Browsing by Subject "BIOCHEMICAL-MODEL"

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  • Maignan, Fabienne; Abadie, Camille; Remaud, Marine; Kooijmans, Linda M. J.; Kohonen, Kukka-Maaria; Commane, Róisín; Wehr, Richard; Campbell, J. Elliott; Belviso, Sauveur; Montzka, Stephen A.; Raoult, Nina; Seibt, Ulli; Shiga, Yoichi P.; Vuichard, Nicolas; Whelan, Mary E.; Peylin, Philippe (2021)
    Land surface modellers need measurable proxies to constrain the quantity of carbon dioxide (CO2) assimilated by continental plants through photosynthesis, known as gross primary production (GPP). Carbonyl sulfide (COS), which is taken up by leaves through their stomates and then hydrolysed by photosynthetic enzymes, is a candidate GPP proxy. A former study with the ORCHIDEE land surface model used a fixed ratio of COS uptake to CO2 uptake normalised to respective ambient concentrations for each vegetation type (leaf relative uptake, LRU) to compute vegetation COS fluxes from GPP. The LRU approach is known to have limited accuracy since the LRU ratio changes with variables such as photosynthetically active radiation (PAR): while CO2 uptake slows under low light, COS uptake is not light limited. However, the LRU approach has been popular for COS-GPP proxy studies because of its ease of application and apparent low contribution to uncertainty for regional-scale applications. In this study we refined the COS-GPP relationship and implemented in ORCHIDEE a mechanistic model that describes COS uptake by continental vegetation. We compared the simulated COS fluxes against measured hourly COS fluxes at two sites and studied the model behaviour and links with environmental drivers. We performed simulations at a global scale, and we estimated the global COS uptake by vegetation to be -756 Gg S yr(-1) , in the middle range of former studies (-490 to -1335 Gg S yr(-1)). Based on monthly mean fluxes simulated by the mechanistic approach in ORCHIDEE, we derived new LRU values for the different vegetation types, ranging between 0.92 and 1.72, close to recently published averages for observed values of 1.21 for C-4 and 1.68 for C-3 plants. We transported the COS using the monthly vegetation COS fluxes derived from both the mechanistic and the LRU approaches, and we evaluated the simulated COS concentrations at NOAA sites. Although the mechanistic approach was more appropriate when comparing to high-temporal-resolution COS flux measurements, both approaches gave similar results when transporting with monthly COS fluxes and evaluating COS concentrations at stations. In our study, uncertainties between these two approaches are of secondary importance compared to the uncertainties in the COS global budget, which are currently a limiting factor to the potential of COS concentrations to constrain GPP simulated by land surface models on the global scale.
  • Kolari, Pasi; Chan, Tommy; Porcar-Castell, Albert; Back, Jaana; Nikinmaa, Eero; Juurola, Eija (2014)
  • Bacour, C.; Maignan, F.; MacBean, N.; Porcar-Castell, A.; Flexas, J.; Frankenberg, C.; Peylin, P.; Chevallier, F.; Vuichard, N.; Bastrikov, V. (2019)
    Abstract 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 gross primary productivity (GPP) simulated by global terrestrial biosphere models. SIF can be used to improve GPP simulations by optimizing critical model parameters through statistical Bayesian data assimilation techniques. A prerequisite is the availability of a functional link between GPP and SIF in terrestrial biosphere models. Here we present the development of a mechanistic SIF observation operator in the ORCHIDEE (Organizing Carbon and Hydrology In Dynamic Ecosystems) terrestrial biosphere model. It simulates the regulation of photosystem II fluorescence quantum yield at the leaf level thanks to a novel parameterization of non-photochemical quenching as a function of temperature, photosynthetically active radiation, and normalized quantum yield of photochemistry. It emulates the radiative transfer of chlorophyll fluorescence to the top of the canopy using a parametric simplification of the SCOPE (Soil Canopy Observation Photosynthesis Energy) model. We assimilate two years of monthly OCO-2 (Orbiting Carbon Observatory-2) SIF product at 0.5° (2015?2016) to optimize ORCHIDEE photosynthesis and phenological parameters over an ensemble of grid points for all plant functional types. The impact on the simulated GPP is considerable with a large decrease of the global scale budget by 28 GtC/year over the period 1990?2009. The optimized GPP budget (134/136 GtC/year over 1990?2009/2001?2009) remarkably agrees with independent GPP estimates, FLUXSAT (137 GtC/year over 2001?2009) in particular and FLUXCOM (121 GtC/year over 1990?2009). Our results also suggest a biome dependency of the SIF-GPP relationship that needs to be improved for some plant functional types.
