Genomic and metabolomic characterization of Acinetobacter calcoaceticus (DT1) and Citrobacter braakii (S10) reveal functional traits for plant stress alleviation and sustainable agriculture

Plant growth-promoting rhizobacteria (PGPR) enhance plant growth and development through diverse mechanisms, including phytohormone production, nutrient acquisition, and stress mitigation. This study describes the isolation and characterization of two bacterial strains, DT1 and S10, from the rhizospheres of Diplotaxis tenuifolia and Cynodon dactylon , respectively capable of solubilizing phosphate and zinc, fix nitrogen and produce indole acetic acid (IAA) and siderophores. Using whole genome sequencing and taxonomic analyses, these two strains were identified as Acinetobacter calcoaceticus (DT1) and Citrobacter braakii (S10). Functional genomic annotation revealed numerous genes associated with key plant growth-promoting traits, including those involved in indole-3-acetic acid (IAA) ( trpABCDE , ipdC ), cytokinin ( miaABE ), and riboflavin biosynthesis, confirmed by targeted metabolomics. In addition, genes associated with nitrogen metabolism ( nirB , narGHI ) and phosphate solubilization ( gcd , phoARP , pstABCS , pqqEFG ) were identified and supported by phenotypic assays. Interestingly, biosynthetic gene clusters for the secondary metabolites enterobactin, bacillibactin, and staphyloferrin B, known to contribute to plant growth promotion, were identified in both genomes. Both strains also harbored genes encoding ACC deaminase, an enzyme known to enhance plant tolerance to abiotic stress. Furthermore, non-targeted metabolomic analysis revealed that DT1 and S10 produced a range of intracellular and extracellular metabolites associated with plant growth promotion and stress resilience, including cadaverine, biotin, arginine, and GABA. Collectively, these findings position DT1 and S10 as promising bioinoculant candidates, offering an integrative genomic and metabolic foundation for their application in next-generation sustainable agricultural strategies.