Draft Genome Sequence of Bacillus pumilus Fairview, an Isolate Recovered from a Microbial Methanogenic Enrichment of Coal Seam Gas Formation Water from Queensland, Australia

Abstract

Despite its global abundance, Bacillus pumilus is poorly studied. The Fairview strain was obtained from a methanogenic anaerobic coal digester. The draft genome sequence was 3.8 Mbp long and contained 3,890 protein-coding genes. Like the SAFR-032 strain, it includes B. pumilus-specific proteins that likely confer enhanced resistance to environmental stresses.

GENOME ANNOUNCEMENT

Bacillus pumilus Fairview was isolated from a 45°C methanogenic anaerobic digester sample obtained from a coal seam gas formation water sample growing with a highly volatile bituminous Bowen Basin coal as the feedstock. The formation water was sourced from the Fairview coal seam gas field near Injune, Queensland, Australia (S25°51; E148°34) from a borehole intersecting a coal seam at approximately 600 m subsurface. On collection, the water was 45°C (pH 8.9) and had an electrical conductivity (EC) of 1,400 µS cm^–1. The digester was incubated at 45°C for 8 weeks before attempts were made to culture microbes from the consortium. These efforts included dilution on a range of media, including peptone, yeast-extract, and glucose (PYG) (all 1 g liter^–1) agar (1), followed by incubation to isolate facultative aerobes. One of the colonies isolated was the B. pumilus Fairview strain described. The pure culture was grown in liquid PYG, DNA was extracted, and Illumina (HiSeq, 100-bp paired-end [PE] library) sequencing was undertaken. Of the reads, 99.95% were assembled using Velvet 1/2/07 (k = 41) into the draft genome.

The draft genome of Fairview was 3,838,013 bp long and had coverage of ~200×. The genome was composed of 67 large contigs (>200 bp). Excluding the short contigs, mean and median contig lengths were 57,284 bp and 18,358 bp, respectively, with a maximum contig length of 568,093 bp. (The short contigs [<200 bp] are available at http://dx.doi.org/10.4225/08/531CF5598D431.) Genome annotation was undertaken with Integrated Microbial Genomes Expert Review (IMG ER) (2), which predicted 3,890 protein-coding genes. Based on coverage, we estimated that B. pumilus Fairview had five copies of the 16S gene. This 16S sequence has 99 to 100% identity with an array of B. pumilus, including the well-known SAFR-032 strain (3). Genomic comparisons of B. pumilus genomes available to date indicate that the Fairview strain is closely related to the CCMA-560 strain isolated from an oil-affected sediment (4) with which it shares ~89% of its genome. Further analyses of the genome using the SignalP (5) and dbCAN (6) pipelines revealed a small number of proteins which probably were extracellular β-glucosidase, pectin, or pectate lyase enzymes. Despite its presence in the digester, with coal as a sole source of carbon, no polyphenol oxidase or laccases were detected; however, a vanillyl-alcohol oxidase was identified and may be involved in some aromatic degradative processes.

It remains unclear whether the taxon was growing in the digestor or was present as a spore; genes for respiratory nitrate reduction were not detected. Furthermore, spores of B. pumilus have been shown to have extreme resistance to a range of stressors (7–9) and this may be conferred by a range of repair proteins unique to B. pumilus (3). Like SAFR-032, the Fairview strain possesses analogs of a B. pumilus-specific DNA photo-lyase enzyme (csirobg2_00392) that may confer resistance properties to this strain. Despite occurring in many environments, B. pumilus is relatively poorly studied compared to its relative B. subtilis. The ability of B. pumilus to survive in extreme environments, host unusual genes, and produce a range of metabolites warrants further examination.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JFBY00000000. The version described in this paper is the first version, JFBY01000000.