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

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.