基于基因组的 Haloarcula 和 Halomicroarcula 属的分类学研究，以及六种新型 Haloarcula 物种的描述。

Genome-based taxonomy of genera Haloarcula and Halomicroarcula, and description of six novel species of Haloarcula.

机构信息

School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China.

出版信息

Extremophiles. 2024 Jan 12;28(1):10. doi: 10.1007/s00792-023-01329-9.

DOI:10.1007/s00792-023-01329-9

PMID:38214762

Abstract

The genera Haloarcula and Halomicroarcula are the most closely related genera within the family Haloarculaceae (class Halobacteria). The respective 16S rRNA genes of type strains from the genus Haloarcula showed 94.7-96.5% similarities to their homologous genes of type strains from the genus Halomicroarcula. The Haloarcula species showed 89.3-92.8% rpoB' gene similarities to Halomicroarcula species. These similarities were higher than the proposed genus boundary. Phylogenomic analysis revealed that these two genera formed a tight cluster separated from Halomicrobium with high bootstrap confidence. The average amino acid identity (AAI) values among Haloarcula and Halomicroarcula were 70.1-74.5%, higher than the cutoff value (67.0%) to differentiate the genera Haloarcula and Halomicroarcula from Halomicrobium. These results indicated that the genus Halomicroarcula should be merged with Haloarcula. Then, six novel species are described based on strains DFY41, GDY20, SHR3, XH51, YJ-61-S, and ZS-22-S1 isolated from coarse sea salt, marine solar saltern, and salt lake (China). These six strains formed separate clades (90.1-99.3% 16S rRNA and 89.0-94.9% rpoB' gene similarities) and then clustered with current Haloarcula and Halomicroarcula species (89.4-99.1% 16S rRNA and 87.6-95.0% rpoB' gene similarities), as revealed by phylogenetic analyses. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and AAI values among these six strains and current Haloarcula and Halomicroarcula species were 76.2-89.8%, 25.3-46.0%, and 70.3-89.7%, respectively, clearly below the species demarcation threshold. These six strains were distinguished from current Haloarcula and Halomicroarcula species according to differential phenotypic characteristics. Six novel species, Haloarcula halophila sp. nov., Haloarcula litorea sp. nov., Haloarcula rara sp. nov., Haloarcula halobia sp. nov., Haloarcula pelagica sp. nov., and Haloarcula ordinaria sp. nov., are proposed to accommodate strains DFY41, GDY20, SHR3, XH51, YJ-61-S, and ZS-22-S1, respectively.

摘要

属 Haloarcula 和 Halomicroarcula 是 Haloarculaceae 科（Class Halobacteria）中最密切相关的属。属 Haloarcula 模式菌株的 16S rRNA 基因与属 Halomicroarcula 模式菌株的同源基因相似性为 94.7-96.5%。属 Haloarcula 物种的 rpoB'基因与 Halomicroarcula 物种的相似性为 89.3-92.8%。这些相似性高于提议的属界。系统基因组分析表明，这两个属与 Halomicrobium 形成了一个紧密的聚类，置信度高。Haloarcula 和 Halomicroarcula 之间的平均氨基酸同一性 (AAI) 值为 70.1-74.5%，高于区分属 Haloarcula 和 Halomicroarcula 与属 Halomicrobium 的截断值（67.0%）。这些结果表明，属 Halomicroarcula 应与 Haloarcula 合并。然后，基于从粗海盐、海洋太阳能盐场和盐湖（中国）中分离的菌株 DFY41、GDY20、SHR3、XH51、YJ-61-S 和 ZS-22-S1，描述了六个新物种。这六个菌株形成了单独的分支（16S rRNA 的 90.1-99.3%和 rpoB'基因的 89.0-94.9%相似性），然后与当前的 Haloarcula 和 Halomicroarcula 物种聚类（16S rRNA 的 89.4-99.1%和 rpoB'基因的 87.6-95.0%相似性），正如系统发育分析所示。这六个菌株与当前的 Haloarcula 和 Halomicroarcula 物种之间的平均核苷酸同一性 (ANI)、数字 DNA-DNA 杂交 (dDDH) 和 AAI 值分别为 76.2-89.8%、25.3-46.0%和 70.3-89.7%，明显低于种的划分阈值。这六个菌株根据表型特征的差异与当前的 Haloarcula 和 Halomicroarcula 物种区分开来。六个新物种，即 Haloarcula halophila sp. nov.、Haloarcula litorea sp. nov.、Haloarcula rara sp. nov.、Haloarcula halobia sp. nov.、Haloarcula pelagica sp. nov. 和 Haloarcula ordinaria sp. nov.，分别被提议用于容纳菌株 DFY41、GDY20、SHR3、XH51、YJ-61-S 和 ZS-22-S1。