Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill

Abstract

Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05) once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass) suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems.

Figure 1. Study site.

(A) Map of Point Aux Pins peninsula. Study site indicated by box in inset. (B) Sediment samples collected ∼25 m from shore outside the marsh stands (designated “Inlet”) and 2–4 m from shore within the marsh stands (designated “Marsh”).

Figure 2. Boxplots of TPH concentrations in (a) Inlet and (b) Marsh surface and subsurface sediments.

Each box represents the concentration range of 50% of the observations. Lines within the boxes represent the median values, open squares are the averages, and the whisker lines connect to outliers.

Figure 3. GCMS analysis of MC252 oil and oil-contaminated sediment.

(A) GCMS chromatogram of 10 ppm Macondo oil (MC252); (B) concentrations of n-alkanes in tar balls and sediment from July Marsh samples as determined by GCMS.

Figure 4. Non-metric multi-dimensional scaling (nMDS) ordination of the bacterial community in salt marsh sediments.

Resemblance matrix generated using Bray Curtis similarity and based on the relative abundance of taxa identified by PhyloChip analysis.

Figure 5. Relative abundance of phyla in salt marsh sediments.

Groups I, II, and III determined from nMDS analysis.

Figure 6. Functional gene distribution in Inlet and Marsh sediments.

Gene relative abundance determined by GeoChip for samples compared between June and July 2010. Categories with significant changes indicated by *for p<0.05.

Figure 7. Hydrocarbon degradation genes in Inlet sediments.

Average abundances of hydrocarbon degradation genes in Inlet sediments compared between June and July. Significant changes indicated by *for p<0.05 and **for p<0.01.

Figure 8. Hydrocarbon degradation genes in Marsh sediments.

Average abundances of hydrocarbon degradation genes in Marsh sediments compared between June and July. Significant changes indicated by *for p<0.05 and **for p<0.01.