Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation.

Xian Zhang,Yunhua Xiao,Xue Feng,Xueduan Liu,Jiemeng Tao,Liyuan Ma,Yili Liang,Huaqun Yin

doi:10.3390/ijms17081355

Xian Zhang, Yunhua Xiao + Show 6 more

Open Access

https://doi.org/10.3390/ijms17081355

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Abstract

Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.

Highlights

Extreme environments [1,2,3] are the habitats for extremophiles, they were previously thought of as almost insurmountable physical and chemical barriers to life [4]
General Features of Acidithiobacillus thiooxidans (A. thiooxidans) Genomes Six new genomic DNA were subjected to Illumina MiSeq sequencing platform, and an average of MSbixranwewregaednso(mshicorDtNDANwAesreeqsuuebnjeccetse)dintoeIalcluhmgiennaoMmieSewqasseyqiueeldnceidn.gApfltaetrfoqruma,liatnydcoantarvoel ruasgieng
Comparative genomics provided useful information on the genetic and functional features of A. thiooxidans strains. Phylogeny based on their core genome revealed that genetic diversity was potentially related to the geographic distribution and geochemical conditions of their habitats

Summary

Introduction

Extreme environments [1,2,3] are the habitats for extremophiles, they were previously thought of as almost insurmountable physical and chemical barriers to life [4]. In contrast to standard genetic researches, which have inherent limits to elucidate the hereditary traits of species, acquisition of genomic sequences generated by high-throughput sequencing provides plentiful gene contents and further enables future studies to explore the primary issues that investigators are interested in. Acidophiles such as Acidithiobacillus, Sulfobacillus, and Leptospirillum were isolated from the extremely acidic environments, and their sequenced genomes were used for comparative survey [6,9,10]. It remains unclear whether these intriguing findings concerning the genomic analyses of other organisms could be applied to acidophiles isolated from the harsh environments that are physico-chemically and ecologically distinct from the “normal” environments

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