Comparative Genomics and Rhizosphere Microbiome Profiling Reveal Crop-Dependent Responses to Closely Related Bacillus subtilis Strains in Chickpea and Maize
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Plant growth-promoting rhizobacteria (PGPR) are considered sustainable alternatives to chemical fertilizers; however, their effectiveness is often influenced by strain–crop compatibility. In this study, two closely related strains of Bacillus subtilis (HM01 and HM04) were investigated to understand crop-specific growth responses and associated rhizosphere dynamics. Although both strains exhibited comparable in vitro Plant growth-promoting (PGP) traits, seed germination assays revealed distinct host-dependent effects. HM01 significantly enhanced chickpea root growth by 95%, whereas HM04 increased maize root growth by 86%. Comparative genomic analysis identified distinct accessory genes that may contribute to crop-specific plant-microbe interactions. Rhizosphere microbial profiling further indicated strain-dependent and crop-specific microbial restructuring. In chickpea, HM01 inoculation showed a higher relative abundance of Paenibacillus mucilaginosus and Neobacillus niacini , whereas HM04 treatment in maize promoted taxa including Sphingobium yanoikuyae , Citrobacter koseri , and Pantoea dispersa . Predictive functional profiling suggested that these inoculation-driven shifts were associated with crop-dependent metabolic potential, with chickpea-associated communities enriched in carbohydrate and aromatic compound degradation pathways, while maize-associated communities showed greater lipid and amino acid degradation potential. Overall, the findings suggest that closely related PGPR strains can produce contrasting plant responses that are associated with strain-specific genomic traits and differential modulation of rhizosphere microbial communities, highlighting the importance of strain–crop compatibility in bioinoculant development. Future studies integrating functional validation and field evaluation will further advance the understanding and application of these interactions.
