Multi-omics Integration Reveals Metabolic Regulatory Mechanisms of Plant-Microbe Interactions in Subtropical Agroforestry Systems

Abstract:

Subtropical agroforestry systems (AFSs) harbor complex plant-microbe interactions that drive metabolic flux networks and support ecosystem stability. However, the metabolic regulatory mechanisms underlying these interactions remain poorly elucidated. Here, we integrated metabolomics, transcriptomics, metagenomics, and metatranscriptomics to characterize plant-microbe metabolic interactions in three typical subtropical AFSs (alley cropping, silvopasture, forest garden). Root exudate metabolomes, plant transcriptomes, rhizosphere microbial communities, and microbial metabolic pathways were systematically analyzed. Results showed that forest garden exhibited the most diverse root exudate profile (128 unique metabolites) and highest microbial alpha diversity (Shannon index = 7.82). Key metabolites (e.g., flavonoids, organic acids) in root exudates shaped rhizosphere microbial communities by selecting for specific taxa (e.g., Pseudomonas, Arbuscular Mycorrhizal Fungi). Transcriptomic analysis revealed that plant genes involved in flavonoid biosynthesis (e.g., CHS, FLS) were significantly upregulated in forest garden, which correlated with increased microbial genes encoding flavonoid degradation enzymes. Metabolic network reconstruction identified 18 core metabolic modules mediating plant-microbe interactions, including nitrogen cycling, carbon sequestration, and secondary metabolite synthesis. These modules were more interconnected in forest garden, indicating a more stable metabolic network. Our findings provide a comprehensive understanding of metabolic regulatory mechanisms in AFS plant-microbe interactions, offering novel insights for optimizing AFS design via metabolic engineering.