Complete Genome Sequence of Bacillus pumilus PDSLzg-1, a Hydrocarbon-Degrading Bacterium Isolated from Oil-Contaminated Soil in China.

Bacillus pumilus strain PDSLzg-1, an efficient hydrocarbon-degrading bacterium, was isolated from oil-contaminated soil. Here, we present the complete sequence of its circular chromosome and circular plasmid. The genomic information is essential for the study of degradation of oil by B. pumilus PDSLzg-1.

GENOME ANNOUNCEMENT

Bacillus pumilus strain PDSLzg-1 is a novel bacterium isolated from oil-contaminated soil of the Shengli oil field (Shandong, People’s Republic of China) in 2015. The bacterium is characterized as Gram-positive, aerobic, motile, rod-shaped, and forming endospores. According to 16s rRNA sequencing analysis, the bacterium is identified as a strain of Bacillus pumilus. This strain, designated PDSLzg-1, has the ability to effectively degrade petroleum hydrocarbons, especially C8 to C18 alkanes, and was shown to produce at least one bio-surfactant and may be of interest for an industrial application of oil pollution degradation.

B. pumilus PDSLzg-1 genomic DNA was isolated from overnight culture using a Wizard Genomic DNA purification kit (Promega). Total DNA obtained was subjected to quality control by agarose gel electrophoresis and quantified by Qubit. The genome of B. pumilus PDSLzg-1 was sequenced by single molecule real-time (SMRT) technology. Sequencing was performed at the Beijing Novogene Bioinformatics Technology Co., Ltd., producing 95,240 reads with 358× coverage. SMRT Analysis 2.3.0 was used to filter low-quality reads and the filtered reads were assembled to generate one contig without gaps. The genome of B. pumilus PDSLzg-1 had a 3,698,973-bp circular chromosome and an 11,801-bp circular plasmid with G+C contents of 41.96% and 39.36%, respectively. Gene prediction was performed on the B. pumilus PDSLzg-1 genome by GeneMarkS, resulting in the identification of 3,895 genes with an average length of 848 bp (1). 81 tRNA genes were predicted with tRNAscan-SE, 24 rRNA genes were predicted with rRNAmmer, and seven sRNAs were predicted by a BLAST search against the Rfam database (2–4). A whole-genome BLAST search (E value less than 1e−5, minimal alignment length percentage larger than 40%) was performed against KEGG, COG, nr, Swiss-Prot, GO, and TrEMBL (5–9). 3,689 (94.7%) genes were annotated to at least one database.

There were a group of genes in genome of B. pumilus strain PDSLzg-1 encoding alcohol dehydrogenase, aldehyde dehydrogenase, and monooxygenase, which are probably related to oil degradation (10, 11). This study presents the first fully sequenced and annotated hydrocarbon-degrading strain of B. pumilus, which is valuable for studying its evolution, hydrocarbon-degrading mechanism, and industrial applications.

Accession number(s).

The complete annotated genome and plasmid sequences of B. pumilus strain PDSLzg-1 were deposited in GenBank under the accession numbers CP016784 and CP016785, respectively.