Roots: metabolic architects of beneficial microbiome assembly

Abstract The increasing demand for sustainable agricultural practices has driven a renewed interest in plant–microbiome interactions as a basis for the next “green revolution.” Central to these interactions are root-derived metabolites that act as mediators of microbial recruitment and function. Plants exude a chemically diverse array of compounds that influence the assembly, composition, and stability of the root microbiome. These metabolites can act as nutrients, chemical signals, or antimicrobial barriers, orchestrating beneficial relationships while defending against pathogenic threats. This review highlights the multifaceted role of plant metabolites in root microbiome assembly, focusing on their dynamic regulation by plant genotype, environmental conditions, and immune responses. We discuss the emerging concept of roots as metabolic architects of their associated microbiomes, wherein plant–metabolite–microbiome interactions coevolved alongside critical life-support systems such as immunity and nutrient acquisition. We propose that elucidating the mechanisms of metabolite-driven microbial selection can guide the development of future crops optimized for beneficial microbiome recruitment and enhanced resilience.