抄録
Soil microbiomes play a central role in regulating agricultural ecosystem functioning by linking soil biogeochemical processes with crop productivity; however, traditional agroecosystems increasingly face constraints in resource efficiency, environmental sustainability, and system stability under intensifying global change and agricultural practices. Recent advances in multi-omics technologies, including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, have enabled a shift from reductionist analyses of individual microorganisms toward integrated, system-level investigations of microbial communities and their interactions with plants and the environment. Current evidence indicates that soil microbiomes regulate ecosystem productivity, stability, and resilience through the mediation of carbon, nitrogen, and phosphorus cycling, the modulation of soil structure formation, and the coordination of plant nutrient acquisition, stress adaptation, and immune responses. In addition, microbial interaction networks and plant–microbe regulatory feedbacks jointly determine functional stability and environmental responsiveness at the ecosystem scale. Despite these advances, major challenges remain in moving from correlation-based observations to causal mechanistic understanding, integrating laboratory and field-scale evidence, and improving predictive modeling of dynamic microbial networks under environmental variability. This review synthesizes recent progress in soil microbiome research enabled by multi-omics approaches, critically evaluates their functional mechanisms and ecosystem-level roles, and compares emerging regulatory strategies across scales and application contexts. By integrating current knowledge, this study establishes a conceptual framework for soil microbiome–driven regulation of agricultural ecosystems and highlights key pathways toward mechanistic understanding and predictive management of microbiome functions for sustainable agriculture.
