Coevolution of Rhizosphere Microbiome and Plant Stress-Resistant Metabolism Enhances Adaptability of Subtropical Agroforestry Systems to Combined Abiotic Stresses

Abstract:

Subtropical agroforestry systems (AFSs) are increasingly challenged by combined abiotic stresses (e.g., drought + high temperature), which severely threaten ecosystem stability and productivity. The coevolution of rhizosphere microbiome and plant stress-resistant metabolism is hypothesized to be a key adaptive mechanism, but the underlying processes and driving factors remain unclear. Here, we conducted a long-term field survey (5 years) and controlled simulation experiments to explore the coevolutionary patterns of rhizosphere microbiome and plant stress-resistant metabolism in four typical subtropical AFSs (bamboo-tea intercropping, camphor-corn intercropping, mango-grass intercropping, and natural secondary forest-agricultural crop mixed system) under drought-high temperature (D-HT) combined stress. Integrating metabolomics, metagenomics, and transcriptomics, we characterized plant stress-resistant metabolite profiles, rhizosphere microbial community structure, and functional gene co-expression networks. Results showed that the natural secondary forest-agricultural crop mixed system (high plant diversity) exhibited the strongest adaptive capacity to D-HT stress, with the highest plant survival rate (82.3%) and yield stability (yield reduction rate: 12.7%). This was accompanied by distinct coevolutionary patterns: (1) Plant stress-resistant metabolites (e.g., abscisic acid, jasmonic acid, phenols) and rhizosphere beneficial microbes (e.g., Arthrobacter, Bacillus, mycorrhizal fungi) formed stable co-occurrence networks, with 32.5% of metabolites significantly correlating with microbial functional genes; (2) Transcriptomic analysis revealed that plants in high-diversity AFSs upregulated genes involved in metabolite synthesis (e.g., PAL, LOX, NCED) and microbial recruitment (e.g., LYK3, NFP), while rhizosphere microbes upregulated genes encoding stress-responsive enzymes (e.g., superoxide dismutase, peroxidase) and nutrient transporters (e.g., NRT2, PHT1); (3) Coevolutionary selection pressure drove the enrichment of microbial functional traits related to metabolite degradation and stress adaptation, and plant metabolic traits related to microbial recruitment. Moreover, the coevolutionary degree was positively correlated with AFS adaptability (r = 0.87, p < 0.01). Our findings demonstrate that the coevolution of rhizosphere microbiome and plant stress-resistant metabolism enhances the adaptability of subtropical AFSs to combined abiotic stresses, and plant diversity is a key driver of this coevolution. This provides a new theoretical basis for constructing stress-resistant AFSs by regulating plant-microbe coevolutionary relationships.