Plant Growth-Promoting Bacillus Strains Modulate Early Soybean Development via Proteome Remodelling

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 (), 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 strains (HT1, HT2, and HT3) isolated previously from the soybean root microbiome for their potential plant growth-promoting and biocontrol activities. -HT1 and HT2 significantly enhanced soybean seed germination, while -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 HT1 and HT2 associated with pathways linked to cellular component organization, microtubule dynamics, and organelle function, and -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 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.