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Primers: functional marker genes for methylotrophs and methanotrophs

Primers: functional marker genes for methylotrophs and methanotrophs
Primers: functional marker genes for methylotrophs and methanotrophs
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 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 beta-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.
1949-2448
1-21
Springer Verlag
Dumont, Marc G.
ad1ad358-0ed9-4f15-b5eb-7c6f54547eb5
McGenity, T.J.
Dumont, Marc G.
ad1ad358-0ed9-4f15-b5eb-7c6f54547eb5
McGenity, T.J.

Dumont, Marc G. (2014) Primers: functional marker genes for methylotrophs and methanotrophs. In, McGenity, T.J. (ed.) Hydrocarbon and Lipid Microbiology Protocols. (Springer Protocols Handbooks, , (doi:10.1007/8623_2014_23)) Berlin, DE. Springer Verlag, pp. 1-21. (doi:10.1007/8623_2014_23).

Record type: Book Section

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 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 beta-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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Published date: December 2014
Organisations: Centre for Biological Sciences

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Local EPrints ID: 387929
URI: http://eprints.soton.ac.uk/id/eprint/387929
ISSN: 1949-2448
PURE UUID: 7c017a9e-0acd-4489-8476-741acd4f45e4

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Date deposited: 13 Apr 2016 11:53
Last modified: 08 Apr 2019 16:32

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