Abstract
The role of soil microorganisms in supporting multiple ecosystem functions (multifunctionality) remains poorly understood across diverse environmental conditions. Here, we investigate 484 soils from 27 European countries spanning a range of climatic and edaphic contexts. We assess the contribution of climate, soil properties, and soil microbiome traits (i.e., the relative abundance of co-occurring taxa) to explain six key functional proxies related to soil structure, biochemical activity, and productivity. We find the highest multifunctionality values in grasslands, woodlands, loamy and acidic soils, and temperate humid regions, and the lowest in croplands, alkaline soils, and drier regions. Soil properties explain 12–31% of variation in multifunctionality, with microbial biomass and nitrogen content emerging as the strongest predictors. The soil microbiome accounts for 2–14% of unique variance in multifunctionality but explains more than 25% of variation in enzymatic activities and primary productivity in clay-rich soils and soils originating from temperate dry regions. Specific taxa, particularly within Actinobacteria, Acidobacteria, and the fungal genus Mortierella consistently emerge as strong predictors of ecosystem multifunctionality. Our findings highlight that ecosystem multifunctionality is jointly shaped by soil properties and microbial communities. We argue that specific taxa hold potential as context-dependent indicators for multifunctionality monitoring across environmental gradients.
Data availability
The data that supports the findings of this study are freely available in figshare with the identifier https://doi.org/10.6084/m9.figshare.28645625. Raw DNA sequences can be accessed through the European Soil Data Centre (ESDAC) portal: https://esdac.jrc.ec.europa.eu/content/soil-biodiversity-dna-bacteria-and-fungi. The raw data (DNA sequences) generated in this study have been deposited in the Sequence Read Archive (SRA) database under BioProject ID PRJNA952168. Detailed information on the taxonomic composition of bacterial and fungal modules is available as Supplementary Dataset 1. Detailed information on Structural Equation Models (SEMs) results is availabel as Supplementary Dataset 2.
Code availability
Code used to perform all analyses described in this study is freely available at https://github.com/fromerob/Multifunctionality.git.
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Acknowledgements
F.R. acknowledges funding from the Novo Nordisk Foundation through a Postdoctoral fellowship (grant reference number NNF24OC0094454). The LUCAS Survey is coordinated by Unit E4 of the Statistical Office of the European Union (EUROSTAT). The LUCAS Soil sample collection is supported by the Directorate-General Environment (DG-ENV), Directorate-General Agriculture and Rural Development (DG-AGRI) and Directorate-General Climate Action (DG-CLIMA) of the European Commission. 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. M.v.d.H and F.R. acknowledge funding from the Swiss National Science Foundation (Switzerland) through grant no. 310030–188799 and from the European Union Horizon 2020 research and innovation program under grant agreement no. 862695 EJP SOIL-MINOTAUR.
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F.R. contributed to conceptualization, methodology, formal analysis, investigation, data curation, writing – original draft, writing – review & editing, and visualization. M.L. contributed to conceptualization, methodology, formal analysis, investigation, writing – review & editing, and data curation. A.O. contributed to conceptualization, methodology, resources, writing – review & editing, and data curation. C.B. contributed to methodology and resources. P.P. contributed to conceptualization, methodology, resources, writing – review & editing, project administration, and data curation. A.J. contributed to conceptualization, methodology, resources, writing – review & editing, project administration, and data curation. L.T. and M.B. contributed to resources, writing – review & editing, and data curation. N.E., M.S., and C.A.G. contributed to resources and writing – review & editing. D.T. contributed to methodology. I.R. and S.J. contributed to writing – review & editing. S.M. contributed to project administration and funding acquisition. M.C.R. and A.L. contributed to resources and writing – review & editing. M.D.B. contributed to writing – review & editing. M.v.d.H. contributed to conceptualization, methodology, resources, writing – original draft, writing – review & editing, supervision, project administration, and funding acquisition.
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Romero, F., Labouyrie, M., Orgiazzi, A. et al. The soil microbiome as an indicator of ecosystem multifunctionality in European soils.
Nat Commun (2025). https://doi.org/10.1038/s41467-025-67353-9
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DOI: https://doi.org/10.1038/s41467-025-67353-9
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