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Alkane hydroxylase gene (alkB) phylotype composition and diversity in northern Gulf of Mexico bacterioplankton.

Smith CB, Tolar BB, Hollibaugh JT, King GM - Front Microbiol (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA.

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.

No MeSH data available.


AlkB diversity indices as a function of depth; open symbols, ACE index and closed symbols, Shannon index.
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Figure 5: AlkB diversity indices as a function of depth; open symbols, ACE index and closed symbols, Shannon index.

Mentions: Statistical measures of diversity (e.g., Chao1, ACE, Shannon and Inverse Simpson's indices, and evenness indices) also did not vary consistently with depth or sampling station (Figure 5, SI Table 1). Values for the Shannon index, for example, fell between 0.0 (MR1-2 m, 1 OPU) and 1.79, but there were no systematic differences among samples. Likewise, there were no systematic differences among samples for other diversity indices. In this respect, spatial trends for AlkB diversity were comparable to those for bulk nGoM bacterioplankton based on 16S rRNA gene sequences; diversity metrics for the latter also did not vary with depth or geographic location on the shelf (King et al., 2013).


Alkane hydroxylase gene (alkB) phylotype composition and diversity in northern Gulf of Mexico bacterioplankton.

Smith CB, Tolar BB, Hollibaugh JT, King GM - Front Microbiol (2013)

AlkB diversity indices as a function of depth; open symbols, ACE index and closed symbols, Shannon index.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3860262&req=5

Figure 5: AlkB diversity indices as a function of depth; open symbols, ACE index and closed symbols, Shannon index.
Mentions: Statistical measures of diversity (e.g., Chao1, ACE, Shannon and Inverse Simpson's indices, and evenness indices) also did not vary consistently with depth or sampling station (Figure 5, SI Table 1). Values for the Shannon index, for example, fell between 0.0 (MR1-2 m, 1 OPU) and 1.79, but there were no systematic differences among samples. Likewise, there were no systematic differences among samples for other diversity indices. In this respect, spatial trends for AlkB diversity were comparable to those for bulk nGoM bacterioplankton based on 16S rRNA gene sequences; diversity metrics for the latter also did not vary with depth or geographic location on the shelf (King et al., 2013).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA.

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.

No MeSH data available.