Genome Sequence of an Alkane-Degrading Bacterium, Alcanivorax pacificus Type Strain W11-5, Isolated from Deep Sea Sediment

Abstract

Alcanivorax pacificus W11-5^T was isolated from a pyrene-degrading consortium, enriched from the deep sea sediment of the Pacific Ocean. Strain W11-5^T can degrade various n-alkanes. Here we report the draft genome of W11-5^T and genes associated with alkane degradation.

GENOME ANNOUNCEMENT

Alcanivorax pacificus W11-5^T (MCCC 1A00474^T, CCTCC AB 208236^T, LMG 25514^T) was isolated from deep sea sediments of the Pacific Ocean enriched with pyrene as the sole carbon and energy source (3, 4). By now, only three strains of this species were isolated from marine environments, two in our lab (http://www.mccc.org.cn) and one strain (with 100% 16S rRNA gene sequence similarity) that can be retrieved in NCBI. In addition, 19 uncultured bacterial clones of 16S rRNA gene sequences with 99% 16S similarity were detected from skin of human plantar heel (2). A. pacificus strain W11-5^T grows well in mineral medium with an n-alkane carbon source with chain lengths from C₁₄ to C₂₈, but it cannot use pyrene as the sole carbon source for growth. Only one alkane hydroxylase was detected in strain W11-5^T by PCR prior to this study.

The genome sequence of A. pacificus W11-5^T was determined by Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China), using Solexa paired-end sequencing technology (1). A total of 5,855,964 paired-end reads (500-bp library) were generated to reach a 143-fold depth of coverage with Illumina/Solexa Genome Analyzer IIx (Illumina, SanDiego, CA), and the gaps among scaffolds were closed by custom primer walks or by PCR amplification followed by DNA sequencing. The obtained genome sequence of A. pacificus W11-5^T consists of 42 contigs (N₉₀ = 19) of 4,137,438 bp and had an average G+C content of 62.62%. Automatic gene annotation was carried out by the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html), which was followed by manual editing. The genome contains 3,762 candidate protein-encoding genes (with an average size of 964 bp), giving a coding intensity of 87.7%. A total of 2,870 proteins were assigned to cluster of orthologous groups (COG) families. Forty-one tRNA genes for 19 amino acids (lack of Ile) and one 16S-23S-5S rRNA operon were identified.

We particularly analyzed genes possibly responsible for alkane degradation. Genes encoding four integral-membrane alkane monooxygenases (AlkB) and three cytochrome P450 enzymes were found in the genome. Moreover, four genes encoding flavin-binding family monooxygenases (AlmA) responsible for long-chain n-alkane hydroxylation were found in the draft genome sequence. The W11-5^T genome sequence and its curated annotation are important assets to better understand the physiology and metabolic potential of A. pacificus and will open up new opportunities in the functional genomics of this species.

Nucleotide sequence accession number.

The draft genome sequence of Alcanivorax pacificus W11-5^T has been deposited at GenBank under accession number AJGP00000000 (chromosome).