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Green manuring relocates microbiomes in driving the soil functionality of nitrogen cycling to obtain preferable grain yields in thirty years

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Abstract

Fertilizers are widely used to produce more food, inevitably altering the diversity and composition of soil organisms. The role of soil biodiversity in controlling multiple ecosystem services remains unclear, especially after decades of fertilization. Here, we assess the contribution of the soil functionalities of carbon (C), nitrogen (N), and phosphorus (P) cycling to crop production and explore how soil organisms control these functionalities in a 33-year field fertilization experiment. The long-term application of green manure or cow manure produced wheat yields equivalent to those obtained with chemical N, with the former providing higher soil functions and allowing the functionality of N cycling (especially soil N mineralization and biological N fixation) to control wheat production. The keystone phylotypes within the global network rather than the overall microbial community dominated the soil multifunctionality and functionality of C, N, and P cycling across the soil profile (0–100 cm). We further confirmed that these keystone phylotypes consisted of many metabolic pathways of nutrient cycling and essential microbes involved in organic C mineralization, N2O release, and biological N fixation. The chemical N, green manure, and cow manure resulted in the highest abundances of amoB, nifH, and GH48 genes and Nitrosomonadaceae, Azospirillaceae, and Sphingomonadaceae within the keystone phylotypes, and these microbes were significantly and positively correlated with N2O release, N fixation, and organic C mineralization, respectively. Moreover, our results demonstrated that organic fertilization increased the effects of the network size and keystone phylotypes on the subsoil functions by facilitating the migration of soil microorganisms across the soil profiles and green manure with the highest migration rates. This study highlights the importance of the functionality of N cycling in controlling crop production and keystone phylotypes in regulating soil functions, and provides selectable fertilization strategies for maintaining crop production and soil functions across soil profiles in agricultural ecosystems.

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Availability of data and materials

The obtained sequences were submitted to the NCBI Sequence Read Archive (SRA) with accession number PRJNA841854 and PRJNA841974 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA841854 and https://dataview.ncbi.nlm.nih.gov/object/PRJNA841974). Other data and results supporting the findings of the study are available in this article and its supplementary information files.

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Acknowledgement

This work was supported by the National Key Research and Development Program of China (2021YFD1700200), the earmarked fund for CARS-Green manure (CARS-22), and the Agricultural Science and Technology Innovation Program of CAAS. The authors would like to thank Xingguo Bao, Kesheng Wu, Yue Luo, Rui Liu, Hui Wang, Peng Jiang, Yarong Song and Qiaolin Chang for their assistance in field management, soil sampling, and laboratory work.

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Authors and Affiliations

  1. State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Guopeng Zhou, Danna Chang, Ting Liang & Weidong Cao

  2. State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China

    Kunkun Fan

  3. College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China

    Songjuan Gao, Hai Liang & Shun Li

  4. Institute of Soil & Fertilizer and Resource & Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China

    Guilong Li

  5. Institute of Soil and Fertilizer and Water-saving Agriculture, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China

    Jiudong Zhang & Zongxian Che

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  1. Guopeng Zhou
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Correspondence to Zongxian Che or Weidong Cao.

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Zhou, G., Fan, K., Gao, S. et al. Green manuring relocates microbiomes in driving the soil functionality of nitrogen cycling to obtain preferable grain yields in thirty years. Sci. China Life Sci. 67, 596–610 (2024). https://doi.org/10.1007/s11427-023-2432-9

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  • DOI: https://doi.org/10.1007/s11427-023-2432-9

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