The effect of atmospheric turbulence and chamber deployment period on autochamber CO2 and CH4 flux measurements in an ombrotrophic peatland

Accurate quantification of soil-atmosphere gas exchange is essential for understanding the magnitude and controls of greenhouse gas emissions. We used an automatic, closed, dynamic chamber system to measure the fluxes of CO2 and CH4 for several years at the ombrotrophic Mer Bleue peatland near Ottawa, Canada and found that atmospheric turbulence and chamber deployment period had a considerable influence on the observed flux rates. With a short deployment period of 2.5 min, CH4 flux exhibited strong diel patterns and both CH4 and nighttime CO2 effluxes were highly and negatively correlated with ambient friction velocity as were the CO2 concentration gradients in the top 20 cm of peat. This suggests winds were flushing the very porous and relatively dry near-surface peat layers and reducing the belowground gas concentration gradient, which then led to flux underestimations owing to a decrease in turbulence inside the headspace during chamber deployment compared to the ambient windy conditions. We found a 9 to 57% underestimate of the net biological CH4 flux at any time of day and a 13 to 21% underestimate of nighttime CO2 effluxes in highly turbulent conditions. Conversely, there was evidence of an overestimation of 100% of net biological CH4 and nighttime CO2 fluxes in calm atmospheric conditions possibly due to enhanced near-surface gas concentration gradient by mixing of chamber headspace air by fans. These problems were resolved by extending the deployment period to 30 min. After 13 min of chamber closure, the flux rate of CH4 and nighttime CO2 became constant and were not affected by turbulence thereafter, yielding a reliable estimate of the net biological fluxes. The measurement biases we observed likely exist to some extent in all chamber flux measurements made on porous and aerated substrate, such as peatlands, organic soils in tundra and forests, and snow-covered surfaces, but would be difficult to detect unless high frequency, semi-continuous observations were made.