Emerging constraints of photosynthesis (including chlorophyll fluorescence), respiration and transpiration at ecosystem to global scales

Gross photosynthetic CO2 uptake is the single largest component of the global carbon cycle and a crucial variable for monitoring and understanding global biogeochemical cycles and fundamental ecosystem services. Nowadays routine measurements of the net biosphere-atmosphere CO2 exchange are conducted at the ecosystem scale in a large variety of ecosystem types across the globe. Gross photosynthetic and ecosystem respiratory fluxes are then typically inferred from the net CO2 exchange and used for benchmarking of terrestrial biosphere models or as backbones for upscaling exercises. Uncertainty in the responses of photosynthesis and respiration to the climate and environmental conditions is a major source of uncertainty in predictions of ecosystem-atmosphere feedbacks under climate change. On the other hand, transpiration estimates both at ecosystem to global scales are highly uncertain with estimates ranging from 20 to 90 % of total evapotranspiration. The most important bottleneck to narrow down the uncertainty in transpiration estimates is the fact that direct measurements of transpiration are uncertain and techniques like eddy covariance measure only the total evapotranspiration.
During the last decade, technological developments in field spectroscopy, including remote and proximal sensing of sun-induced fluorescence, as well as in isotope flux measurements and quantum cascade lasers have enabled alternative approaches for constraining ecosystem-scale photosynthesis, respiration and transpiration. On the other hand, a variety of approaches have been developed to directly assess the gross fluxes of CO2 and transpiration by using both process based and empirical models, and machine learning techniques.
In this session, we aim at reviewing recent progress made with novel approaches of constraining ecosystem gross photosynthesis, respiration and transpiration and at discussing their weaknesses and future steps required to reduce the uncertainty of present-day estimates. To this end, we are seeking contributions that use emerging constrains to improve the ability to quantify respiration and photosynthesis processes, transpiration and water use efficiency, at scales from leaf to ecosystem and global. Particularly welcome are studies reporting advancements and new developments in CO2 and evapotranspiration flux partitioning from eddy covariance data, the use of carbonyl sulfide, stable isotopes approaches and sun-induced fluorescence.

Convener: Karolina SakowskaECSECS | Co-conveners: Timothy Griffis, Markus Reichstein, Mirco Migliavacca, Georg Wohlfahrt
vPICO presentations
| Tue, 27 Apr, 15:30–17:00 (CEST)

Session assets

Session materials

vPICO presentations: Tue, 27 Apr

Chairpersons: Karolina Sakowska, Mirco Migliavacca, Georg Wohlfahrt
Nicole Salvatori

In natural environments plants are subjected to variable light conditions and therefore need an efficient regulatory system to regulate photosynthesis and the downstream metabolism. Most of the measurements available are taken at steady state and at leaf level but those may overestimate total carbon uptake in a more dynamic environment. Furthermore, some plants may be more adapted than others to deal with light fluctuations and therefore is difficult to draw general conclusions. We then grew a commercial soybean variety and a chlorophyll deficient mutant in a recently developed growth chamber system (DYNAMISM) which allowed to obtain instantaneous gas exchange data at canopy level for several weeks. By doing so we could investigate both short term responses and long term adaptations to light dynamic conditions of the two varieties. At steady state, chlorophyll deficient crops are thought to have a similar or even a higher photosynthetic rate compared to the green wildtypes, enhanced by a higher light transmittance throughout the canopy. But little is known about how they respond to fluctuations in light. The two varieties were grown either in fluctuating (F) or non-fluctuating (NF) light conditions to evaluate how variable light would affect biomass accumulation. Two different light treatments were applied, low light (LL) and high light (HL) with different light intensities and amplitude of fluctuations. The LL treatment did not entail any difference among F and NF in both varieties. The chlorophyll-deficient mutant was instead found to be susceptible to the fluctuations of light in the HL treatment, by accumulating less biomass. It is hypothesised that this might be due to its longer non‐photochemical quenching relaxation time  in light transitions, but other acclimatation mechanisms need to be investigated.

How to cite: Salvatori, N.: The effect of fluctuating light on canopy photosynthesis: a focus on a chlorophyll-deficient Soybean mutant, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-12543,, 2021.

