Abstract
Natural and anthropogenic activities introduce alkanes into marine systems where they are degraded by alkane hydroxylases expressed by phylogenetically diverse bacteria. Partial sequences for alkB, one of the structural genes of alkane hydroxylase, have been used to assess the composition of alkane-degrading communities, and to determine their responses to hydrocarbon inputs. We present here the first spatially extensive analysis of alkB in bacterioplankton of the northern Gulf of Mexico (nGoM), a region that experiences numerous hydrocarbon inputs. We have analyzed 401 partial alkB gene sequences amplified from genomic extracts collected during March 2010 from 17 water column samples that included surface waters and bathypelagic depths. Previous analyses of 16S rRNA gene sequences for these and related samples have shown that nGoM bacterial community composition and structure stratify strongly with depth, with distinctly different communities above and below 100 m. Although we hypothesized that alkB gene sequences would exhibit a similar pattern, PCA analyses of operational protein units (OPU) indicated that community composition did not vary consistently with depth or other major physical-chemical variables. We observed 22 distinct OPUs, one of which was ubiquitous and accounted for 57% of all sequences. This OPU clustered with AlkB sequences from known hydrocarbon oxidizers (e.g., Alcanivorax and Marinobacter). Some OPUs could not be associated with known alkane degraders, however, and perhaps represent novel hydrocarbon-oxidizing populations or genes. These results indicate that the capacity for alkane hydrolysis occurs widely in the nGoM, but that alkane degrader diversity varies substantially among sites and responds differently than bulk communities to physical-chemical variables.
Highlights
Alkanes enter marine environments from many natural and anthropogenic sources (Head et al, 2006; Hu et al, 2009)
(8 and 2, respectively) were too few for meaningful comparisons. Both of these sites harbored alkB-containing populations based on results from a prior survey of 16S rRNA genes (King et al, 2013), they appeared to be dominated by taxa that contained divergent genes that were amplified with alkB primers
Resulted in a cluster of shallow water samples (≤100 m depth) that included one deeper water sample (A6-350 m); the remaining deep-water samples were dispersed across both axes (SI Figure 3). This suggests that the less abundant operational protein units (OPU) in surface waters might form similar assemblages across sites, but that variability in the more abundant OPUs obscures patterns. Results similar to those for a PCA with all AlkB OPUs were obtained from a PCA analysis of the relative abundances in each sample of 16S rRNA gene sequences for Alcanivorax, Marinobacter, Pseudomonas, Hydrocarboniphaga, and Kordiimonas, the primary alkane-oxidizing reference taxa with which some of the clone sequences were identified
Summary
Alkanes enter marine environments from many natural and anthropogenic sources (Head et al, 2006; Hu et al, 2009). The particulate (or membrane-associated) non-heme iron alkane hydroxylases (alkane 1-monooxygenases) oxidize substrates with chain lengths ≥C5 -C16 These “alkB” hydroxylases are widely distributed among bacteria (Vomberg and Klinner, 2000; van Beilen www.frontiersin.org et al, 2003; Liu and Shao, 2005; Liu et al, 2007; van Beilen and Funhoff, 2007; Wasmund et al, 2009). They are encoded by three genes, alkB for the catalytically active alkane hydroxylase, and alkG and alkT for rubredoxin and rubredoxin reductase, respectively, (Cappelletti et al, 2011). AlkB sequence conservation has been exploited in a variety of molecular ecological studies to assess the distribution and diversity of alkane degraders in hydrocarbon-contaminated soils and sediments
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