A survey of deepwater horizon (DWH) oil-degrading bacteria from the Eastern oyster biome and its surrounding environment

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Abstract

The deepwater horizon (DWH) accident led to the release of an estimated 794,936,474 L of crude oil into the northern Gulf of Mexico over an 85 day period in 2010, resulting in the contamination of the Gulf of Mexico waters, sediments, permeable beach sands, coastal wetlands, and marine life. This study examines the potential response of the Eastern oyster's microbiome to hydrocarbon contamination and compares it with the bacterial community responses observed from the overlaying water column (WC) and the oyster bed sediments. For this purpose, microcosms seeded with DWH crude oil were established and inoculated separately with oyster tissue (OT), mantle fluid (MF), overlaying WC, and sediments (S) collected from Apalachicola Bay, FL, USA. Shifts in the microbial community structure in the amended microcosms was monitored over a 3-month period using automated ribosomal intergenic spacer region analysis, which showed that the microbiome of the OT and MF were more similar to the sediment communities than those present in the overlaying WC. This pattern remained largely consistent, regardless of the concentration of crude oil or the enrichment period. Additionally, 72 oil-degrading bacteria were isolated from the microcosms containing OT, MF, WC, and S and identified using 16S ribosomal RNA gene sequencing and compared by principal component analysis, which clearly showed that the WC isolates were different to those identified from the sediment. Conversely, the OT and MF isolates clustered together; a strong indication that the oyster microbiome is uniquely structured relative to its surrounding environment. When selected isolates from the OT, MF, WC, and S were assessed for their oil-degrading potential, we found that the DWH oil was biodegraded between 12 and 42%, under the existing conditions. © 2014 Thomas, Wafula, Chauhan, Green, Gragg and Jagoe.

Figures

  • FIGURE 1 | Shown are (A) non-metric multidimensional scaling plot (NMDS) of ARISA data obtained from oyster tissue (blue triangle), mantle fluid (green triangle), water column (red diamond), and sediments (turquoise square) with sample source as the grouping factor. The bacterial communities from enrichment stages are shown as
  • FIGURE 2 | Shown are the non-metric multidimensional scaling plot (NMDS) of ARISA data obtained from the first enrichment phase (E1; green triangle), second enrichment phase (E2; blue triangle), and the third enrichment phase (VE; turquoise square) with enrichment time as the grouping factor. Shown in (A–D) are bacterial community profiles within the samples enriched with oyster tissue (A), mantle fluid (B), sediments (C), and water (D), respectively. (E) Shows pooled ARISA data from the oyster
  • Table 1 | Summary of oil-degrading bacterial strains isolated from DWH oil-amended microcosms containing oyster tissue (OT), mantle fluid (MF), water column (WC), and sediment (S) samples obtained from Dry Bar, Apalachicola Bay, FL, USA.
  • Table 2 |Taxonomic affiliation shown of the 72 oil-degrading bacterial strains that were isolated from DWH oil-amended microcosms containing oyster tissue (OT), mantle fluid (MF), water column (WC), and sediment (S) samples obtained from Dry Bar, Apalachicola Bay, FL, USA.
  • FIGURE 3 |Taxonomic affiliations of representative isolates shown as neighbor-joining dendrograms.The optimal tree with the sum of branch length = 0.65751938 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the
  • FIGURE 4 | Shown is a principal component analysis (PCA) obtained from UniFrac analysis of the 16S rRNA sequences of 72 isolated strains from the oyster tissue (yellow triangle), mantle fluid (red circle), water column (green triangle), and sediment (blue square).The percentages on each of the axes show the percent variation explained by each axes.
  • FIGURE 5 | Growth profiles of 10 selected isolated strains obtained from microcosms spiked with 0.75% DWH crude oil as the sole source of carbon and energy over the course of 7 days.
  • Table 3 | Growth kinetics and oil degradation abilities of nine selected strains isolated from oyster tissue (OT), mantle fluid (MF), water column (WC), and sediment (S) samples obtained from Dry Bar, Apalachicola Bay, FL, USA.

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Thomas, J. C., Wafula, D., Chauhan, A., Green, S. J., Gragg, R., & Jagoe, C. (2014). A survey of deepwater horizon (DWH) oil-degrading bacteria from the Eastern oyster biome and its surrounding environment. Frontiers in Microbiology, 5(APR). https://doi.org/10.3389/fmicb.2014.00149

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