The application of <i>Rhizobium subbaraonis</i> TY15 increased soybean growth and disease resistance by modifying rhizosphere microbial communities

Microbial biofertilizers present a sustainable approach to enhancing agricultural productivity by reducing reliance on chemical inputs. A total of 193 bacterial strains were isolated from the soybean rhizosphere using culture-dependent methods and high-throughput sequencing. Genetic diversity analysis via IS-PCR fingerprinting identified 19 representative strains, followed by 16S rRNA sequencing that delineated <i>Bacillus</i>, <i>Rhizobium</i>, and <i>Paenibacillus</i> as dominant genera. We chose <i>Rhizobium subbaraonis</i> TY15 on the basis of its dominant position and plant growth-promoting rhizobacteria characteristics. Functional screening highlighted strains exhibiting phosphate and potassium solubilization, plant growth-promoting traits (e.g., auxin production and enzyme synthesis), and antagonistic activity against phytopathogens such as <i>Fusarium oxysporum</i>, <i>Rhizoctonia solani</i>, and <i>Pseudomonas solanacearum</i>. Notably, <i>Rhizobium subbaraonis</i> TY15 demonstrated dual benefits in promoting soybean growth and modulating rhizosphere microbial communities, significantly increasing the abundance of beneficial genera like <i>Bacillus</i> and <i>Rhizobium</i>. These findings underscore the potential of targeted microbial inoculants to improve crop resilience and nutrient efficiency, offering insights for developing sustainable biofertilizers through plant-microbe interaction optimization.IMPORTANCEPersistent challenges in soybean production demand sustainable solutions leveraging plant growth-promoting rhizobacteria. While biofertilizers enhance crop resilience, understanding how elite strains reconfigure rhizosphere microbiomes remains limited. Our study demonstrates that <i>Rhizobium subbaraonis</i> TY15 uniquely enriches beneficial genera (e.g., <i>Bacillus</i> and <i>Rhizobium</i>) while suppressing oligotrophic taxa, synergistically boosting nutrient mobilization and pathogen resistance-effects overlooked by conventional screening methods. By integrating culture-dependent isolation with high-throughput sequencing, we expose limitations of standard protocols in capturing strain-specific microbiome modulation. These insights establish a framework for precision microbial consortia design, advancing biofertilizer development to sustainably address global food security challenges.