Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Defending Earth’s terrestrial microbiome

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.

This is a preview of subscription content, access via your institution

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

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).

References

  1. Mora, C., Tittensor, D. P., Adl, S., Simpson, A. G. B. & Worm, B. How many species are there on earth and in the ocean? PLoS Biol. 9, e1001127 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Costello, M. J., May, R. M. & Stork, N. E. Can we name earth’s species before they go extinct? Science 339, 413–416 (2013).

    Article  CAS  PubMed  Google Scholar 

  3. Corlett, R. T. Plant diversity in a changing world: status, trends, and conservation needs. Plant Divers. 38, 10–16 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Baldrian, P., Větrovský, T., Lepinay, C. & Kohout, P. High-throughput sequencing view on the magnitude of global fungal diversity. Fungal Divers. 114, 539–547 (2022).

    Article  CAS  Google Scholar 

  5. Taylor, D. L. et al. A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning. Ecol. Monogr. 84, 3–20 (2014).

    Article  Google Scholar 

  6. Locey, K. J. & Lennon, J. T. Scaling laws predict global microbial diversity. Proc. Natl Acad. Sci. USA 113, 5970–5975 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Schopf, J. W. Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic. Proc. Natl Acad. Sci. USA 91, 6735–6742 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Seager, S., Huang, J., Petkowski, J. J. & Pajusalu, M. Laboratory studies on the viability of life in H2-dominated exoplanet atmospheres. Nat. Astron. 4, 802–806 (2020).

    Article  Google Scholar 

  9. Halme, P., Holec, J. & Heilmann-Clausen, J. The history and future of fungi as biodiversity surrogates in forests. Fungal Ecol. 27, 193–201 (2017).

    Article  Google Scholar 

  10. Arnolds, E. Decline of ectomycorrhizal fungi in Europe. Agric. Ecosyst. Environ. 35, 209–244 (1991).

    Article  Google Scholar 

  11. Boddy, L. in The Fungi (eds Watkinson, S. C. et al.) 361–400 (Elsevier, 2016); https://doi.org/10.1016/B978-0-12-382034-1.00011-6

  12. Zimmerman, M. The mushroom message. Sun 11A (1992).

  13. Bader, P., Jansson, S. & Jonsson, B. G. Wood-inhabiting fungi and substratum decline in selectively logged boreal spruce forests. Biol. Conserv. 72, 355–362 (1995).

    Article  Google Scholar 

  14. Weinbauer, M. G. & Rassoulzadegan, F. Extinction of microbes: evidence and potential consequences. Endanger. Species Res. 3, 205–215 (2007).

    Article  Google Scholar 

  15. Chomicki, G., Kiers, E. T. & Renner, S. S. The evolution of mutualistic dependence. Annu. Rev. Ecol. Evol. Syst. 51, 409–432 (2020).

    Article  Google Scholar 

  16. Blaser, M. J. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol. 17, 461–463 (2017).

    Article  CAS  PubMed  Google Scholar 

  17. Carthey, A. J., Blumstein, D. T., Gallagher, R. V., Tetu, S. G. & Gillings, M. R. Conserving the holobiont. Funct. Ecol. 34, 764–776 (2020).

    Article  Google Scholar 

  18. Schapheer, C., Pellens, R. & Scherson, R. Arthropod-microbiota integration: its importance for ecosystem conservation. Front. Microbiol. 12, 2094 (2021).

    Article  Google Scholar 

  19. Zhou, Z., Wang, C. & Luo, Y. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat. Commun. 11, 3072 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Anthony, M. A., Stinson, K. A., Moore, J. A. M. & Frey, S. D. Plant invasion impacts on fungal community structure and function depend on soil warming and nitrogen enrichment. Oecologia 194, 659–672 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Lilleskov, E., Hobbie, E. A. & Horton, T. Conservation of ectomycorrhizal fungi: exploring the linkages between functional and taxonomic responses to anthropogenic N deposition. Fungal Ecol. 4, 174–183 (2011).

