Methane (CH₄) is a potent greenhouse gas and management strategies have been proposed to limit CH₄ emissions from freshwater wetlands. Methane-oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse active CH₄ gas produced in wetlands before it can be emitted to the atmosphere. The methanotrophic bacteria can intercept much of the CH₄ produced by methanogenic archaea and thus management protocols for wetlands could conceivably include manipulations not only to limit the production of CH₄ by methanogens, but also to enhance the consumption of CH₄ by benthic or planktonic methanotrophs.

The hydrological characteristics of a wetland are a major determinant of the CH₄ emission rates. One important factor is whether a wetland is static or flowing (wetlands connected to rivers and streams) which would likely affect abundance and activity of methanotrophs. Very little is known about the effects of hydrologic pulsing on wetland carbon dynamics and especially CH₄ oxidation. Furthermore, although it has been established that methanotrophs are very active at the oxic sediment-water interface of wetlands, little is known about the ecology of methanotrophs in the “at the fringe” of flowing or pulsing wetlands.

Microbial Phospholipid Fatty Acid (PLFA) profiling provides a culture-independent method that has biomarkers for methanotrophs. PLFAs are an integral part of the membrane of all living cells and can serve as “fingerprints” of microbial communities in environmental samples. Combining this approach with stable isotope probing (SIP) that utilizes ¹³C (isotopically labeled carbon) provide a means to connect CH₄ oxidation to specific methanotrophs and track the shifts in community structure. This is done by exposing environmental samples to ¹³CH₄ followed by separation of signature PLFAs for methanotrophs on a gas chromatograph, followed by subsequent ¹³C analysis of PLFAs on a mass spectrometer. This SIP method offers the novel opportunity to track ¹³CH₄ flow through methanotrophs and into secondary microbial feeders and soil organic carbon pools.

Based on the presence of “fingerprint” PLFAs, the methanotrophs are divided into two major categories, viz. Type I (detected by the presence of fatty acids: 16:ω5c, 16:ω7c 16:ω8c) and Type II (detected by the presence of fatty acids: 18:ω8c, 18:ω9c and 18:ω7c). The Type II methanotrophs are physiologically active at higher methane concentrations (>40 ppm) and the Type II methanotrophs are active at atmospheric concentrations of methane (~ 2 ppm). The use of SIP techniques enable us to not only identify the key players in methane oxidation but also, to track the flow of C and thereby, the significance of these bacteria in C sequestration in different hydrologic situations.