Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.
The Academy of Scientific and Innovative Research, Ghaziabad, India.
Curr Microbiol. 2022 Sep 5;79(10):304. doi: 10.1007/s00284-022-03001-5.
Xanthomonas is a major group of pathogenic bacteria infecting staple food crops like rice. Increasingly it is being recognized that non-pathogenic Xanthomonas (NPX) are also important members of a healthy plant microbiome. However, the vast majority of the species described in this genus are of pathogenic nature, and only a few NPX species have been reported till now. Genomic and taxonogenomic analysis of NPX is needed for the management of this important group of bacteria. In this study, two yellow-pigmented bacterial isolates were obtained from healthy rice seeds in Punjab, India. The isolates designated PPL560 and PPL568 were identified as members of the genus Xanthomonas based on biochemical tests and 16S rRNA gene sequence analysis retrieved from the whole-genome sequences. Isolates formed a distinct monophyletic lineage with Xanthomonas sontii and Xanthomonas sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by the representative species of the genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560 and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. The absence of type III secretion system-related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of the genus Xanthomonas with PPL560 = MTCC 13185 = CFBP 9039 = ICMP 24394 as its type strain and PPL568 as another constituent member.
黄单胞菌是感染水稻等主要粮食作物的重要致病菌群体。越来越多的证据表明，非致病性黄单胞菌（NPX）也是健康植物微生物组的重要成员。然而，该属中描述的绝大多数物种都具有致病性，迄今为止仅报道了少数几个 NPX 物种。为了管理这一重要的细菌群体，需要对 NPX 进行基因组和分类基因组分析。在这项研究中，从印度旁遮普邦健康水稻种子中获得了两个黄色色素细菌分离株。根据生化试验和从全基因组序列中检索到的 16S rRNA 基因序列分析，将这些分离株鉴定为黄单胞菌属的成员。基于代表种属的核心基因内容，分离株与黄单胞菌属的黄单胞菌属和黄单胞菌属蔗糖相似，在系统发育树上形成了一个独特的单系谱系。根据计算的种属之间的平均核苷酸同一性和数字 DNA-DNA 杂交值，与其他黄单胞菌属物种相比，这些值都低于各自的截止值。在体内研究中发现，PPL560 和 PPL568 通过叶片夹接种对水稻植物没有致病性。缺乏 III 型分泌系统相关基因和效应子进一步支持了它们的非致病性状态。在此，我们提出了印度黄单胞菌 sp. nov. 作为黄单胞菌属的一个新种，PPL560 = MTCC 13185 = CFBP 9039 = ICMP 24394 作为其模式株，PPL568 作为另一个组成成员。
