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Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252)

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Abstract

The indigenous bacterial communities in sediment microcosms from Dauphin Island (DI), Petit Bois Island (PB) and Perdido Pass (PP) of the coastal Gulf of Mexico were compared following treatment with Macondo oil (MC252) using pyrosequencing and culture-based approaches. After quality-based trimming, 28,991 partial 16S rRNA sequence reads were analyzed by rarefaction, confirming that analyses of bacterial communities were saturated with respect to species diversity. Changes in the relative abundances of Proteobacteria, Bacteroidetes and Firmicutes played an important role in structuring bacterial communities in oil-treated sediments. Proteobacteria were dominant in oil-treated samples, whereas Firmicutes and Bacteroidetes were either the second or the third most abundant taxa. Tenericutes, members of which are known for oil biodegradation, were detected shortly after treatment, and continued to increase in DI and PP sediments. Multivariate statistical analyses (ADONIS) revealed significant dissimilarity of bacterial communities between oil-treated and untreated samples and among locations. In addition, a similarity percentage analysis showed the contribution of each species to the contrast between untreated and oil-treated samples. PCR amplification using DNA from pure cultures of Exiguobacterium,  Pseudoalteromonas,  Halomonas and Dyadobacter, isolated from oil-treated microcosm sediments, produced amplicons similar to polycyclic aromatic hydrocarbon-degrading genes. In the context of the 2010 Macondo blowout, the results from our study demonstrated that the indigenous bacterial communities in coastal Gulf of Mexico sediment microcosms responded to the MC252 oil with altered community structure and species composition. The rapid proliferation of hydrocarbonoclastic bacteria suggests their involvement in the degradation of the spilt oil in the Gulf of Mexico ecosystem.

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Acknowledgments

This work was supported by the Gulf of Mexico Research Initiative (GoMRI) grant, which was distributed by Alabama Marine Environmental Science Consortium (MESC) (project number: T1-001-DISL); we thank John Valentine of DISL, Patricia Sobecky of University of Alabama, Tuscaloosa (UA) and Ronald Kiene of DISL and USA for selecting the proposal for funding; Ronald Kiene to share the sediment samples for the microcosm study; Jonathan Huang for helping with the Bioinformatics analysis. We also thank David A. Pillared, GCRO Reference Material Account Manager, KSA Project Manager, AECOM Environment (The GRAIS Team) for providing the Macondo oil (MC252); John Delton Hanson of Research and Testing Laboratory, TX for assisting us with the pyrosequencing of the samples; Maria Salazar of UAB Center for AIDS Research (CFAR) DNA Sequencing core (Grant #P30AU027767) for sequencing of DNA from pure culture of bacterial isolates. Also, we thank Katherine DV Hughes and Matthew Pace of UAB CAS IT for computer support necessary for the bioinformatics analyses of the pyrosequencing data. Additional support was provided by the National Science Foundation (DEB 1208340).

Conflict of interest

The authors declare no conflict of interest associated with this study and was conducted solely for the purpose of a scientific study.

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  1. Nazia Mojib

    Present address: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

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  1. Department of Biology, University of Alabama at Birmingham, Birmingham, AL, 35204, USA

    Hyunmin Koo, Nazia Mojib, Robert W. Thacker & Asim K. Bej

  2. Department of Biology, University of Alabama at Birmingham, Birmingham, AL, 35294-1170, USA

    Asim K. Bej

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Koo, H., Mojib, N., Thacker, R.W. et al. Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252). Antonie van Leeuwenhoek 106, 993–1009 (2014). https://doi.org/10.1007/s10482-014-0268-3

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