We built an automatic chamber system to measure greenhouse gas (GHG) exchange in forested peatland ecosystems. We aimed to build a system robust enough which would work throughout the year and could measure through a changing snowpack in addition to producing annual GHG fluxes by integrating the measurements without the need of using models. The system worked rather well throughout the year, but it was not service free. Gap filling of data was still necessary. We observed problems in carbon dioxide (CO₂) respiration flux estimation during calm summer nights, when a CO₂ concentration gradient from soil/moss system to atmosphere builds up. Chambers greatly overestimated the night-time respiration. This was due to the disturbance caused by the chamber to the soil-moss CO₂ gradient and consequent initial pulse of CO₂ to the chamber headspace. We tested different flux calculation and measurement methods to solve this problem. The estimated flux was strongly dependent on (1) the starting point of the fit after closing the chamber, (2) the length of the fit, (3) the type of the fit (linear and polynomial), (4) the speed of the fan mixing the air inside the chamber, and (5) atmospheric turbulence (friction velocity, u*). The best fitting method (the most robust, least random variation) for respiration measurements on our sites was linear fitting with the period of 120–240 s after chamber closure. Furthermore, the fan should be adjusted to spin at minimum speed to avoid the pulse-effect, but it should be kept on to ensure mixing. If night-time problems cannot be solved, emissions can be estimated using daytime data from opaque chambers.

We measured methane (CH₄) exchange rates with automatic chambers at the forest floor of a nutrient-rich drained peatland in 2011–2013. The fen, located in southern Finland, was drained for forestry in 1969 and the tree stand is now a mixture of Scots pine, Norway spruce, and pubescent birch. Our measurement system consisted of six transparent chambers and stainless steel frames, positioned on a number of different field and moss layer compositions. Gas concentrations were measured with an online cavity ring-down spectroscopy gas analyzer. Fluxes were calculated with both linear and exponential regression. The use of linear regression resulted in systematically smaller CH₄ fluxes by 10–45 % as compared to exponential regression. However, the use of exponential regression with small fluxes ( < 2.5 µg CH₄ m⁻² h⁻¹) typically resulted in anomalously large absolute fluxes and high hour-to-hour deviations. Therefore, we recommend that fluxes are initially calculated with linear regression to determine the threshold for low fluxes and that higher fluxes are then recalculated using exponential regression. The exponential flux was clearly affected by the length of the fitting period when this period was < 190 s, but stabilized with longer periods. Thus, we also recommend the use of a fitting period of several minutes to stabilize the results and decrease the flux detection limit. There were clear seasonal dynamics in the CH₄ flux: the forest floor acted as a CH₄ sink particularly from early summer until the end of the year, while in late winter the flux was very small and fluctuated around zero. However, the magnitude of fluxes was relatively small throughout the year, ranging mainly from −130 to +100 µg CH₄ m⁻² h⁻¹. CH₄ emission peaks were observed occasionally, mostly in summer during heavy rainfall events. Diurnal variation, showing a lower CH₄ uptake rate during the daytime, was observed in all of the chambers, mainly in the summer and late spring, particularly in dry conditions. It was attributed more to changes in wind speed than air or soil temperature, which suggest that physical rather than biological phenomena are responsible for the observed variation. The annual net CH₄ exchange varied from −104 ± 30 to −505 ± 39 mg CH₄ m⁻² yr⁻¹ among the six chambers, with an average of −219 mg CH₄ m⁻² yr⁻¹ over the 2-year measurement period.