Quentin Beauclaire and Bernard Longdoz

Understanding how plant crops respond to drought is essential for both improving photosynthesis modelling and predicting the impacts of climate change on agricultural production. Over the past years, researches have focused on identifying the stomatal processes that restrict the net photosynthetic rate and quantifying the importance and how different factors limit it. However, the constraints to photosynthesis coming from perturbation in the mechanisms taking place from sub-stomatal cavities to carboxylation sites in chloroplasts are not yet fully understood especially in plant crops. The aim of our study was to investigate the impact of drought on the light-limited photosynthesis rate for potato (Solanum Tubersosum) by measuring the photosynthesis limitations and partitioning them between stomatal, mesophyll and biochemical constrains during a field-experiment that took place in Wallonia during the summer 2020. Gas-exchange and fluorescence techniques were used to quantify mesophyll conductance (gm), stomatal conductance (gs), Rubisco carboxylation rate (Vcmax) and electron transport rate (Jmax) in response to low soil water content during the tuber development stage. We obtained a clear reduction of the leaf assimilation and performed a limitation analysis identifying which factor contributed the most to the light-saturated photosynthetic rate (An) decrease. During the one-month drought treatment, An, gm, Jmax and Vcmax significantly decreased when the relative extractable water (REW) passed below a threshold ranging from 0.5 to 0.7 . On the opposite, g1, the slope of the gs dependence on environmental factors, remained constant. When soil water was not limiting, most of the light-saturated photosynthetic rate variation was explained by VPD while mesophyll and biochemical influence progressively increased when soil water content declined. At the maximum drought intensity, gm and Vcmax reduction explained respectively 40 % and 30% of the light-saturated photosynthetic rate decrease. The coexistence of aerial drought (high VPD) accounted only for 3% of the total limitation. This highlights the importance of mesophyll and biochemical limitations on potato photosynthesis and development.

How to cite: Beauclaire, Q. and Longdoz, B.: Estimating mesophyll and biochemical limitations to carbon assimilation of potato crop during drought, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-11021,, 2021.

Michaela Schwarz, Karolina Sakowska, Klaudia Ziemblińska, Paulina Dukat, Marek Urbaniak, Janusz Olejnik, Albin Hammerle, and Georg Wohlfahrt

Solar-induced chlorophyll fluorescence (SIF) has been shown as a promising approach for the estimation of gross primary productivity (GPP), but whether SIF is merely a function of canopy structure or also contains precious physiological information, is presently heavily discussed. In this study, the SIF-GPP relationship was quantified at a Pinus sylvestris forest (Mezyk, Poland) during a series of short-term cold spells throughout the spring awakening to investigate the potential of SIF as a proxy for GPP during this period characterized by cold stress. GPP was inferred from the net ecosystem CO2 exchange measured by the eddy covariance technique. Canopy-scale SIF was measured using a high-resolution spectrometer system and retrieved via spectral fitting (SFM) algorithms. Active leaf-scale chlorophyll fluorescence measurements were conducted on seven branches using an automated field-deployable fluorometer system. Our results demonstrate a clear difference in GPP and the utilization of chlorophyll-absorbed energy between cold spell and warm days. At short, sub-daily time scales, the correlation between SIF and GPP was minor, but increased significantly when observed over extended temporal periods, when SIF exhibited a seasonal pattern that was more closely aligned with the GPP. Furthermore, the strong relationship between non-photochemical quenching (NPQ) and the photochemical reflectance index (PRI) shows good potential to better estimate GPP when integrated in the SIF-GPP model, as the integration of PRI overall increased the relation between SIF and GPP.

How to cite: Schwarz, M., Sakowska, K., Ziemblińska, K., Dukat, P., Urbaniak, M., Olejnik, J., Hammerle, A., and Wohlfahrt, G.: Chlorophyll fluorescence-gross primary productivity relationships during the spring awakening of an evergreen needleleaf forest, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-3094,, 2021.

Albin Hammerle, Mirco Migliavacca, Felix Spielmann, Javier Pacheco-Labrador, and Georg Wohlfahrt

Solar radiation absorbed by chlorophyll in plants is either used for photosynthesis, dissipated as heat or is re-emitted as fluorescence at a slightly higher wavelength. Sun induced chlorophyll fluorescence (SIF) has thus the potential to act as a sensitive indicator for early stress detection in ecosystems. SIF signals at the top of the canopy are however influenced by canopy structure and not only by plant physiology, due to light scattering and (re)absorption.

In this study we present the first results of a mesocosm experiment on the effect of drought stress on chlorophyll fluorescence in two plant stands differing in their canopy structure. In total we investigated 24 plots of planophile (Trifolium repens) and erectophile (Lolium perenne) plant stands. 12 plots acted as a control plots, while the remaining 12 plots underwent a progressively intensifying drought stress treatment. During the course of the experiment regular measurements of SIF using a passive spectrometer system were conducted. Furthermore, active chlorophyll fluorescence measurements with a multiplexed field spectrometer system were used to derive the maximum PSII efficiency (Fvm) and non-photochemical quenching (NPQ). Ancillary measurements included meteorological, leaf physiological, soil water and canopy structure variables.

The drought treatment led to a relatively stronger decrease in NDVI and a relatively higher increase in PRI in the Trifolium repens stand, which also experienced a more pronounced increase in NPQ, especially during hot days. For both stands surface temperatures were clearly higher in the treatment groups, with a larger effect in the Trifolium stand. SIF-yield (SIF/aPAR) did remain more or less constant or increased slightly for the control groups. In both stands it dropped towards the end of the experiment for both treatment groups at very low soil water content levels, about at the same time when the active chlorophyll fluorescence measurements started to indicate persistent reductions in Fvm. The relative decrease in SIF and SIF-yield for the treatment groups was not significantly different between the two stands.

