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Vulnerability of soil food webs to chemical pollution and climate change

Abstract

Soil food webs are critical for maintaining ecosystem functions but are challenged by various stressors including climate change, habitat destruction and pollution. Although complex multitrophic networks can, in theory, buffer environmental stress, the effects of anthropogenic chemicals on soil food webs under climate change remain poorly understood. Here we propose that the effects of chemical pollution on soil communities have been largely underestimated, particularly for climate change-affected ecosystems. We explore the interactive effects of environmental stressors on soil food webs and the importance of integrating chemical pollution impacts into assessing soil food web stability. We also discuss a conceptual framework involving microbiome manipulation, community compensatory dynamics and interaction modulation to mitigate the combined effects of chemical pollution and climate change on soil food webs.

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Fig. 1: Adverse effects of chemical pollution on soil biota and the food web.
Fig. 2: Combined effects of chemical pollution and climate change on soil communities, food webs and ecosystem functions.
Fig. 3: Strategies for regulating soil multifunctionality and ecosystem services.

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References

  1. Petters, S. et al. The soil microbial food web revisited: predatory myxobacteria as keystone taxa? ISME J. 15, 2665–2675 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Scheu, S. The soil food web: structure and perspectives. Eur. J. Soil Biol. 38, 11–20 (2002).

    Article  Google Scholar 

  3. Sigmund, G. et al. Addressing chemical pollution in biodiversity research. Glob. Change Biol. 29, 3240–3255 (2023).

    Article  CAS  Google Scholar 

  4. Thakur, M. P. et al. Towards an integrative understanding of soil biodiversity. Biol. Rev. 95, 350–364 (2020).

    Article  PubMed  Google Scholar 

  5. van der Putten, W. H. et al. Soil biodiversity needs policy without borders. Science 379, 32–34 (2023).

    Article  PubMed  Google Scholar 

  6. Groh, K., Vom Berg, C., Schirmer, K. & Tlili, A. Anthropogenic chemicals as underestimated drivers of biodiversity loss: scientific and societal implications. Environ. Sci. Technol. 56, 707–710 (2022).

    Article  CAS  PubMed  Google Scholar 

  7. Sylvester, F. et al. Better integration of chemical pollution research will further our understanding of biodiversity loss. Nat. Ecol. Evol. 7, 1552–1555 (2023).

    Article  PubMed  Google Scholar 

  8. International Network on Soil Pollution (INSOP). fao.org https://www.fao.org/global-soil-partnership/global-soil-partnershipinsopen/en/ (2022).

  9. Wang, F. et al. Emerging contaminants: a one health perspective. Innovation 5, 100612 (2024).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Wang, Z., Walker, G. W., Muir, D. C. & Nagatani-Yoshida, K. Toward a global understanding of chemical pollution: a first comprehensive analysis of national and regional chemical inventories. Environ. Sci. Technol. 54, 2575–2584 (2020).

    Article  CAS  PubMed  Google Scholar 

  11. Bernhardt, E. S., Rosi, E. J. & Gessner, M. O. Synthetic chemicals as agents of global change. Front. Ecol. Environ. 15, 84–90 (2017).

    Article  Google Scholar 

  12. Liu, Y.-R. et al. Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide. Nat. Commun. 14, 1706 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. UNEP Global Assessment of Soil Pollution: Summary for Policymakers (FAO, 2021).

  14. Zero pollution action plan. European Commission https://environment.ec.europa.eu/strategy/zero-pollution-action-plan_en (2021).

  15. EU Biodiversity Strategy for 2030–Bringing Nature Back Into Our Lives (Publications Office of the European Union, 2021).

  16. Li, Y., Wang, X. & Sun, Z. Ecotoxicological effects of petroleum-contaminated soil on the earthworm Eisenia fetida. J. Hazard. Mater. 393, 122384 (2020).

    Article  CAS  PubMed  Google Scholar 

  17. Liu, Y.-R., Delgado-Baquerizo, M., Bi, L., Zhu, J. & He, J.-Z. Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China. Microbiome 6, 183 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  18. Wang, Y., Slotsbo, S., Damgaard, C. F. & Holmstrup, M. Influence of soil moisture on bioaccumulation, growth, and recruitment of Folsomia candida exposed to phenanthrene-polluted soil. Environ. Sci. Technol. 57, 3085–3094 (2023).

    Article  CAS  PubMed  Google Scholar 

  19. Kelly, B. C., Ikonomou, M. G., Blair, J. D., Morin, A. E. & Gobas, F. A. Food web specific biomagnification of persistent organic pollutants. Science 317, 236–239 (2007).

