Rhizosphere Metabolites Mediate Microbial Functional Plasticity in Subtropical Agroforestry Systems Under Environmental Disturbances

Abstract:

Microbial functional plasticity, the ability of microbial communities to adjust metabolic activities in response to environmental changes, is critical for maintaining ecosystem stability of subtropical agroforestry systems (AFSs) under increasing environmental disturbances. However, the role of rhizosphere metabolites in regulating microbial functional plasticity remains unclear. Here, we conducted a field experiment combined with controlled pot trials to investigate the effects of drought disturbance on rhizosphere metabolite profiles and microbial functional plasticity in three subtropical AFSs (alley cropping, silvopasture, forest garden). Multi-omics approaches (metabolomics, metagenomics, metatranscriptomics) were used to characterize rhizosphere metabolite dynamics, microbial taxonomic composition, and functional gene expression. Results showed that forest garden exhibited the highest rhizosphere metabolite diversity (286 metabolites) and strongest microbial functional plasticity (functional redundancy index = 0.82) under drought, compared to silvopasture (243 metabolites, redundancy index = 0.71) and alley cropping (198 metabolites, redundancy index = 0.58). Key rhizosphere metabolites (e.g., flavonoids, polyamines, amino acids) significantly correlated with the expression of microbial functional genes involved in drought resistance (e.g., osmolyte synthesis, antioxidant enzymes) and nutrient cycling (e.g., nitrogen fixation, phosphorus solubilization). Specifically, flavonoids in forest garden rhizosphere induced the upregulation of microbial genes encoding trehalose synthase (RPKM = 102.3) and catalase (RPKM = 89.7), enhancing microbial drought tolerance. Metabolic network analysis revealed that rhizosphere metabolites formed functional modules that mediated microbial functional shifts, with the flavonoid-amino acid module being the core regulator of microbial plasticity in forest garden. Our findings demonstrate that rhizosphere metabolites drive microbial functional plasticity in subtropical AFSs under drought disturbance, highlighting the importance of plant diversity in shaping rhizosphere metabolite profiles to enhance AFS resilience. This provides a theoretical basis for optimizing AFS design by selecting plant species with drought-adaptive rhizosphere metabolite traits.