Similar methane fluxes measured by transparent and opaque chambers point at belowground connectivity of Phragmites australis beyond the chamber footprint

• Phragmites CH4 emissions strongly influenced by PAR but not by chamber shading.
• Shading by chambers likely compensated by pressure propagation from outside plants.
• Lack of headspace mixing with fans slightly reduced CH4 emissions.
• Opaque chambers with headspace mixing suitable for reliable CH4 measurements.

In daylight, methane (CH4) emissions from green Phragmites australis culms are dominated by internal convective through-flow controlled by relative air humidity (RH), air temperature and photosynthetic active radiation (PAR). As shading by opaque chambers may attenuate emissions, it is generally recommended to use temperature-controlled transparent chambers for measuring CH4 emissions. However, experimental data on the actual impact of opaque chambers are contradictory, and full-day measurements integrating the entire range of solar radiation are rare. Moreover, the impact of chamber headspace mixing with fans on measured CH4 fluxes remains to be determined.We conducted high resolution CH4 measurements over 8–24 h at two rewetted fen sites with dense reed stands featuring different water depths. Methane emissions were measured with short enclosure times (8–12 min) using temperature-controlled transparent chambers and opaque chambers both with and opaque chambers without continuous headspace mixing by fans.The use of transparent or opaque chambers with fans did not lead to significant differences in measured CH4 emission rates. At the deep water reed site, chambers without fans resulted in lower flux estimates compared to chambers with fans, but differences were not significant. Methane emission rates closely reflected changes of PAR, even during drastic and fast changes between clouded and clear skies, indicating that PAR is the dominant factor influencing CH4 flux rates of Phragmites. We explain the contradiction between the high importance of outside PAR and the negligible influence of chamber shading by pressure propagation along horizontal rhizomes connecting non-illuminated culms inside and illuminated culms outside the chamber. For plant species with interconnected gas exchange and pressurization exceeding the boundary of a measurement plot, both opaque and transparent chambers may therefore be used to reliably determine CH4 emission.