一株嗜酸硫杆菌M4-422-6的分离及其全基因组测序和比较基因组学分析

Isolation, whole genome sequencing, and comparative genomic analysis of Acidithiobacillus strain M4-422-6

摘要:

【目的】开展具有硫氧化能力的嗜酸硫杆菌属(Acidithiobacillus)的分离及其比较基因组学分析，不仅可以丰富硫氧化细菌菌种资源，而且有助于加深理解嗜酸硫杆菌的分子进化与生态适应机制。【方法】利用以硫代硫酸钠为唯一能源的培养基分离具有硫氧化能力的细菌；利用Illumina HiSeq X和Oxford Nanopore测序平台对一株嗜酸硫杆菌M4-422-6进行全基因组测序；利用相关生物信息学分析软件对原始数据进行组装和基因组注释，并与一株亲缘关系最近的菌株Igneacidithiobacillus copahuensis VAN18-1进行比较基因组学分析。【结果】分离获得一株具有硫氧化能力的嗜酸硫杆菌M4-422-6。基因组注释结果显示，菌株M4-422-6基因组由1个染色体和2个质粒组成，基因组大小为2 917 823 bp，G+C含量为58.54%，共编码2 925个蛋白。16S rRNA基因和基因组系统发育树显示，菌株M4-422-6代表嗜酸硫杆菌属的一个潜在新种。功能基因注释结果显示，菌株Acidithiobacillus sp. M4-422-6拥有与菌株特性相关的众多基因，包括硫氧化相关基因、CO₂固定相关基因和耐酸相关基因。比较基因组学分析发现，虽然菌株M4-422-6与VAN18-1的亲缘关系最近，但两者仍拥有众多的差异基因，主要包括噬菌体抗性相关基因和移动元件编码基因。【结论】菌株M4-422-6代表嗜酸硫杆菌属的一个潜在新种，该菌株具有同种内菌株所不具有的特有基因，并据此推测嗜酸硫杆菌种内分化可归因于对特定生态位的适应。

Abstract:

[Objective] The isolation and comparative genomic analysis of Acidithiobacillus capable of oxidizing sulfur will enrich our knowledge about not only sulfur-oxidizing bacterial strains but also the molecular evolution and ecological adaptation mechanisms of Acidithiobacillus.[Methods] The medium with sodium thiosulfate as the sole energy source was used to isolate the strain capable of oxidizing sulfur, which was followed by Illumina HiSeq X and Oxford Nanopore sequencing of strain M4-422-6. Bioinformatics tools were used for sequence assembly and gene annotation, and the comparative genomic analysis was performed with Ignacidithiobacillus copahuensis VAN18-1. [Results] An Acidithiobacillus strain M4-422-6 capable of oxidizing sulfur was isolated. The genome annotation results showed that the genome of strain M4-422-6 consisted of one chromosome and two plasmids, with a length of 2 917 823 bp and G+C content of 58.54%, encoding a total of 2 925 proteins. The 16S rRNA gene sequence and the phylogenetic tree built by the type (strain) genome server (TYGS) revealed that strain M4-422-6 represented a novel species of Acidithiobacillus. Functional gene annotation showed that strain M4-422-6 carried numerous genes involved in sulfur oxidation, CO₂ fixation, and acid resistance. The comparative genomic analysis revealed that although strain M4-422-6 had the closest genetic relationship with Ignacidithiobacillus copahuensis VAN18-1, and the two strains possessed numerous different genes, which were mainly involved in phage resistance and mobile element encoding. [Conclusion] Strain M4-422-6 represents a novel species of Acidithiobacillus and has unique genes that are not present in strains of the same species. Therefore, we hypothesize that the intra-species differentiation of Acidithiobacillus can be attributed to adaptation to specific niches.