In-Depth Insights into the Complex Interplay Between Microbial Diversity, Ecological Functionality, and Soil Health in Rice Agroecosystems

Although microbial communities in rice agroecosystems regulate nitrogen transformations, methane dynamics, crop residue decomposition, and pathogen suppression, their integration into agronomic decision-making remains limited. Existing rice microbiome reviews largely describe taxonomic diversity without critically linking microbial processes to management trade-offs, greenhouse gas mitigation, and productivity outcomes. This review synthesizes current knowledge through a process-based and management-oriented framework, emphasizing how water and crop residue management, fertilization, tillage, and genotype selection shape microbial functionality rather than merely community composition. Advances in stable isotope probing (SIP), metatranscriptomics, and multi-omics have improved functional inference, yet a persistent gap remains between genetic potential and in situ process rates. By integrating microbiome science within a One Health perspective, we propose a conceptual framework linking microbial network structure to interconnected dimensions of ecosystem, plant, and human health. This framework addresses not only agronomic outcomes but also food safety concerns, including mycotoxin contamination by fungal pathogens, microbial contributions to nutritional quality, and pathways through which soil and plant microbiomes influence human health via the food chain. We critically examine how microbiome management can simultaneously target productivity, environmental sustainability, and health risk mitigation. We identify priority research needs in predictive microbial ecology, activity-based validation, and microbiome-informed management strategies. Rather than framing microbiomes as a universal solution to global food security, this review critically examines their realistic and context-dependent contribution to improving sustainability, resilience, and resource-use efficiency in rice production under climatic and environmental constraints, while safeguarding food safety and public health.