Draft Genome Sequence of Pseudomonas abietaniphila KF701 (NBRC110664), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated Soil.

Pseudomonas abietaniphila KF701 utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (PCBs). Here, we report the 6,886,250-bp draft genome sequence of KF701, which contains 6,315 coding sequences and 59.4 mol% G+C content. The strain possesses genes for biphenyl catabolism and other genes that mediate the degradation of benzoate, salicylate, and phenol.

GENOME ANNOUNCEMENT

Polychlorinated biphenyls (BCBs) have been recognized as serious environmental pollutants (1). Biphenyl-utilizing bacteria cometabolize certain PCB congeners into chlorobenzoic acids through oxidation by biphenyl-catabolic enzymes. The biphenyl catabolic bph genes were first cloned from Pseudomonas pseudoalcaligenes KF707 (2). Since then, a number of PCB-degrading bacteria have been identified, including both Gram-negative and Gram-positive bacteria (3). Some strains possess very similar, if not identical, bph genes, while others possess diversified bph genes (4). The purpose of this study was to explore how bph genes are organized, transferred, and rearranged by sequencing the genomes of various PCB degraders isolated from the same site. We isolated 14 PCB-degrading bacterial strains (KF strains), including Pseudomonas abietaniphila KF701 (formerly Pseudomonas graminis KF701) from biphenyl-contaminated soil in Kitakyushu, Japan (4).

Whole-genome shotgun sequencing of P. abietaniphila KF701 was performed by the National Institute of Technology and Evaluation (NITE) using a combination of shotgun sequencing on a 454 Roche GS FLX+ system (Roche) and paired-end sequencing on a HiSeq sequencing system (Illumina). The Newbler software package (version 2.6; Roche) was used for genome assembly. The draft genome was composed of 140 contigs (>537 bp) totaling 6,886,250 bases, with a G+C content of 59.4 mol%. The N50 contig size and the largest contig size were 90,844 bp and 392,029 bp, respectively.

Rapid genome annotation using the RAST annotation server (5) described 6,315 coding sequences (CDSs), 58 tRNA sequences, and 4 rRNA sequences. The coding sequences were classified into 547 subsystems, including cofactors, vitamins, prosthetic groups, and pigments (n = 328 CDSs), phages, prophages, transposable elements, and plasmids (n = 17 CDSs), motility and chemotaxis (n = 152 CDSs), metabolism of aromatic compounds (n = 146 CDSs), and metabolism of carbohydrates (n = 526 CDSs). A comparison of P. abietaniphila KF701 with other Pseudomonas strains within the RAST server database identified Pseudomonas syringae pv. syringae B728a (taxonomy ID, 205918.7) as its closest neighbor, with a score of 515, followed by P. syringae pv. phaseolicola 1448A (taxonomy ID, 264730.9), with a score of 481.

Functional annotations were compared with the Kyoto Encyclopedia of Genes and Genomes (KEGG) (6). Strain KF701 possessed bph genes very similar to those of Pseudomonas putida KF715 (7), benzoate-degrading genes via the hydroxylation pathway, and entire genes of the salicylate and phenol degradation pathways.

Nucleotide sequence accession numbers.

The draft genome sequence of P. abietaniphila KF701 has been deposited at DDBJ/EMBL/GenBank under the accession numbers BBQJ01000001 to BBQJ01000140.