Microbiome succession on the pomegranate phylloplane during bacterial blight dysbiosis: Functional implications for blight suppression

Bacterial blight of pomegranate caused by Xanthomonas axonopodis pv. punicae poses significant challenges to sustainable cultivation, necessitating eco-friendly management strategies, and this study explores the role of the phylloplane microbiome in disease suppression through metabarcoding, traditional microbiology, and antibacterial screening of microbial candidates. Here, we mapped the phylloplane microbiome of pomegranate cultivar 'Bhagwa' during bacterial blight development using metabarcoding sequencing (2443,834 reads), traditional microbiological methods (nutrient-rich and minimal media), and scanning electron microscopy. We observed shifts in microbial diversity, with Xanthomonas typically released through stomata as the blight progressed from water-soaked early lesion to advanced necrotic lesion. The Shannon diversity index peaked at 2.6 in early necrotic stages but dropped to 2.1 in advanced blight. Proteobacteria and Firmicutes were the dominant phyla, with significant compositional changes between disease stages. Bacillus species were prevalent throughout, peaking in both early and severe lesions. Pantoea and Curtobacterium increased during severe blight, while Exiguobacterium thrived on the abaxial surface. A core microbiome, including Pantoea, Enterobacter, and Pseudomonas, remained consistent across stages. Antibacterial screening of 116 bacterial candidates, dominated by Pantoea (32), Bacillus (18), and Pseudomonas (11), revealed multipronged activities against X. axonopodis pv. punicae. Bacillus amyloliquefaciens P2-1 and Pantoea dispersa Pg-Slp-6 suppressed the pathogen through secreted metabolites, while Pantoea dispersa Pg-Slp-6, Pseudomonas oryzihabitans Pg-Slp-82, and Pantoea dispersa Pg-slp-117 exhibited volatile-mediated suppression. Among these, Bacillus amyloliquefaciens P2-1 and Pantoea dispersa Pg-slp-6 showed 55 % and 42 % blight suppression, respectively, highlighting their potential as biocontrol agents.