Plant–Microbiome Interactions in Medicinal Plants: A Synergistic Partnership for Biomass Production and Secondary Metabolite Accumulation

Medicinal plants are important sources of secondary metabolites (SMs), but their production is constrained by resource shortages, low cultivation efficiency, and continuous cropping obstacles. As the “second genome” of host plants, the plant microbiome is deeply involved in plant growth and development, stress adaptation, and the accumulation of bioactive compounds, providing new pathways for the sustainable utilization of traditional Chinese medicine resources. This review summarizes the mechanisms by which the plant microbiome regulates biomass formation and SM accumulation in medicinal plants. Microorganisms can promote plant nutrient acquisition, enhance resistance to biotic and abiotic stresses, and regulate root architecture and hormonal signaling. Meanwhile, microorganisms can also participate in the remodeling of secondary metabolic networks in medicinal plants through elicitor- and effector protein-mediated signal transduction, regulation of metabolic gene expression, redistribution of photosynthetic carbon sources and metabolic precursors, and their own biosynthetic capacities. From the perspective of co-evolution, plants and their microbiomes constitute symbiotic systems formed through long-term interactions. Plants can selectively recruit specific microbial taxa through root exudates, SMs, and signaling molecules, whereas microorganisms influence plant adaptability and medicinal material quality through colonization, metabolic feedback, and horizontal gene transfer. This review proposes that a synergistic regulatory pattern of “close phylogenetic relatedness-similar secretions-similar microbial communities” may exist between medicinal plants and microorganisms. This pattern suggests that closely related medicinal plants may share similar core microbial taxa, which may help reveal the intrinsic mechanisms underlying specific microbial recruitment and the quality formation of geo-authentic medicinal materials. Furthermore, the design of synthetic microbial communities (SynComs) can be achieved based on the identification of shared functional genes and the screening of indigenous core functional strains.