Complete Genome Sequence of the Extremophilic Bacillus cereus Strain Q1 with Industrial Applications

Bacillus cereus strain Q1 was isolated from a deep-subsurface oil reservoir in the Daqing oil field in northeastern China. This strain is able to produce biosurfactants and to survive in extreme environments. Here we report the finished and annotated genome sequence of this organism.Bacillus cereus strain Q1 was isolated from a deep-subsurface oil reservoir in the Daqing oil field in northeastern China. This strain can facilitate oil recovery when added to an oil reservoir. This attribute may be partially due to its ability to produce biosurfactants, which assist microbial enhanced oil recovery by lowering interfacial tension at the oil-rock interface (data not shown).The complete genome sequence of B. cereus Q1 was determined by the whole-genome shotgun strategy. Draft assemblies were based on 55,790 high-quality reads. All libraries provided sixfold coverage of the genome. Gap closure was accomplished by primer walking on gap-spanning clones and direct sequencing of combinatorial PCR products. Open reading frame (ORF) predictions were obtained and annotation was performed as described previously (4). GenomeComp was used for genomic comparison with default parameters (5).The genome of B. cereus Q1 is composed of one circular chromosome of 5,214,195 bp and two circular plasmids (pBc239 239,246 bp] and pBc53 52,766 bp]) with mean G+C contents of 35.6, 33.5, and 35.1%, respectively. There are 5,657 predicted ORFs, 13 rRNA operons, and 94 tRNA genes for all 20 amino acids, covering 86% of the genome. Putative functions were assigned to 3,946 ORFs. Of the remainder, 1,561 showed similarity to hypothetical proteins and 140 had no detectable homologs in the public protein database (E value, <10⁻¹⁰). Twelve phage-related genes were identified, but no complete prophages were found. Whole-genome comparison showed that Q1 has extensive similarity to the genomes of other members of the B. cereus group and the greatest similarity to nonpathogenic strain B. cereus ATCC 10987 (5,224,283 bp).Genome analysis revealed that B. cereus Q1 contains several genes related to niche-specific adaptations. As a thermophilic bacterium, Q1 can easily adapt to geothermal oil reservoirs. Three thermophily-associated genes (BC1015, BC1017, and BC1018) found in Q1 have orthologs in Moorella thermoacetica ATCC 39073. The latter genes encode the structural maintenance of chromosome protein, exonuclease SbcC, and subunit A of DNA topoisomerase VI, respectively. The presence of the genes involved in the utilization of l-fucose (BC2995 to BC3006) and d-mannose (BC5091 to BC5094, BC5097 to BC5102, and BC5105 to BC5111) helps Q1 use these carbohydrates as carbon sources under glucose-limited conditions. Q1 also contains the nitrate utilization gene cluster (BC2100 to BC2123), including a typical narGHJI operon that encodes membrane-bound nitrate reductase. The nitrate utilization gene cluster might play an important role in helping the strain use nitrate as a nitrogen source and survive under anaerobic or oxygen-limited conditions. Moreover, we found an operon that encodes proteins responsible for producing a novel type of lantibiotic (2), which we designated cereicidin. All of the above-mentioned genes were not found in the other B. cereus group bacteria.One of the notable features of Q1 is its ability to produce biosurfactants. The dhb operon (dhbACEBF), which is involved in nonribosomal peptide synthesis and encodes the biosynthetic template for the catecholic siderophore in B. subtilis (1), was identified in Q1. Downstream of the operon, the sfp gene, which encodes phosphopantetheinyl transferase and is required for production of the lipopeptide antibiotic surfactin in B. subtilis (3), was found. No surfactin synthetase gene (srfAA, srfAB, or srfAC) was found, but the mbtH gene involved in mycobactin synthesis and a gene (BC2300) with an unknown function were found in the region between the dhb operon and the sfp gene. We therefore speculated that these three genes located downstream of the dhbF gene might belong to the dhb operon, which is involved in antibiotic-siderophore-surfactin biosynthesis.The B. cereus Q1 genome provides an excellent platform for the further improvement of this organism for biosurfactant production and extends our understanding of the evolutionary relationships among B. cereus group organisms.