Christiaan van der Tol

Linking chlorophyll a fluorescence to photosynthesis for remote sensing applications: mechanisms and challenges

Chlorophyll a fluorescence (ChlF) has been used for decades to study the organization, functioning, and physiology of photosynthesis at the leaf and subcellular levels. ChlF is now measurable from remote sensing platforms. This provides a new optical means to track photosynthesis and gross primary productivity of terrestrial ecosystems. Importantly, the spatiotemporal and methodological context of the new applications is dramatically different compared with most of the available ChlF literature, which raises a number of important considerations. Although we have a good mechanistic understanding of the processes that control the ChlF signal over the short term, the seasonal link between ChlF and photosynthesis remains obscure. Additionally, while the current understanding of in vivo ChlF is based on pulse amplitude-modulated (PAM) measurements, remote sensing applications are based on the measurement of the passive solar-induced chlorophyll fluorescence (SIF), which entails important differences and new challenges that remain to be solved. In this review we introduce and revisit the physical, physiological, and methodological factors that control the leaf-level ChlF signal in the context of the new remote sensing applications. Specifically, we present the basis of photosynthetic acclimation and its optical signals, we introduce the physical and physiological basis of ChlF from the molecular to the leaf level and beyond, and we introduce and compare PAM and SIF methodology. Finally, we evaluate and identify the challenges that still remain to be answered in order to consolidate our mechanistic understanding of the remotely sensed SIF signal.

Forest productivity and water stress in Amazonia: observations from GOSAT chlorophyll fluorescence

It is unclear to what extent seasonal water stress impacts on plant productivity over Amazonia. Using new Greenhouse gases Observing SATellite (GOSAT) satellite measurements of sun-induced chlorophyll fluorescence, we show that midday fluorescence varies with water availability, both of which decrease in the dry season over Amazonian regions with substantial dry season length, suggesting a parallel decrease in gross primary production (GPP). Using additional SeaWinds Scatterometer onboard QuikSCAT satellite measurements of canopy water content, we found a concomitant decrease in daily storage of canopy water content within branches and leaves during the dry season, supporting our conclusion. A large part (r2 = 0.75) of the variance in observed monthly midday fluorescence from GOSAT is explained by water stress over moderately stressed evergreen forests over Amazonia, which is reproduced by model simulations that include a full physiological representation of photosynthesis and fluorescence. The strong relationship between GOSAT and model fluorescence (r2 = 0.79) was obtained using a fixed leaf area index, indicating that GPP changes are more related to environmental conditions than chlorophyll contents. When the dry season extended to drought in 2010 over Amazonia, midday basin-wide GPP was reduced by 15 per cent compared with 2009.

Reprint of: Estimation of forest above-ground biomass using multi-parameter remote sensing data over a cold and arid area

Remote sensing is a valuable tool for estimating forest biomass in remote areas. This study explores retrieval of forest above-ground biomass (AGB) over a cold and arid region in Northwest China, using two different methods (non-parametric and parametric), field data, and three different remote sensing data: a SPOT-5 HRG image, multi-temporal dual-polarization ALOS PALSAR and airborne LiDAR data. The non-parametric method was applied in 300 different configurations, varying both the mathematical formulation and the data input (SPOT-5 and ALOS PALSAR), and the quality of the performance of each configuration was evaluated by Leave One Out (LOO) cross-validation against ground measurements. For the parametric method (the multivariate linear regression), the same remote sensing data were used, but in one additional configuration the airborne LiDAR data were used for stepwise multiple regression. The result of the best performing non-parametric configuration was satisfactory (R = 0.69 and RMSE = 20.7 tons/ha). The results for the parametric method were notoriously inaccurate, except for the case where airborne LiDAR data were included. The regression method with airborne low density LiDAR point cloud data was the best of all tested methods (R = 0.84 and RMSE = 15.2 tons/ha). A cross comparison of the two best results showed that the non-parametric method performs nearly as well as the parametric method with LiDAR data, except for some areas where forests have a very heterogeneous structure. It is concluded that the non-parametric method with SPOT data is able to map forest AGB operatively over the cold and arid region as an alternative to the more expensive airborne LiDAR data.

Estimating montane forest above-ground biomass in the upper reaches of the Heihe River Basin using Landsat-TM data

