Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
Institute of Agrobiological Sciences, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
Int J Syst Evol Microbiol. 2023 Jun;73(6). doi: 10.1099/ijsem.0.005942.
The search for bacteria that can be used as biocontrol agents to control crop diseases yielded a promising candidate, Sm006, which was isolated from the rhizosphere of eggplant () growing in a field in Aichi Prefecture, Japan, in 2006. The cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with one polar flagellum. The results of homology searches and phylogenetic analyses based on the 16S rRNA gene sequence indicated that Sm006 represents a member of the genus . The genomic DNA G+C content was 66.3 mol% and the major cellular fatty acids (more than 5 % of the total fatty acids) were summed feature 8 (Cω7 and/or Cω6), summed feature 3 (Cω7 and/or Cω6), C and C. Phylogenetic analyses using the gene sequence and phylogenomic analysis of the whole genome sequence revealed that Sm006 represents a member of the group; however, its phylogenetic position does not match that of any known species of the genus . The average nucleotide identity and digital DNA-DNA hybridisation values between the strain and closely related species were lower than the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for TUM18999 (92.05 and 46.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and possession of 2,4-diacetylphloroglucinol biosynthetic gene cluster could be used to differentiate the strain from its closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained during this study indicated that Sm006 represents a novel species of the genus , for which we propose the name sp. nov., with Sm006 (= MAFF 212523 = ICMP 24689) as the type strain.
从日本爱知县农田茄子根际中分离到一株细菌 Sm006，它对多种作物病害具有生防潜力，可作为生物防治剂使用。该菌细胞呈革兰氏阴性、需氧、不产芽孢、杆状、单极生鞭毛、运动。根据 16S rRNA 基因序列的同源性搜索和系统发育分析结果，Sm006 代表伯克霍尔德氏菌属的一个种。基因组 DNA G+C 含量为 66.3mol%，主要细胞脂肪酸（占总脂肪酸的 5%以上）为 sumF 8（Cω7 和/或 Cω6）、sumF 3（Cω7 和/或 Cω6）、C 和 C。基因序列的系统发育分析和全基因组序列的系统发育分析表明，Sm006 代表伯克霍尔德氏菌群的一个种；然而，它的系统发育位置与该属的任何已知种都不匹配。该菌株与密切相关的种之间的平均核苷酸同一性和数字 DNA-DNA 杂交值均低于原核生物种定义的阈值（分别为 95-96%和 70%），与 TUM18999 的最高值（分别为 92.05%和 46.3%）。表型特征、细胞脂肪酸组成和具有 2,4-二乙酰基间苯三酚生物合成基因簇可用于将该菌株与最接近的亲缘关系区分开来。在这项研究中获得的表型、化学分类和基因型数据表明，Sm006 代表伯克霍尔德氏菌属的一个新种，我们建议将其命名为 sp. nov.，其模式菌株为 Sm006（=MAFF 212523=ICMP 24689）。
