Original Article

Subject Category: Microbial population and community ecology

The ISME Journal (2013) 7, 2091–2104; doi:10.1038/ismej.2013.98; published online 20 June 2013

Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP

Tony Gutierrez1,2, David R Singleton1, David Berry3, Tingting Yang4, Michael D Aitken1 and Andreas Teske4

  1. 1Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
  2. 2School of Life Sciences, Heriot-Watt University, Edinburgh, UK
  3. 3Department of Microbial Ecology, Vienna Ecology Centre, Faculty of Sciences, University of Vienna, Vienna, Austria
  4. 4Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, USA

Correspondence: T Gutierrez, School of Life Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK. E-mail: tony.gutierrez@hw.ac.uk

Received 29 January 2013; Revised 12 May 2013; Accepted 17 May 2013
Advance online publication 20 June 2013

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Abstract

The massive influx of crude oil into the Gulf of Mexico during the Deepwater Horizon (DWH) disaster triggered dramatic microbial community shifts in surface oil slick and deep plume waters. Previous work had shown several taxa, notably DWH Oceanospirillales, Cycloclasticus and Colwellia, were found to be enriched in these waters based on their dominance in conventional clone and pyrosequencing libraries and were thought to have had a significant role in the degradation of the oil. However, this type of community analysis data failed to provide direct evidence on the functional properties, such as hydrocarbon degradation of organisms. Using DNA-based stable-isotope probing with uniformly 13C-labelled hydrocarbons, we identified several aliphatic (Alcanivorax, Marinobacter)- and polycyclic aromatic hydrocarbon (Alteromonas, Cycloclasticus, Colwellia)-degrading bacteria. We also isolated several strains (Alcanivorax, Alteromonas, Cycloclasticus, Halomonas, Marinobacter and Pseudoalteromonas) with demonstrable hydrocarbon-degrading qualities from surface slick and plume water samples collected during the active phase of the spill. Some of these organisms accounted for the majority of sequence reads representing their respective taxa in a pyrosequencing data set constructed from the same and additional water column samples. Hitherto, Alcanivorax was not identified in any of the previous water column studies analysing the microbial response to the spill and we discuss its failure to respond to the oil. Collectively, our data provide unequivocal evidence on the hydrocarbon-degrading qualities for some of the dominant taxa enriched in surface and plume waters during the DWH oil spill, and a more complete understanding of their role in the fate of the oil.

Keywords:

biodegradation; Deepwater Horizon; Gulf of Mexico; marine bacteria; polycyclic aromatic hydrocarbons; stable-isotope probing