Integrative Genomics and Metabolomics Analyses Provide New Insights into the Molecular Basis of Plant Growth Promotion by Pantoea agglomerans

Plant Growth-Promoting Rhizobacteria (PGPR) are emerging as a sustainable alternative in agriculture due to their environmentally friendly properties and their ability to enhance crop productivity. Among these, <i>Pantoea agglomerans</i> has gained attention for its versatility as both a biofertilizer and a biocontrol agent. In this study, we use comparative genomics to gain insight into the genetic diversity and functional specialization of members of this species. The pan-genome analysis of 20 representative <i>P. agglomerans</i> strains revealed that 32% of the genes constitute the core genome (2856 out of 8899), while the remaining 68% are classified as accessory or singleton genes, indicating a high level of genomic diversity within the species. Functional annotation showed that core genes are predominantly involved in central metabolic processes, whereas genes associated with specialized metabolic functions are found within the accessory and singleton categories. The comparative analysis demonstrated a mosaic distribution of genes related to nitrogen and sulfur metabolism, heavy metal resistance, defense mechanisms, and oligopeptide uptake, suggesting niche-specific adaptations and metabolic capabilities within this species. Exometabolome profiling of strains associated with different hosts, specifically plant (C1) or human (DSM3493^T), demonstrated that omics-centered approaches can be utilized to select <i>P. agglomerans</i> strains tailored to specific agronomic requirements.