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Most studies implicitly consider soil carbon dioxide (CO2) efflux as the instantaneous soil respiration and thereby neglect possible changes in the amount of CO2 stored in the soil pore‐space. We measured the CO2 concentration profile of a well‐aerated soil continuously to evaluate the dynamics of the stored CO2 and to analyse the influence of environmental factors. For 25% of the observation period, changes in the amount of stored CO2 accounted for more than 15% of the soil‐CO2 efflux. The following factors were identified to interfere with steady‐state CO2 storage: (i) the fluctuating groundwater table altered the volume of the vadose zone, causing viscous airflow in air‐filled soil pores, (ii) atmospheric turbulence caused pressure‐pumping at the soil–atmosphere interface and (iii) intense rain greatly reduced the diffusivity of the uppermost soil layer. The friction velocity above the canopy was strongly correlated with fluctuations in the differential pressure between soil air and atmosphere, but no static pressure gradient could be detected because of the permeable nature of the soil. Unexpected short‐term declines in the soil CO2 concentration were observed during intense rainfall events. These declines were explained by the intensified CO2 saturation deficit of the infiltrating rainwater caused by the carbonate chemistry of the soil solution.

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Quantifying and understanding fluxes of methane (CH4) and carbon dioxide (CO2) in natural soil–plant–atmosphere systems are crucial to predict global climate change. Wetland herbaceous species or tree species at waterlogged sites are known to emit large amounts of CH4. Upland forest soils are regarded as CH4 sinks and tree species like upland beech are not known to significantly emit CH4. Yet, data are scarce and this assumption needs to be tested. We combined measurements of soil–atmosphere and stem–atmosphere fluxes of CO2 and CH4, and soil gas profiles to assess the contribution of the different ecosystem compartments at two upland beech forest sites in Central Europe in a case study. Soil was a net CH4 sink at both sites, though emissions were detected consistently from beech stems at one site. Although stem emissions from beech stems were high compared to known fluxes from other upland tree species, they were substantially lower compared to the strong CH4 sink of the soil. Yet, we observed extraordinarily large CH4 emissions from one beech tree that was 140% of the CH4 sink of the soil. The soil gas profile at this tree indicated CH4 production at a soil depth > 0.3 m, despite the net uptake of CH4 consistently observed at the soil surface. Field soil assessment showed strong redoximorphic color patterns in the adjacent soil and supports this evaluation. We hypothesize that there is a transport link between the soil and stem via the root system representing a preferential transport mechanism for CH4 despite the fact that beech roots usually do not bear aerenchyma. The high mobility of gases requires a holistic view on the soil–plant–atmosphere system. Therefore, we recommend including field soil assessment and soil gas profiles measurements when investigating soil–atmosphere and stem–atmosphere fluxes to better understand the sources of gases and their transport mechanisms.

High-precision differential air pressure measurements were conducted in the below-canopy space of a Scots pine forest and in the forest soil to investigate small air pressure fluctuations and their effect on soil gas flux. In addition to air pressure measurements, tracer gas concentration in the soil and airflow characteristics above and below the canopy were measured. Results suggest that air pressure fluctuations in the frequency range of 0.01 Hz-0.1 Hz are strongly dependent on abovecanopy wind speed. While amplitudes of the observed air pressure fluctuations (<10 Pa) increase significantly with increasing above-canopy wind speed, the periods decrease significantly with increasing above-canopy wind speed. These air pressure fluctuations are associated with the pressure-pumping effect in the soil. A pressure-pumping coefficient was defined, which describes the strength of the pressure-pumping effect. During the measurement period, pressure-pumping coefficients up to 0.44 Pa·s −1 were found. The dependence of the pressure-pumping coefficient on mean above-canopy wind speed can be described well with a polynomial fit of second degree. The knowledge of this relation simplifies the quantification of the pressure-pumping effect in a Scots pine forest considerably, since only the mean above-canopy wind speed has to be measured. In addition, empirical modeling revealed that the pressure-pumping coefficient explains the largest fraction of the variance of tracer gas concentration in the topsoil.

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Naturally produced by microbial processes in soil, nitrous oxide (N2O) is an important greenhouse gas contributing to climate change. Accordingly, there is a need to accurately quantify the capability of forest ecosystems to exchange N2O with the atmosphere. While N2O emissions from soils have been well studied, trees have so far been overlooked in N2O inventories. Here, we show that stems of mature beech trees (Fagus sylvatica) may act as a substantial sink of N2O from the atmosphere under conditions of soils consuming N2O. Consistent consumption of N2O by all stems investigated (ranging between −2.4 and −3.8 µg m−2 h−1) is a novel finding in contrast to current studies presenting trees as N2O emitters. To understand these fluxes, N2O exchange of photoautotrophic organisms associated with beech bark (lichens, mosses and algae) was quantified under laboratory conditions. All these organisms were net N2O sinks at full rehydration and temperature of 25 °C. The consumption rates were comparable to stem consumption rates measured under field conditions. Cryptogamic stem covers could be a relevant sink of N2O in European beech forests.