The application of Rhizobium subbaraonis 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 Bacillus, Rhizobium, and Paenibacillus as dominant genera. We chose Rhizobium subbaraonis 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 Fusarium oxysporum, Rhizoctonia solani, and Pseudomonas solanacearum. Notably, Rhizobium subbaraonis TY15 demonstrated dual benefits in promoting soybean growth and modulating rhizosphere microbial communities, significantly increasing the abundance of beneficial genera like Bacillus and Rhizobium. 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 Rhizobium subbaraonis TY15 uniquely enriches beneficial genera (e.g., Bacillus and Rhizobium) 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.