Genome-based characterization of Pantoea cypripedii APP145 reveals secondary replicon-associated functional diversity and aromatic metabolic potential

Abstract Background Forest soils contain diverse microorganisms adapted to plant-derived aromatic compounds released during lignin decomposition. Genome-based characterization of these microorganisms provides insights into their genomic diversity and metabolic potential. In this study, strain APP145 was isolated from forest soil using enrichment cultures containing lignin-derived aromatic compounds, and integrated phenotypic, phylogenetic, and comparative genomic analyses were performed to determine its taxonomic position and genomic characteristics. Results Genome-based analyses identified strain APP145 as Pantoea cypripedii . Whole-genome sequencing revealed a multipartite genome comprising one chromosome and four large secondary replicons. Comparative genomic analyses demonstrated a large accessory genome, with many APP145-specific gene clusters within the analyzed genome set located on secondary replicons and assigned to diverse functional categories, including transport, metabolism, regulation, and defense-related functions. Genome mining identified genes associated with portions of the β-ketoadipate pathway together with diverse oxidoreductases, transporters, carbohydrate-active enzymes, and stress response systems, suggesting the potential for aromatic compound metabolism and responses to diverse environmental conditions. Several biosynthetic gene clusters, including terpene-related, and siderophore-related clusters, were also identified. Overall, the chromosome predominantly encoded core metabolic functions, whereas secondary replicons contained a substantial proportion of accessory genes associated with diverse predicted functions. Conclusions The genome of Pantoea cypripedii APP145 exhibits a modular organization consisting of a conserved chromosomal backbone and a large secondary-replicon-associated accessory genome. These genomic features illustrate strain-level genomic diversity within the genus Pantoea and provide a genomic resource for future studies of aromatic compound metabolism and the functional roles of accessory genes in soil-associated bacteria.