Functional divergence within mulberry-associated Pantoea ananatis : Insights from comparative genomics and host-contact metabolomics

Pantoea ananatis is a widely distributed plant-associated bacterium that can exhibit contrasting ecological functions, ranging from plant-beneficial activities to pathogenicity. However, the genomic and metabolic features associated with such functional divergence among closely related strains remain poorly understood. Here, we characterized 18 mulberry-associated P. ananatis isolates using phenotypic assays and selected Pa-6 and YSFJ as representatives of two predominant functional types for comparative genomic and host-contact metabolomic analyses. Pa-6 exhibited a beneficial-associated phenotype characterized by several plant growth-promoting and antagonistic traits, comparatively limited tissue damage, and lower disease severity during the later stages of co-inoculation with Ralstonia pseudosolanacearum XZqk. In contrast, YSFJ caused progressive wilt accompanied by bacterial aggregation, xylem occlusion, vascular disorganization, and tissue damage. Despite these contrasting phenotypes, Pa-6 and YSFJ shared approximately 98.9% average nucleotide identity. Comparative genomic analyses revealed differences in accessory-gene content, plasmid composition, and strain-specific homologous clusters. Annotation comparisons highlighted a GH19-associated locus in Pa-6 and wbpZ- and feoB-associated loci in YSFJ as putative gene-content differences. Exploratory pathway mapping of host-contact extracellular metabolomic profiles highlighted central-carbon, organic-acid, and redox-related processes in the Pa-6 treatment and carbohydrate transport and utilization, aromatic-compound metabolism, and stress-related processes in the YSFJ treatment. These results document contrasting host-associated phenotypes and provide genomic and metabolic context for further investigation, while the contributions of individual loci and phylogenetic background remain unresolved.