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Bacterial richness enhances the thermostability of soil organic matter via a long-term trade-off between molecular diversity and thermodynamic stability

Nature Food volume 6, pages 1032–1041 (2025)Cite this article

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Abstract

The persistence of soil organic matter (SOM) is shaped by its molecular features and stability, but the temporal dynamics of these features remain unclear. Here we investigate the molecular diversity (the number of molecules) and molecular thermodynamic stability (the theoretical Gibbs free energy for the half reaction of carbon oxidation) of SOM in soils from long-term (>30 years) paddy and upland experimental fields. Thermogravimetric analysis shows that enhanced SOM thermostability aligns with the temporal variation of molecular thermodynamic stability in these soils. Increased SOM molecular thermodynamic stability occurs alongside decreased molecular diversity over decades, and this temporal trade-off (negative relationship) is modulated by increased bacterial richness. These findings highlight the role of microbial diversity in enhancing SOM thermostability and support strategies that promote bacterial richness for improved SOM persistence in agriculture.

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Fig. 1: Changes in molecular diversity, molecular thermodynamic stability and thermostability index of SOM over time under four treatments in paddy soils and upland soils.
Fig. 2: Relationship between SOM thermostability and molecular thermodynamic stability, and the temporal variation of SOM molecular features in farmland soils.
Fig. 3: Relationships between bacterial richness and SOM molecular features in farmland soils.
Fig. 4: Variation of SOM molecular features at different times in the verification test.
Fig. 5: The conceptual framework for the evolution of SOM features over time in farmland soils.

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Data availability

The sequences have been deposited in the National Center for Biotechnology Information’s Sequence Read Archive under BioProject nos PRJNA995319 (bacteria in paddy soil), PRJNA995321 (fungi in paddy soil), PRJNA997090 (bacteria in upland soils) and PRJNA997086 (fungi in upland soil). The data on the properties of soil microorganisms and SOM are available via Figshare at https://doi.org/10.6084/m9.figshare.25824097.v2 (ref. 48). Source data are provided with this paper.

Code availability

No unique code is applied to this work.

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Acknowledgements

This work was supported by the National Key R&D Program of China (grant nos 2021YFD1500300 and 2022YFD2300300); the National Natural Science Foundation of China (grant no. 42077021); the Independent Deployment Project of Institute of Soil Science, Chinese Academy of Sciences (grant no. ISSAS2403); and the Natural Science Foundation of Jiangsu Province (grant no. BK20221005). We acknowledge A. T. Nottingham (University of Leeds) for his valuable suggestions during the preparation of the first version of the manuscript.

Author information

Authors and Affiliations

  1. State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China

    Meng Wu, Ming Liu, Jun Shan, Xiaoyuan Yan & Zhongpei Li

  2. University of Chinese Academy of Sciences, Beijing, China

    Meng Wu, Ming Liu, Jun Shan, Xiaoyuan Yan & Zhongpei Li

  3. Joint Research Centre, European Commission, Ispra, Italy

    Emanuele Lugato

  4. College of Life Sciences, Nanjing Agricultural University, Nanjing, China

    Pengfa Li

  5. Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China

    Jia Liu

  6. Zhenjiang College, Zhenjiang, China

    Cunpu Qiu

  7. Heilongjiang Academy of Black Soil Conservation & Utilization, Harbin, China

    Shuang Wang, Xingzhu Ma & Xiaoyu Hao

  8. State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China

    Shuang Wang

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Contributions

Z.L., M.W., J.S. and X.Y. designed the framework. S.W., X.M., X.H. and M.L. collected the samples. C.Q. and J.L. conducted the verification experiment. M.W. and P.L. performed the data analysis. M.W. and J.S. wrote and revised the paper with input from the other authors. E.L. provided comments on the results and revised the original manuscript.

Corresponding authors

Correspondence to Shuang Wang, Jun Shan or Zhongpei Li.

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Nature Food thanks Anna Gunina, Sören Thiele-Bruhn and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Tables 1–3 and Figs. 1–7.

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Supplementary Data 1

Source data for Supplementary Figs. 1–7.

Source data

Source Data Fig. 1

Source data on SOM features in the field experiment.

Source Data Fig. 2

Source data for the correlations.

Source Data Fig. 3

Source data for the correlations.

Source Data Fig. 4

Source data on SOM features in the verification test.

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Wu, M., Lugato, E., Li, P. et al. Bacterial richness enhances the thermostability of soil organic matter via a long-term trade-off between molecular diversity and thermodynamic stability. Nat Food 6, 1032–1041 (2025). https://doi.org/10.1038/s43016-025-01253-5

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