How to cite: Hammerle, A., Migliavacca, M., Spielmann, F., Pacheco-Labrador, J., and Wohlfahrt, G.: Canopy structure and stress induced changes in chlorophyll fluorescence – a mesocosm experiment, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-16102,, 2021.

Amnon Cochavi, Eyal Rotenberg, Fyodor Tatarinov, Philipp Kӧhler, Christian Frankenberg, and Dan Yakir

Dry Mediterranean forests are characterized by a short rainy season followed by a long dry period with high temperatures and radiation levels. These ecosystem are also exposed to large interannual variations in precipitation. Taking advantage of contrasting rainfall years, we investigated the opportunistic nature of pine trees in this region.  In our study site (the Yatir forest) mean annual precipitation is 288 mm, but it was 220 and 420 mm in the hydrological years 2018/19 and 2019/20, respectively. We used fluorescence measurements at the leaf, tower, and satellite scales, together with reflectance indices and eddy covariance measurements to assess the physiological response in the dry stressful season in these contrasting years.

The results showed that following a low rainfall season, soil moisture contes (SWC) reaches the 16% threshold of no traspirable water in spring, followed by larg decrease in carbon uptake and quantum yield of photosynthesis and the activation of protection mechanisms, such as decrease in chlorophyll content, large NPQ, and drop in the chlorophyll to cartenoid ratio (CCI index, obtained from canopy reflectance). Following the high rainfall year, the active season is extended (as indicated also by the satellite data), but even after the SWC threshold is reached, and mid-day VPD reaches ~5 KPa), carbon uptake continues, the amount of energy allocated to photochemistry remains high (high Fv/Fm and Y(II) levels), without the onset of protective mechanisms: No decrease in leaf chlorophyll and in NPQ, or decrease in CCI. We hypothesize that the opportunistic response of the dry-land forest must rely on yet unidentified water storage outside the root zone (e.g. deep soil pockets within the bedrock, or within the plants), which allow the plant to maintain high, with the only apparent adjustment reflected in shift of activity to early morning hours, when VPD is still low but the PAR levels are sufficiently high.

How to cite: Cochavi, A., Rotenberg, E., Tatarinov, F., Kӧhler, P., Frankenberg, C., and Yakir, D.: Combining SIF, reflectance, and leaf scale measuremnts to assess the effcets of interannual changes in winter rainfall on tree physiology during the following summer drought period in a dry Mediterranean pine forest, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-15086,, 2021.

Rafat Qubaja, Rafael Stern, Itay Oz, Amnon Cochavi, Jonathan Muller, and Dan Yakir

During the regular seasonal drought conditions in our semi-arid pine forest, soil water content decrease below the 16% threshold of no transpirable soil water availability, and VPD increase to values of >5 kPa. Soil drought in one forest plot was eliminated by using supplemental drip irrigation during summer. We used automatic branch chambers to measure CO2/H2O exchange together with laser-based COS exchange, and retrieving canopy sun induced fluorescence (SIF) using a high-resolution spectrometer above the canopy that was moved between the control and irrigated plots on a weekly basis. Using these research tools, we investigated the ecophysiological response (including rates of gas exchange, conductances, and photochemical response) of the mature pine trees to the differential effects of soil and atmospheric droughts. Leaf relative uptake (LRU) ratio of COS to CO2 fluxes was used to constrain estimates of carbon assimilation (An) and changes in the An/gl ratio (where gl is leaf conductance), and leaf COS and H2O exchange fluxes were also used to partition leaf conductance. We will report on the first seasonal cycle of COS and CO2 fluxes, LRU and SIFA of mature pine trees under field conditions in the semi-arid forest, which includes the summer dry stress period, the recovery during the transition to the winter wet season, and the spring peak activity period.

How to cite: Qubaja, R., Stern, R., Oz, I., Cochavi, A., Muller, J., and Yakir, D.: Combining branch-scale COS/CO2 exchange and canopy-scale SIF measurements to disentangle the effects of high VPD and low soil moisture in mature pine trees under field conditions, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-6430,, 2021.

Sebastian Wieneke, Ana Bastos, Manuela Balzarolo, José Miguel Barrios, and Ivan Janssens

Sun Induced Chlorophyll Fluorescence (SIF) is considered as a good proxy for photosynthesis given its closer link to the photosynthetic light reactions compared to remote sensing vegetation indices typically used for ecosystem productivity modelling (eg. NDVI). Satellite-based SIF shows significant linear relationships with gross primary production (GPP) from in-situ measurements across sites, biomes and seasons. While SIF can be considered a good proxy for large scale spatial and seasonal variability in GPP, much of the SIF-GPP co-variance can be explained by their common dependence on the absorbed photosynthetically active radiation. Whether SIF can be an equally good proxy for interannual variability in GPP especially during periods of vegetation stress (drought/heat) is, so far, not clear.

