Rhizobium-Enhanced Drought Tolerance in Red Kidney Beans Through Modification of Transcriptome and Microbial Communities

Drought is a significant abiotic stressor affecting crops globally. Beneficial microorganisms, such as rhizobia, have been shown to enhance crop resilience to such stresses. In this study, we isolated a highly efficient rhizobacterial strain (<i>Rhizobium</i> sp. PV-6) from the root system of <i>Phaseolus vulgaris</i> and systematically investigated the phenotypic and physiological responses of the plants across seven growth stages under four treatments: W-NO (watering without inoculation of <i>rhizobium</i>), W-RHI (watering with inoculation of <i>rhizobium</i>), D-NO (drought without inoculation of <i>rhizobium</i>), and D-RHI (drought with inoculation of <i>rhizobium</i>). We also examined the variation in microbial communities in rhizosphere and root compartments. Physiological analyses revealed that <i>rhizobium</i> inoculation significantly enhanced plant height, fresh weight and dry weight, root length, lateral root number, and nodule number of red kidney beans. Alpha diversity analysis suggested that the microbial communities in the roots and rhizosphere of red kidney beans show different variant distributions. Beta diversity and species difference analysis revealed that drought treatments (D-NO, D-RHI) recruit <i>Shinella</i>, <i>Nocardioides</i>, <i>Agromyces</i>, <i>Pseudomonas</i>, and <i>Ensifer</i> at rhizosphere compartments, while D-RHI enrich <i>Pseudomonas</i>, <i>Sphingobacterium</i>, <i>Paenibacillus</i>, <i>Bacillus</i>, <i>Massilia</i>, and <i>Lysobacter</i> at root compartments in the T5 stage. Further, transcriptomic analysis revealed that PV-6 enhances drought tolerance in red kidney beans by modulating the expression of genes associated with abiotic stress-related genes. Our findings highlight the potential of <i>Rhizobium</i> sp. PV-6 as a bioinoculant for improving drought tolerance in red kidney beans (<i>Phaseolus vulgaris</i>), providing a foundation for designing synthetic microbial communities for crop stress resilience.