Phylloplane bacterial exometabolites suppress Xanthomonas axonopodis pv. punicae: Metabolomic and genomic insights for bacterial blight management in pomegranate

Bacterial blight, caused by Xanthomonas axonopodis pv. punicae, remains a significant constraint to pomegranate cultivation, necessitating sustainable alternatives to chemical and antibiotic-based control. In this study, 24 epiphytic bacterial strains isolated from the pomegranate phylloplane were evaluated for their biocontrol potential through integrated metabolomic, volatilomic, in vitro, and greenhouse analyses. LC-MS/MS profiling revealed the presence of bioactive metabolites such as Bacillomycin D, Fengycin, and Iturin A in Bacillus spp.; Macrolactin (6.3 μg/mL), Macrolactin W (4.1 μg/mL), and sucrose palmitate (2.8 μg/mL) in Erwinia; and Cyclo (l-Pro-l-Tyr), Tryptophol, Dapdiamide A and B, and Pantocin A and B in Pantoea. GC-MS analysis identified (E)-3-Butylidene-4,5-dihydroisobenzofuran-1(3H)-one as a dominant volatile compound across multiple isolates. Among the strains, Pantoea dispersa Pg-Slp6 emerged as the most promising, exhibiting the highest phosphate solubilization (84.5 μg/mL), indole-3-acetic acid production (28.6 μg/mL), siderophore activity (CAS index 0.86), and significant pathogen suppression (72.3 % inhibition in vitro; 61.5 % disease reduction in greenhouse trials). Metabolite-mediated bioassays confirmed complete inhibition of X. axonopodis pv. punicae by secondary metabolites from Bacillus amyloliquefaciens P2-1 and P. dispersa Pg-Slp6. Whole-genome sequencing of P. dispersa Pg-Slp6 revealed gene clusters associated with secondary metabolite biosynthesis, xenobiotic degradation, and plant growth-promoting traits, affirming its multifunctional capabilities. Phylogenetic analysis based on 100 conserved protein-coding genes placed P. dispersa Pg-Slp6 in a distinct clade, underscoring its unique genomic identity. These findings establish P. dispersa Pg-Slp6 as a robust candidate for developing phylloplane-adapted microbial formulations aimed at the eco-friendly and effective management of bacterial blight in pomegranate.