In this study, we evaluate the relationship between satellite-based SIF and in-situ GPP measurements during vegetation stress periods (drought/heat), compared to non-stress periods. GPP is obtained from eddy-covariance measurements from a set of forest sites pre-filtered to ensure homonegeous footprints. SIF is obtained from GOME-2 covering the period 2007-2018. Because of scale mismatch between each site’s footprint (in the order of hundred meters) and the spatial resolution of GOME-2 (ca. 50km), we additionally use SIF from the downscale product from Duveiller et al. 2020 (ca. 5km) and the more recent dataset from TROPOMI (ca. 7 x 3.5 km), covering only the last year of the study period.

We develop a classification of stress periods that is based on both the occurrence of drought/heat extreme events and the presence of photosynthetic downregulation. We then evaluate the relationship between SIF and GPP and their yields, for different plant functional types and at site-level. We evaluate how these relationships vary depending on environmental conditions and in particular for “stress” versus “non-stress” days.

Duveiller, G., Filipponi, F., Walther, S., Köhler, P., Frankenberg, C., Guanter, L., and Cescatti, A.: A spatially downscaled sun-induced fluorescence global product for enhanced monitoring of vegetation productivity, Earth Syst. Sci. Data, 12, 1101–1116,, 2020.

How to cite: Wieneke, S., Bastos, A., Balzarolo, M., Barrios, J. M., and Janssens, I.: Evaluating the relationship between SIF and GPP under climate extremes, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8939,, 2021.

Tomoki Kiyono, Hibiki Noda, Tomo’omi Kumagai, Haruki Oshio, Yukio Yoshida, Tsuneo Matsunaga, and Kouki Hikosaka

Atmospheric aridity and soil drought control vegetation water use and affect the terrestrial water and carbon cycles. Separating these two types of drought is difficult but crucial because they relate to different ecosystem properties and their impacts depend on vegetation types. We examine how well satellite-observed solar-induced chlorophyll fluorescence (SIF) captures the drought responses of taiga and steppe in semiarid areas on the Mongolian plateau, which have experienced a historic drought since the late 1990s. Ten-year records of the GOSAT SIF and the MODIS-band-1 photochemical reflectance index (PRI, also known as chlorophyll/carotenoid index) from Aqua consistently suggest that the taiga is sensitive to vapor-pressure deficit but insensitive to surface-soil drought, and that the opposite is the case for the steppe. The MODIS PRI changes reasonably with temperature and drought stress, and also with canopy shades, which is attributable to the xanthophyll cycle. However the most influential factor on the PRI is leaf area in both vegetations, and temperature is the second in the taiga, indicating the dominant effect of its pigment-pool size. The leaf area index of the taiga has almost similar values and seasonal patterns in each year, while the SIF shows remarkable interannual changes. The SIF yield in the taiga decreases 36–48% on average with the increase of vapor-pressure deficit from 1 kPa to 3 kPa under high-PRI conditions. Almost all detectable information from the SIF yield in the steppe is correlated with PRI on a monthly basis. The SIF in the steppe decreases nonlinearly when the surface-soil-water content fell below ∼0.154 m3 m−3, which agrees well with an eddy-covariance result in this region and implies the capability of satellite-based wilting-point estimation. We will further clarify which biological factors affected the observed results of SIF and PRI using the process-based model 'Soil-Canopy-Observation of Photosynthesis and Energy fluxes' (SCOPE) and show the impact of drought on the gross primary production in the past decade.

How to cite: Kiyono, T., Noda, H., Kumagai, T., Oshio, H., Yoshida, Y., Matsunaga, T., and Hikosaka, K.: Detecting the Drought-Response Difference in Semiarid Ecosystems on the Mongolian Plateau: 10-Year Observation Using GOSAT SIF and MODIS PRI, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-3583,, 2021.

Athanasios Paschalis, Pierre Gentine, Duncan Graham, and Simone Fatichi

A deep understanding of the responses of terrestrial vegetation to environmental forcing is crucial for understanding the global carbon dynamics, especially under a changing climate. Vegetation responses to stress can manifest first as plant physiological responses, and at later stages through changes in canopy structure. Remote sensing of vegetation has been proven very valuable in providing such understanding. One of the major breakthroughs has been the use of multi and hyper spectral sensors on board satellites that can retrieve Solar Induced Fluorescence (SIF), which is closely linked with plant photosynthesis.

In this study we assess whether (SIF), as observed by instruments on board of satellites, can adequately capture both of those responses. Using 7 different global SIF products, water and CO2 flux data from 120 eddy-covariance towers and climate reanalysis products, we found a good agreement between the 16-day responses of flux tower observed gross primary productivity (GPP) and SIF to soil moisture and light, and a weaker agreement regarding the responses to temperature and atmospheric humidity. Overall, we found that current satellite SIF responses to environmental stressors mostly reflect structural changes in vegetation structure, and that satellite SIF has limited skill in capturing early stress plant physiological responses except for the light availability response at higher latitudes. While satellite SIF significantly outperforms more traditional vegetation indices (EVI, NDVI), as it does not saturate unlike the latter ones, it does not provide major additional information regarding vegetation physiological responses to either hydrological or atmospheric droughts.

