Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium

Abstract

Background: Antimonite [Sb(III)]-oxidizing bacterium have great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 isolated from antimony-contaminated soil showed high Sb(III) resistance and Sb(III) oxidation efficiency. However, very little genomic information and evolutionary relationships that bacterial oxidation of Sb(III) is available. Results: Here, we identified a 5579638 bp chromosome with 40.30% GC content and a 241339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contains key aioB gene potentially encoding As(III)/Sb(III) oxidase, is not shared with other Bacillus strains. Further, a series of genes associated with Sb(III) and other heavy metal(loid) were also ascertained, reflecting adaptive advantage for growth in the harsh eco-environment. It is noteworthy that Bacillus sp. S3 is a novel species within the Bacillus genus as indicated by phylogenetic relationship and the average nucleotide identities (ANI) analysis. The presence of genomic plasticity demonstrated a high number of mobile genetic elements (MGEs) that were mainly distributed on chromosomes within the Bacillus genus. The core genome contained 554 core genes and many unique genes were dissected in analyzed genomes, indicating a conserved core but adaptive pan repertoire. Whole genomic alignment indicates that frequently genomic reshuffling and rearrangements, genetic gain and loss, and other recombination events occurred during the evolutionary history of Bacillus genus. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed that evolutionary relationships and events of horizontal gene transfer (HGT) among the Bacillus genus. The assessment of functionality of heavy metal(loid) resistance genes emphasized its indispensable roles in the harsh eco-environment of Bacillus genus. The real-time Quantitative PCR(RT-qPCR) results of Sb(III)-related genes indicated that the Sb(III) resistance was constantly increased under the Sb(III) stress. Conclusions: The insights provided in this study shed light on the molecular details of Bacillus sp. S3 coping with Sb(III), which extended our understanding on the evolutionary relationship between Bacillus sp. S3 and other closely related species and will enrich the Sb(III) resistance genetic data sources.