In this work, the results of above-ground biomass (AGB) estimates from Landsat Thematic Mapper 5 (TM) images and field data from the fragmented landscape of the upper reaches of the Heihe River Basin (HRB), located in the Qilian Mountains of Gansu province in northwest China, are presented. Estimates of AGB are relevant for sustainable forest management, monitoring global change, and carbon accounting. This is particularly true for the Qilian Mountains, which are a water resource protection zone. We combined forest inventory data from 133 plots with TM images and Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) global digital elevation model (GDEM) V2 products (GDEM) in order to analyse the influence of the sun-canopy-sensor plus C (SCS+C) topographic correction on estimations of forest AGB using the stepwise multiple linear regression (SMLR) and k-nearest neighbour (k-NN) methods. For both methods, our results indicated that the SCS+C correction was necessary for getting more reliable forest AGB estimates within this complex terrain. Remotely sensed AGB estimates were validated against forest inventory data using the leave-one-out (LOO) method. An optimized k-NN method was designed by varying both mathematical formulation of the algorithm and remote-sensing data input, which resulted in 3000 different model configurations. Following topographic correction, performance of the optimized k-NN method was compared to that of the regression method. The optimized k-NN method (R2 = 0.59, root mean square error (RMSE) = 24.92 tonnes ha–1) was found to perform much better than the regression method (R2 = 0.42, RMSE = 29.74 tonnes ha–1) for forest AGB retrieval over this montane area. Our results indicated that the optimized k-NN method is capable of operational application to forest AGB estimates in regions where few inventory data are available.

Analysis of Red and Far-Red Sun-Induced Chlorophyll Fluorescence and Their Ratio in Different Canopies Based on Observed and Modeled Data

Sun-induced canopy chlorophyll fluorescence in both the red (FR) and far-red (FFR) regions was estimated across a range of temporal scales and a range of species from different plant functional types using high resolution radiance spectra collected on the ground. Field measurements were collected with a state-of-the-art spectrometer setup and standardized methodology. Results showed that different plant species were characterized by different fluorescence magnitude. In general, the highest fluorescence emissions were measured in crops followed by broadleaf and then needleleaf species. Red fluorescence values were generally lower than those measured in the far-red region due to the reabsorption of FR by photosynthetic pigments within the canopy layers. Canopy chlorophyll fluorescence was related to plant photosynthetic capacity, but also varied according to leaf and canopy characteristics, such as leaf chlorophyll concentration and Leaf Area Index (LAI). Results gathered from field measurements were compared to radiative transfer model simulations with the Soil-Canopy Observation of Photochemistry and Energy fluxes (SCOPE) model. Overall, simulation results confirmed a major contribution of leaf chlorophyll concentration and LAI to the fluorescence signal. However, some discrepancies between simulated and experimental data were found in broadleaf species. These discrepancies may be explained by uncertainties in individual species LAI estimation in mixed forests or by the effect of other model parameters and/or model representation errors. This is the first study showing sun-induced fluorescence experimental data on the variations in the two emission regions and providing quantitative information about the absolute magnitude of fluorescence emission from a range of vegetation types.

Remote Sensing of Grass Response to Drought Stress Using Spectroscopic Techniques and Canopy Reflectance Model Inversion

The aim of this study was to follow the response to drought stress in a Poa pratensis canopy exposed to various levels of soil moisture deficit. We tracked the changes in the canopy reflectance (450–2450 nm) and retrieved vegetation properties (Leaf Area Index (LAI), leaf chlorophyll content (Cab), leaf water content (Cw), leaf dry matter content (Cdm) and senescent material (Cs)) during a drought episode. Spectroscopic techniques and radiative transfer model (RTM) inversion were employed to monitor the gradual manifestation of drought effects in a laboratory setting. Plots of 21 cm × 14.5 cm surface area with Poa pratensis plants that formed a closed canopy were divided into a well-watered control group and a group subjected to water stress for 36 days. In a regular weekly schedule, canopy reflectance and destructive measurements of LAI and Cab were taken. Spectral analysis indicated the first sign of stress after 4–5 days from the start of the experiment near the water absorption bands (at 1930 nm, 1440 nm) and in the red (at 675 nm). Spectroscopic techniques revealed plant stress up to 6 days earlier than visual inspection. Of the water stress-related vegetation indices, the response of Normalized Difference Water Index (NDWI_1241) and Normalized Photochemical Reflectance Index (PRI_norm) were significantly stronger in the stressed group than the control. To observe the effects of stress on grass properties during the drought episode, we used the RTMo (RTM of solar and sky radiation) model inversion by means of an iterative optimization approach. The performance of the model inversion was assessed by calculating R2 and the Normalized Root Mean Square Error (RMSE) between retrieved and measured LAI (R2 = 0.87, NRMSE = 0.18) and Cab (R2 = 0.74, NRMSE = 0.15). All parameters retrieved by model inversion co-varied with soil moisture deficit. However, the first strong sign of water stress on the retrieved grass properties was detected as a change of Cw followed by Cab and Cdm in the earlier stages. The results from this study indicate that the spectroscopic techniques and RTMo model inversion have a promising potential of detecting stress on the spectral reflectance and grass properties before they become visibly apparent.