    Article  CAS  PubMed  Google Scholar 

  20. Sánchez-Bayo, F. Impacts of agricultural pesticides on terrestrial ecosystems. Ecol. Impacts Toxic Chem. 2011, 63–87 (2011).

    Google Scholar 

  21. Tison, L., Beaumelle, L., Monceau, K. & Thiéry, D. Transfer and bioaccumulation of pesticides in terrestrial arthropods and food webs: state of knowledge and perspectives for future research. Chemosphere 357, 142036 (2024).

    Article  CAS  PubMed  Google Scholar 

  22. Sánchez-Bayo, F., Ward, R. & Beasley, H. A new technique to measure bird’s dietary exposure to pesticides. Anal. Chim. Acta 399, 173–183 (1999).

    Article  Google Scholar 

  23. Yamamuro, M. et al. Neonicotinoids disrupt aquatic food webs and decrease fishery yields. Science 366, 620–623 (2019).

    Article  CAS  PubMed  Google Scholar 

  24. Roodt, A. P., Huszarik, M., Entling, M. H. & Schulz, R. Aquatic-terrestrial transfer of neonicotinoid insecticides in riparian food webs. J. Hazard. Mater. 455, 131635 (2023).

    Article  CAS  PubMed  Google Scholar 

  25. Douglas, M. R., Rohr, J. R. & Tooker, J. F. EDITOR’S CHOICE: neonicotinoid insecticide travels through a soil food chain, disrupting biological control of non‐target pests and decreasing soya bean yield. J. Appl. Ecol. 52, 250–260 (2015).

    Article  Google Scholar 

  26. Ni, B., Lin, D., Cai, T., Du, S. & Zhu, D. Soil plastisphere reinforces the adverse effect of combined pollutant exposure on the microfood web. Environ. Sci. Technol. 58, 21641–21652 (2024).

    Article  CAS  PubMed  Google Scholar 

  27. Wang, X. et al. Heavy metal contamination collapses trophic interactions in the soil microbial food web via bottom-up regulation. Soil Biol. Biochem. 184, 109058 (2023).

    Article  CAS  Google Scholar 

  28. Zhu, D., Ding, J., Wang, Y.-F. & Zhu, Y.-G. Effects of trophic level and land use on the variation of animal antibiotic resistome in the soil food web. Environ. Sci. Technol. 56, 14937–14947 (2022).

    Article  CAS  PubMed  Google Scholar 

  29. Liu, M., Wang, C. & Zhu, B. Drought alleviates the negative effects of microplastics on soil micro-food web complexity and stability. Environ. Sci. Technol. 57, 11206–11217 (2023).

    Article  CAS  PubMed  Google Scholar 

  30. Thakur, M. P. & Geisen, S. Trophic regulations of the soil microbiome. Trends Microbiol. 27, 771–780 (2019).

    Article  CAS  PubMed  Google Scholar 

  31. Wu, C., Chao, Y., Shu, L. & Qiu, R. Interactions between soil protists and pollutants: an unsolved puzzle. J. Hazard. Mater. 429, 128297 (2022).

    Article  CAS  PubMed  Google Scholar 

  32. Du, S. et al. Stronger responses of soil protistan communities to legacy mercury pollution than bacterial and fungal communities in agricultural systems. ISME Commun. 2, 69 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  33. Soliman, M. M., Hesselberg, T., Mohamed, A. A. & Renault, D. Trophic transfer of heavy metals along a pollution gradient in a terrestrial agro-industrial food web. Geoderma 413, 115748 (2022).

    Article  CAS  Google Scholar 

  34. Potts, L. D. et al. Chronic environmental perturbation influences microbial community assembly patterns. Environ. Sci. Technol. 56, 2300–2311 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Liu, J. et al. Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities. Environ. Sci. Technol. 49, 6438–6447 (2015).

    Article  CAS  PubMed  Google Scholar 

  36. Beauchesne, D., Cazelles, K., Archambault, P., Dee, L. E. & Gravel, D. On the sensitivity of food webs to multiple stressors. Ecol. Lett. 24, 2219–2237 (2021).

    Article  PubMed  Google Scholar 

  37. Rillig, M. C. et al. Increasing the number of stressors reduces soil ecosystem services worldwide. Nat. Clim. Change 13, 478–483 (2023).

    Article  Google Scholar 

  38. Zhu, X. et al. Substantial halogenated organic chemicals stored in permafrost soils on the Tibetan Plateau. Nat. Geosci. 16, 989–996 (2023).

