Wang Xing, He Shan-Wen, Guo He-Bao, Han Ji-Gang, Thin Kyu Kyu, Gao Ju-Sheng, Wang Yao, Zhang Xiao-Xia
Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
College of life science, The Yangtze University, Jingzhou, 434025, PR China.
Int J Syst Evol Microbiol. 2020 Jul;70(7):4171-4178. doi: 10.1099/ijsem.0.004265.
A novel Gram-stain-negative strain, designated ZYY5, was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5 was a member of the genus , with a highest similarity to DSM 18068 (98.5%). The major fatty acids were summed feature 3 (C ω7 and/or C ω6), C and summed feature 8 (C ω7 and/or C ω6). Multi-locus sequence analysis using five concatenated genes (16S rRNA, , , and ) and phylogenomic analysis based on 2940 core gene sequences showed that strain ZYY5 formed a robust cluster with strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of . The orthologous average nucleotide identity (ANI) and digital DNA-DNAhybridization (dDDH) values among these six strains ranged from 96.8-99.9% and 73.7-99.8%, which supported that they were belonged to the same species. However, strain ZYY5 shared 58.4 of dDDH and 94.5% of ANI values with type strain DSM 18068, which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5 contained virulence-associated genes, which is same as the phylogenetic-related strains of the genus . Based on the results of the polyphasic approaches, we propose that strain ZYY5 represents a novel species in the genus , for which the name sp. nov. (=JCM 33020 =ACCC 61554 ) is proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be classified in the same genomospecies of same as ZYY5.
从水稻根部分离出一株新型革兰氏阴性菌株，命名为ZYY5。16S rRNA基因分析结果表明，菌株ZYY5属于 属，与DSM 18068的相似度最高（98.5%）。主要脂肪酸为总和特征3（C ω7和/或C ω6）、C以及总和特征8（C ω7和/或C ω6）。使用五个串联基因（16S rRNA、 、 、 和 ）进行的多位点序列分析以及基于2940个核心基因序列的系统基因组分析表明，菌株ZYY5与菌株EC1、ZJU1202、DZ2Q、NCPPB 3531和CSL RW192形成了一个稳定的聚类，同时与 属的其他菌株分离。这六个菌株之间的直系同源平均核苷酸同一性（ANI）和数字DNA-DNA杂交（dDDH）值范围分别为96.8 - 99.9%和73.7 - 99.8%，这支持它们属于同一物种。然而，菌株ZYY5与模式菌株DSM 18068的dDDH值为58.4，ANI值为94.5%，低于提议的dDDH和ANI物种界限临界值。基因组分析表明，菌株ZYY5含有与毒力相关的基因，这与 属的系统发育相关菌株相同。基于多相分类方法的结果，我们提议菌株ZYY5代表 属中的一个新物种，为此提出名称 sp. nov.（=JCM 33020 =ACCC 61554 ）。菌株EC1、ZJU1202、DZ2Q、NCPPB 3531和CSL RW192也应与ZYY5归为 属的同一基因组种。
