Comparing ecosystem and soil respiration: Review and key challenges of tower-based and soil measurements

The net ecosystem exchange (NEE) is the difference between ecosystem CO₂ assimilation and CO₂ losses to the atmosphere. Ecosystem respiration (R_eco), the efflux of CO₂ from the ecosystem to the atmosphere, includes the soil-to-atmosphere carbon flux (i.e., soil respiration; R_soil) and aboveground plant respiration. Therefore, R_soil is a fraction of R_eco and theoretically has to be smaller than R_eco at daily, seasonal, and annual scales. However, several studies estimating R_eco with the eddy covariance technique and measuring R_soil within the footprint of the tower have reported higher R_soil than R_eco at different time scales. Here, we compare four different and contrasting ecosystems (from forest to grasslands, and from boreal to semiarid) to test if measurements of R_eco are consistently higher than R_soil. In general, both fluxes showed similar temporal patterns, but R_eco was not consistently higher than R_soil from daily to annual scales across sites. We identified several issues that apply for measuring NEE and measuring/upscaling R_soil that could result in an underestimation of R_eco and/or an overestimation of R_soil. These issues are discussed based on (a) nighttime measurements of NEE, (b) R_soil measurements, and (c) the interpretation of the functional relationships of these fluxes with temperature (i.e., Q₁₀). We highlight that there is still a need for better integration of R_soil with eddy covariance measurements to address challenges related to the spatial and temporal variability of R_eco and R_soil.