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Primers: Functional Genes for Nitrogen-Cycling Microbes in Oil Reservoirs

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Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

Microbial communities found in the subsurface are important in the biogeochemical cycling of nitrogen (N) both in the oxidative and reductive processes, and changes in their functional structure might affect the stability of a petroleum reservoir. In petroleum reservoirs, where in situ conditions are predominantly anoxic, denitrification involving the stepwise reduction of nitrate (NO3 −) via nitrite (NO2 −) and nitric oxide (NO) to nitrous oxide (N2O) or dinitrogen gas (N2) is a major process. Microorganisms may also decompose organic N to ammonium (NH4 +) by ammonification, which can subsequently be oxidised to NO3 − via NO2 − by the process of nitrification. Autotrophic ammonia oxidation is known in three groups of microorganisms: aerobic autotrophic ammonia-oxidising bacteria (AOB) and Archaea (AOA) and anaerobic ammonia-oxidising bacteria (anammox). Since the microorganisms involved in many of these N transformations are taxonomically diverse, 16S rRNA-based methods are generally not suitable. Instead, a common approach has been to target the protein-encoding genes involved in the transformation of N as biomarkers. This chapter describes the common PCR primers that have been used to target the major functional genes involved in the cycling of N, with the key N transformations likely to occur in petroleum reservoirs highlighted throughout.

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Authors and Affiliations

  1. School of Natural Sciences, National University of Ireland, University Road, Galway, UK

    C. J. Smith

  2. School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK

    B. A. McKew, A. Coggan & C. Whitby

Authors
  1. C. J. Smith
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  2. B. A. McKew
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  3. A. Coggan
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  4. C. Whitby
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Corresponding author

Correspondence to C. Whitby .

Editor information

Editors and Affiliations

  1. Dept. Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

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© 2015 Springer-Verlag Berlin Heidelberg

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Smith, C.J., McKew, B.A., Coggan, A., Whitby, C. (2015). Primers: Functional Genes for Nitrogen-Cycling Microbes in Oil Reservoirs. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_184

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  • DOI: https://doi.org/10.1007/8623_2015_184

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-50427-7

  • Online ISBN: 978-3-662-50428-4

  • eBook Packages: Springer Protocols

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