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Abstract. Recent technological advances have enabled the wider application of automated chambers for soil greenhouse gas (GHG) flux measurements, several of them commercially available. However, few studies addressed the challenges associated with operating these systems. In this contribution we compared two commercial soil GHG chamber systems – the LI-8100A Automated Soil CO2 Flux System and the greenhouse gas monitoring system AGPS. From April until August 2014, the two systems monitored in parallel soil respiration (SR) fluxes at a recently harvested poplar (Populus) plantation, which provided a bare field situation directly after the harvest as well as a closed canopy later on. For the bare field situation (15 April–30 June 2014), the cumulated average SR obtained from the unfiltered data sets of the LI-8100A and the AGPS were 520 and 433 g CO2 m−2 respectively. For the closed canopy phase (1 July–31 August 2014), which was characterized by a higher soil moisture content, the cumulated average SR estimates were not significantly different with 507 and 501 g CO2 m−2 for the AGPS and the LI-8100A respectively. Flux quality control and filtering did not significantly alter the results obtained by the LI-8100A, whereas the AGPS SR estimates were reduced by at least 20 %. The main reasons for the observed differences in the performance of the two systems were (i) a lower data coverage provided by the AGPS due to technical problems; (ii) incomplete headspace mixing in the AGPS chambers; (iii) lateral soil CO2 diffusion below the collars during AGPS chamber measurements; and (iv) a possible overestimation of nighttime SR fluxes by the LI-8100A. Additionally, increased root growth was observed within the LI-8100A collars but not within the AGPS collars, which might have also contributed to the observed differences. In contrast to the LI-8100A, the AGPS had the gas sample inlets installed inside the collars and not the chambers. This unique design feature enabled for the first time the detection of disturbed chamber measurements during nights with a stratified atmosphere, resulting in unbiased nighttime SR estimates. Thus besides providing high temporal frequency flux data, automated chamber systems offer another possibility to greatly improve our understanding of SR fluxes.

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