    Article  Google Scholar 

  22. Gibbons, S. M. et al. Invasive plants rapidly reshape soil properties in a grassland ecosystem. mSystems 2, e00178-16 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Rillig, M. C. et al. The role of multiple global change factors in driving soil functions and microbial biodiversity. Science 366, 886–890 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Certini, G., Moya, D., Lucas-Borja, M. E. & Mastrolonardo, G. The impact of fire on soil-dwelling biota: a review. For. Ecol. Manage. 488, 118989 (2021).

    Article  Google Scholar 

  25. Caruso, T., Hempel, S., Powell, J. R., Barto, E. K. & Rillig, M. C. Compositional divergence and convergence in arbuscular mycorrhizal fungal communities. Ecology 93, 1115–1124 (2012).

    Article  CAS  PubMed  Google Scholar 

  26. Anthony, M., Frey, S. & Stinson, K. Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion. Ecosphere 8, e01951 (2017).

    Article  Google Scholar 

  27. Guerra, C. A. et al. Global projections of the soil microbiome in the Anthropocene. Glob. Ecol. Biogeogr. 30, 987–999 (2021).

    Article  PubMed  Google Scholar 

  28. Enright, D. J., Frangioso, K. M., Isobe, K., Rizzo, D. M. & Glassman, S. I. Mega‐fire in redwood tanoak forest reduces bacterial and fungal richness and selects for pyrophilous taxa that are phylogenetically conserved. Mol. Ecol. 31, 2475–2493 (2022).

    Article  CAS  PubMed  Google Scholar 

  29. Anthony, M. A. et al. Forest tree growth is linked to mycorrhizal fungal composition and function across Europe. ISME J. 16, 1327–1336 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Crowther, T. W. et al. The global soil community and its influence on biogeochemistry. Science 365, eaav0550 (2019).

    Article  CAS  PubMed  Google Scholar 

  31. Ceballos, G. et al. Accelerated modern human–induced species losses: entering the sixth mass extinction. Sci. Adv. 1, e1400253 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Novacek, M. J. & Cleland, E. E. The current biodiversity extinction event: scenarios for mitigation and recovery. Proc. Natl Acad. Sci. USA 98, 5466–5470 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Guerra, C. A. et al. Tracking, targeting, and conserving soil biodiversity. Science 371, 239–241 (2021).

    Article  CAS  PubMed  Google Scholar 

  34. Guerra, C. A. et al. Blind spots in global soil biodiversity and ecosystem function research. Nat. Commun. 11, 3870 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Cameron, E. K. et al. Global mismatches in aboveground and belowground biodiversity. Conserv. Biol. 33, 1187–1192 (2019).

    Article  PubMed  Google Scholar 

  36. Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).

    Article  PubMed  Google Scholar 

  37. Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).

    Article  CAS  PubMed  Google Scholar 

  38. Delgado-Baquerizo, M. et al. A global atlas of the dominant bacteria found in soil. Science 359, 320–325 (2018).

    Article  CAS  PubMed  Google Scholar 

  39. Peixoto, R. S. et al. Harnessing the microbiome to prevent global biodiversity loss. Nat. Microbiol. https://doi.org/10.1038/s41564-022-01173-1 (2022).

  40. Box, G. E. P. & Draper, N. R. Empirical Model-building and Response Surfaces (Wiley, 1987).

  41. Box, G. E. P., Hunter, W. G. & Hunter, J. S. Statistics for Experimenters: an Introduction to Design, Data Analysis, and Model Building (Wiley, 1978).

  42. Kothamasi, D., Spurlock, M. & Kiers, E. T. Agricultural microbial resources: private property or global commons? Nat. Biotechnol. 29, 1091–1093 (2011).

    Article  CAS  PubMed  Google Scholar 

  43. Davison, J. et al. Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science 349, 970–973 (2015).

    Article  CAS  PubMed  Google Scholar 

  44. van der Linde, S. et al. Environment and host as large-scale controls of ectomycorrhizal fungi. Nature 558, 243–248 (2018).

