Peatlands are interesting as a carbon storage option, but are also natural emitters of the greenhouse gas methane (CH4). Phragmites peatlands are particularly interesting due to the global abundance of this wetland plant (Phragmites australis) and the highly efficient internal gas transport mechanism, which is called humidity-induced convection (HIC). The research aims were to (1) clarify how this plant-mediated gas transport influences the CH4 fluxes, (2) which other environmental variables influence the CO2 and CH4 fluxes, and (3) whether Phragmites peatlands are a net source or sink of greenhouse gases. CO2 and CH4 fluxes were measured with the eddy covariance technique within a Phragmites-dominated fen in southwest Germany. One year of flux data (March 2013–February 2014) shows very clear diurnal and seasonal patterns for both CO2 and CH4. The diurnal pattern of CH4 fluxes was only visible when living, green reed was present. In August the diurnal cycle of CH4 was the most distinct, with 11 times higher midday fluxes (15.7 mg CH4 m−2 h−1) than night fluxes (1.41 mg CH4 m−2 h−1). This diurnal cycle has the highest correlation with global radiation, which suggests a high influence of the plants on the CH4 flux. But if the cause were the HIC, it would be expected that relative humidity would correlate stronger with CH4 flux. Therefore, we conclude that in addition to HIC, at least one additional mechanism must be involved in the creation of the convective flow within the Phragmites plants. Overall, the fen was a sink for carbon and greenhouse gases in the measured year, with a total carbon uptake of 221 g C m−2 yr−1 (26 % of the total assimilated carbon). The net uptake of greenhouse gases was 52 g CO2 eq. m−2 yr−1, which is obtained from an uptake of CO2 of 894 g CO2 eq. m−2 yr−1 and a release of CH4 of 842 g CO2 eq. m−2 yr−1.
