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.

我们报告了三种黄色色素、革兰氏阴性、需氧、杆状、能动的细菌分离株，它们被指定为来自健康巴斯马蒂水稻种子的PPL1 ^T、PPL2 和 PPL3。表型和 16S rRNA 基因序列分析将这些分离株 归入黄单胞菌属。16S rRNA 与甘蔗病原体X. sacchari  CFBP 4641 ^T具有 99.59% 的相似 性。此外，生化和脂肪酸分析表明它更接近 X. sacchari。尽管如此，它总体上还是不同于其他物种和已知的稻米相关物种，例如X. oryzae  （致病性）和X. maliensis （非致病性）特别是。有趣的是，本研究中的分离株是从健康的水稻植株中分离出来的，但与从患病甘蔗中分离的致病物种密切相关。因此，在植物中的研究表明，PPL1 ^T、PPL2 和 PPL3 在叶片接种后对水稻植株是非致病性的。基于直系同源平均核苷酸同一性 (OrthoANI) 和数字 DNA-DNA 杂交 (dDDH) 值与黄单胞菌属 物种类型菌株的分类基因 组学研究低于推荐的物种划分阈值。基于全基因组的系统基因组分析表明，这些分离株与X.  sacchari  CFBP 4641 ^T形成了一个独特的单系进化枝 作为他们最近的邻居。此外，泛基因组分析显示 PPL1 ^T、PPL2 和 PPL3 分离株包含 NRPS 簇以及大量与新物种相关的独特基因。基于多相和基因组方法，一种与健康水稻种子相关的新谱系和物种，其名称为 Xanthomonas sontii  sp。十一月 被提议。X. sontii  sp.的类型菌株 。十一月 是 PPL1 ^T (JCM 33631 ^T  = CFBP 8688 ^T  = ICMP 23426 ^T  = MTCC 12491 ^T ) 和 PPL2 (JCM 33632 = CFBP 8689 = ICMP 23427 = MTCC 12492) 和 PPL3 (JCM 33632 = CFBP 8689 = MTCC 12492) 和 PPL3 (JCM 33632 ICMP 23426 ICMP 23393933CM)作为该物种的其他菌株。