    Article  PubMed  Google Scholar 

  45. Davison, J. et al. Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi. New Phytol. 231, 763–776 (2021).

    Article  CAS  PubMed  Google Scholar 

  46. Ramirez, K. S. et al. Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nat. Microbiol. 3, 189–196 (2018).

    Article  CAS  PubMed  Google Scholar 

  47. Wild, S. Quest to map Africa’s soil microbiome begins. Nature 539, 152 (2016).

    Article  CAS  PubMed  Google Scholar 

  48. Bissett, A. et al. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. GigaScience 5, 21 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  49. Pan, K., Guo, Z. & Liu, J. Building and materializing of China Soil Microbiome Data Platform. Acta Pedol. Sin. 56, 1023–1033 (2019).

    Google Scholar 

  50. Orgiazzi, A., Ballabio, C., Panagos, P., Jones, A. & Fernández‐Ugalde, O. LUCAS Soil, the largest expandable soil dataset for Europe: a review. Eur. J. Soil Sci. 69, 140–153 (2018).

    Article  Google Scholar 

  51. Hinckley, E. S. et al. The soil and plant biogeochemistry sampling design for The National Ecological Observatory Network. Ecosphere 7, e01234 (2016).

    Article  Google Scholar 

  52. Větrovský, T. et al. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci. Data 7, 228 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Jackson, F. Sustainable agriculture and a low carbon future: are we missing out on mycelium? Forbes https://www.forbes.com/sites/feliciajackson/2021/12/02/sustainable-agriculture-and-a-low-carbon-future-are-we-missing-out-on-mycelium/?sh=3dc1a6d076ed (2021).

  54. Gilbert, J. A., Jansson, J. K. & Knight, R. The Earth Microbiome project: successes and aspirations. BMC Biol. 12, 69 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  55. Fedrowitz, K. et al. Can retention forestry help conserve biodiversity? A meta‐analysis. J. Appl. Ecol. 51, 1669–1679 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  56. Schmidt, R., Mitchell, J. & Scow, K. Cover cropping and no-till increase diversity and symbiotroph:saprotroph ratios of soil fungal communities. Soil Biol. Biochem. 129, 99–109 (2019).

    Article  CAS  Google Scholar 

  57. Status of the World’s Soil Resources: Main Report (FAO, 2015).

  58. Aronson, J., Goodwin, N., Orlando, L., Eisenberg, C. & Cross, A. T. A world of possibilities: six restoration strategies to support the United Nation’s Decade on Ecosystem Restoration. Restor. Ecol. 28, 730–736 (2020).

    Article  Google Scholar 

  59. Seymour, F. Seeing the forests as well as the (trillion) trees in corporate climate strategies. One Earth 2, 390–393 (2020).

    Article  Google Scholar 

  60. Dinerstein, E. et al. A global deal for nature: guiding principles, milestones, and targets. Sci. Adv. 5, eaaw2869 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Philipson, C. D. et al. Active restoration accelerates the carbon recovery of human-modified tropical forests. Science 369, 838–841 (2020).

    Article  CAS  PubMed  Google Scholar 

  62. Coleman, E. A. et al. Limited effects of tree planting on forest canopy cover and rural livelihoods in Northern India. Nat. Sustain. 4, 997–1004 (2021).

    Article  Google Scholar 

  63. Neuenkamp, L., Prober, S. M., Price, J. N., Zobel, M. & Standish, R. J. Benefits of mycorrhizal inoculation to ecological restoration depend on plant functional type, restoration context and time. Fungal Ecol. 40, 140–149 (2019).

    Article  Google Scholar 

  64. Koziol, L. et al. Manipulating plant microbiomes in the field: native mycorrhizae advance plant succession and improve native plant restoration. J. Appl. Ecol. https://doi.org/10.1111/1365-2664.14036 (2021).

  65. Wubs, E. R. J., van der Putten, W. H., Bosch, M. & Bezemer, T. M. Soil inoculation steers restoration of terrestrial ecosystems. Nat. Plants 2, 16107 (2016).

