Three yellow pigmented, Gram negative, aerobic, rod shaped, motile bacterial strains designated as PPL1, PPL2 and PPL3 were isolated from healthy basmati rice seeds. Phenotypic, biochemical and 16S rRNA gene sequence analysis assigned these strains to the genus Xanthomonas. The 16S rRNA gene sequence was having 99.59% similarity with X. sacchari CFBP4641T. However, whole genome based phylogenomic analysis revealed that these strains formed a distinct monophyletic clade with X. sacchari CFBP4641T as their closest neighbour. Taxonogenomic studies based on average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH) values of these strains with type strains (or representative strains) of different Xanthomonas species including X. sacchari showed below recommended threshold values of ANI (<96%) and dDDH (70%) for species delineation. Furthermore, at the whole genome level, PPL1 and PPL2 were found to be clonal, while PPL3 was not a clonal, but belonging to the same species. Our in planta pathogenicity studies revealed that the strains PPL1, PPL2 and PPL3 are non-pathogenic to rice plants. Hence, based on the present study, they form a novel lineage and species associated with rice seeds for which the name Xanthomonas sontii sp. nov. is proposed. The type strain for the X. sontii sp. nov. is PPL1T (CFBP8688T = ICMP23426T = MTCC12491T) and strains PPL2 (CFBP8689 = ICMP23427 = MTCC12492) and PPL3 (CFBP8690 =ICMP23428 = MTCC12492) as other strains of the species.

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