    Article  CAS  Google Scholar 

  39. Noyes, P. D. et al. The toxicology of climate change: environmental contaminants in a warming world. Environ. Int. 35, 971–986 (2009).

    Article  CAS  PubMed  Google Scholar 

  40. Peng, Z. et al. Agricultural subsoil microbiomes and functions exhibit lower resistance to global change than topsoils in Chinese agroecosystems. Nat. Food 6, 375–388 (2025).

    Article  PubMed  Google Scholar 

  41. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Jackson, M. C., Pawar, S. & Woodward, G. The temporal dynamics of multiple stressor effects: from individuals to ecosystems. Trends Ecol. Evol. 36, 402–410 (2021).

    Article  PubMed  Google Scholar 

  43. Merz, E. et al. Disruption of ecological networks in lakes by climate change and nutrient fluctuations. Nat. Clim. Change 13, 389–396 (2023).

    Article  Google Scholar 

  44. Lau, J. A. & Lennon, J. T. Rapid responses of soil microorganisms improve plant fitness in novel environments. Proc. Natl Acad. Sci. USA 109, 14058–14062 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Valliere, J. M., Wong, W. S., Nevill, P. G., Zhong, H. & Dixon, K. W. Preparing for the worst: utilizing stress‐tolerant soil microbial communities to aid ecological restoration in the Anthropocene. Ecol. Solut. Evid. 1, e12027 (2020).

    Article  Google Scholar 

  46. Andrade‐Linares, D. R., Lehmann, A. & Rillig, M. C. Microbial stress priming: a meta‐analysis. Environ. Microbiol. 18, 1277–1288 (2016).

    Article  PubMed  Google Scholar 

  47. Hawkes, C. V. & Keitt, T. H. Resilience vs. historical contingency in microbial responses to environmental change. Ecol. Lett. 18, 612–625 (2015).

    Article  PubMed  Google Scholar 

  48. Arias-Sánchez, F. I., Vessman, B., Haym, A., Alberti, G. & Mitri, S. Artificial selection improves pollutant degradation by bacterial communities. Nat. Commun. 15, 7836 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  49. Liu, C. et al. Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils. Nat. Food 4, 912–924 (2023).

    Article  CAS  PubMed  Google Scholar 

  50. Ruan, Z. et al. Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling. Nat. Commun. 15, 4694 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Großkopf, T. & Soyer, O. S. Synthetic microbial communities. Curr. Opin. Microbiol. 18, 72–77 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  52. Jansson, J. K., McClure, R. & Egbert, R. G. Soil microbiome engineering for sustainability in a changing environment. Nat. Biotechnol. 41, 1716–1728 (2023).

    Article  CAS  PubMed  Google Scholar 

  53. Mueller, U. G. & Sachs, J. L. Engineering microbiomes to improve plant and animal health. Trends Microbiol. 23, 606–617 (2015).

    Article  CAS  PubMed  Google Scholar 

  54. Berg, S. et al. Effects of commercial microbial biostimulants on soil and root microbial communities and sugarcane yield. Biol. Fertil. Soils 56, 565–580 (2020).

    Article  CAS  Google Scholar 

  55. Wong, W. S. et al. Limited efficacy of a commercial microbial inoculant for improving growth and physiological performance of native plant species. Conserv. Physiol. 12, coae037 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Connell, S. D. & Ghedini, G. Resisting regime-shifts: the stabilising effect of compensatory processes. Trends Ecol. Evol. 30, 513–515 (2015).

    Article  PubMed  Google Scholar 

  57. Gonzalez, A. & Loreau, M. The causes and consequences of compensatory dynamics in ecological communities. Annu Rev. Ecol. Evol. Syst. 40, 393–414 (2009).

    Article  Google Scholar 

  58. Hamilton, C. D., Kovacs, K. M., Ims, R. A., Aars, J. & Lydersen, C. An Arctic predator–prey system in flux: climate change impacts on coastal space use by polar bears and ringed seals. J. Anim. Ecol. 86, 1054–1064 (2017).

    Article  PubMed  Google Scholar 

  59. Myers, R. A. & Worm, B. Rapid worldwide depletion of predatory fish communities. Nature 423, 280–283 (2003).

    Article  CAS  PubMed  Google Scholar 

  60. Sahasrabudhe, S. & Motter, A. E. Rescuing ecosystems from extinction cascades through compensatory perturbations. Nat. Commun. 2, 170 (2011).

