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

Abstract

We report three yellow-pigmented, Gram-negative, aerobic, rod-shaped, motile bacterial isolates designated as PPL1T, PPL2, and PPL3 from healthy basmati rice seeds. Phenotypic and 16S rRNA gene sequence analysis assigned these isolates to the genusXanthomonas. The 16S rRNA showed a 99.59% similarity withX. sacchariCFBP 4641T, a sugarcane pathogen. Further, biochemical and fatty acid analysis revealed it to be closer toX. 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 PPL1T, PPL2, and PPL3 are non-pathogenic to rice plants upon leaf inoculation. Taxonogenomic studies based onorthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values with type strains ofXanthomonasspecies were below the recommended threshold values for species delineation. Whole genome-based phylogenomic analysis revealed that these isolates formed a distinct monophyletic clade withX.sacchariCFBP 4641T as their closest neighbour. Further, pangenome analysis revealed PPL1T, PPL2, and PPL3 isolatesto 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 nameXanthomonas sontiisp. nov. is proposed. The type strain for theX. sontiisp. nov. is PPL1T (JCM 33631T = CFBP 8688T = ICMP 23426T = MTCC 12491T) 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.