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Research progress on the structure, function, and agricultural applications of the rice microbiome

Liu Yuan-Hui**,Tang Hong-Wei**,Zhu Xin-Xia,Yu Kai,Xu Chun-Mei,Wang Dan-Ying*   

  1. China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
  • Received:2026-04-13 Revised:2026-08-17 Accepted:2026-08-17 Published:2026-08-21
  • Supported by:
    This study was supported by the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-CNRRI-2025-01) and the Central Public-interest Scientific Institution Basal Research Fund -CNRRI (No. 10).

Abstract:

Symbiotic microbiomes of rice act as core biological components underpinning green and high-yield rice production and balancing paddy field ecosystems, which profoundly regulate rice growth and development throughout its whole life cycle, nutrient cycling and multiple stress resistances. This paper systematically sorts out the species composition, abundance distribution and spatiotemporal dynamics of microbial communities in three microhabitats including rhizosphere, phyllosphere and endosphere, and elaborates the hierarchical regulatory rules of microbial community assembly driven by multiple factors such as rice genotype, water and fertilizer management, farming practices and regional climate. The core functional mechanisms of microorganisms are analyzed from four dimensions: nutrient activation, growth regulation, biotic stress defense and abiotic stress alleviation. Special focus is placed on molecular and physiological pathways through which nitrogen-fixing, phosphate-solubilizing and potassium-mobilizing microbiota activate insoluble soil minerals, biocontrol microbes antagonize rice blast, bacterial leaf blight and other diseases, and functional microorganisms enhance rice tolerance to drought, salinity and heavy metals. On this basis, three major practical application orientations of microorganisms in rice production are summarized: the development of multi-functional compound microbial fertilizers (strain compounding and innovation of novel carrier materials), integrated green disease prevention combining microorganisms with chemical pesticides, and microbe-driven soil improvement systems under straw returning and crop rotation regimes. Finally, the bottlenecks restricting current research on rice microbiomes are summarized, and prospects are proposed regarding targeted editing of microbiomes, in-depth elucidation of host-microbe interaction mechanisms, and integrated application in ecological agriculture. This work aims to provide comprehensive theoretical support and practical technical references for reducing chemical fertilizers and pesticides, improving paddy soil fertility, and realizing sustainable agricultural development.

Key words: rice, microbiome, nutrient activation, growth regulation, stress alleviation, microbial fertilizer, sustainable agriculture

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