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Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil

Lookup NU author(s): Dr Casey Hubert, Thomas Oldenburg, Emeritus Professor Neil GrayORCiD, Professor Stephen Larter, Dr Arlene Rowan, Dr Angela SherryORCiD, Richard Swainsbury, Professor Ian Head



The subsurface microbiology of an Athabasca oil sands reservoir in western Canada containing severely biodegraded oil was investigated by combining 16S rRNA gene- and polar lipid-based analyses of reservoir formation water with geochemical analyses of the crude oil and formation water. Biomass was filtered from formation water, DNA was extracted using two different methods, and 16S rRNA and gene fragments were amplified with several different primer pairs prior to cloning and sequencing or community fingerprinting by DGGE. Similar results were obtained irrespective of the DNA extraction method or primers used. Archaeal libraries were dominated by Methanomicrobiales (410 of 414 total sequences formed a dominant phylotype affiliated with a Methanoregula sp.), consistent with the proposed dominant role of CO2-reducing methanogens in crude oil biodegradation. In two bacterial 16S rRNA clone libraries generated with different primer pairs, >99% and 100% of the sequences were affiliated with Epsilonproteobacteria (n=382 and 72 total clones, respectively). This massive dominance of Epsilonproteobacteria sequences was again obtained in a third library (99% of sequences; n=96 clones) using a third universal bacterial primer pair (inosine-341f and 1492r). Sequencing of bands from DGGE profiles and intact polar lipid analyses were in accordance with the bacterial clone library results. Epsilonproteobacterial OTUs were affiliated with Sulfuricurvum, Arcobacter and Sulfurospirillum spp. detected in other oil field habitats. The dominant organism revealed by the bacterial libraries (87% of all sequences) is a close relative of Sulfuricurvum kujiense—an organism capable of oxidizing reduced sulfur compounds in crude oil. Geochemical analysis of organic extracts from bitumen at different reservoir depths down to the oil water transition zone of these oil sands indicated active biodegradation of dibenzothiophenes, and stable sulfur isotope ratios for elemental sulfur and sulfate in formation waters were indicative of anaerobic oxidation of sulfur compounds. Microbial desulfurization of crude oil may be an important metabolism for Epsilonproteobacteria indigenous to oil reservoirs with elevated sulfur content and may explain their prevalence in formation waters from highly biodegraded petroleum systems.

Publication metadata

Author(s): Hubert CRJ, Oldenburg TBP, Fustic M, Gray ND, Larter SR, Penn K, Rowan AK, Seshadri R, Sherry A, Swainsbury R, Voordouw G, Voordouw JK, Head IM

Publication type: Article

Publication status: Published

Journal: Environmental Microbiology

Year: 2012

Volume: 14

Issue: 2

Pages: 387-404

Print publication date: 08/08/2011

Date deposited: 06/11/2012

ISSN (print): 1462-2912

ISSN (electronic): 1462-2920

Publisher: Wiley-Blackwell Publishing Ltd


DOI: 10.1111/j.1462-2920.2011.02521.x


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