Abstract
Mineral fertilizers have sustained food security for decades, yet the long-term impacts on soil microbial communities underpinning soil health remain virtually unknown. We combine standardized field surveys with a meta-analysis to assemble a global dataset of 501 long-term agricultural experiments (≥5 years, median duration 25 years) to evaluate the impacts of sustained mineral fertilization on soil properties and microbial communities. Long-term mineral fertilization increases soil organic carbon by 14% and decreases soil pH by 0.31 units on average relative to unfertilized controls. Soil organic carbon accumulation largely explains increased microbial biomass carbon and living bacterial biomass. Mineral fertilizer-induced acidification primarily reshapes dominant bacterial taxa, with the relative abundance of Proteobacteria increasing and Firmicutes declining, whereas fungal community composition remains stable. Virulent bacteriophages increase in association with shifts in bacterial hosts. Microbial activities reveal a decoupling of more nitrogen- and phosphorus-acquisition enzymes from the unchanged production of carbon-mineralization enzymes. Microbial communities are taxonomically reorganized without reducing richness or promoting fungal pathogens. These responses are evaluated in the context of agroecosystem type, fertilization regime, and cropping regime. Our findings provide global-scale evidence for the consequences of long-term mineral fertilization on soil health, which is integral to guiding fertilizer management for sustainable agriculture.
Similar content being viewed by others
Contrasting response of fungal versus bacterial residue accumulation within soil aggregates to long-term fertilization
Field study of compound microbial agents for soil improvement and microbial community dynamics on rocky slopes in Southwest China
Soil structure and microbiome functions in agroecosystems
Acknowledgements
We sincerely thank all colleagues who provided published data for this analysis and apologize for the inability to cite everyone who has contributed to this field. We are grateful to W. Ding, X. Zhao, and M. Liu (Institute of Soil Science, Chinese Academy of Sciences); X. Meng, X. Zhang, and X. Tian (College of Natural Resources and Environment, Northwest A&F University); S. Qin and X. Liu (Institute of Genetics and Developmental Biology, Chinese Academy of Sciences); J. Ma (Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences); Y. Li (Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences); W. Zhang (College of Resources and Environment, China Agricultural University); and H. Liao and J. Long (Guizhou Normal University) for invaluable assistance in soil sampling. We also acknowledge the Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, for generously providing soil samples. S.X. thanks Y. Bai, Y. Wu, S. Lin, and D. Song for their assistance with soil sample analyses.
Funding
H.Y. discloses support for the research of this work from the National Natural Science Foundation of China (U24A20626, W2412148, 42477135). S.X. discloses support for the research of this work from the China Scholarship Council (202408420228).
Author information
Authors and Affiliations
Corresponding authors
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
Supplementary information (download PDF )
Description of Additional Supplementary Information (download PDF )
Supplementary Data 1 (download XLSX )
Supplementary Data 2 (download XLSX )
Reporting Summary (download PDF )
Transparent Peer Review file (download PDF )
PRISMA checklist (download PDF )
Source data
Source data (download XLSX )
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
Xu, S., Delgado-Baquerizo, M., Yu, Y. et al. Global long-term agricultural experiments reveal consequences of mineral fertilization for soil microbiomes.
Nat Commun (2026). https://doi.org/10.1038/s41467-026-74614-8
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41467-026-74614-8
Source: Ecology - nature.com
