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 has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce. Results: Here, we identified a 5,436,472 bp chromosome with 40.30% GC content and a 241,339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As (III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Furthermore, a wide variety of genes associated with Sb(III) and other heavy metal (loid) s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), Bacillus sp. S3 was proved to a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed the evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal (loid) s resistance genes emphasized its indispensable role in the harsh eco-environment of Bacillus genus. Real-time quantitative PCR (RT-qPCR) analysis indicated that Sb(III)-related genes were all induced under the Sb(III) stress, while arsC gene was down-regulated. Conclusions: The results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationships between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.

Comprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine

“…CRISPR1 and CRISPR2 were located nucleotides at 2456771 to 2457221 bp with five spacers and 2981872 to 2982191 bp with four spacers, respectively. Our results propose that, like other pathogenic bacteria, the B. contaminans could initiate a defense mechanism against foreign gene invasion to maintain the stability of the genetic structure during evolution (Li et al 2020). Moreover, the results indicated that most mobile gene elements were distributed on chromosomes within the B. contaminans.…”

“…Pangenome analysis can be used to investigate the core, auxiliary, and unique genes in pathogenic bacterial genomes (Liang et al 2019). The core gene is frequently found in all strains, the accessory gene is present in two or more strains, and the unique gene is unique to individual members of a species (Bosi et al 2016;Li et al 2020). Five B. contaminans genomes yielded a pangenome size of 8832 genes; of these, the core genome is composed of 5452 genes (61.73%), and the accessory genome is composed of 2128 genes (24.09%).…”

Comprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine

“…CRISPR1 and CRISPR2 were located nucleotides at 2,456,771 to 2,457,221 bp with ve spacers and 2,981,872 to 2,982,191 bp with four spacers, respectively. Our results propose that, like other pathogenic bacteria, the B. contaminans could initiate a defense mechanism against foreign gene invasion to maintain the stability of the genetic structure during evolution (Li et al, 2020). Moreover, the results indicated that most mobile gene elements were distributed on chromosomes within the B. contaminans.…”

“…Pangenome analysis can be used to investigate the core, auxiliary, and unique genes in pathogenic bacterial genomes (Liang et al, 2019). The core gene is frequently found in all strains, the accessory gene is present in two or more strains, and the unique gene is unique to individual members of a species (Bosi et al, 2016;Li et al, 2020). Five B. contaminans genomes yielded a pangenome size of 8,832 genes; of these, the core genome is composed of 5,452 genes (61.73%), and the accessory genome is composed of 2,128 genes (24.09%).…”

Characterization of a Novel Bacillus glycinifermentans Strain MGMM1 Based on Full Genome Analysis and Phenotypic Properties for Biotechnological Applications

“…This may be a good indicator for its application in sewage treatments, as it can withstand these harsh conditions. Although there is no research on its application for bioremediation, an article by Li et al [ 67 ] compared the genome of Bacillus sp. S3 to other Bacillus species to determine its resistance to heavy metal antimony (Sb(III)-related genes).…”