Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

Abstract

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using (14)C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of (14)C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem.

Figure 1

(a) Map of 64 sample sites and (b) Their corresponding TPH, alkane, cycloalkane, PAH, total nitrogen and DIN concentrations. Note that the data shown represent discontinuous samples. For the sake of comparison, an effort was made to scale down to the lowest hydrocarbon concentration (cycloalkane); the maximum TPH concentration was 65 643 μg kg⁻¹, 29 338 μg kg⁻¹ for alkanes and 9075 μg kg⁻¹ for PAH. Total nitrogen and DIN were not scaled down.

Figure 2

Non-metric multidimensional scaling ordination of 16S rRNA gene iTag sequence data. (a) The main ordination shows sample similarity and the correlations between environmental variables and ordination axes. The three most abundant OTUs in the contaminated samples (uncultured Gammaproteobacterium, Colwellia and Rhodobacteraceae) are represented by arrows. Sample BP366 is indicated by a blue square. Samples that exceeded the EPA's aquatic benchmark for PAHs are denoted by red circles. (b) For this same ordination, the concentrations of TPH, total nitrogen, DIN, nitrate and ammonium are indicated by bubble size and contour lines. (c) Rarified abundance of an uncultured Gammaproteobacterium OTU and a Colwellia OTU are shown for the same ordination, with bubble size and contour lines indicating abundance. P-values indicate the significance for the variable shown and are based on 999 permutations.

Figure 3

Metagenomic data annotated by comparing raw reads with a database of genes involved in hydrocarbon degradation. (a) The heatmap shows abundance of genes involved in degradation of a particular hydrocarbon. (b) The dominant hydrocarbon degradation pathway is shown, along with (c) A statistical comparison of these gene abundances in samples that exceeded the EPA-BM and those that did not. *Genes that were statistically significantly different and more abundant in samples that exceeded EPA-BM ; **Those that were more abundant in the nonexceed samples.

Figure 4

Mineralization data for sediments incubated with ¹⁴C-labeled propylene glycol as a model component of the dispersant (COREXIT) and ¹⁴C model compounds found in oil.

Figure 5

Genes involved in nitrogen cycling. (a) Only those genes that were statistically different when comparing samples that exceed EPA-BM with those that did not. (b) Nitrogen cycle displaying statistically significant differences when comparing samples that exceed EPA-BM with those that did not. Solid lines depict strong support for a pathway (on the basis of the metagenomic data sequence abundance), whereas dashed lines indicate little to no support for a pathway. Abbreviations: amo, ammonia monooxygenase; hao, hydroxylamine oxidoreductase; hh, hydrazine hydrolase; nar, nitrate reductase (dissimilartory); nas, nitrate reductase (assimilatory); nif, nitrogenase (various types); nir (Fe/Cu), nitrite reductase (Fe/Cu containing); nor, nitric oxide reductase; nos, nitrous oxide reductase; nrf, nitrate reductase (associated with nap); nxr, nitrite oxidoreductase.