Abstract
The stability of soil microbiomes is critical for ecosystem functioning under climate change, yet its assessment is confounded by the overlooked problem of observational temporal scale dependency. Here, we introduce a multi-temporal window framework to resolve this problem. Applied to a decade-long warming experiment, our approach reveals that the perceived stability of bacterial and fungal communities nonlinearly decays with observational temporal scale, and short windows systematically overestimate it. Crucially, we document a temporal scale-driven mechanistic shift. Community stability shifts from species resistance to compensatory asynchrony once the window exceeds a threshold. This transition occurs over a broader temporal scale range for fungi than for bacteria. Our work establishes that microbiome stability is an intrinsically temporal scale-dependent property and provides a scalable, bioinformatic-friendly framework that challenges conventional single-temporal-scale assessments. This paradigm is critical for accurately predicting the fate of soil carbon and other microbiome-governed functions in a warming world.
Data availability
Data are available from Figshare: https://doi.org/10.6084/m9.figshare.31651414
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Acknowledgements
This study was funded by Xizang Autonomous Region Science and Technology Project [XZ202401JD0029, XZ202501ZY0086, XZ202501ZY0056], China National Natural Science Foundation [31600432], Lhasa Science and Technology Plan Project [LSKJ202422], Chinese Academy of Sciences Youth Innovation Promotion Association [2020054 l and Construction of Zhongba County Fixed Observation and Experiment Station of First Support System for Agriculture Green Development. We sincerely thank the editors and reviewers for their extremely constructive and valuable comments, which are very helpful in improving the quality of this study.
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G.F. designed the research and performed the experiments; G.F. and W.S. analyzed the data, drafted the paper, and revised it.
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Communications Earth & Environment thanks Samuel Bickel and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editors: Somaparna Ghosh. A peer review file is available
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Fu, G., Sun, W. A multi-temporal window framework reveals the temporal-scale-dependent stability of soil microbiomes under warming.
Commun Earth Environ (2026). https://doi.org/10.1038/s43247-026-03471-6
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DOI: https://doi.org/10.1038/s43247-026-03471-6
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