Phylloplane-Adapted Pseudomonas oryzihabitans as a biocontrol agent: omics insights into antibiosis and defense against bacterial blight of pomegranate.

Phylloplane-associated bacteria contribute significantly to sustainable plant disease management by modulating host defense mechanisms and directly antagonizing pathogens. In this study, Pseudomonas oryzihabitans Pg-Slp82, a dominant phylloplane isolate from pomegranate, was evaluated for its potential as a biocontrol agent against Xanthomonas axonopodis pv. punicae, the causal agent of bacterial blight. Whole-genome sequencing revealed a 5.0 Mb genome comprising 7,193 coding sequences, including 1,029 hypothetical proteins, 15 tRNAs, 15 rRNAs, and 60 repetitive elements, indicating a genomically diverse strain with potential biocontrol traits. Transcriptomic analysis of P. oryzihabitans Pg-Slp82-treated pomegranate leaves generated 403 million reads (GC content 49-50%) and showed peak host gene expression at 24 h post-inoculation (hpi), with activation of 28.3% of unique transcripts. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations revealed enrichment in pathways related to stress response, secondary metabolism, and defense signaling, notably phenylpropanoid and shikimate biosynthesis. Antioxidant assays indicated early activation of SOD at 24 hpi, with maximum activity of POX, PAL, and PPO at 72 hpi. qPCR validation confirmed early upregulation of defense-related genes (SIRK1, CAT1, RLP47) at 72 hpi, followed by a decline in expression of immune regulatory genes (EMS1, PR1, PR5, POX) at 120 hpi, suggesting a transition toward immune modulation. These findings demonstrate the ability of P. oryzihabitans Pg-Slp82 to induce a transient but effective defense response, followed by successful epiphytic adaptation. The integrated genomic and transcriptomic data support its potential as a biocontrol agent for managing bacterial blight in pomegranate.