2.3.1 Ecosystem CO2 and trace gas fluxes

Authors: Vicca S1, Stuart-Haëntjens E2, Althuizen IHJ3, Mand P4

Reviewers: Lee H5, Christansen CT5, De Boeck HJ1


Measurement unit: carbon per area and time; Measurement scale: plot; Equipment costs: €€€€€; Running costs: €€€; Installation effort: medium to high; Maintenance effort: low to high; Knowledge need: medium to high; Measurement mode: manual or data logger

The exchange of CO2 between terrestrial ecosystems and the atmosphere is a key aspect of the climate system as it determines the capacity of ecosystems to sequester anthropogenic CO2 emissions. Moreover, gas exchange measurements offer a non-destructive way to follow the system’s response to environmental changes. Net CO2 exchange (NEE) is the difference between plant CO2 uptake (GPP) and ecosystem respiration (ER). The latter combines plant and microbial respiration. All these processes are sensitive to environmental changes such as increasing atmospheric CO2, climate change, nitrogen deposition, and biodiversity loss (e.g. De Boeck et al., 2007; Vicca et al., 2007; Schmitt et al., 2010; Xu et al., 2016; Ryan et al., 2017; Nogueira et al., 2019). The combined responses will determine to what extent terrestrial ecosystems remain a carbon sink or become a source of carbon to the atmosphere.

Besides CO2, plants and soil exchange trace gases such as CH4, N2O, and biogenic volatile organic compounds (BVOCs, for example: methanol and isoprene; see protocol 5.14 BVOCs, emissions from plants and soils) with the atmosphere. Whereas CH4 and N2O are greenhouse gases with a high global warming potential, isoprene and monoterpene emissions play major roles in the ecological relationships among plants and between plants and herbivores (Peñuelas et al., 2013) as well as in climate (e.g. influencing cloud formation; Zhao et al., 2017). What and how to measure?

In experiments with short vegetation (e.g. grassland, heathland), ecosystem CO2 and trace gas fluxes are typically measured using a closed system, including soil and plants. For CO2, GPP and ER can be distinguished by combining measurements in the light and in the dark (by using a dark chamber or covering the transparent chamber with a cloth). The CO2 flux measured from a transparent chamber is NEE, the CO2 flux from a darkened chamber provides an estimate of ER. GPP can then be calculated as the difference between NEE and ER.

A transparent chamber (often custom-built) is fitted on pre-installed collars (e.g. a collar equipped with a rubber sealing or a water-filled groove; Pumpanen et al., 2004) to ensure airtight sealing. If the soil, roots, and water flow are to remain intact one can connect a windshield to the bottom of the chamber and weigh it down with a heavy chain to ensure a closed system. These chambers also require one or more fans to improve air mixing. It is important to ensure that the air inside the chamber is neither pressurised nor underpressured, as a pressure difference will create an advective flux through the soil underneath the chamber edge (Pumpanen et al., 2004). The chamber should be equipped with a sensor to measure light intensity or photosynthetically active radiation (PAR) and a temperature sensor to measure air temperature within the chamber. The chamber is connected to, for example, an infra-red gas analyser to measure the changes in the CO2 concentration continuously during the measurement period.

Ecosystem flux measurements in forest experiments are more challenging because of the size of the trees. Eddy covariance is rarely an option as plots are much smaller than the footprint. Ecosystem CO2 fluxes in forests are therefore typically derived by upscaling leaf, branch, stem, and soil flux measurements (e.g. Tang et al., 2008; see protocols 2.1.4 Plant respiration and 2.3.3 Upscaling from the plot scale to the ecosystem and beyond), although whole-tree chambers have also been used (e.g. Medhurst et al., 2006).


Where to start

De Boeck et al. (2007), Medhurst et al. (2006), Xu et al. (2016)


Installation, field operation

Chambers are typically placed on permanently installed collars. Because collar installation may disturb the gas fluxes, some equilibration time needs to be allowed (a few days should suffice, but this can be monitored). Collar insertion depth should be as shallow as possible to avoid root cutting (Wang et al., 2005); 1–2 cm insertion depth is sufficient to gain a sealing effect between soil and collar/chamber.

