Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
Halophiles Research Institute, Noda, Chiba 278-0043, Japan.
Int J Syst Evol Microbiol. 2011 Dec;61(Pt 12):2984-2995. doi: 10.1099/ijs.0.029298-0. Epub 2011 Feb 4.
Members of the order Halobacteriales are obligate extreme halophiles that belong to the domain Archaea. The classification of the Halobacteriales currently relies on a polyphasic approach, which integrates phenotypic, genotypic and chemotaxonomic characterization. However, the most utilized genetic marker for phylogeny, the 16S rRNA gene, has multiple drawbacks for use with the Halobacteriales: the species of many genera exhibit large intragenic differences between multiple ribosomal RNA operons, the gene is too conserved to discriminate reliably at the species level and it appears to be the most frequently recombined gene between closely related species. Moreover, the Halobacteriales is a rapidly expanding group due to recent successes at cultivating novel strains from a diverse set of hypersaline environments; a fast, reliable, inexpensive, portable molecular method for discriminating species is required for their investigation. Recently, multilocus sequence analysis (MLSA) has been shown to be an effective tool for strain identification and taxonomic designation, even for those taxa that experience frequent lateral gene transfer and homologous recombination. In this study, MLSA was utilized for evolutionary and taxonomic investigation of the Halobacteriales. Efficacy of the MLSA approach was tested across a hierarchical gradient using 52 halobacterial strains, representing 33 species (including names without standing in nomenclature) and 14 genera. A subset of 21 strains from the genus Haloarcula was analysed separately to test the sensitivity and relevance of the MLSA approach among closely related strains and species. The results demonstrated that MLSA differentiated individual strains, reliably grouped strains into species and species into genera and identified potential novel species and also family-like relationships. This study demonstrates that MLSA is a rapid and informative molecular method that will probably accommodate strain analysis at any taxonomic level within the Halobacteriales.
嗜盐菌目成员是专性极端嗜盐古菌，属于古菌域。目前，嗜盐菌目的分类依赖于多相方法，该方法综合了表型、基因型和化学生态特征。然而，用于系统发育的最常用遗传标记 16S rRNA 基因对于嗜盐菌目有多个缺点：许多属的物种在多个核糖体 RNA 操纵子之间表现出较大的种内差异，该基因过于保守，无法在种水平上可靠地区分，并且似乎是密切相关物种之间最频繁重组的基因。此外，由于最近从各种高盐环境中成功培养了新菌株，嗜盐菌目是一个快速扩张的群体；需要一种快速、可靠、廉价、便携的分子方法来区分物种，以对其进行研究。最近，多位点序列分析 (MLSA) 已被证明是一种有效的工具，用于菌株鉴定和分类指定，即使对于那些经历频繁水平基因转移和同源重组的分类群也是如此。在这项研究中，MLSA 被用于嗜盐菌目的进化和分类研究。使用代表 33 个种（包括无命名的名称）和 14 个属的 52 株嗜盐菌菌株，在一个层次梯度上测试了 MLSA 方法的有效性。从 Haloarcula 属中分析了 21 株菌株的子集，以测试 MLSA 方法在密切相关的菌株和物种中的敏感性和相关性。结果表明，MLSA 可以区分单个菌株，可靠地将菌株分组为种，将种分组为属，并鉴定出潜在的新种和类似家族的关系。这项研究表明，MLSA 是一种快速而有信息量的分子方法，可能适应嗜盐菌目中任何分类水平的菌株分析。
