Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

Baruch Marine Field Laboratory, Belle W. Baruch Institute for Marine and Coastal Sciences, University of South Carolina Georgetown, SC, USA.
Frontiers in Microbiology (Impact Factor: 3.94). 03/2013; 4:50. DOI: 10.3389/fmicb.2013.00050
Source: PubMed

ABSTRACT Marine subsurface environments such as deep-sea sediments, house abundant and diverse microbial communities that are believed to influence large-scale geochemical processes. These processes include the biotransformation and mineralization of numerous petroleum constituents. Thus, microbial communities in the Gulf of Mexico are thought to be responsible for the intrinsic bioremediation of crude oil released by the Deepwater Horizon (DWH) oil spill. While hydrocarbon contamination is known to enrich for aerobic, oil-degrading bacteria in deep-seawater habitats, relatively little is known about the response of communities in deep-sea sediments, where low oxygen levels may hinder such a response. Here, we examined the hypothesis that increased hydrocarbon exposure results in an altered sediment microbial community structure that reflects the prospects for oil biodegradation under the prevailing conditions. We explore this hypothesis using metagenomic analysis and metabolite profiling of deep-sea sediment samples following the DWH oil spill. The presence of aerobic microbial communities and associated functional genes was consistent among all samples, whereas, a greater number of Deltaproteobacteria and anaerobic functional genes were found in sediments closest to the DWH blowout site. Metabolite profiling also revealed a greater number of putative metabolites in sediments surrounding the blowout zone relative to a background site located 127 km away. The mass spectral analysis of the putative metabolites revealed that alkylsuccinates remained below detection levels, but a homologous series of benzylsuccinates (with carbon chain lengths from 5 to 10) could be detected. Our findings suggest that increased exposure to hydrocarbons enriches for Deltaproteobacteria, which are known to be capable of anaerobic hydrocarbon metabolism. We also provide evidence for an active microbial community metabolizing aromatic hydrocarbons in deep-sea sediments of the Gulf of Mexico.

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Available from: Terry C Hazen, Aug 29, 2015
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    • "The most abundant OTUs identified in the sediment and floc samples are consistent with previously examined DWH impacted samples, in particular the subsurface plume (Kessler et al., 2011, Redmond and Valentine, 2012) and deep-sea sediments (Kimes et al., 2013, Mason et al., 2014) as well as indigenous microbial communities from the GoM including those found in natural hydrocarbon seep sites and sediments (Teske et al., 2002, Lloyd et al., 2010, Biddle et al., 2011, Orcutt et al., 2010, Kleindienst et al., 2012). Determining the full extent to which the DWH oil spill has perturbed the microbial community at this site is challenging, as pre-spill data regarding microbes associated with corals in the deep GoM is limited. "
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    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, 16 S 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 16 S 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.
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    • "Examples of applications are widespread across diverse areas of research from human medicine (Jin et al. 2014) to deep-sea microbial ecology (Kimes et al. 2013). While only limitedly applied to aquaculture research thus far, specific metabolomics-based investigations are starting to provide useful information for various sectors within the aquaculture industry. "
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    • "Aerobes initiate biodegradation via mono-and dioxygenase enzymes (Haddock, 2010; Pérez-Pantoja et al., 2010; Rojo, 2010; Austin and Groves, 2011; Austin and Callaghan, 2014; Figure 1). One of the most well studied oildegrading microorganisms is Alcanivorax borkumensis, which is a marine gammaproteobacterium known to utilize a broad range of aliphatic hydrocarbons (Schneiker et al., 2006; Yakimov et al., 2006; dos Santos et al., 2010) through multiple routes of terminal oxidation via several hydroxylating enzymes (i.e., alkB1, P450 cytochrome monooxygenase, and a putative flavinbinding monooxygenase) (Sabirova et al., 2006). Also important in marine ecosystems, especially marine sediments, is the anaerobic biodegradation of hydrocarbons (Coates et al., 1997; Davidova et al., 2007). "
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    ABSTRACT: The Deepwater Horizon blowout, which occurred on April 20, 2010, resulted in an unprecedented oil spill. Despite a complex effort to cap the well, oil and gas spewed from the site until July 15, 2010. Although a large proportion of the hydrocarbons was depleted via natural processes and human intervention, a substantial portion of the oil remained unaccounted for and impacted multiple ecosystems throughout the Gulf of Mexico. The depth, duration and magnitude of this spill were unique, raising many questions and concerns regarding the fate of the hydrocarbons released. One major question was whether or not microbial communities would be capable of metabolizing the hydrocarbons, and if so, by what mechanisms and to what extent? In this review, we summarize the microbial response to the oil spill as described by studies performed during the past four years, providing an overview of the different responses associated with the water column, surface waters, deep-sea sediments, and coastal sands/sediments. Collectively, these studies provide evidence that the microbial response to the Deepwater Horizon oil spill was rapid and robust, displaying common attenuation mechanisms optimized for low molecular weight aliphatic and aromatic hydrocarbons. In contrast, the lack of evidence for the attenuation of more recalcitrant hydrocarbon components suggests that future work should focus on both the environmental impact and metabolic fate of recalcitrant compounds, such as oxygenated oil components.
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