Chambers are typically closed for only a few minutes. In case of very small fluxes, however, closure time may need to be lengthened to ensure robust flux calculation. In that case, extra caution is required to ensure conditions inside the cuvettes (especially temperature and humidity) do not change significantly over the time of the closure.

See also protocols 2.1.4 Plant respiration and 2.2.3 Soil CO2 (and other trace gas) fluxes for further information regarding field operation.



While GPP reflects only plant processes, ER combines plant and microbial respiration. When the primary interest is in plant processes, aboveground (plant) respiration (Rabove) can be estimated by combining measurements of ER and soil CO2 efflux (see protocol 2.2.3 Soil CO2 (and other trace gas) fluxes); Rabove is the difference between ER and soil CO2 efflux (see e.g. de boeck et al., 2007). Ecosystem CO2 fluxes depend strongly on the environmental conditions: GPP is strongly driven by light, while respiration is primarily related to temperature. In order to usefully compare these fluxes between plots, light response curves are fitted to the GPP data and and temperature response curves are fitted to the ER and Rabove data. Commonly used equations are provided in, for instance, Casella & Soussana (1997) and De Boeck et al. (2007). Subsequently, ecosystem CO2 fluxes can be compared at standard conditions. Depending on the research question, normalisation for plant cover or biomass may be desirable (see e.g. Vicca et al., 2007; see protocol 2.1.1 Aboveground plant biomass). Depending on the aim of the study, one may need to take into account that leaf respiration is partially inhibited in the light, and deriving GPP from NEE and ER measurements may result in a 5–10% overestimation of GPP (Atkin et al., 2000). Special cases, emerging issues, and challenges

In recent years, advanced infrastructures – so-called ecotrons – have been developed in which ecosystem gas fluxes can be measured continuously while at the same time allowing precise conditioning of environmental factors such as temperature, relative humidity, precipitation, and CO2 concentration (see e.g. Roy et al., 2016). More of such infrastructures will be developed in the near future within the European infrastructure network ANAEE. References

Theory, significance, and large datasets

Kutzbach et al. (2007), Lu et al. (2013), Schmitt et al. (2010)


More on methods and existing protocols

Kutzbach et al. (2007), Wohlfart et al. (2005)


All references

Atkin, O. K., Evans, J. R., Ball, M. C., Lambers, H., & Pons, T. L. (2000). Leaf respiration of snow gum in the light and dark. Interactions between temperature and irradiance. Plant Physiology122(3), 915-924.

Casella, E., & Soussana, J. F. (1997). Long-term effects of CO2 enrichment and temperature increase on the carbon balance of a temperate grass sward. Journal of Experimental Botany48(6), 1309-1321.

De Boeck, H. J., Lemmens, C. M., Vicca, S., Van den Berge, J., Van Dongen, S., Janssens, I. A., … Nijs, I. (2007). How do climate warming and species richness affect CO2 fluxes in experimental grasslands? New Phytologist, 175(3), 512-522.

Kutzbach, L., Schneider, J., Sachs, T., Giebels, M., Nykänen, H., Shurpali, N. J., … Wilmking, M. (2007). CO2 flux determination by closed-chamber methods can be seriously biased by inappropriate application of linear regression. Biogeosciences4(6), 1005-1025.

Lu, M., Zhou, X., Yang, Q., Li, H., Luo, Y., Fang, C., … & Li, B. (2013). Responses of ecosystem carbon cycle to experimental warming: a meta‐analysis. Ecology, 94(3), 726-738.

Medhurst, J., Parsby, J. A. N., Linder, S., Wallin, G., Ceschia, E., & Slaney, M. (2006). A whole‐tree chamber system for examining tree‐level physiological responses of field‐grown trees to environmental variation and climate change. Plant, Cell & Environment29(9), 1853-1869.