How to cite: Paschalis, A., Gentine, P., Graham, D., and Fatichi, S.: Solar Induced Fluorescence measured from satellite sensors captures mostly structural than physiological responses to environmental stressors, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7321,, 2021.

Lena Schreiner, Katja Grossmann, André Butz, Sanam N. Vardag, and Eva-Marie Schömann

The Eurasian boreal ecosystem acts as a major terrestrial carbon sink in the northern hemisphere. Under changing climatic conditions, it is crucial to monitor biogenic carbon fluxes in this area. The Siberian in-situ CO2 data are, however, sparse in spatial coverage and limit model-validation there. Satellite observations of CO2 and Sun-Induced Fluorescence (SIF) can provide essential information to constrain the Eurasian boreal biogenic carbon-cycle and further, to improve carbon cycle inverse models.

In this study, we investigate the Eurasian boreal carbon cycle with satellite observations of the Orbiting Carbon Observatory 2 (OCO-2) and the Greenhouse gase Observing SATellite (GOSAT). We compare the observed carbon cycle dynamics to model data such as provided by CarbonTracker (CT2019, CT-NRT.v2020-1) and find differences in the ppm range. Various sensitivity studies with respect to region selection, sampling biases and model choices are used to consolidate the robustness of the detected pattern. Using SIF and FLUXCOM GPP data, we will show first attempts to attribute the model-measurement differences to uncertainties in biogenic carbon fluxes.

How to cite: Schreiner, L., Grossmann, K., Butz, A., Vardag, S. N., and Schömann, E.-M.: Constraining the Eurasian biogenic boreal carbon-cycle with satellite-SIF, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-15375,, 2021.

Aparnna Ravi P, Dhanyalekshmi K Pillai, Christoph Gerbig, Julia Marshall, and Chandra Shekhar Jha

Several countries across the world have initiated considerable efforts to curb Greenhouse Gas emissions to limit the increase in global temperature to 2°C. However, planning of proper emission reduction policies and their successful implementation require accurate carbon budgeting. The objective of this study is to accurately quantify various sources and sinks of carbon dioxide over Indian domain using inverse modelling techniques. 

In order to better represent and quantify the atmosphere-biosphere CO2 exchange fluxes and ecosystem behaviour in the inverse modeling framework, the Vegetation Photosynthesis and Respiration Model (VPRM) is employed over Indian region. VPRM is a satellite based assimilation scheme with very simple model structure, so as to facilitate successive optimization of parameters in the inverse modelling framework. As an initial step, we evaluated the VPRM model with eddy covariance observations over India from two different vegetation types (Betul; Deciduous forest and Sundarbans; Evergreen forest) for the year 2017. The comparison reveals that the model needs further refinement in parametrization even though the VPRM showed better performance than other existing terrestrial biosphere models (e.g ., TRENDY and Carbon Tracker (CT)) over Indian domain. Among the VPRM products (Net ecosystem exchange (NEE), Gross Primary Productivity (GPP), and Ecosystem Respiration (Re)), the ecosystem respiration shows large deviations from observation. The analysis, based on the soil moisture (SM) data from IITM monsoon mission project shows that the SM plays a significant role, which is currently missing in the VPRM respiration calculations. Further, the study attempts to utilize Solar induced Fluorescence (SIF) as a proxy to estimate GPP and to be included in VPRM for the better representation of biospheric fluxes over India. Preliminary results will be presented and discussed.

How to cite: Ravi P, A., K Pillai, D., Gerbig, C., Marshall, J., and Jha, C. S.: Towards improved estimation of the atmosphere - terrestrial biosphere CO2 exchange over India using a diagnostic satellite based model, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-7019,, 2021.

Cédric Bacour, Luis Guanter, Andreas Schneider, Ilse Aben, Fabienne Maignan, Leo Grignon, Mahmoud El Hajj, and Christian Retscher

The total amount of CO2 absorbed and turned into organic matter through photosynthesis can be quantified as Gross Primary Productivity (GPP). Terrestrial vegetation GPP is responsible for offsetting about 30% of carbon dioxide emissions released by anthropogenic activities into the atmosphere. This corresponds to approximately 120 to 170 PgC/year, making terrestrial vegetation both the largest and most uncertain component of the global carbon cycle. Over the last few years, solar- induced chlorophyll fluorescence (SIF) observations from space have emerged as a promising resource for evaluating the spatio-temporal distribution of GPP by terrestrial ecosystems. SIF is an electromagnetic signal emitted by the chlorophyll a of green plants: part of the absorbed energy not used for photosynthesis is emitted at longer wavelengths as a two-peak spectrum roughly covering the 650–850 nm spectral range. The SIF signal responds instantaneously to perturbations in  environmental conditions such as light and water stress, which makes it a direct proxy for photosynthetic activity.

