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 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.