Draft Genome Sequence of Nocardioides luteus Strain BAFB, an Alkane-Degrading Bacterium Isolated from JP-7-Polluted Soil.

Nocardioides luteus strain BAFB is a Gram-positive bacterium that efficiently degrades C8 to C11 alkanes aerobically. The draft genome of N. luteus BAFB is 5.76 Mb in size, with 5,358 coding sequences and 69.9% G+C content. The genes responsible for alkane degradation are present in this strain.

GENOME ANNOUNCEMENT

Nocardioides luteus strain BAFB is a Gram-positive, high G+C, aerobic actinomycete bacterium isolated from soil contaminated with JP-7, a light petroleum hydrocarbon distillate fuel, from Beale Air Force Base in Northern California. This strain was shown to degrade alkanes in the range of C8 to C11 efficiently (1). Our results confirmed that N. luteus BAFB exhibits efficient degradation of C8 to C11 normal and mono-branched alkane compounds. Several Nocardioides spp. have been isolated from environments contaminated with hydrocarbons and shown to degrade aromatics and alkanes (2 – 4). Based on BLAST analysis (http://blast.ncbi.nlm.nih.gov/Blast.cgi) of the 16S rRNA gene sequence, N. luteus BAFB is 100% similar in 98% of the sequence to N. albus KAUST1; 96% similar to Nocardioides sp. CF8 (5) and N. nitrophenolicus JCM 10703; and 94% similar to N. aromaticivorans JCM 11674. We have sequenced the genome of N. luteus BAFB to understand the mechanisms controlling its hydrocarbon-adaptation and alkane-degradation activities.

N. luteus BAFB was sequenced on an Illumina HiSeq platform using a whole-genome shotgun approach, producing 8,457,792 reads. Roche de novo assembly software (Newbler version 2.9) aligned the reads into 86 large (>500 bp) contigs with an average coverage of 111× and an N50 of 121,485 bp. The largest contig extended 261,750 bp. The draft genome sequence was 5,761,811 bp in length with a G+C content of 69.9%. The NCBI Prokaryotic Genome Annotation Pipeline (PGAP; https://www.ncbi.nlm.nih.gov/genome/annotation_prok) predicted 5,476 genes, including 5,358 coding sequences (CDSs), two rRNAs, 48 tRNAs, and 118 pseudogenes. Rapid genome annotations using the RAST server (6) assigned the coding sequences to 442 subsystems, of which amino acids and derivatives (n = 561 CDSs), carbohydrates (n = 492), cofactors, vitamins, prosthetic groups, and pigments (n = 328), protein metabolism (n = 286), fatty acids, lipids, and isoprenoids (n = 255), stress response (n = 138), metabolism of aromatic compounds (n = 119), respiration (n = 117), RNA metabolism (n = 111), DNA metabolism (n = 110), nucleosides and nucleotides (n = 127), and virulence, disease, and defense (n = 95) were most abundant.

The NCBI PGAP predicted a large number of oxygenases and hydrolases, including three predicted alkane monooxygenase genes (alkB), two with at least 76% homology to Nocardioides sp. CF8 and one with 78% similarity to Streptomyces sp. CdTB01. Also, genes for two methane monooxygenase subunits were observed. Twelve P450 genes, with one presenting 79% homology to the Gordonia sp. TF6 cytochrome P450 alkane hydroxylase, were predicted. P450 cytochromes were shown to be involved in the degradation of branched alkanes (7). Other important genes involved in the degradation of hydrocarbons and aromatic compounds include phenol monooxygenase, catechol 1,2-dioxygenase, homogentisate 1,2-dioxygenase, 2-nitropropane dioxygenase, benzoate 1,2-dioxygenase, alkanesulfonate monooxygenase, and dimethyl sulfone monooxygenase. The genes of the central protocatechuate catabolic pathway for aromatic degradation, including protocatechuate 3,4-dioxygenase, 3-carboxymuconate cycloisomerase, and 4-carboxymuconolactone decarboxylase, were present. However, this bacterium lacked key aromatic hydroxylating enzymes such as benzene 1,2-dioxygenase and naphthalene 1,2-dioxygenase, which are required for the degradation of benzene and naphthalene hydrocarbons, respectively. The N. luteus BAFB genome will facilitate the study of pathways and adaptive mechanisms leading to the degradation and bioremediation of recalcitrant hydrocarbon compounds.

Accession number(s).

This project has been deposited at DDBJ/EMBL/GenBank under the accession number JZDQ00000000.