对大柴旦盐杆菌与塘沽盐杆菌分类地位的修订

Revision of the taxonomic status of Halobacterium dachaidanensis and Halobacterium tangguensis

摘要:

【背景】 1984年，我国学者在国内学术期刊上首次发表了分离自我国内陆盐湖和海滨盐田的极端嗜盐菌新物种：大柴旦盐杆菌(Halobacterium dachaidanensis)和塘沽盐杆菌(Halobacterium tangguensis)。40年来，嗜盐古菌的分类体系不断完善，但这2个物种的分类地位仍不明确。【目的】 基于系统基因组学、比较基因组学方法以及表型特征分析，明确Hbt. dachaidanensis F3和Hbt. tangguensis F5的分类地位。【方法】 扩增、测定2个菌株的16S rRNA基因与rpoB′基因，基于系统发育分析，初步鉴定上述菌株；测定菌株的基因组框架图，通过系统基因组学和比较基因组学方法明确2个菌株的分类学地位；通过KEGG注释确定菌株的主要代谢途径；通过表型特征分析比较菌株的主要理化特征。【结果】 系统基因组学分析结果表明，菌株F3和F5分别与解淀粉盐盒菌(Haloarcula amylolytica) BD-3^T和耐热需苏打线菌(Natrinema thermotolerans) JCM 11050^T聚为一支。基因组测序结果显示，菌株F3和F5的G+C含量分别为62.2%和65.5%。比较基因组学分析显示，菌株F3与Har. amylolytica BD-3^T的平均核苷酸一致性(average nucleotide identity, ANI)、DNA-DNA杂交同源性(digital DNA-DNA hybridization, dDDH)和平均氨基酸一致性(average amino acid identity, AAI)分别为98.3%、88.1%、97.9%，而菌株F5与Nnm. thermotolerans JCM 11050^T的这3个值分别为98.0%、85.2%、97.9%，均高于原核生物关于种的界定阈值。表型特征结果表明，菌株F3的最适生长盐度、温度和pH值分别为2.6 mol/L、37 ℃和7.5，而菌株F5则分别为3.4 mol/L、40 ℃和7.0。2个菌株与相近物种在多个表型特征上存在差异。功能基因注释结果表明，碳水化合物代谢和氨基酸代谢为2株菌的主要代谢途径。【结论】 通过多相分类，明确了菌株F3和F5的分类地位，分别归属于Har. amylolytica和Nnm. thermotolerans。菌株F3代表一个新的亚种，建议命名为“解淀粉盐盒菌大柴旦亚种”。

Abstract:

[Background] In 1984, two novel halophilic archaea species, Halobacterium dachaidanensis sp. nov. and Hbt. tangguensis sp. nov., were isolated from an inland saline lake and a marine solar saltern in China, and first published on Acta Microbiologica Sinica by Chinese researchers. Over the past four decades, the taxonomic system of halophilic archaea has been continuously updated, while the precise taxonomic status of these two species remains unclear. [Objective] To clarify the taxonomic status of Hbt. dachaidanensis F3 and Hbt. tangguensis F5 by phylogenomic and comparative genomic analyses and phenotypic characterization. [Methods] We performed the phylogenetic analysis based on amplified and sequenced 16S rRNA and rpoB' genes. The draft genomes of these two strains were sequenced and the taxonomic status of them was elucidated by phylogenomic and comparative genomic analyses. The major metabolic pathways of both strains were identified through KEGG annotation. The key physiological and biochemical characteristics were comparatively analyzed via phenotypic assays. [Results] Phylogenetic analyses revealed that strains F3 and F5 formed tight clusters with Har. amylolytica BD-3^T and Natrinema thermotolerans JCM 11050^T, respectively. The genomic G+C content of strains F3 and F5 was 62.2% and 65.5%, respectively. Comparative genomic analysis showed that the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) between strain F3 and Har. amylolytica BD-3^T were 98.3%, 88.1%, and 97.9%, respectively, and these three values between strain F5 and Nnm. thermotolerans JCM 11050^T were 98.0%, 85.2%, and 97.9%, respectively. These values were higher than the thresholds for species demarcation in prokaryotes. The phenotypic characterization showed that the optimum growth salinity, temperature, and pH for strain F3 were 2.6 mol/L, 37 ℃, and 7.5, while those for strain F5 were 3.4 mol/L, 40 ℃, and 7.0, respectively. Diverse differential phenotypic characteristics were found among these two strains and their related species. Functional gene annotations identified carbohydrate metabolism and amino acid metabolism as the predominant metabolic pathways in both strains. [Conclusion] The taxonomic status of Hbt. dachaidanensis F3 and Hbt. tangguensis F5 was reclarified by polyphasic taxonomic characterization as Har. amylolytica and Nnm. thermotolerans, respectively. Strain F3 may represent a novel subspecies, for which the name, Haloarcula amylolytica subsp. dachaidanensis subsp. nov., is proposed.