Unlocking Genomics of Multifunctional Endophytic Strain Citrobacter sp. HSTU-ABk15 from Rice Focusing Pesticide Bioremediation and Plant Health

Endophytic bacteria represent a promising biological solution for sustainable agriculture and pesticide bioremediation. This study reports the isolation and comprehensive characterization of the novel endophytic bacterial strain Citrobacter sp. HSTU-ABk15 from Oryza sativa L. tissues exposed to pesticide stress. Integrated biochemical, genomic, and in silico analyses revealed their dual functionality in chlorpyrifos degradation and plant growth promotion. The genome sequence analysis (ANI, dDDH, pangenomics, Progressive Mauve, and phylogenetic analysis) confirmed the strains belong to the Citrobacter species. The isolates exhibited phosphate solubilization, indole-3-acetic acid (IAA) production, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing genes in their annotated genome. Genome annotation identified organophosphate-degrading genes (opd, phn, ampD, pepD), suggesting potential for pesticide degradation. In silico docking analyses validated strong interactions (–6.5 to –8.0 kcal·mol⁻¹) between key enzymes (AmpD, PepE, GlpQ, carboxylesterase, amidohydrolase, and phosphonatase) and cypermethrin, diazinon, and crotoxiphos. Phylogenomic analyses (ANI and dDDH) confirmed their distinct taxonomic positions, indicating functionally distinct endophytic strains. Citrobacter sp. strain HSTU-ABk15 as a genetically robust, multifunctional endophyte with significant potential for eco-friendly pesticide remediation and sustainable rice cultivation.