Abstract
Soils host highly diverse microbial communities that regulate nutrient cycling, carbon storage, and ecosystem resilience, yet the mechanisms linking microbial diversity to function remain incompletely understood. Here we synthesize soil microbiome research through a function-centred framework based on recent studies across ecological, agricultural, and environmental systems. We identify four conserved functional axes, secondary metabolism, nutrient cycling, community interactions, and stress tolerance, that collectively govern ecosystem processes and environmental outcomes. Evidence indicates that these functions influence plant productivity, climate regulation, and pollutant transformation, although their expression is strongly context dependent. We propose that soil operates as a self-organizing system in which microbial interactions generate emergent ecosystem behaviour. This framework provides a basis for predictive, ecology-informed approaches to manage soil systems and to harness microbial functions for sustainable agriculture, environmental remediation, and climate mitigation.
Similar content being viewed by others
Soil microbiome engineering for sustainability in a changing environment
Soil structure and microbiome functions in agroecosystems
Defending Earth’s terrestrial microbiome
Acknowledgements
The authors acknowledge the support of the European Union’s Horizon Europe programme (SOILCRATES project), which contributed to the development of this work. This work has received funding from the European Union’s HORIZON-MISS-2023-SOIL-01-08 programme under grant agreement no. 101157354 (SOILCRATES project: http://soilcrates.eu).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Transparent Peer Review file (download PDF )
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
Reprints and permissions
About this article
Cite this article
Hassan-Dalléac, S., Guiga, W. & Suau-Pernet, A. Soil microbes are the tiny bioengineers running Earth’s underground factory.
Commun Earth Environ (2026). https://doi.org/10.1038/s43247-026-03544-6
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s43247-026-03544-6
Source: Ecology - nature.com
