Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio.
Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio.
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DOI：
10.1371/journal.pone.0173517
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Muyzer G
中科院分区：
文献类型：
--
作者：
Ahn AC;Meier-Kolthoff JP;Overmars L;Richter M;Woyke T;Sorokin DY;Muyzer G
硫碱弧菌是一种专性化能自养的嗜盐碱性硫氧化细菌。它们的栖息地是苏打湖，这是一种双重极端环境，pH值范围从9.5到11，盐浓度达到饱和。目前已从世界各地的碱湖中分离出100多株该属真菌，但目前仅描述了10个种。因此，将剩余的菌株分配给现有的或新的物种是重要的，将进一步阐明其基因组多样性，以及更好地了解这个属。最近，对76株硫碱弧菌的基因组进行了测序。在这些方面，我们应用了不同的方法，包括（i）16S rRNA基因序列分析，（ii）基于八个管家基因的多位点序列分析（MLSA），（iii）基于BLAST（ANIb）和MUMmer（ANIm）的平均核苷酸同一性，（iv）四核苷酸频率相关系数（TETRA），（v）数字DNA：DNA杂交（dDDH）以及（vi）基于核苷酸和氨基酸的基因组BLAST距离系统发育（GBDP）分析。除了已经描述的10个物种之外，我们还发现了15个新的“基因组”物种和16个新的“基因组”亚种，检测到了高基因组多样性。系统发育和基因组分析表明，属是不是单系，因为四个菌株明显分开，从其他属的模式菌株从其他硫碱弧菌。因此，建议将后者分类为一个新属。硫碱弧菌的地理分布表明，不同的“基因组”物种可以被归类为候选间断或候选特有种。本研究是一个详细的基于基因组的分类和鉴定属内的成员硫碱弧菌。然而，未来的表型和化学分类学的研究将需要一个完整的物种描述本属。
Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but only ten species have been effectively described yet. Therefore, the assignment of the remaining strains to either existing or novel species is important and will further elucidate their genomic diversity as well as give a better general understanding of this genus. Recently, the genomes of 76 Thioalkalivibrio strains were sequenced. On these, we applied different methods including (i) 16S rRNA gene sequence analysis, (ii) Multilocus Sequence Analysis (MLSA) based on eight housekeeping genes, (iii) Average Nucleotide Identity based on BLAST (ANIb) and MUMmer (ANIm), (iv) Tetranucleotide frequency correlation coefficients (TETRA), (v) digital DNA:DNA hybridization (dDDH) as well as (vi) nucleotide- and amino acid-based Genome BLAST Distance Phylogeny (GBDP) analyses. We detected a high genomic diversity by revealing 15 new “genomic” species and 16 new “genomic” subspecies in addition to the ten already described species. Phylogenetic and phylogenomic analyses showed that the genus is not monophyletic, because four strains were clearly separated from the other Thioalkalivibrio by type strains from other genera. Therefore, it is recommended to classify the latter group as a novel genus. The biogeographic distribution of Thioalkalivibrio suggested that the different “genomic” species can be classified as candidate disjunct or candidate endemic species. This study is a detailed genome-based classification and identification of members within the genus Thioalkalivibrio. However, future phenotypical and chemotaxonomical studies will be needed for a full species description of this genus.