Alcanivorax pacificus
Alcanivorax pacificus is a pyrene-degrading marine gammaprotobacterium. It is of the genus "Alcanivorax", a group of marine bacteria known for degrading hydrocarbons. When originally proposed, the genus "Alcanivorax" comprised six distinguishable species. However, "A. pacificus", a seventh strain, was isolated from deep sea sediments in the West Pacific Ocean by Shanghai Majorbio Bio-pharm Technology Co., Ltd. in 2011. "A. pacificus’s" ability to degrade hydrocarbons can be employed for cleaning up oil-contaminated oceans through bioremediation. The genomic differences present in this strain of "Alcanivorax" that distinguish it from the original consortium are important to understand  to better utilize this bacteria for bioremediation. Characteristics. "A. pacificus" is a non-motile, Gram-negative bacillus. It is oxidase- and catalase-positive. It forms light grey colonies that are between 1 and 2 millimeters in diameter when grown on 216L marine agar medium containing seawater, sodium acetate, tryptone, yeast extract, ammonium nitrate, and sodium citrate. "A. pacificus" is mesophilic and moderately halophilic, growing best in an environment between 10-42 degrees Celsius that contains 0.5-12% NaCl. Genome. Shanghai Majorbio Bio-pharm Technology Co., Ltd. sequenced a total of 5,855,964 paired ends of "A. pacificus" using Solexa paired-end  sequencing technology. The obtained type strain of "A. pacificus" is W11-5 (=MCCC 1A00474 =CCTCC AB 208236 =LMG 25514). The GC-content of strain W11-5 is 62.62%. Strain W11-5 is made of 42 contigs ("N" = 19) of 4,137,438 bp. Results from automatic gene annotation, which was completed by the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP), revealed that the genome of strain W11-5 contains 3,762 candidate protein-encoding genes. Out of these genes, 2,870 proteins were assigned to orthologous groups. Additionally identified were 41 tRNA genes for 19 amino acids and one 16S-23S-5S  rRNA operon. Particularly close attention was paid to genes that potentially coded for alkane degradation. Found were genes encoding for four integral-membrane alkane monooxygenases, three cytochrome P450 enzymes, and four genes encoding flavin-binding family monooxygenases. These monooxygenases are especially important, as they account for long-chain "n"-alkane hydroxylation. Diversity. "A. Pacificus" is closely related to other strains in the genus "Alcanivorax". It shares 16S rRNA gene sequence similarities of 93.9, 93.1, 93.1, 93.0, 93.0 and 92.9% with neighboring strains "A." "dieselolei" B-5 , "A. balearicus" MACL04 , "A. hongdengensis" A-11-3 , "A. venustensis" ISO4 , "A. borkumensis" SK2 and "A. jadensis  T9 respectively. However, as the gene sequence of A. Pacificus" diverges more than 3% from all other strains, it is different enough to represent a novel bacterial strain. Part of this difference results from a 549 nucleootide fragment of the alkane hydroxylase gene "alkB", which was amplified from the strand W11-5. The gene alkB is a protein that is produced by "A. pacificus" and other strains in the genus "Alcanivorax" that reverses the damage of alkylation, the process by which an alkane missing one hydrogen is transferred from one molecule to another. The amino acid sequences deduced from this  fragment show that there is not a clear grouping between the species of "Alcanivorax", as some strains within this genus contain multiple alkB sequences, which places them on different branches of the phylogenetic tree.