    Article  PubMed  Google Scholar 

  66. Bever, J. & Schultz, P. Prairie mycorrhizal fungi inoculant may increase native plant diversity on restored sites (Illinois). Ecol. Restor. 21, 311–312 (2003).

    Google Scholar 

  67. Vahter, T. et al. Co-introduction of native mycorrhizal fungi and plant seeds accelerates restoration of post-mining landscapes. J. Appl. Ecol. 57, 1741–1751 (2020).

    Article  CAS  Google Scholar 

  68. Egan, C. P. et al. Restoration of the mycobiome of the endangered Hawaiian mint Phyllostegia kaalaensis increases its resistance to a common powdery mildew. Fungal Ecol. 52, 101070 (2021).

    Article  Google Scholar 

  69. Wubs, E. R. J. et al. Single introductions of soil biota and plants generate long‐term legacies in soil and plant community assembly. Ecol. Lett. 22, 1145–1151 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  70. Abrego, N. et al. Reintroduction of threatened fungal species via inoculation. Biol. Conserv. 203, 120–124 (2016).

    Article  Google Scholar 

  71. Salomon, M. J. et al. Global evaluation of commercial arbuscular mycorrhizal inoculants under greenhouse and field conditions. Appl. Soil Ecol. 169, 104225 (2022).

    Article  Google Scholar 

  72. Maltz, M. R. & Treseder, K. K. Sources of inocula influence mycorrhizal colonization of plants in restoration projects: a meta-analysis: mycorrhizal inoculation in restoration. Restor. Ecol. 23, 625–634 (2015).

    Article  Google Scholar 

  73. Busby, P. E., Newcombe, G., Neat, A. S. & Averill, C. Facilitating reforestation through the plant microbiome: perspectives from the phyllosphere. Annu. Rev. Phytopathol. https://doi.org/10.1146/annurev-phyto-021320-010717 (2022).

  74. van der Heijden, M. G. A., Martin, F. M., Selosse, M.-A. & Sanders, I. R. Mycorrhizal ecology and evolution: the past, the present, and the future. New Phytol. 205, 1406–1423 (2015).

    Article  PubMed  Google Scholar 

  75. Crowther, T. W. et al. Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study. Glob. Change Biol. 20, 2983–2994 (2014).

    Article  Google Scholar 

  76. Lilleskov, E. A., Kuyper, T. W., Bidartondo, M. I. & Hobbie, E. A. Atmospheric nitrogen deposition impacts on the structure and function of forest mycorrhizal communities: a review. Environ. Pollut. 246, 148–162 (2019).

    Article  CAS  PubMed  Google Scholar 

  77. Smith, G. R., Steidinger, B. S., Bruns, T. D. & Peay, K. G. Competition–colonization tradeoffs structure fungal diversity. ISME J. 12, 1758–1767 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Ceballos, I. et al. The in vitro mass-produced model mycorrhizal fungus, Rhizophagus irregularis, significantly increases yields of the globally important food security crop cassava. PLoS ONE 8, e70633 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Buysens, C., César, V., Ferrais, F., de Boulois, H. D. & Declerck, S. Inoculation of Medicago sativa cover crop with Rhizophagus irregularis and Trichoderma harzianum increases the yield of subsequently-grown potato under low nutrient conditions. Appl. Soil Ecol. 105, 137–143 (2016).

    Article  Google Scholar 

  80. Antunes, P. M. et al. Influence of commercial inoculation with Glomus intraradices on the structure and functioning of an AM fungal community from an agricultural site. Plant Soil 317, 257–266 (2009).

    Article  CAS  Google Scholar 

  81. Emam, T. Local soil, but not commercial AMF inoculum, increases native and non‐native grass growth at a mine restoration site. Restor. Ecol. 24, 35–44 (2016).

    Article  Google Scholar 

  82. Hoeksema, J. D. et al. A meta-analysis of context-dependency in plant response to inoculation with mycorrhizal fungi. Ecol. Lett. 13, 394–407 (2010).

