Integrative microbial and omic-based approaches reveal the molecular mechanisms of composite PGPR-mediated growth promotion in plants

Plant growth-promoting rhizobacteria (PGPR) are important due to their biostimulant activity. However, most studies focus on single-strain effects, leaving the cooperative mechanisms of multistrain consortia underexplored. In this study, seven PGPR strains were isolated from mangrove forests. Among them, Sinorhizobium sp. N2-2 and Pseudomonas putida S5 were selected to form a composite PGPR based on their complementary plant growth-promoting traits and enhanced IAA production during co-culture. Pot experiments and a subsequent field validation trial revealed that the composite PGPR significantly promoted the growth of pakchoi (increasing plant fresh weight by 80.25% in pots and 49.3% in the field), improved soil physicochemical properties (soil pH, enzyme activity, available potassium and phosphorus levels). Metagenomic analysis showed that inoculation enriched beneficial microbial taxa and upregulated functional genes related to nitrogen fixation ( nifDHK ), phosphorus solubilization ( gcd , pstS , phoD ), and carbohydrate metabolism (CAZymes) in the rhizosphere. Transcriptomic analysis of plant roots further indicated that the PGPR consortium activated key pathways involved in energy metabolism, MAPK signaling, and cell wall biogenesis. The results suggest that the “composite PGPR” co-promoted plant growth by driving transformations in rhizosphere nutrient cycling, regulating microbial metabolism, and balancing plant physiology. This study provides insights into the coordination between PGPR strains and highlights their potential for sustainable agriculture development.