SIF has been estimated at the global scale from several space-borne spectrometers originally intended for atmospheric research because they provide the necessary spectral  resolution and radiometric sensitivity. However, the exploitation of SIF estimates has remained limited by their coarse spatial resolution (GOSAT, GOME-2) or low number of observations (OCO-2). This has been strongly alleviated by the advent of the TROPOspheric Monitoring Instrument (TROPOMI) onboard Sentinel-5 Precursor which combines a global continuous spatial sampling with a 5.5 km x 3.5 km pixel size at nadir, a daily  revisit time, a wide spectral coverage and an enormous increase in the number of clear-sky measurements per day in comparison to previous missions, as demonstrated by the first SIF retrievals from TROPOMI derived by Caltech (Köhler et al. 2018).

In this study, we present a new independent SIF product derived from TROPOMI observations using two fitting windows at 743-758 nm (all sky SIF) and 735-758 nm (clear sky SIF). The first one is very robust against atmospheric effects (especially cloud contamination) whereas the second one is less sensitive to estimation errors (due to the greater number of spectral points in the fitting window). The retrieval scheme is not much different from the one from Caltech (in 743-758 nm) but relies on different cloud fraction inputs. We will present the principles of the retrieval scheme, the format of the output TROPOSIF product, and the results of the comparison of our SIF estimates against the Caltech ones as well as SIF data derived from OCO-2 which show a very good consistency between all SIF products.

How to cite: Bacour, C., Guanter, L., Schneider, A., Aben, I., Maignan, F., Grignon, L., El Hajj, M., and Retscher, C.: A new SIF (solar‐induced chlorophyll fluorescence) product derived from TROPOMI onboard Sentinel-5 Precursor, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8420,, 2021.

Camille Abadie, Fabienne Maignan, Marine Remaud, Linda M. J. Kooijmans, Kukka-Maaria Kohonen, Róisín Commane, Richard Wehr, J. Elliott Campbell, Sauveur Belviso, Stephen A. Montzka, Nina Raoult, Ulli Seibt, Yoichi Shiga, Nicolas Vuichard, Mary Whelan, and Philippe Peylin

Better constraining the ecosystem gross photosynthetic CO2 uptake (GPP) is necessary to reduce the uncertainties on continental vegetation response to climate change. As GPP cannot be directly measured at the ecosystem scale, different proxies of vegetation CO2 uptake have emerged. These proxies are essential for land surface modelers to estimate GPP at large scale. Carbonyl sulfide (COS) shows many similarities with CO2, following the same diffusional pathways through the leaves. However, unlike CO2 that is also emitted by plants during respiration, COS is essentially only taken up by leaves and not re-emitted back to the atmosphere. Therefore, COS is a promising proxy of photosynthetic activity. In previous studies, fixed values of the leaf relative uptake (LRU) ratio of COS to CO2 fluxes normalized by their respective concentration have typically been used to infer GPP for the different biomes. However, it has been shown that LRU ratio changes with varying Photosynthetically Active Radiation (PAR), which limits its accuracy to constrain photosynthetic activity. Therefore, we redefined the COS-based GPP estimation approach to better capture GPP response to changing environmental conditions, by implementing a mechanistic model of COS exchange by continental vegetation in the ORCHIDEE land surface model. We compared the modelled fluxes against field measurements at two sites and studied the model behavior and environmental drivers. Then, we ran global simulations and computed the annual COS vegetation uptake that was found in the middle range values of previous reported budgets (-490 to -1335 Gg S yr-1), with -756 Gg S yr-1. The simulated fluxes were transported, and COS concentrations were evaluated against measurements from the NOAA atmospheric stations. Our results show that the mechanistic approach is more appropriate when studying photosynthetic activity at high temporal resolution, but similar results in concentrations are obtained between the mechanistic and LRU approaches at the global scale. Accurate evaluation of the continental vegetation COS uptake is necessary as it is the main COS sink. However, COS can also be absorbed or emitted by soils, a flux that complicates the use of eddy covariance COS flux measurements or atmospheric COS measurements to derive information on GPP estimates. Therefore, the soil COS exchange should also be represented in land surface models. We implemented two soil COS exchange models in ORCHIDEE, a mechanistic model (based on Ogée et al. 2016) and a second model based on an empirical relationship with soil respiration (following Berry et al., 2013). We evaluated the two models at several sites against field measurements. We also performed global simulations to evaluate the spatial distribution of soil COS fluxes and their seasonal variations. Finally, we estimated the contributions of the combined impact of soil COS exchange and leaf COS uptake (both from the ORCHIDEE model) to the global COS budget and on the COS atmospheric concentration latitudinal gradient.

How to cite: Abadie, C., Maignan, F., Remaud, M., Kooijmans, L. M. J., Kohonen, K.-M., Commane, R., Wehr, R., Campbell, J. E., Belviso, S., Montzka, S. A., Raoult, N., Seibt, U., Shiga, Y., Vuichard, N., Whelan, M., and Peylin, P.: Implementation of vegetation and soil carbonyl sulfide exchanges in the ORCHIDEE land surface model to better constrain ecosystem gross primary production, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-8335,, 2021.

