Biochemical Interactions in the Rhizosphere: Roles of Root Exudates, Flavonoids and Phytoalexins in Plant–Microbe Communication

The rhizosphere functions as a biochemical interface where plants and microbes exchange signals that regulate growth, defense, and adaptation. Root exudates, including sugars, amino acids, organic acids, and specialized metabolites, shape microbial communities, mobilize nutrients, and influence plant stress responses. Among secondary metabolites, flavonoids act as key chemo-attractants and signaling molecules in legume–rhizobia symbiosis while also contributing to antimicrobial defense and redox balance. Phytoalexins, synthesized de novo upon pathogen attack, provide potent antimicrobial activity and trigger systemic acquired resistance. Recent advances in metabolomics, transcriptomics, and microbiome research reveal the complexity of these biochemical pathways and their role in rhizosphere communication. Integrating this knowledge offers opportunities for rhizosphere engineering, development of microbial inoculants, and breeding strategies that exploit metabolite-mediated signaling for crop resilience. This review highlights the roles of root exudates, flavonoids, and phytoalexins in plant–microbe biochemical interactions with implications for sustainable agriculture.