial life.
Fig. 2: A map of sampling priorities for the soil fungal microbiome.
Fig. 3: Response of plant biomass to inoculation with soil organisms from intact reference habitats relative to control (N = 81).

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Acknowledgements

C.A. was supported by Ambizione grant no. PZ00P3_17990 from the Swiss National Science Foundation. T.W.C. was supported by grants from DOB Ecology and the Bernina Foundation.

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Authors and Affiliations

  1. Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland

    Colin Averill, Mark A. Anthony, Felix Finkbeiner, Johan van den Hoogen, Eliane Hirt, Gabriel Reuben Smith & Tom W. Crowther

  2. Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic

    Petr Baldrian & Petr Kohout

  3. Department of Ecological Science, Vrije Universiteit, Amsterdam, the Netherlands

    Toby Kiers

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Contributions

C.A. and T.W.C. conceived the project. C.A., E.H., F.F. and G.R.S. conducted the meta-analysis. C.A. and J.v.d.H. performed all mapping analyses. C.A., M.A.A., P.B., P.K., F.F., J.v.d.H., T.K., E.H., G.R.S. and T.W.C. contributed to the writing and revising of the manuscript.

Corresponding author

Correspondence to Colin Averill.

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Competing interests

T.W.C. is the founder of Restor, a non-governmental organization that facilitates the global restoration movement. T.K. and C.A. are the founders of the Society for the Protection of Underground Networks, an organization that advocates for the protection of belowground network forming fungi. C.A. is the founder of Funga, an organization that facilitates the restoration of belowground fungal biodiversity.

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Peer review information

Nature Microbiology thanks David Relman, Brajesh Singh and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

A description of all methods used for analyses presented in the main text.

Supplementary Data 1

A table of all covariate layers and associated references used in creating the sampling uncertainty product.

Supplementary Data 2

All data used in the meta-analysis of plant biomass responses to soil microbiome restoration.

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Averill, C., Anthony, M.A., Baldrian, P. et al. Defending Earth’s terrestrial microbiome. Nat Microbiol 7, 1717–1725 (2022). https://doi.org/10.1038/s41564-022-01228-3

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