Marine Remaud, Camille Abadie, Sauveur Belviso, Antoine Berchet, Frédéric Chevallier, Fabienne Maignan, and Philippe Peylin

Carbonyle Sulphide, a trace gas exhibiting a striking similarity with CO2 in the biochemical diffusion path of leaves, has been recognized to be a promising surrogate of CO2 for estimating carbon storage in the terrestrial vegetation. Based on the similarity between COS and CO2, an empirical linear model relating both gas concentrations provides constraints on the estimation of the Gross Primary Productivity (GPP), the amount of carbon dioxide that is absorbed by ecosystems. However, large uncertainties on the other components of its atmospheric budget prevent us from directly relating the atmospheric COS measurements to the the GPP at global scale. The largest uncertainty arises from the closure of its atmospheric budget, with a source component missing. We explore here the benefit of assimilating both COS and CO2 measurements into the LMDz atmospheric transport model to gain insight on the COS budget. We develop an analytic inverse system which optimized the biospheric fluxes within the 14 Plant functional Type (PFTs) as defined in the ORCHIDEE land surface model. The vegetation uptake of COS is parameterized as a linear function of GPP and of the leaf relative uptake (LRU), which is the ratio of COS to CO2 deposition velocities in plants. A possible scenario leads to a global biospheric sink between 800-900 GgS/y, with a higher GPP in the high latitudes and higher total oceanic emissions between 400 and 600 GgS/y over the tropics. The COS inter-hemispheric gradient is in better agreement with HIPPO independent aircraft measurements. The comparison against NOAA COS airborne profiles and Solar Induced Fluorescence shed light on a too strong GPP in spring in ORCHIDEE in northern America,  leaving room for improvements. We also show that uncertainty in the location of hot spots in the prior anthropogenic inventory limits the use of atmospheric COS measurements in inverse modeling.

How to cite: Remaud, M., Abadie, C., Belviso, S., Berchet, A., Chevallier, F., Maignan, F., and Peylin, P.: A description of the Carbonyl Sulfide (COS) budget inferred by inverse modelling, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-15957,, 2021.

Gerbrand Koren, Getachew A. Adnew, Jordi Vilà-Guerau de Arellano, Michiel K. van der Molen, Bart Kruijt, Thomas Röckmann, and Wouter Peters

The triple oxygen isotope signature Δ17O in atmospheric CO2 is a potential tracer for gross primary production (GPP). However, interpretation of Δ17O in atmospheric CO2 is complicated by the contributions from respired CO2, isotopic exchange with soil and ocean water, and the release of CO2 by fossil fuel combustion and biomass burning. We studied Δ17O in CO2 at the ecosystem level, which is the domain that integrates the contributions from vegetation and soil to the atmospheric signal.  

We report for the first time the observed diurnal variation of Δ17O in CO2, measured from air samples collected on 15-16 August 2019 at the mid-latitude pine forest Loobos (ICOS L2 ecosystem site). We also measured the isotopic signatures δ13C and δ18O in CO2 close to the surface (at 0.5 m height, inside the canopy) and from the top of the tower (1-2 m above the canopy). To support the interpretation of the measurements, we used a land-atmosphere model that satisfactorily reproduces the diurnal variability of the interaction between leaf/canopy and the convective boundary layer using mixed-layer theory assumptions (CLASS). Also, we used the global atmospheric transport model TM5 to (1) quantify the contribution of different sources that affect Δ17O in CO2 at Loobos; and (2) extend our analysis of the diurnal cycle to the global scale.  

Our methodology demonstrates the added value of isotope measurements at ICOS ecosystem and tall-tower sites, and how to integrate meteorological and ecological observations from the canopy up to the atmospheric boundary layer. This study contributes to our ongoing effort of creating an overview of different methods for quantifying photosynthesis from a top-down perspective (concentration-based methods and remote sensing) in a review paper for which we are open to other contributions. 

How to cite: Koren, G., Adnew, G. A., Vilà-Guerau de Arellano, J., van der Molen, M. K., Kruijt, B., Röckmann, T., and Peters, W.: Exploring the diurnal cycle of Δ17O in CO2 at the ecosystem level, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-13322,, 2021.

Klaus Steenberg Larsen, Johannes Wilhelmus Maria Pullens, Linsey Avila, Sander Bruun, Ji Chen, Jesper Riis Christiansen, Andreas Ibrom, Poul Larsen, Poul Erik Lærke, Preben Jørgensen, and Azeem Tariq

In experimental ecosystem ecology, plot sizes are most often too small to apply eddy flux techniques and estimation of ecosystem gas exchange rates relies on various chamber measurement technologies. Furthermore, drained areas often results in increased growth of trees which complicates application of eddy flux measurements on small plots.