    Article  PubMed  Google Scholar 

  83. Policelli, N., Horton, T. R., Hudon, A. T., Patterson, T. R. & Bhatnagar, J. M. Back to roots: the role of ectomycorrhizal fungi in boreal and temperate forest restoration. Front. For. Glob. Change 3, 97 (2020).

    Article  Google Scholar 

  84. Hoeksema, J. D. et al. Ectomycorrhizal plant-fungal co-invasions as natural experiments for connecting plant and fungal traits to their ecosystem consequences. Front. Glob. Change 3, 84 (2020).

    Article  Google Scholar 

  85. Land Use Statistics and Indicators. Global, Regional and Country Trends 1990– 2019 FAOSTAT Analytical Brief Series No. 28 (FAO, 2021).

  86. Stewart, W. M., Dibb, D. W., Johnston, A. E. & Smyth, T. J. The contribution of commercial fertilizer nutrients to food production. Agron. J. 97, 1–6 (2005).

    Article  Google Scholar 

  87. Harlander, S. K. The evolution of modern agriculture and its future with biotechnology. J. Am. Coll. Nutr. 21, 161S–165S (2002).

    Article  PubMed  Google Scholar 

  88. Cooper, J. & Dobson, H. The benefits of pesticides to mankind and the environment. Crop Prot. 26, 1337–1348 (2007).

    Article  CAS  Google Scholar 

  89. Zsögön, A., Peres, L. E. P., Xiao, Y., Yan, J. & Fernie, A. R. Enhancing crop diversity for food security in the face of climate uncertainty. Plant J. https://doi.org/10.1111/tpj.15626 (2021).

  90. IPCC Climate Change 2013: The Physical Science Basis (eds Stocker, T. F. et al.) (Cambridge Univ. Press, 2013).

  91. McDonald, B. A. & Stukenbrock, E. H. Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security. Phil. Trans. R. Soc. Lond. B 371, 20160026 (2016).

    Article  Google Scholar 

  92. Avelino, J. et al. The coffee rust crises in Colombia and Central America (2008–2013): impacts, plausible causes and proposed solutions. Food Sec. 7, 303–321 (2015).

    Article  Google Scholar 

  93. Goss, E. M. et al. The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes. Proc. Natl Acad. Sci. USA 111, 8791–8796 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Ploetz, R. C. Panama disease: a classic and destructive disease of banana. Plant Health Prog. https://doi.org/10.1094/PHP-2000-1204-01-HM (2000).

  95. Craven, D. et al. Multiple facets of biodiversity drive the diversity–stability relationship. Nat. Ecol. Evol. 2, 1579–1587 (2018).

    Article  PubMed  Google Scholar 

  96. Thibaut, L. M. & Connolly, S. R. Understanding diversity–stability relationships: towards a unified model of portfolio effects. Ecol. Lett. 16, 140–150 (2013).

    Article  PubMed  Google Scholar 

  97. Isbell, F. et al. Biodiversity increases the resistance of ecosystem productivity to climate extremes. Nature 526, 574–577 (2015).

    Article  CAS  PubMed  Google Scholar 

  98. Prieto, I. et al. Complementary effects of species and genetic diversity on productivity and stability of sown grasslands. Nat. Plants 1, 15033 (2015).

    Article  CAS  PubMed  Google Scholar 

  99. Liang, J. et al. Positive biodiversity-productivity relationship predominant in global forests. Science 354, aaf8957 (2016).

    Article  PubMed  Google Scholar 

  100. Cornell, C. et al. Do bioinoculants affect resident microbial communities? A meta-analysis. Front. Agron. 3, 753474 (2021).

    Article  Google Scholar 

  101. Manning, L. Groundwork BioAg raises $11m to expand mycorrhizal inputs business. AgFunder Network https://agfundernews.com/groundwork-bioag-raises-11m-to-expand-mycorrhizal-inputs-business (2021).

  102. Egidi, E. et al. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat. Commun. 10, 2369 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  103. Olle, M. & Williams, I. H. Effective microorganisms and their influence on vegetable production—a review. J. Hortic. Sci. Biotechnol. 88, 380–386 (2013).

