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Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs

Nature volume 451, pages 176–180 (2008)Cite this article

Abstract

Biodegradation of crude oil in subsurface petroleum reservoirs has adversely affected the majority of the world’s oil, making recovery and refining of that oil more costly1. The prevalent occurrence of biodegradation in shallow subsurface petroleum reservoirs2,3 has been attributed to aerobic bacterial hydrocarbon degradation stimulated by surface recharge of oxygen-bearing meteoric waters2. This hypothesis is empirically supported by the likelihood of encountering biodegraded oils at higher levels of degradation in reservoirs near the surface4,5. More recent findings, however, suggest that anaerobic degradation processes dominate subsurface sedimentary environments6, despite slow reaction kinetics and uncertainty as to the actual degradation pathways occurring in oil reservoirs. Here we use laboratory experiments in microcosms monitoring the hydrocarbon composition of degraded oils and generated gases, together with the carbon isotopic compositions of gas and oil samples taken at wellheads and a Rayleigh isotope fractionation box model, to elucidate the probable mechanisms of hydrocarbon degradation in reservoirs. We find that crude-oil hydrocarbon degradation under methanogenic conditions in the laboratory mimics the characteristic sequential removal of compound classes seen in reservoir-degraded petroleum. The initial preferential removal of n-alkanes generates close to stoichiometric amounts of methane, principally by hydrogenotrophic methanogenesis. Our data imply a common methanogenic biodegradation mechanism in subsurface degraded oil reservoirs, resulting in consistent patterns of hydrocarbon alteration, and the common association of dry gas with severely degraded oils observed worldwide. Energy recovery from oilfields in the form of methane, based on accelerating natural methanogenic biodegradation, may offer a route to economic production of difficult-to-recover energy from oilfields.

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Figure 1: Gas chromatograms of total hydrocarbon fractions from field and laboratory degraded oils.
Figure 2: Plot of the ratios of pristane to n-heptadecane against 4-methylbiphenyl to 3-methylbiphenyl abundances.
Figure 3: n -alkane depletion and methane production during oil degradation.
Figure 4: Measured and modelled methane and carbon dioxide stable carbon isotopic compositions from degraded oil reservoir gases.

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References

  1. Roadifer, R. E. in Exploration for Heavy Crude Oil and Natural Bitumen (ed. Meyer, R.F.) 3–23 (American Association of Petroleum Geologists, Tulsa, 1987)

    Google Scholar 

  2. Winters, J. C. & Williams, J. A. Microbial Alteration of Crude Oil in the reservoir. Am. Chem. Soc. Div. Petrol. Chem. Preprints 14, E22–E31 (1969)

    CAS  Google Scholar 

  3. Connan, J. in Advances in Petroleum Geochemistry Vol. 1 (eds Brooks, J. & Welte, D. H.) 299–335 (Academic Press, London, 1984)

    Book  Google Scholar 

  4. Krejci-Graf, K. Rule of density of oils. Bull. Am. Assoc. Petrol. Geol. 16, 1038 (1932)

    Google Scholar 

  5. Palmer, S. E. in Organic Geochemistry (eds Macko, S. A. & Engel, M. H.) 511–534 (Plenum Press, New York, 1993)

    Book  Google Scholar 

  6. Head, I. M., Jones, D. M. & Larter, S. R. Biological activity in the deep subsurface and the origin of heavy oil. Nature 426, 344–352 (2003)

    Article  ADS  CAS  Google Scholar 

  7. Horstad, I., Larter, S. R. & Mills, N. A. Quantitative model of biological petroleum degradation within the Brent Group reservoir in the Gullfaks field, Norwegian North Sea. Org. Geochem. 19, 1–3,–107–117 (1992)

    Article  Google Scholar 

  8. Bastin, E. Microorganisms in oilfields. Science 63, 21–24 (1926)

    Article  ADS  CAS  Google Scholar 

  9. Magot, M., Connan, J. & Crolet, J.-L. Les bactéries des gisements pétroliers. Recherche 228, 936–937 (1994)

    Google Scholar 

  10. Reuter, P. et al. Anaerobic oxidation of hydrocarbons in crude oil by new types of sulfate-reducing bacteria. Nature 372, 455–458 (1994)

    Article  ADS  Google Scholar 

  11. Zengler, K., Richnow, H. H., Rossello-Mora, R., Michaelis, W. & Widdel, F. Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401, 266–269 (1999)

