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Restoring soil and sediment microbiomes in the Anthropocene

Nature Reviews Microbiology (2026) Cite this article

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Abstract

Soil and sediment microbiomes have a central role in biogeochemical cycling, climate regulation and ecosystem resilience. However, they are increasingly degraded by land use change, pollution and climate change. Despite their foundational roles in ecosystems, these microbiomes remain under-represented in ecosystem restoration science, practice and policy. Improving the integration of microbiomes across the restoration science–practice–policy nexus is essential for achieving more effective and resilient restoration outcomes. Without this, global restoration risks neglecting the microbial foundations of functional ecosystems and long-term resilience. In this Review, we synthesize the current state of knowledge of soil and sediment microbiome restoration. We describe the major anthropogenic stressors that are degrading these microbiomes, highlighting the linked and context-dependent nature of these impacts, and evaluate existing strategies to restore them. To improve restoration effectiveness, we propose a research workflow that encompasses baseline establishment, degradation diagnostics, designing and testing interventions, research methodology selection and best practice principles. We also outline key theoretical frameworks and propose future research priorities to help soil and sediment microbiome restoration to move towards a predictive, theory-led discipline.

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Fig. 1: Microbiomes in soil and sediment ecosystems.
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Fig. 2: Schematic of anthropogenic degradation of soil and sediment microbiomes.
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Fig. 3: Strategies to restore degraded soil and sediment microbiomes.
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Acknowledgements

This work was supported by funding from the Australian Research Council (DE260101763, DE260101877, DP250101476, IE230100464 and LP240100073), the New Zealand Ministry of Business, Innovation and Employment (grant UOWX2101) and the Australian Government under the National Environmental Science Program’s Resilient Landscapes Hub. The authors acknowledge the Kaurna People, the traditional owners of the lands of the Adelaide (Tarntanya) region in Australia, on which most of this review was written.

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    Georgina V. Wood, Craig Liddicoat, Jake M. Robinson & Martin F. Breed

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Wood, G.V., Liddicoat, C., Robinson, J.M. et al. Restoring soil and sediment microbiomes in the Anthropocene. Nat Rev Microbiol (2026). https://doi.org/10.1038/s41579-026-01307-w

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