Active microbiome succession in the rhizosphere of growing plants

Plant root exudates dynamically shape rhizosphere microbiomes, yet how they drive the succession of active microbial communities across development remains unclear.  Through a novel integration of quantitative stable isotope probing (qSIP), metagenomics and metabolomics, we established a direct link between dynamic root exudate profiles and the succession of active rhizosphere microbiota in watermelon rhizosphere. The results showed that microbial activity in the rhizosphere increased progressively from the seedling to the flowering stage. The microbial codon usage bias increased, with genomes becoming progressively streamlined, suggesting rhizosphere selection toward a microbial community with enhanced growth potential but lower functional redundancy. From seedling to flowering, the metabolic network of rhizosphere microbes utilising root exudates became simpler. Dominant active taxa provided persistent core functions for the plant (e.g., root development and pathogen suppression), and specifically produced siderophores during flowering, thus stabilising rhizosphere ecosystem functioning. Overall, these results reveal how plants orchestrate microbial succession through exudate chemistry, optimising rhizosphere function across development.