    Article  ADS  CAS  Google Scholar 

  12. Aitken, C. M., Jones, D. M. & Larter, S. R. Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs. Nature 431, 291–294 (2004)

    Article  ADS  CAS  Google Scholar 

  13. Rabus, R. & Widdel, F. Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch. Microbiol. 163, 96–103 (1995)

    Article  CAS  Google Scholar 

  14. Lovley, D. R. et al. Oxidation of aromatic contaminants coupled to microbial iron reduction. Nature 339, 297–300 (1989)

    Article  ADS  CAS  Google Scholar 

  15. Anderson, R. T. & Lovley, D. R. Biogeochemistry—hexadecane decay by methanogenesis. Nature 404, 722–723 (2000)

    Article  ADS  CAS  Google Scholar 

  16. Larter, S. et al. The controls on the composition of biodegraded oils in the deep subsurface. Part II. Geological controls on subsurface biodegradation fluxes and constraints on reservoir fluid property prediction. Bull. Am. Assoc. Petrol. Geol 90, 921–938 (2006)

    CAS  Google Scholar 

  17. Larter, S. R. et al. in Petroleum Geology: North-West Europe and Global Perspectives (eds Doré, A. G. & Vining, B. A.) 633–639 (Geological Society, London, 2005)

    Google Scholar 

  18. Larter, S. & di Primio, R. Effects of biodegradation on oil and gas field PVT properties and the origin of oil rimmed gas accumulations. Org. Geochem. 36, 299–310 (2005)

    Article  CAS  Google Scholar 

  19. Boreham, C. J., Hope, J. M. & Hartung-Kagi, B. Understanding source, distribution and preservation of Australian natural gas: A geochemical perspective. Aus. Petrol. Explor. Assoc. J. 41, 523–547 (2001)

    CAS  Google Scholar 

  20. Pallaser, R. J. Recognising biodegradation in gas/oil accumulations through the δ13C composition of gas components. Org. Geochem. 31, 1363–1373 (2000)

    Article  Google Scholar 

  21. Masterson, W. D., Dzou, L. I. P., Holba, A. G., Fincannon, A. L. & Ellis, L. Evidence for biodegradation and evaporative fractionation in West Sak, Kuparuk and Prudhoe Bay field areas, North Slope, Alaska. Org. Geochem. 32, 411–441 (2001)

    Article  CAS  Google Scholar 

  22. Volkman, J. K., Alexander, R., Kagi, R. I., Rowland, S. J. & Sheppard, P. N. Biodegradation of aromatic hydrocarbons in crude oils from the Barrow Sub-basin of Western Australia. Org. Geochem. 6, 619–632 (1984)

    Article  CAS  Google Scholar 

  23. Peters, K. E. & Moldowan, J. M. The Biomarker Guide 252–265 (Prentice Hall, New York, 1993)

    Google Scholar 

  24. Wenger, L. M., Davis, C. L. & Isaksen, G. H. Multiple controls on petroleum biodegradation and impact in oil quality. SPE Reservoir Eval. Engin. 5, 375–383 (2002)

    Article  CAS  Google Scholar 

  25. Williams, J. A. et al. Biodegradation in South Texas oils—effects on aromatics and biomarkers. Org. Geochem. 10, 451–461 (1986)

    Article  CAS  Google Scholar 

  26. Fedorak, P. M. & Westlake, D. W. S. Microbial degradation of aromatics and saturates in Prudhoe Bay crude oil. Can. J. Microbiol. 27, 432–443 (1981)

    Article  CAS  Google Scholar 

  27. Townsend, G. T., Prince, R. C. & Suflita, J. M. Anaerobic oxidation of crude oil hydrocarbons by the resident microorganisms of a contaminated anoxic aquifer. Environ. Sci. Technol. 37, 5213–5218 (2003)

    Article  ADS  CAS  Google Scholar 

  28. Karlsson, W. in Habitat of Hydrocarbons on the Norwegian Continental Shelf (eds Spencer, A. M. et al.) 181–197 (Graham & Trotman, London, 1986)

    Google Scholar 

  29. Larter, S. et al. The controls on the composition of biodegraded oils. Part 1. Biodegradation rates in petroleum reservoirs in the deep subsurface. Org. Geochem. 34, 601–613 (2003)

    Article  CAS  Google Scholar 

  30. Adams, J. J., Riediger, C. L., Fowler, M. G. & Larter, S. R. Thermal controls on biodegradation around the Peace River tar sands: paleo-pasteurization to the west. J. Geochem. Explor. 89, 1–4 (2006)