  • Thum, Tea; Zaehle, Sönke; Köhler, Philipp; Aalto, Tuula; Aurela, Mika; Guanter, Luis; Kolari, Pasi; Laurila, Tuomas; Lohila, Annalea; Magnani, Federico; Van der Tol, Christiaan; Markkanen, Tiina (2017)
    Recent satellite observations of sun-induced chlorophyll fluorescence (SIF) are thought to provide a large-scale proxy for gross primary production (GPP), thus providing a new way to assess the performance of land surface models (LSMs). In this study, we assessed how well SIF is able to predict GPP in the Fenno-Scandinavian region and what potential limitations for its application exist. We implemented a SIF model into the JSBACH LSM and used active leaf-level chlorophyll fluorescence measurements (Chl F) to evaluate the performance of the SIF module at a coniferous forest at Hyytiala, Finland. We also compared simulated GPP and SIF at four Finnish micrometeorological flux measurement sites to observed GPP as well as to satellite-observed SIF. Finally, we conducted a regional model simulation for the Fenno-Scandinavian region with JSBACH and compared the results to SIF retrievals from the GOME-2 (Global Ozone Monitoring Experiment-2) space-borne spectrometer and to observation-based regional GPP estimates. Both observations and simulations revealed that SIF can be used to estimate GPP at both site and regional scales. At regional scale the model was able to simulate observed SIF averaged over 5 years with r(2) of 0.86. The GOME-2-based SIF was a better proxy for GPP than the remotely sensed fA-PAR (fraction of absorbed photosynthetic active radiation by vegetation). The observed SIF captured the seasonality of the photosynthesis at site scale and showed feasibility for use in improving of model seasonality at site and regional scale.
  • Dewar, Roderick; Mauranen, Aleksanteri; Makela, Annikki; Holtta, Teemu; Medlyn, Belinda; Vesala, Timo (2018)
    Optimization models of stomatal conductance (g(s)) attempt to explain observed stomatal behaviour in terms of cost-benefit tradeoffs. While the benefit of stomatal opening through increased CO2 uptake is clear, currently the nature of the associated cost(s) remains unclear. We explored the hypothesis that g(s) maximizes leaf photosynthesis, where the cost of stomatal opening arises from nonstomatal reductions in photosynthesis induced by leaf water stress. We analytically solved two cases, CAP and MES, in which reduced leaf water potential leads to reductions in carboxylation capacity (CAP) and mesophyll conductance (g(m)) (MES). Both CAP and MES predict the same one-parameter relationship between the intercellular:atmospheric CO2 concentration ratio (c(i)/c(a)) and vapour pressure deficit (VPD, D), viz. c(i)/c(a) approximate to xi/xi (xi+D), as that obtained from previous optimization models, with the novel feature that the parameter xi is determined unambiguously as a function of a small number of photosynthetic and hydraulic variables. These include soil-to-leaf hydraulic conductance, implying a stomatal closure response to drought. MES also predicts that g(s)/g(m) is closely related to c(i)/c(a) and is similarly conservative. These results are consistent with observations, give rise to new testable predictions, and offer new insights into the covariation of stomatal, mesophyll and hydraulic conductances.
  • Mäkela, Jarmo; Knauer, Juergen; Aurela, Mika; Black, Andrew; Heimann, Martin; Kobayashi, Hideki; Lohila, Annalea; Mammarella, Ivan; Margolis, Hank; Markkanen, Tiina; Susiluoto, Jouni; Thum, Tea; Viskari, Toni; Zaehle, Soenke; Aalto, Tuula (2019)
    We calibrated the JSBACH model with six different stomatal conductance formulations using measurements from 10 FLUXNET coniferous evergreen sites in the boreal zone. The parameter posterior distributions were generated by the adaptive population importance sampler (APIS); then the optimal values were estimated by a simple stochastic optimisation algorithm. The model was constrained with in situ observations of evapotranspiration (ET) and gross primary production (GPP). We identified the key parameters in the calibration process. These parameters control the soil moisture stress function and the overall rate of carbon fixation. The JSBACH model was also modified to use a delayed effect of temperature for photosynthetic activity in spring. This modification enabled the model to correctly reproduce the springtime increase in GPP for all conifer sites used in this study. Overall, the calibration and model modifications improved the coefficient of determination and the model bias for GPP with all stomatal conductance formulations. However, only the coefficient of determination was clearly improved for ET. The optimisation resulted in best performance by the Bethy, Ball-Berry, and the Friend and Kiang stomatal conductance models. We also optimised the model during a drought event at a Finnish Scots pine forest site. This optimisation improved the model behaviour but resulted in significant changes to the parameter values except for the unified stomatal optimisation model (USO). Interestingly, the USO demonstrated the best performance during this event.