Draft Genome Sequence of Pseudomonas frederiksbergensis SI8, a Psychrotrophic Aromatic-Degrading Bacterium.

Pseudomonas frederiksbergensis strain SI8 is a psychrotrophic bacterium capable of efficient aerobic degradation of aromatic hydrocarbons. The draft genome of P. frederiksbergensis SI8 is 6.57 Mb in size, with 5,904 coding sequences and 60.5% G+C content. The isopropylbenzene (cumene) degradation pathway is predicted to be present in P. frederiksbergensis SI8.

GENOME ANNOUNCEMENT

Pseudomonas frederiksbergensis strain SI8 was isolated from a desert soil sample from under a fuel storage bladder in Kuwait. This strain grows in temperatures ranging from 4°C to 30°C and metabolizes toluene, ethylbenzene, and propylbenzene, among other compounds. Based on the 16S rRNA gene sequence, P. frederiksbergensis SI8 is at least 99.0% similar to P. frederiksbergensis strains V1R0E2, JW-SD2, DSM13022, CB2B1. An alkane-degrading psychrophilic P. frederiksbergensis strain and a psychrotrophic strain from soil at a coal gasification plant have been reported (1, 2). Due to the importance of cold-tolerant microorganisms in the environment and their potential application in bioremediation, we have sequenced the genome of P. frederiksbergensis SI8, to understand the underlying aromatic-degradation mechanisms.

P. frederiksbergensis SI8 was sequenced on a Roche 454-GS Junior platform using a whole-genome shotgun (WGS) approach, resulting in 728,652 reads. The sequence reads were assembled with the Roche de novo Assembly software. More than 99% or 724,816 reads were assembled into 65 large (>500 bp) contigs, with an N50 of 320,712 bp. The longest contig was 684,101 bp. The draft genome sequence was 6,569,267 bases in length, with a G+C content of 60.5%. Rapid genome annotation using RAST annotation server (3) described 5,904 coding sequences (CDSs) and 64 RNAs. The coding sequences were classified into 546 subsystems of which amino acids and derivatives (n = 671 CDSs); carbohydrates (n = 509); membrane transport (n = 282); protein metabolism (n = 235); fatty acids, lipids, and isoprenoids (n = 222); RNA metabolism (n = 210); stress response (n = 206); cell wall and capsule (n = 186); virulence, disease, and defense (n = 159); respiration (n = 155); metabolism of aromatic compounds (n = 146); motility and chemotaxis (n = 143); regulation and cell signaling (n = 127); and DNA metabolism (n = 144) were the most abundant.

The NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/) predicted the benzene 1,2-dioxygenase, vanillate monooxygenase, catechol 1,2-dioxygenase (catA), homogentisate 1,2-dioxygenase, and 4-hydroxybenzoate 3-monooxygenase genes. The cum gene cluster (4) for isopropylbenze (cumene) degradation was present. This cluster is 99% similar to that of P. fluorescens, accession number D37828. P. frederiksbergensis SI8 showed at least 71% homology with twenty of the twenty one genes, with the exception of ditE, of the dit cluster for abietane diterpenoids catabolism of P. abietaniphila, accession number AF119621 (5). Additionally, the genes encoding protocatechuate 3,4-dioxygenase (ligA and ligB), 3-carboxymuconate cycloisomerase, and 4-carboxymuconolactone decarboxylase, of the central protocatechuate catabolic pathway for aromatic degradation were observed (6). The gentisate 1,2-dioxygenase (gdo) gene essential for the gentisate catabolic pathway of polycyclic aromatics was not detected (6). Important hydrocarbon degradation genes encoding 2,4-dichlorophenol 6-monooxygenase, alkanesulfonate monooxygenase, 2-polyprenyl-6-methoxyphenol hydroxylase, aminobenzoate oxygenase, and 2-nitropropane dioxygenase were observed. A gene cluster with at least 80% homology to the ttg2 operon encoding an ABC-type transporter essential for toluene resistance in P. Putida and P. aeruginosa, was observed (7, 8). The alkB genes were not detected, explaining its inability to degrade n-alkanes. This genome will provide valuable insight into the genetics and metabolism of hydrocarbon-degrading psychrotrophic bacteria.

Nucleotide sequence accession number.

This project has been deposited in DDBJ/EMBL/GenBank under the accession number JQGJ00000000.