Xanthomonas sontii sp. nov., a non-pathogenic bacterium isolated from healthy basmati rice (Oryza sativa) seeds from...

We report three yellow-pigmented, Gram-negative, aerobic, rod-shaped, motile bacterial isolates designated as PPL1^T, PPL2, and PPL3 from healthy basmati rice seeds. Phenotypic and 16S rRNA gene sequence analysis assigned these isolates to the genus Xanthomonas. The 16S rRNA showed a 99.59% similarity with X. sacchari CFBP 4641^T, a sugarcane pathogen. Further, biochemical and fatty acid analysis revealed it to be closer to X. sacchari. Still, it differed from other species in general and known rice associated species such as X. oryzae (pathogenic) and X. maliensis (non-pathogenic) in particular. Interestingly, the isolatess in this study were isolated from healthy rice plants but are closely related to species that is pathogenic and isolated from diseased sugarcane. Accordingly, in planta studies revealed that PPL1^T, PPL2, and PPL3 are non-pathogenic to rice plants upon leaf inoculation. Taxonogenomic studies based on orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values with type strains of Xanthomonas species were below the recommended threshold values for species delineation. Whole genome-based phylogenomic analysis revealed that these isolates formed a distinct monophyletic clade with X. sacchari CFBP 4641^T as their closest neighbour. Further, pangenome analysis revealed PPL1^T, PPL2, and PPL3 isolates to comprise NRPS cluster along with a large number of unique genes associated with the novel species. Based on polyphasic and genomic approaches, a novel lineage and species associated with healthy rice seeds for which the name Xanthomonas sontii sp. nov. is proposed. The type strain for the X. sontii sp. nov. is PPL1^T (JCM 33631^T = CFBP 8688^T = ICMP 23426^T = MTCC 12491^T) and PPL2 (JCM 33632 = CFBP 8689 = ICMP 23427 = MTCC 12492) and PPL3 (JCM 33633 = CFBP 8690 = ICMP 23428 = MTCC 12493) as other strains of the species.