青藏高原戈壁生境中一株链霉菌新种Streptomyces haixigobicum sp. nov. Qhu-G9的多相分类学鉴定及其次级代谢产物的基因组挖掘

Polyphasic identification and genome mining of secondary metabolites of a novel species Streptomyces haixigobicum sp. nov. Qhu-G9 isolated from the Gobi habitat of the Qinghai-Tibetan Plateau

摘要:

【背景】青藏高原极端生境具有丰富的微生物资源，同时也是微生物药物的重要来源，但是大量微生物新资源尚待开发利用。【目的】对从青藏高原戈壁土壤中分离得到的一株链霉菌Qhu-G9进行多相分类鉴定及次级代谢产物生物合成潜力分析。【方法】通过16S rRNA基因扩增、测序和系统发育分析，结合形态、生理生化、细胞化学组分及基因组测序等多相分类特征，确定链霉菌Qhu-G9的分类地位。【结果】Qhu-G9与链霉菌Streptomyces dioscori A217^T和Streptomyces auranttⅡacus NBRC 13017^T相似度最高，均为99.22%，结合形态观察，说明该菌是一株链霉菌。基于16S rRNA基因序列构建的系统发育树显示Qhu-G9独立成支，并且其生理生化和细胞化学成分特征与最相似模式菌存在较大差异。通过基因组测序评估了与最相似模式菌的数字DNA-DNA杂交值(digital DNA-DNA hybridization, dDDH)和平均核苷酸一致性(average nucleotide identity, ANI)，发现Qhu-G9与最相似菌S. auranttⅡacus NBRC 13017^T的dDDH与ANI值最高，分别为36.65%和88.21%，但是均低于判定新菌的阈值，进一步表明Qhu-G9为一株链霉菌属新种，并命名为Streptomyces haixigobicum sp. nov. Qhu-G9。此外，通过antiSMASH分析发现Qhu-G9基因组中存在大量编码已知和未知次级代谢产物的生物合成基因簇。【结论】从青藏高原戈壁土壤中分离得到的Qhu-G9是一株链霉菌新种，并且具有进一步挖掘活性次级代谢产物的潜力。

Abstract:

[Background] The extreme habitats of the Qinghai-Tibet Plateau (QTP) harbor rich microbial resources and are important sources of microbial drugs, with abundant microbial resources remaining to be exploited.[Objective] A Streptomyces strain Qhu-G9 isolated from Gobi soil of the QTP was identified by polyphasic taxonomy, and its biosynthesis potential of secondary metabolites was analyzed. [Methods] The taxonomic status of Streptomyces Qhu-G9 was determined by 16S rRNA gene amplification, sequencing, and phylogenetic analysis, combined with polyphasic taxonomy based on genome sequencing and morphological, physiochemical, and cytochemical characteristics. [Results] Qhu-G9 had the highest similarity (99.22%) with the type strains Streptomyces dioscori A217^T and S. auranttⅡacus NBRC 13017^T, which, combined with morphological characteristics, indicated that Qhu-G9 belonged to Streptomyces. However, the phylogenetic tree constructed based on the 16S rRNA gene sequence displayed that Qhu-G9 branched independently. Moreover, the physiochemical and cytochemical characteristics of this strain were quite different from those of the most similar model bacteria. We then employed genome sequencing to evaluate the digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between Qhu-G9 and the model bacteria. The dDDH and ANI values were the highest between Qhu-G9 and S. auranttⅡacus NBRC 13017^T, reaching 36.65% and 88.21%, respectively, both of which were lower than those determining a novel species. The results further confirmed that Qhu-G9 was a novel species of Streptomyces and named as S. haixigobicum sp. nov. Qhu-G9. In addition, antiSMASH revealed a large number of gene clusters for the biosynthesis of known and unknown secondary metabolites in the Qhu-G9 genome. [Conclusion] Qhu-G9 isolated from Gobi soil of the QTP is a novel Streptomyces species and has great potential for the production of active secondary metabolites.