Plant Immunity-Microbiome Interactions: Assembly, Stress Adaptation, and Translation

Plants harbor complex microbial communities that play fundamental roles in nutrient acquisition, stress tolerance, and disease resistance. Current evidence indicates that plant immunity influences microbiome assembly through context-dependent microbial filtering rather than deterministic recruitment of beneficial taxa. Pattern-triggered immunity, phytohormone signaling, reactive oxygen species, and defense-associated metabolites alter microbial colonization and community structure, whereas direct evidence for effector-triggered immunity as a major regulator of microbiome assembly remains limited. Immune-driven changes in root exudation provide a key mechanistic link between host defense, nutrient status, and microbial selection, although resulting communities also depend strongly on the environmental species pool, microbial competition, priority effects, plant genotype, developmental stage, and abiotic stress. In the reciprocal direction, beneficial microorganisms enhance plant defense through induced systemic resistance, immune priming, bioactive metabolites, and community-level pathogen suppression. Evidence is strongest for root-associated systems and rhizobacteria-mediated resistance, while mechanisms operating in the phyllosphere, endosphere, and field-grown crops remain less resolved. Multi-omics, synthetic microbial communities, spatial imaging, and computational approaches are increasingly enabling causal and spatially resolved analyses; however, simplified experimental systems often incompletely represent the ecological complexity of agricultural soils. Collectively, available studies support an immunity–metabolism–microbiome framework in which host signaling and microbial ecological processes jointly determine community stability and plant adaptation. Translational application will require crop- and stress-specific validation, improved persistence of introduced microorganisms, and strategies that account for native microbiome competition and environmental variability.

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