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Effects of replacing chemical fertilizer with organic fertilizer on organic carbon mineralization and carbon cycle functional genes in yellow soil

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Abstract

Fertilization-mediated soil organic carbon (SOC) mineralization is a key process in agroecosystem carbon cycling, yet the microbial mechanisms involved under different fertilization regimes remain unclear. This study, based on a three-year field experiment in acidic yellow soil (Ultisol) in Guizhou, integrated SOC mineralization incubation and metagenomic sequencing to compare SOC mineralization and functional gene profiles under no fertilization (CK), chemical fertilizer alone (NP), and replacing chemical fertilizer with 50% or 100% organic fertilizer (1/2NPM and M). Fertilization significantly increased cumulative mineralized SOC (Ct) (p < 0.05); NP showed high mineralization, whereas organic-fertilizer replacement reduced the cumulative mineralization ratio (Ct/SOC). Metagenomic analysis indicated NP did not substantially alter carbon-cycling genes but lowered the C/N ratio, increasing microbial diversity and driving “carbon-compensation” mineralization. Conversely, 1/2NPM and M improved soil pH, available phosphorus (AP), and nitrate nitrogen (NO₃−-N), reshaped microbial community structure, up-regulated carbon-fixation genes (korA, facA, coxS), and suppressed carbon-degradation genes (pel, chi), enhancing carbon sequestration capacity. Partial least squares path modeling confirmed a “stoichiometry-community diversity” cascade significantly regulated SOC mineralization (p < 0.01), with organic-fertilizer replacement shifting functional profiles from carbon degradation to carbon fixation.

Data availability

The datasets generated and/or analyzed during the current study are not publicly available due to privacy concerns; however, the data presented in this study are available upon request from the corresponding author.

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Acknowledgements

This work was supported by the National Key R&D Program Project (2022YFD1901500, 2022YFD1901505), Guizhou Key Laboratory of Cultivated Land Quality (Qian Ke He Platform ZSYS[2025]035), Construction of High Quality and Efficient Mechanized Scientific and Technological Innovation Talent Team of Characteristic Coarse Cereals in Guizhou Province (grant number BQW[2024]009), We thank research staffs for their contributions to this work.

Funding

This work was supported by the National Key R&D Program Project (2022YFD1901500, 2022YFD1901505), Guizhou Key Laboratory of Cultivated Land Quality (Qian Ke He Platform ZSYS[2025]035), and the Construction of High Quality and Efficient Mechanized Scientific and Technological Innovation Talent Team of Characteristic Coarse Cereals in Guizhou Province (grant number BQW[2024]009). The funders had no role instudy design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Authors and Affiliations

  1. College of Agriculture, Guizhou University, Guiyang, 550025, China

    Shengmei Yang, Xiaoli Wang, Sanwei Yang, Jin He, Chen Fang & Yizhu Huang

  2. Key Laboratory of Tobacco Quality Research of Guizhou Province, College of Tobacco, Guizhou University, Guiyang, 550025, China

    Jianjun Duan

  3. Nanhu Sub-district Office, People’s Government of Pu’an County, Pu’an, 561500, Guizhou, China

    Na Zhao

Authors

  1. Shengmei Yang
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  2. Xiaoli Wang
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  4. Sanwei Yang
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  5. Jin He
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  6. Chen Fang
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Contributions

X.W., S.Y., and J.D. conceptualized and led the work. S.Y., J.H., and C.F. contributed to data analysis including validation and interpretation of the results. S.Y. wrote the manuscript. S.Y., N.Z., and Y.H. provide the measured data. X.W., S.Y., J.D. reviewed and edited the manuscript. All authors contributed to the final version of the manuscript.

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Correspondence to
Xiaoli Wang or Jianjun Duan.

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Yang, S., Wang, X., Duan, J. et al. Effects of replacing chemical fertilizer with organic fertilizer on organic carbon mineralization and carbon cycle functional genes in yellow soil.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-47725-x

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