Community-level analysis: key genes of aerobic methane oxidation

Aerobic methane-oxidizing bacteria (methanotrophs) are a diverse group of bacteria that are currently represented by 13 recognized genera. They play a major role in the global methane cycle and are widespread in nature with representatives found in soils, freshwater, seawater, freshwater and marine sediments, peat bogs and at extremes of temperature, salinity, and pH. There has been an interest in methanotrophs for their potential in bioremediation processes. Methanotroph diversity and ecology are often studied using the "functional" genes pmoA, mmoX, and mxaF, encoding subunits of the particulate methane monooxygenase, soluble methane monooxygenase, and the methanol dehydrogenase, respectively. This chapter describes methods used to detect and analyze these functional genes.