Examining the diversity of microbes in a deep-sea coral community impacted by the Deepwater Horizon oil spill

Abstract

Deep-sea surface sediments and flocculent material (floc) associated with corals containing oil originating from the Deepwater Horizon (DWH) oil spill were examined to determine the diversity of microbes and the presence of functional genes involved in oil degradation. For all samples, 16S rRNA clone libraries were constructed to obtain full-length sequences and Illumina amplicon sequencing was used to further probe the diversity of the microbial community. The 16S rRNA gene data obtained by Illumina amplicon sequencing revealed Proteobacteria (55–64%) as the dominant bacteria in both sediment and floc samples. The floc samples were comprised of mostly aerobic or facultative aerobic phylotypes including Rhizobiales, Rhodobacterales, Sphingomonadales, Rickettsiales, Alteromonadales, Pseudomonadales, whereas mixtures of the aforementioned aerobic species and anaerobic phylotypes such as Desulfobacterales, Desulfuromonadales and Desulfarculales were present in the sediment samples. Genera affiliated with oil-degrading bacteria were identified in both sediment and floc samples. To evaluate the potential of the microbial community to degrade oil, clone libraries were constructed for the alkB gene (one of the structural genes of alkane hydroxylase involved in the aerobic degradation of n-alkanes of chain length >C5–C16) and the alkylsuccinate synthase/benzylsuccinate synthases (assA/bssA) gene (involved in the anaerobic degradation of n-alkanes [via assA] and polycyclic aromatic hydrocarbons [PAHs; via bssA]). The alkB gene was present in all samples with the majority of sequences clustering to members of the Proteobacteria closely aligned to environmental sequences from hydrocarbon seep environments. The assA/bssA genes were only detected in sediment samples and were closely affiliated with δ-Proteobacteria previously detected in oil-contaminated sediments and oil-enrichment cultures. These data provide insight into the differences between environments impacted by the DWH oil spill and highlight the functional diversity of oil-degrading microbes associated with a deep-sea coral community.