Draft Genome Sequence of Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Pseudomonas bauzanensis Strain W13Z2.

Pseudomonas bauzanensis W13Z2 is a halotolerant polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from petroleum-contaminated drill cuttings in the Bohai Sea. Here, we report the 8.6-Mb draft genome sequence of this strain, which will provide insights into the diversity of Pseudomonas and the mechanism of PAHs degradation in drill cuttings.

GENOME ANNOUNCEMENT

Microbial populations in drill cuttings have been well documented (1, 2). However, little is known about polycyclic aromatic hydrocarbon (PAH)-degrading bacteria in such an environment. Pseudomonas bauzanensis W13Z2, which can degrade phenanthrene and pyrene with 5% NaCl, was isolated from petroleum-contaminated drill cuttings in the Bohai Sea of China. However, genomic information about P. bauzanensis is still unknown, which limits understanding of the mechanism of PAH degradation in drill cuttings. Here, the draft genome sequence of P. bauzanensis W13Z2 is presented for the first time.

Genomic DNA was extracted and sequenced using an Illumina HiSeq 2000 platform. The shotgun sequencing produced 14,417,292 paired-end reads with an average insert size of 300 bp (yielding approximately 170-fold coverage), which were filtered by NGS QC toolkit v 2.3 (3). Filtered reads were assembled, scaffolded, gap filled, and validated using SOAPdenovo v. 2.04 (4), SSPACE v. 2.0 (5), GapFiller v. 1.10 (6), and bwa v. 0.7.4 (7). Final assembly consisted of 69 contigs with an N50 length of 289,896 bp and the largest length of 1,692,974 bp. The genome sequence was annotated using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/).

The genome consists of 8.6 Mb, with a G+C content of 61.8%. A total of 7,839 coding sequences (CDS), 139 pseudogenes, 97 tRNA genes, and 2 noncoding RNA (ncRNA) and 11 rRNA genes were identified. Of the CDS, 76.5% were assigned to clusters of orthologous groups (COGs) with amino acid transport and metabolism as the most abundant class, and 43.3% can be annotated into 2,479 KEGG orthologous groups by using KAAS (8), involving 218 metabolic pathways. A total of 209 tandem repeats were detected by Tandem Repeats Finder v. 4.07 (9). The IS5 family dominated the insertion sequence (IS) elements as revealed by ISFinder (10). A total of 695 potentially secreted proteins were identified by SignalP v. 4.0 (11). One clustered regularly interspaced short palindromic repeat (CRISPR) element with 20 spacers was identified by CRISPRFinder (12). Average nucleotide identity (ANI) analysis (13) revealed that P. bauzanensis W13Z2 is phylogenetically related to Pseudomonas aeruginosa PAO1 (70.5%) (14), P. brassicacearum NFM421 (69.55%) (15), P. denitrificans ATCC 13867 (70.7%) (16), P. entomophila L48 (70.2%) (17), P. mendocina NK01 (70.5%) (18), P. monteilii SB3078 (70.0%) (19), P. poae RE*1/1/14 (69.7%) (20), P. putida KT2440 (69.8%) (21), P. resinovorans NBRC106553 (70.8%) (22), P. stutzeri A1501 (70.8%) (23), and P. syringae pv. tomato DC3000 (69.2%) (24).

Thirteen genes responsible for the degradation of alkanes and PAHs were identified, including 1 alkane 1-monooxygenase gene, 5 catechol 1,2-dioxygenase genes, 2 benzene 1,2-dioxygenase genes, and 5 naphthalene 1,2-dioxygenase genes. Moreover, 9 genes were identified as involved in compatible solute synthesis and uptake, including 3 betaine-aldehyde dehydrogenase, 5 glycine/betaine ABC transporter genes, and 1 ectoine synthase genes. Copper-, mercury-, and tellurium-resistant genes were detected, which may enhance the resistance to heavy metal. Eleven cold shock protein genes were detected, which are helpful for the survival in seawater at low temperatures.

Nucleotide sequence accession number.

The draft genome sequence of P. bauzanensis W13Z2 has been deposited in GenBank under the accession number JFHS00000000. The version described in this paper is the first version.