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Slower-growing species promote interspecific cooperation and coexistence under acid stress through cross-feeding

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Abstract

Acid stress is a central environmental factor shaping the structure and function of microbial communities worldwide. However, there is a lack of predictive understanding of how microbial communities respond physiologically and metabolically to acid stress. Here, we find that higher acid stress favors slower-growing species, promoting population growth and coexistence. Our experiments show that acid stress influences the spatial structure of communities, wherein coexistence is ordered over centimeter-length scales and determined by growth-tolerance trade-offs. We find that interspecific interactions are highly dynamic during acid stress changes, with shifts from competition to cooperation, enhancing resilience under high-stress intensities. Slower-growing species may bolster interspecific coexistence through stress-dependent excretion and cross-feeding of public goods. We construct a resource-consumer-based mathematical model to unravel the processes experienced by species in stress-induced coexistence and their distinct physiological states. Finally, our pairwise bacterial-fungal interaction experiments elucidate universalities in stress-induced coexistence between closely related and phylogenetically distant species with complementary phenotypic profiles. Overall, our work provides insights into how acid stress affects physiological and metabolic responses, as well as overall fitness, resilience, and coexistence.

Data availability

All data that support the findings of this study are provided in the Supplementary Information, Source Data file, and databases. Raw mass spectral data is deposited to MassIVE and accessible with the accession code MSV000099939. Source data are provided with this paper, and can also be found at https://doi.org/10.5281/zenodo.1732030972. Source data are provided as a Source Data file. Source data are provided with this paper.

Code availability

Based on the mathematical model provided in the Supplementary Notes, the code can be found at https://zenodo.org/records/17330958.

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Acknowledgements

This work was funded by a grant from the National Natural Science Foundation of China (31972064 (X.X.)), the Basic Research Program of Jiangsu (BK20252085 (X.X.), BK20251603 (H.L.)), and Jiangsu Funding Program for Excellent Postdoctoral Talent (2025ZB880 (H.L.)).

Author information

Author notes

  1. These authors contributed equally: Hui Liao, Liming Wu.

Authors and Affiliations

  1. The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangnan, China

    Hui Liao, Yi Luo, Hussain Asif, Xinlei Huang & Xiaole Xia

  2. College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China

    Liming Wu & Xiaole Xia

Authors

  1. Hui Liao
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  2. Liming Wu
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  3. Yi Luo
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  4. Hussain Asif
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  5. Xinlei Huang
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  6. Xiaole Xia
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Contributions

H.L., L.W., Y.L., and X.H. performed the experiments. H.L. analyzed the experimental data. A.H. and X.X. carried out manuscript revisions. X.X. directed the study. H.L. and L.W. wrote the manuscript, and all authors read and approved the final manuscript.

Corresponding author

Correspondence to
Xiaole Xia.

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The authors declare no competing interests.

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Nature Communications thanks Wenping Cui, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.

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Liao, H., Wu, L., Luo, Y. et al. Slower-growing species promote interspecific cooperation and coexistence under acid stress through cross-feeding.
Nat Commun (2025). https://doi.org/10.1038/s41467-025-67395-z

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