Nogueira, C., Werner, C., Rodrigues, A., & Caldeira, M. C. (2019). A prolonged dry season and nitrogen deposition interactively affect CO2 fluxes in an annual Mediterranean grassland. Science of the Total Environment, 654, 978-986.

Peñuelas, J., Marino, G., LLusia, J., Morfopoulos, C., Farré-Armengol, G., & Filella, I. (2013). Photochemical reflectance index as an indirect estimator of foliar isoprenoid emissions at the ecosystem level. Nature Communications, 4, art2604.

Pumpanen, J., Kolari, P., Ilvesniemi, H., Minkkinen, K., Vesala, T., Niinistö, S., … Janssens, I. (2004). Comparison of different chamber techniques for measuring soil CO2 efflux. Agricultural and Forest Meteorology, 123(3), 159-176.

Roy, J., Picon-Cochard, C., Augusti, A., Benot, M. L., Thiery, L., Darsonville, O., … Escape, C. (2016). Elevated CO2 maintains grassland net carbon uptake under a future heat and drought extreme. Proceedings of the National Academy of Sciences USA113(22), 6224-6229.

Ryan, E. M., Ogle, K., Peltier, D., Walker, A. P., Kauwe, M. G., Medlyn, B. E., … Harper, A. B. (2017). Gross primary production responses to warming, elevated CO2, and irrigation: quantifying the drivers of ecosystem physiology in a semiarid grassland. Global Change Biology, 23(8), 3092-3106.

Schmitt, M., Bahn, M., Wohlfahrt, G., Tappeiner, U., & Cernusca, A. (2010). Land use affects the net ecosystem CO2 exchange and its components in mountain grasslands. Biogeosciences7(8), 2297.

Tang, J., Bolstad, P. V., Desai, A. R., Martin, J. G., Cook, B. D., Davis, K. J., & Carey, E. V. (2008). Ecosystem respiration and its components in an old-growth forest in the Great Lakes region of the United States. Agricultural and Forest Meteorology148(2), 171-185.

Vicca, S., Serrano-Ortiz, P., De Boeck, H. J., Lemmens, C. M. H. M., Nijs, I., Ceulemans, R., … Janssens, I. A. (2007). Effects of climate warming and declining species richness in grassland model ecosystems: acclimation of CO2 fluxes.

Wang, W. J., Zu, Y. G., Wang, H. M., Hirano, T., Takagi, K., Sasa, K., & Koike, T. (2005). Effect of collar insertion on soil respiration in a larch forest measured with a LI-6400 soil CO2 flux system. Journal of Forest Research10(1), 57-60.

Wohlfahrt, G., Anfang, C., Bahn, M., Haslwanter, A., Newesely, C., Schmitt, M., … Cernusca, A. (2005). Quantifying nighttime ecosystem respiration of a meadow using eddy covariance, chambers and modelling. Agricultural and Forest Meteorology128(3-4), 141-162.

Xu, X., Shi, Z., Chen, X., Lin, Y., Niu, S., Jiang, L., … Luo, Y. (2016). Unchanged carbon balance driven by equivalent responses of production and respiration to climate change in a mixed‐grass prairie. Global Change Biology22(5), 1857-1866.

Zhao, D. F., Buchholz, A., Tillmann, R., Kleist, E., Wu, C., Rubach, F., … Mentel, T. F. (2017). Environmental conditions regulate the impact of plants on cloud formation. Nature Communications, 8, art14067.



Authors: Vicca S1, Stuart-Haëntjens E2, Althuizen IHJ3, Mand P4

Reviewers: Lee H5, Christansen CT5, De Boeck HJ1



1 Centre of Excellence PLECO (Plants and Ecosystems), Biology Department, University of Antwerp, Wilrijk, Belgium

2 Department of Biology, Virginia Commonwealth University, Richmond, USA

3Department of Biological Sciences and Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway

4 Institute of Ecology and Earth Sciences, Tartu University, Tartu, Estonia

5 NORCE Norwegian Research Centre and Bjerknes Centre for Climate Research, Bergen, Norway