We combined ECO2FluX ecosystem-level automatic chambers ( with an LI-8100/LI-8150 multiplexer systems ( in a range of Danish and Norwegian ecosystems experiments spanning agriculture, grassland/heathlands and peatland ecosystems. The automatic closed, none-steady state chambers each cover an area of 3,117 cm2 (63 cm diameter), are 80 cm tall (volume: 250L), and are capable of switching automatically between transparent and darkened mode, enabling separation of light-sensitive and light-indifferent processes in the ecosystems covered. For CO2 fluxes, net exchange (NEE) was estimated as the flux in transparent mode, ecosystem respiration (RE) in darkened mode, while Gross Ecosystem Productivity (GPP) was estimated as NEE – RE.

Chambers were set up to measure gas concentrations every second using enclosure times of 4-5 minutes, first in light mode and 10-30 minutes later in dark mode, with 3-48 repetitions per day. The longest time series spans 5 years of measurements and contain >60,000 point measurements.

In this presentation, we will present an analysis of the ability of the light-dark chamber data to infer ecosystem-level rates of gross primary productivity, respiration, net CO2 exchange, and evapotranspiration. In the two Norwegian peatland sites, flux measurements may be compared directly with eddy flux measurements. We also compare the rates of the direct estimates of GPP from the light-dark chamber measurements to estimates inferred from using the light (NEE) measurements only followed by applying methodologies normally used for eddy flux measurements. This comparison may help constrain potential biases in both the closed chamber and eddy flux techniques. Finally, we investigate the ability of using such closed chambers to estimate ecosystem evapotranspiration rates at the plot scale. Such application may be useful for estimating the effects on evapotranspiration in field-scale experiments manipulating the ecosystem water balance either directly or indirectly.

How to cite: Larsen, K. S., Pullens, J. W. M., Avila, L., Bruun, S., Chen, J., Christiansen, J. R., Ibrom, A., Larsen, P., Lærke, P. E., Jørgensen, P., and Tariq, A.: Inferring ecosystem-level rates of gross primary productivity, respiration, and evapotranspiration with automatic light-dark measurement chambers, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-12464,, 2021.

Weijie Zhang, Jacob A. Nelson, Rafael Poyatos, Diego Miralles, Mirco Migliavacca, Markus Reichstein, and Martin Jung

Eddy covariance (EC) directly measures evapotranspiration (ET), which consists of transpiration and evaporation (E) from the soil and other surfaces. For process understanding it is pivotal to separate ET into its components. Yet, its computation is highly sensitive to the methodology used to estimate T. Among the multiple methods proposed in recent years, T has been estimated from EC via the Transpiration Estimation Algorithm (TEA, Nelson et al., 2020), and from the sap flux measurement network SAPFLUXNET (Poyatos et al., 2020). These methods are applicable to a large number of measurement sites worldwide, and can help constrain the global estimates of the ratio of T to ET, T/ET. While EC measures water and carbon fluxes across ecosystems globally, water vapor flux measurements can be underestimated at high relative humidity (Ibrom et al., 2007; Mammarella et al., 2009) causing errors in the measured ET and propagating into the predicted T.

Here we report a method to detect and correct the high relative humidity error caused by attenuation of high frequency in water vapor measurements of a closed-path EC system. Our results of the comparison between present water use efficiency (WUE) with previous TEA-based WUE show that the corrected WUE is lower at high relative humidity than that derived from previous TEA at the sub-daily scale. Besides, we compare the corrected T estimates from EC to concurrent SAPFLUXNET sites to show an improved relationship between sap flux and EC based T, T/ET, and WUE. Finally, we explore the main abiotic factors, such as vapor pressure deficit, air temperature, and precipitation, influencing WUE estimated from different T estimation methodologies. These results provide an improved data-driven approach to the ongoing research on ET partitioning and the factors influencing the WUE across ecosystems globally.


Ibrom, A. et al. (2007) ‘Strong low-pass filtering effects on water vapour flux measurements with closed-path eddy correlation systems’, Agricultural and Forest Meteorology.

Mammarella, I. et al. (2009) ‘Relative humidity effect on the high-frequency attenuation of water vapor flux measured by a closed-path eddy covariance system’, Journal of Atmospheric and Oceanic Technology.

Nelson, J. A. et al. (2020) ‘Ecosystem transpiration and evaporation: Insights from three water flux partitioning methods across FLUXNET sites’, Global Change Biology. doi: 10.1111/gcb.15314.

Poyatos, R. et al. (2020) ‘Global transpiration data from sap flow measurements: the SAPFLUXNET database’, Earth System Science Data. doi:10.5194/essd-2020-227.

How to cite: Zhang, W., A. Nelson, J., Poyatos, R., Miralles, D., Migliavacca, M., Reichstein, M., and Jung, M.: Improved eddy covariance flux based transpiration estimates at high relative humidity and comparison to sap flux, EGU General Assembly 2021, online, 19–30 Apr 2021, EGU21-14177,, 2021.