The complicate observations and multi-parameter land information constructions on allied telemetry experiment (COMPLICATE)

The Complicate Observations and Multi-Parameter Land Information Constructions on Allied Telemetry Experiment (COMPLICATE) comprises a network of remote sensing experiments designed to enhance the dynamic analysis and modeling of remotely sensed information for complex land surfaces. Two types of experimental campaigns were established under the framework of COMPLICATE. The first was designed for continuous and elaborate experiments. The experimental strategy helps enhance our understanding of the radiative and scattering mechanisms of soil and vegetation and modeling of remotely sensed information for complex land surfaces. To validate the methodologies and models for dynamic analyses of remote sensing for complex land surfaces, the second campaign consisted of simultaneous satellite-borne, airborne, and ground-based experiments. During field campaigns, several continuous and intensive observations were obtained. Measurements were undertaken to answer key scientific issues, as follows: 1) Determine the characteristics of spatial heterogeneity and the radiative and scattering mechanisms of remote sensing on complex land surfaces. 2) Determine the mechanisms of spatial and temporal scale extensions for remote sensing on complex land surfaces. 3) Determine synergist inversion mechanisms for soil and vegetation parameters using multi-mode remote sensing on complex land surfaces. Here, we introduce the background, the objectives, the experimental designs, the observations and measurements, and the overall advances of COMPLICATE. As a result of the implementation of COMLICATE and for the next several years, we expect to contribute to quantitative remote sensing science and Earth observation techniques.

An Overview of the Regional Experiments for Land-atmosphere Exchanges 2012 (REFLEX 2012) Campaign

The REFLEX 2012 campaign was initiated as part of a training course on the organization of an airborne campaign to support advancement of the understanding of land-atmosphere interaction processes. This article describes the campaign, its objectives and observations, remote as well as in situ. The observations took place at the experimental Las Tiesas farm in an agricultural area in the south of Spain. During the period of ten days, measurements were made to capture the main processes controlling the local and regional land-atmosphere exchanges. Apart from multi-temporal, multi-directional and multi-spatial space-borne and airborne observations, measurements of the local meteorology, energy fluxes, soil temperature profiles, soil moisture profiles, surface temperature, canopy structure as well as leaf-level measurements were carried out. Additional thermo-dynamical monitoring took place at selected sites. After presenting the different types of measurements, some examples are given to illustrate the potential of the observations made.

Growing season net ecosystem CO2 exchange of two desert ecosystems with alkaline soils in Kazakhstan

Central Asia is covered by vast desert ecosystems, and the majority of these ecosystems have alkaline soils. Their contribution to global net ecosystem CO2 exchange (NEE) is of significance simply because of their immense spatial extent. Some of the latest research reported considerable abiotic CO2 absorption by alkaline soil, but the rate of CO2 absorption has been questioned by peer communities. To investigate the issue of carbon cycle in Central Asian desert ecosystems with alkaline soils, we have measured the NEE using eddy covariance (EC) method at two alkaline sites during growing season in Kazakhstan. The diurnal course of mean monthly NEE followed a clear sinusoidal pattern during growing season at both sites. Both sites showed significant net carbon uptake during daytime on sunny days with high photosynthetically active radiation (PAR) but net carbon loss at nighttime and on cloudy and rainy days. NEE has strong dependency on PAR and the response of NEE to precipitation resulted in an initial and significant carbon release to the atmosphere, similar to other ecosystems. These findings indicate that biotic processes dominated the carbon processes, and the contribution of abiotic carbon process to net ecosystem CO2 exchange may be trivial in alkaline soil desert ecosystems over Central Asia.

Quantitative Estimation of Fluorescence Parameters for Crop Leaves with Bayesian Inversion

In this study, backward and forward fluorescence radiance within the emission spectrum of 640–850 nm were measured for leaves of soybean, cotton, peanut and wheat using a hyperspectral spectroradiometer coupled with an integration sphere. Fluorescence parameters of crop leaves were retrieved from the leaf hyperspectral measurements by inverting the FluorMODleaf model, a leaf-level fluorescence model able to simulate chlorophyll fluorescence spectra for both sides of leaves. This model is based on the widely used and validated PROSPECT (leaf optical properties) model. Firstly, a sensitivity analysis of the FluorMODleaf model was performed to identify and quantify influential parameters to assist the strategy for the inversion. Implementation of the Extended Fourier Amplitude Sensitivity Test (EFAST) method showed that the leaf chlorophyll content and the fluorescence lifetimes of photosystem I (PSI) and photosystem II (PSII) were the most sensitive parameters among all eight inputs of the FluorMODleaf model. Based on results of sensitivity analysis, the FluorMODleaf model was inverted using the leaf fluorescence spectra measured from both sides of crop leaves. In order to achieve stable inversion results, the Bayesian inference theory was applied. The relative absorption cross section of PSI and PSII and the fluorescence lifetimes of PSI and PSII of the FluorMODleaf model were retrieved with the Bayesian inversion approach. Results showed that the coefficient of determination (R2) and root mean square error (RMSE) between the fluorescence signal reconstructed from the inverted fluorescence parameters and measured in the experiment were 0.96 and 3.14 × 10−6 W·m−2·sr−1·nm−1, respectively, for backward fluorescence, and 0.92 and 3.84 × 10−6 W·m−2·sr−1·nm−1 for forward fluorescence. Based on results, the inverted values of the fluorescence parameters were analyzed, and the potential of this method was investigated.