Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

Abstract

Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. A. borkumensis SK2 has a streamlined genome with a paucity of mobile genetic elements and energy generation-related genes, but with a plethora of genes accounting for its wide hydrocarbon substrate range and efficient oil-degradation capabilities. The genome further specifies systems for scavenging of nutrients, particularly organic and inorganic nitrogen and oligo-elements, biofilm formation at the oil-water interface, biosurfactant production and niche-specific stress responses. The unique combination of these features provides A. borkumensis SK2 with a competitive edge in oil-polluted environments. This genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills.

Figure 1. Circular representations of the A. borkumensis SK2 chromosome displaying relevant genome features.

From the outer to the inner concentric circle: circle 1, genomic position in kb; circles 2 and 3, predicted protein-coding sequences (CDS) on the forward (outer wheel) and the reverse (inner wheel) strands colored according to the assigned COG classes; circles 4, 5 and 6, CDS with homologs in P. aeruginosa (pink), P. putida (light blue) and I. loihiensis (green), respectively; circle 7, G+C content showing deviations from the average (54.7%); circle 8, GC skew. The bar below the plot represents the COG colors for the functional groups (C, energy production and conversion; D, cell cycle control, mitosis and meiosis; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation; K, transcription; L, replication, recombination and repair; M, cell wall/membrane biogenesis; N, cell motility; O, post-translational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking and secretion; V, defense mechanisms).

Figure 2. Phylogenetic affiliation of A. borkumensis SK2 based on 16S rDNA sequence comparison.

Neighborhood-joining tree showing a 16S rDNA gene phylogeny-based placement of A. borkumensis among the γ-Proteobacteria. Sequences were taken from the type strains of the given organisms. Marine organisms with completely sequenced genomes are highlighted in bold. The tree is rooted with Aquifex pyrophilus M83548. The α-proteobacterial strain Silicibacter pomeroyi served as outgroup.

Figure 3. Genetic determinants involved in alkane degradation in A. borkumensis SK2.

(a) Clusters of genes encoding proteins involved in alkane degradation in A. borkumensis SK2 (see text for details). (b) Neighborhood-joining tree showing the phylogenetic affiliation of the P450 cytochromes of A. borkumensis SK2. Two identical alkane-induced cytochromes P450(b) (ABO_2288) and P450(c) (ABO_0201) cluster with the Acinetobacter EB104 cytochrome P450. Cytochrome P450(a) (ABO_2384) is affiliated distantly. The tree is rooted with the methyl-CoM-reductase subunit A from Methanolubus tindarius (gbU22244). (c) Reconstruction of putative alkane degradation pathways in A. borkumensis SK2 (see text for details).

Figure 4. Schematic overview of metabolism and transport in A. borkumensis SK2.

The background is a transmission electron micrograph (TEM) of an A. borkumensis cell grown on hexadecane (courtesy of H. Lünsdorf). The insert in the right upper corner shows a TEM of A. borkumensis SK2 cells at the oil-water interface of hydrocarbon droplets in salt water. Predicted pathways for alkane degradation are depicted in marine blue. Predicted transporters are grouped by substrate specificity: inorganic cations (gray), inorganic anions (dark orange), amino acids/peptides/amines/purines/pyrimidines and other nitrogenous compounds (dark green), carboxylates (light green), drug efflux and other (dark gray). Export or import of solutes is designated by the direction of the arrow through the transporter. The energy coupling mechanisms of the transporters are also shown: solutes transported by channel proteins are shown with a double-headed arrow; secondary transporters are shown with two arrowed lines indicating both the solute and the coupling ion; ATP-driven transporters are indicated by the ATP hydrolysis reaction; transporters with an unknown energy-coupling mechanism are shown with only a single arrow. The P-type ATPases are shown with a double-headed arrow to indicate they include both uptake and efflux systems. Where multiple homologous transporters with similar substrate predictions exist, the number of that type of protein is indicated in parentheses. Abbreviations of less common terms: EPS, extracellular polysaccharides; AA, amino acids: BCCT, betaine/carnitine/choline transporters; GSP, general secretion pathways; PRPP, 5′-phospho-alpha-D-ribose 1-diphosphate; Mhn, complex sodium/proton antiporter involved in sodium excretion.