Ramachandran Hema, Shafie Nur Asilla Hani, Sudesh Kumar, Azizan Mohamad Noor, Majid Mohamad Isa Abdul, Amirul Al-Ashraf Abdullah
School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
Quest International University Perak, 30250, Ipoh, Perak, Malaysia.
Antonie Van Leeuwenhoek. 2018 Mar;111(3):361-372. doi: 10.1007/s10482-017-0958-8. Epub 2017 Oct 11.
Bacterial classification on the basis of a polyphasic approach was conducted on three poly(3 hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] accumulating bacterial strains that were isolated from samples collected from Malaysian environments; Kulim Lake, Sg. Pinang river and Sg. Manik paddy field. The Gram-negative, rod-shaped, motile, non-sporulating and non-fermenting bacteria were shown to belong to the genus Cupriavidus of the Betaproteobacteria on the basis of their 16S rRNA gene sequence analyses. The sequence similarity value with their near phylogenetic neighbour, Cupriavidus pauculus LMG3413, was 98.5%. However, the DNA-DNA hybridization values (8-58%) and ribotyping analysis both enabled these strains to be differentiated from related Cupriavidus species with validly published names. The RiboPrint patterns of the three strains also revealed that the strains were genetically related even though they displayed a clonal diversity. The major cellular fatty acids detected in these strains included C15:0 ISO 2OH/C16:1 ω7c, hexadecanoic (16:0) and cis-11-octadecenoic (C18:1 ω7c). Their G+C contents ranged from 68.0 to 68.6 mol%, and their major isoprenoid quinone was Ubiquinone Q-8. Of these three strains, only strain USMAHM13 (= DSM 25816 = KCTC 32390) was discovered to exhibit yellow pigmentation that is characteristic of the carotenoid family. Their assembled genomes also showed that the three strains were not identical in terms of their genome sizes that were 7.82, 7.95 and 8.70 Mb for strains USMAHM13, USMAA1020 and USMAA2-4, respectively, which are slightly larger than that of Cupriavidus necator H16 (7.42 Mb). The average nucleotide identity (ANI) results indicated that the strains were genetically related and the genome pairs belong to the same species. On the basis of the results obtained in this study, the three strains are considered to represent a novel species for which the name Cupriavidus malaysiensis sp. nov. is proposed. The type strain of the species is USMAA1020 (= DSM 19416 = KCTC 32390).
采用多相分类法对从马来西亚不同环境样本中分离得到的三株聚（3-羟基丁酸酯-co-4-羟基丁酸酯）[P(3HB-co-4HB)]积累菌进行了细菌分类研究。这些样本分别采集自马来西亚的古林湖、槟榔河和马尼克拉稻田。基于16S rRNA基因序列分析，这些革兰氏阴性、杆状、具运动性、不产芽孢且不发酵的细菌被鉴定为β-变形菌纲贪铜菌属。它们与亲缘关系最近的近缘种贪铜菌（Cupriavidus pauculus）LMG3413的序列相似性值为98.5%。然而，DNA-DNA杂交值（8%-58%）和核糖体分型分析均能将这些菌株与已有效发表名称的相关贪铜菌属物种区分开来。这三株菌的核糖体分型图谱也显示，尽管它们表现出克隆多样性，但在遗传上是相关的。这些菌株中检测到的主要细胞脂肪酸包括C15:0 ISO 2OH/C16:1 ω7c、十六烷酸（16:0）和顺式-11-十八碳烯酸（C18:1 ω7c）。它们的G+C含量在68.0%至68.6%之间，主要类异戊二烯醌为泛醌Q-8。在这三株菌中，只有菌株USMAHM13（=DSM 25816 = KCTC 32390）被发现呈现出类胡萝卜素家族特有的黄色色素沉着。它们的组装基因组还显示，这三株菌的基因组大小并不相同，菌株USMAHM13、USMAA1020和USMAA2-4的基因组大小分别为7.82 Mb、7.95 Mb和8.70 Mb，略大于食油假单胞菌（Cupriavidus necator）H16（7.42 Mb）。平均核苷酸同一性（ANI）结果表明，这些菌株在遗传上相关，基因组对属于同一物种。基于本研究获得的结果，这三株菌被认为代表了一个新物种，为此提出了新名称马来西亚贪铜菌（Cupriavidus malaysiensis sp. nov.）。该物种的模式菌株是USMAA1020（=DSM 19416 = KCTC 32390）。
