Pantoea bangladeshensis sp. nov.; a new phytopathogen causing grain discolouration disease of rice in Bangladesh

Pantoea sp. (strains NSTU24ᵀ and NSTU24.1) is an emerging bacterial pathogen isolated from severe rice grain discolouration in Bangladesh. While initial 16 S rRNA sequencing indicated close phylogenetic relationships with species such as P. graminicola and P. phosphatilytica , definitive identification required comprehensive whole-genome sequencing. Therefore, this study aimed to characterize the genomic, phenotypic, and pathogenic features of these strains to determine their precise taxonomic identity and functional properties. Genomic analysis of the 4.35-Mb genome (56.13 mol% GC content) revealed exceptionally low Average Nucleotide Identity (≤ 92.51%) and digital DNA-DNA Hybridization (≤ 48.6%) values compared to its closest relatives, unequivocally establishing it as a distinct novel species. Rigorous in-vivo pathogenicity assays successfully fulfilled Koch’s postulates, confirming its causal role in the disease. Furthermore, comparative pan-genome profiling highlighted significant evolutionary divergence, identifying unique accessory gene clusters absent in related type strains. The new species also exhibits a distinctive functional repertoire; it harbors complete Type I and Type V secretion systems while completely lacking Type III and Type VI machineries, contrasting sharply with the strategies of closely related Pantoea species. Supported by integrated phenotypic, biochemical, and phylogenomic evidence, we formally propose Pantoea bangladeshensis as a novel taxon, underscoring the critical need for genomic surveillance of agricultural pathogens.