Plant growth-promoting Bacillus strains modulate early soybean development via proteome remodeling

Plant adaptation to environmental stress involves tightly regulated cellular, molecular, and biochemical responses. Among these, microbe-assisted strategies have gained attention, particularly the role of the plant microbiome (phytomicrobiome) in promoting growth and stress resilience. Soybean (Glycine max), a major agricultural crop, actively recruits beneficial microbes through root-secreted secondary metabolites, fostering symbiotic interactions with endophytic bacteria. However, the direct and indirect impacts of root-associated endophytes on plant development remain incompletely understood. In this study, we investigated three Bacillus strains (HT1, HT2, and HT3) isolated previously from the soybean root microbiome.16 S rRNA analysis indicates that HT1 and HT2 are closely related to the Bacillus velezensis and HT3 to the Bacillus thuringiensis lineage although more detailed analyses are warranted for genus identification. These strains were selected for their demonstrated plant growth-promoting and biocontrol activities. Bacillus-HT1 and HT2 significantly enhanced soybean seed germination, while Bacillus-HT3 promoted leaf area expansion significantly compared to the control, indicating strain-specific developmental effects. To elucidate the molecular basis of these effects, we conducted shotgun proteomic profiling of soybean leaves. Enrichment analysis revealed distinct functional signatures, with Bacillus HT1 and HT2 associated with pathways linked to cellular component organization, microtubule dynamics, and organelle function, and Bacillus-HT3 inducing broader enrichment of photosynthesis, chloroplast organization, and biosynthetic processes. These findings suggest that HT1 and HT2 promote early developmental transitions, while HT3 enhances vegetative growth through large-scale metabolic reprogramming. Notably, proteins such as anthranilate synthase and proteasome subunit alpha type were differentially abundant, pointing to the potential involvement of auxin biosynthesis and ubiquitin-proteasome-mediated regulation but, the actual roles of these pathways remain to be validated. These findings provide mechanistic insights into how specific Bacillus strains modulate soybean development at the molecular level and highlight their potential for use as bio-inoculants to enhance crop productivity and resilience under stress conditions.