Examining the diversity of microbes and petroleum-hydrocarbon genes, in Gulf of Mexico deep-sea sediments and coral flocculent material.

Deep-sea surface sediments and flocculent material (floc) associated with corals containing oil and dispersant compounds originating from the Deepwater Horizon (DWH) oil spill were examined to determine the diversity of microbes and the presence of functional catabolic genes involved in oil degradation. 16S rRNA clone libraries provided full-length sequences for all sediment and floc samples examined. Illumina amplicon sequencing was used to further probe the diversity of the microbial communities for each sample and was in agreement with the 16S clone libraries. 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. Detection of functional catabolic genes, for evaluating the microbial community potential for the biodegradation of hydrocarbons was assessed by clone library analysis. The alkB gene, one of the structural genes of alkane hydroxylase, which aerobically degrades n-alkanes of chain length >C5-C16 was present in all samples with the majority of sequences clustering to members the Proteobacteria, clustering with environmental sequences from hydrocarbon seep environments. The alkylsuccinate synthase/benzylsuccinate synthases (assA/bssA), which are involved in the anaerobic degradation of n-alkanes (via assA) and polycyclic aromatic hydrocarbons (via bssA), 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 similarities between environments impacted by the DWH oil spill and highlight the functional diversity of oil-degrading microbes associated with a deep-sea coral community.