Bacillus velezensis ES2-4 Modulates Root Exudation and Microbiome Remodeling to Enhance Soybean Resistance Against Gray Mold

Abstract Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.