Plant physiological control of root microbiome assembly and feedback under environmental stress

Root-associated microbiomes contribute to plant nutrition, defense and stress tolerance, but their variable responses across hosts and environments limit the predictability of microbiome-based interventions. This review examines plant physiological regulation of root microbiome assembly and feedback under environmental stress. Evidence from plant and microbial genetics, defined-metabolite assays, synthetic communities and physiological analyses links changes in carbon allocation, nutrient status, hydraulics, redox balance and hormone-immune signaling to root-derived outputs and microbial responses. These outputs influence microbial sensing and resource use, while host immune and metabolic conditions help regulate colonization and persistence. Flavonoid-NodD signaling, strigolactone-induced mycorrhizal fungal responses and coumarin-mediated selection illustrate comparatively well-resolved transitions; the roles of stress-associated purines, nucleotides and compatible solutes remain more context dependent. However, microbial enrichment and metabolite associations alone do not establish plant-controlled recruitment or benefit. Stronger evidence connects plant regulation, microbial response mechanisms and physiological outcomes through causal perturbations. Microbial activity can modify host physiology, although evidence that the altered host state subsequently redirects community assembly remains limited. We integrate these illustrative findings into a framework linking physiological regulation, root outputs, microbial responses, establishment and feedback. This synthesis identifies testable connections for improving microbiome interventions under stress. Translation requires attention to plant carbon and immune costs, competition within resident communities, and validation across host genotypes and environments.