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: 3.99). 03/2013; 4:50. DOI: 10.3389/fmicb.2013.00050
Source: PubMed


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, Oct 04, 2015
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    • "d washing ) , including populations with potential oil degradation capability ( Engel and Gupta , 2014 ) . Oil plumes have been shown to have an impact on microbial communities in marine sediments and other beach areas , with NGS detecting genes and transcripts indicative of pollutant ( monoaromatics and alkanes ) degradation in marine sediments ( Kimes et al . , 2013 ; Mason et al . , 2014 ) and areas along the shorelines ( Lamendella et al . , 2014 ) ."
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    ABSTRACT: Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.
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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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