    Article  CAS  Google Scholar 

  31. Widdel, F. & Bak, W. in The Prokaryotes (eds Balows, A., Trüper, H. G., Dworkin, M., Harder, W. & Schleifer, K.-H.) Vol. 4, 2nd edn 3352–3379 (Springer, New York, 1992)

    Book  Google Scholar 

  32. Bennett, B., Bowler, B. F. J. & Larter, S. R. Determination of C0–C3 alkylphenols in crude oils and waters. Anal. Chem. 68, 3697–3702 (1996)

    Article  CAS  Google Scholar 

  33. Bennett, B. & Larter, S. R. Quantitative separation of aliphatic and aromatic hydrocarbons using silver ion-solid-phase extraction. Anal. Chem. 72, 1039–1044 (2000)

    Article  CAS  Google Scholar 

  34. Edwards, U., Rogall, T., Blöcker, H., Emde, M. & Böttger, C. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 17, 7843–7853 (1989)

    Article  CAS  Google Scholar 

  35. Øvreås, L., Forney, L., Daae, F. L. & Torsvik, V. Distribution of bacterioplankton in meromictic lake Sælenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 63, 3367–3373 (1997)

    PubMed  PubMed Central  Google Scholar 

  36. Barns, S., Fundyga, R. E., Jeffries, M. W. & Pace, N. R. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl Acad. Sci. USA 91, 1609–1613 (1994)

    Article  ADS  CAS  Google Scholar 

  37. Pearson, W. R. & Lipman, D. J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85, 2444–2448 (1988)

    Article  ADS  CAS  Google Scholar 

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Acknowledgements

We thank B. Huizinga, A. Murray, M. Rangel, L. Trindade, R. Patience and M. Whittaker for comments and also the members of the BACCHUS2 biodegradation consortium for support, discussions and permission to publish. The BACCHUS2 members are Agip ENI, BP/Amoco, ChevronTexaco, ConocoPhillips, Norsk Hydro, Petrobras, Saudi Aramco, Shell, Statoil, Total and Woodside. We thank Norsk Hydro for their extended support of our biodegradation research and A. Wilhelms, J. Leyris, T. Liengen and J. Beeder for discussions on the feasibility of biological recovery of crude oil as methane. We also thank N. Mills of Applied Petroleum Technology (APT), Norway, for provision of samples. We acknowledge support from the Natural Environment Research Council (NERC); the Alberta Ingenuity Fund (AIF Scholarships to S.R.L. and J.J.A.), the National Science and Engineering Research Council (NSERC); and the Canada Foundation for Innovation (CFI).

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Authors and Affiliations

  1. School of Civil Engineering and Geosciences, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK ,

    D. M. Jones, I. M. Head, N. D. Gray, A. K. Rowan, C. M. Aitken, A. Brown, B. F. J. Bowler & S. R. Larter

  2. Department of Geology and Geophysics, Petroleum Reservoir Group, University of Calgary, Calgary, Alberta, T2A 1N4, Canada,

    J. J. Adams, B. Bennett, H. Huang, T. Oldenburg & S. R. Larter

  3. Norsk Hydro Oil & Energy, R&D Centre, Bergen, PO 7190, N-5020 Bergen, Norway ,

    M. Erdmann

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Correspondence to S. R. Larter.

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Competing interests

The BACCHUS2 biodegradation consortium (Agip ENI, BP/Amoco, ChevronTexaco, ConocoPhillips, Norsk Hydro, Petrobras, Saudi Aramco, Shell, Statoil, Total and Woodside) contributed financial support for part of this work. There are three patents pending (S.R.L., I.M.H., D.M.J. & M.E.) relating to methane recovery but these do not directly cover the work presented here.

Supplementary information

Supplementary Information

The file contains: a) the isotopic modelling methods used (Supplementary Methods); with explanatory text plus supplementary Figures S1 and S2 and supplementary Table S1; b) Supplementary Notes on the conversion of 13C-hexadecane to 13C-methane in oil degrading microcosms including Supplementary Figure S3; c) microbial community analysis data comprising of supplementary Figure S4 and Supplementary Table S2. (PDF 102 kb)

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Jones, D., Head, I., Gray, N. et al. Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs. Nature 451, 176–180 (2008). https://doi.org/10.1038/nature06484

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