    Article  Google Scholar 

  104. Mayer, J., Scheid, S., Widmer, F., Fließbach, A. & Oberholzer, H.-R. How effective are ‘Effective microorganisms® (EM)’? Results from a field study in temperate climate. Appl. Soil Ecol. 46, 230–239 (2010).

    Article  Google Scholar 

  105. Kodippili, K. P. A. N. & Nimalan, J. Effect of homemade effective microorganisms on the growth and yield of chilli (Capsicum annuum) MI-2. AGRIEAST J. Agric. Sci. https://doi.org/10.4038/agrieast.v12i2.57 (2018).

  106. de Araujo Avila, G. M., Gabardo, G., Clock, D. C. & de Lima Junior, O. S. Use of efficient microorganisms in agriculture. Res. Soc. Dev. https://doi.org/10.33448/rsd-v10i8.17515 (2021).

  107. Saleem, M., Hu, J. & Jousset, A. More than the sum of its parts: microbiome biodiversity as a driver of plant growth and soil health. Annu. Rev. Ecol. Evol. Syst. 50, 145–168 (2019).

    Article  Google Scholar 

  108. Bradford, M. A. et al. Thermal adaptation of soil microbial respiration to elevated temperature. Ecol. Lett. 11, 1316–1327 (2008).

    Article  PubMed  Google Scholar 

  109. Romero-Olivares, A. L., Allison, S. D. & Treseder, K. K. Soil microbes and their response to experimental warming over time: a meta-analysis of field studies. Soil Biol. Biochem. 107, 32–40 (2017).

    Article  CAS  Google Scholar 

  110. Klironomos, J. N. Variation in plant response to native and exotic arbuscular mycorrhizal fungi. Ecology 84, 2292–2301 (2003).

    Article  Google Scholar 

  111. Veen, C. G. F., Snoek, B. L., Bakx-Schotman, T., Wardle, D. A. & van der Putten, W. H. Relationships between fungal community composition in decomposing leaf litter and home-field advantage effects. Funct. Ecol. 33, 1524–1535 (2019).

    Article  Google Scholar 

  112. Wang, Q., Zhong, M. & He, T. Home-field advantage of litter decomposition and nitrogen release in forest ecosystems. Biol. Fertil. Soils 49, 427–434 (2013).

    Article  CAS  Google Scholar 

  113. Hawkes, C. V., Waring, B. G., Rocca, J. D. & Kivlin, S. N. Historical climate controls soil respiration responses to current soil moisture. Proc. Natl Acad. Sci. USA 114, 6322–6327 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Morriën, E. et al. Soil networks become more connected and take up more carbon as nature restoration progresses. Nat. Commun. 8, 14349 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  115. Wagg, C., Bender, S. F., Widmer, F. & van der Heijden, M. G. A. Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proc. Natl Acad. Sci. USA 111, 5266–5270 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Wittebolle, L. et al. Initial community evenness favours functionality under selective stress. Nature 458, 623–626 (2009).

    Article  CAS  PubMed  Google Scholar 

  117. de Graaff, M.-A., Adkins, J., Kardol, P. & Throop, H. A meta-analysis of soil biodiversity impacts on the carbon cycle. Soil 1, 257–271 (2015).

    Article  Google Scholar 

  118. Gao, J. et al. Assessing the effect of leaf litter diversity on the decomposition and associated diversity of fungal assemblages. Forests 6, 2371–2386 (2015).

    Article  Google Scholar 

  119. Selosse, M.-A., Bouchard, D., Martin, F. & Tacon, F. L. Effect of Laccaria bicolor strains inoculated on Douglas-fir (Pseudotsuga menziesii) several years after nursery inoculation. Can. J. Res. 30, 360–371 (2000).

    Article  Google Scholar 

  120. Banerjee, S. et al. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. 13, 1722–1736 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

Authors

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.

Ethics declarations

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.

Peer review

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.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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.

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41564-022-01228-3

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing