Abstract
Soil microbiomes underpin terrestrial ecosystem functioning and drive nutrient cycling, plant productivity and ecological resilience. However, diverse pollutants, ranging from heavy metals and pesticides to plastics, perfluoroalkyl and polyfluoroalkyl substances and nanomaterials, are reshaping microbial communities in ways that threaten soil health and broader ecological stability. Thus, soils are hotspots of microbial evolution under chemical mixtures. Pollution alters microbial diversity, composition and functional capacity through mechanisms such as direct toxicity, shifts in soil chemistry and selective evolutionary pressures. These disruptions impair nutrient cycling, destabilize plant–microorganism interactions and accelerate the spread of antimicrobial resistance, with cascading effects on food webs and human health under a One Health framework. At the same time, soil microbiomes can serve as indicators of ecosystem stress and as tools for bioremediation and ecological restoration. This Review synthesizes current understanding of terrestrial pollution–microbiome interactions, highlights functional and health implications, and explores how microbiome-informed approaches can guide sustainable soil management and environmental protection under global change, while identifying key knowledge gaps and outlining future research directions for predictive and integrative microbiome-based solutions.
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Subjects
- Element cycles
- Microbial ecology
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Acknowledgements
This work was financially supported by the National Key Research and Development Program of China (2024YFE0106300) and National Natural Science Foundation of China (U25A20803, 42577131).
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Y.-G.Z. and Q.-L.C. researched data for the article. Y.-G.Z., D.Z. and Q.-L.C. contributed substantially to discussion of the content. All authors wrote the article. Y.-G.Z., Q.-L.C. and M.C.R. reviewed and/or edited the manuscript before submission.
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Zhu, YG., Zhu, D., Chen, QL. et al. Impacts of pollution on the soil microbiome.
Nat Rev Microbiol (2026). https://doi.org/10.1038/s41579-026-01350-7
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DOI: https://doi.org/10.1038/s41579-026-01350-7
Source: Ecology - nature.com