    Article  PubMed  Google Scholar 

  61. Schwarz, B. et al. Warming alters energetic structure and function but not resilience of soil food webs. Nat. Clim. Change 7, 895–900 (2017).

    Article  Google Scholar 

  62. Nielsen, U. N., Wall, D. H. & Six, J. Soil biodiversity and the environment. Annu. Rev. Environ. Resour. 40, 63–90 (2015).

    Article  Google Scholar 

  63. Ives, A. R., Gross, K. & Klug, J. L. Stability and variability in competitive communities. Science 286, 542–544 (1999).

    Article  CAS  PubMed  Google Scholar 

  64. Vasseur, D. A. & Fox, J. W. Environmental fluctuations can stabilize food web dynamics by increasing synchrony. Ecol. Lett. 10, 1066–1074 (2007).

    Article  PubMed  Google Scholar 

  65. Norberg, J. et al. Phenotypic diversity and ecosystem functioning in changing environments: a theoretical framework. Proc. Natl Acad. Sci. USA 98, 11376–11381 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Bartley, T. J. et al. Food web rewiring in a changing world. Nat. Ecol. Evol. 3, 345–354 (2019).

    Article  PubMed  Google Scholar 

  67. Lu, X. et al. Drought rewires the cores of food webs. Nat. Clim. Change 6, 875–878 (2016).

    Article  Google Scholar 

  68. Li, Z. P. et al. Colonization ability and uniformity of resources and environmental factors determine biological homogenization of soil protists in human land-use systems. Glob. Change Biol. 30, e17411 (2024).

    Article  CAS  Google Scholar 

  69. Tian, Y. et al. Stover management affects soil food webs and regulates the decomposition pathway in a maize field.Agric. Ecosyst. Environ. 376, 109229 (2024).

    Article  Google Scholar 

  70. Yin, R. et al. Nitrogen deposition stimulates decomposition via changes in the structure and function of litter food webs. Soil Biol. Biochem. 166, 108522 (2022).

    Article  CAS  Google Scholar 

  71. Rosenblatt, A. E. & Schmitz, O. J. Climate change, nutrition, and bottom-up and top-down food web processes. Trends Ecol. Evol. 31, 965–975 (2016).

    Article  PubMed  Google Scholar 

  72. DeAngelis, K. M. Chemical communication connects soil food webs. Soil Biol. Biochem. 102, 48–51 (2016).

    Article  CAS  Google Scholar 

  73. Matz, C. & Kjelleberg, S. Off the hook–how bacteria survive protozoan grazing. Trends Microbiol. 13, 302–307 (2005).

    Article  CAS  PubMed  Google Scholar 

  74. DeAngelis, K. M. Rhizosphere microbial communication in soil nutrient acquisition. Mol. Microb. Ecol. Rhizosphere 1, 823–832 (2013).

    Article  Google Scholar 

  75. Hsueh, Y.-P., Mahanti, P., Schroeder, F. C. & Sternberg, P. W. Nematode-trapping fungi eavesdrop on nematode pheromones. Curr. Biol. 23, 83–86 (2013).

    Article  CAS  PubMed  Google Scholar 

  76. de Rooij, M. F. et al. A loss-of-adhesion CRISPR-Cas9 screening platform to identify cell adhesion-regulatory proteins and signaling pathways. Nat. Commun. 13, 2136 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  77. Sharpee, W. C. & Dean, R. A. Form and function of fungal and oomycete effectors. Fungal Biol. Rev. 30, 62–73 (2016).

    Article  Google Scholar 

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Acknowledgements

This research is supported by the National Natural Science Foundation of China (42425701) and the Fundamental Research Funds for the Central Universities (2662025PY010). M.D.-B. acknowledges support from the Spanish Ministry of Science and Innovation for the I+D+i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. B.K.S.ʼs work on soil communities is supported by Australian Research Council (DP230101448).

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Y.-R.L., S.W. and Y.-G.Z. led the conceptualization and writing of the paper. B.K.S., X.H., Y.-Y.H., M.D.-B., W.T., Q.H., M.C.R. and Y.-G.Z. revised the paper. S.W., W.Z. and Z.L. illustrated the figures. All authors reviewed the paper and approved the final version of the manuscript.

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Correspondence to Yu-Rong Liu or Yong-Guan Zhu.

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Nature Ecology & Evolution thanks Mark Tibbett and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Liu, YR., Wen, S., Singh, B.K. et al. Vulnerability of soil food webs to chemical pollution and climate change. Nat Ecol Evol (2025). https://doi.org/10.1038/s41559-025-02736-1

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