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Primers: Functional Marker Genes for Methylotrophs and Methanotrophs

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Hydrocarbon and Lipid Microbiology Protocols

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Abstract

Methylotrophs are a diverse group of microorganisms that use compounds without a carbon–carbon bond as a sole source of carbon and energy for growth. Methylotrophs play an important role in most environments, including terrestrial, aquatic, and marine habitats. Several approaches to detect and identify methylotrophs in environmental samples have been developed. A common approach is to target protein-encoding genes since methylotrophs are phylogenetically diverse, making the design of 16S rRNA primers and probes with wide coverage difficult or impossible. The mxaF gene encoding the active site subunit of the methanol dehydrogenase is one of the more universal targets for methylotrophs, as are some of the genes involved in C1-transfer reactions, such as fhcD gene of methanopterin-linked pathway. The pmoA gene, encoding the β-subunit of the particulate methane monooxygenase, is a common target for methanotrophs. In many cases the evolution of these functional genes is congruent with the 16S rRNA and other phylogenetic markers, making them suitable for inferring taxonomy. This chapter summarizes the available primers and methods to detect or quantify various aerobic methylotrophs in environmental samples.

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Authors and Affiliations

  1. Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str 10, 35043, Marburg, Germany

    Marc G. Dumont

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  1. Marc G. Dumont
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Correspondence to Marc G. Dumont .

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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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Dumont, M.G. (2014). Primers: Functional Marker Genes for Methylotrophs and Methanotrophs. 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_2014_23

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  • DOI: https://doi.org/10.1007/8623_2014_23

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  • 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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