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Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill

Abstract

The Deepwater Horizon blowout in the Gulf of Mexico in 2010, one of the largest marine oil spills1, changed bacterial communities in the water column and sediment as they responded to complex hydrocarbon mixtures24. Shifts in community composition have been correlated to the microbial degradation and use of hydrocarbons2,5,6, but the full genetic potential and taxon-specific metabolisms of bacterial hydrocarbon degraders remain unresolved. Here, we have reconstructed draft genomes of marine bacteria enriched from sea surface and deep plume waters of the spill that assimilate alkane and polycyclic aromatic hydrocarbons during stable-isotope probing experiments, and we identify genes of hydrocarbon degradation pathways. Alkane degradation genes were ubiquitous in the assembled genomes. Marinobacter was enriched with n-hexadecane, and uncultured Alpha- and Gammaproteobacteria populations were enriched in the polycyclic-aromatic-hydrocarbon-degrading communities and contained a broad gene set for degrading phenanthrene and naphthalene. The repertoire of polycyclic aromatic hydrocarbon use varied among different bacterial taxa and the combined capabilities of the microbial community exceeded those of its individual components, indicating that the degradation of complex hydrocarbon mixtures requires the non-redundant capabilities of a complex oil-degrading community.

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Figure 1: Phylogenetic characterization of genomic bins reconstructed from three SIP enrichments.
Figure 2: Abundance of functional categories detected within the reconstructed genomes.
Figure 3: Distribution of key alkane and polycyclic hydrocarbon degradation pathways in reconstructed genomes.

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Acknowledgements

The metagenomic DNA originated from work that was supported by a Marie Curie International Outgoing Fellowship (PIOF-GA-2008-220129) to T.G. within the 7th European Community Framework Programme. Sampling in the Gulf of Mexico and SIP experiments underlying this study were made possible in part by a grant from The Gulf of Mexico Research Initiative and in part by a Marie Curie Fellowship to T.G. A.T. also acknowledges funding from the National Science Foundation (RAPID Response: the microbial response to the Deepwater Horizon Oil Spill; NSF-OCE 1045115). Data are publicly available through the Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC) at https://data.gulfresearchinitiative.org (doi:10.7266/N7GH9FZ8). This is ECOGIG contribution 431.

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N.D., T.G. and B.J.B. conceived this study. N.D. and B.J.B. supervised experiments and analyses. N.D., J.A.D., K.W.S. and B.J.B. performed analyses. N.D., T.G., A.P.T. and B.J.B. wrote the paper with contributions from all authors.

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Correspondence to Brett J. Baker.

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The authors declare no competing financial interests.

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Supplementary Tables 1,2, Figures 1–6 and References. (PDF 1187 kb)

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Dombrowski, N., Donaho, J., Gutierrez, T. et al. Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. Nat Microbiol 1, 16057 (2016). https://doi.org/10.1038/nmicrobiol.2016.57

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