Canopy Chlorophyll Fluorescence Research Articles

Tracking canopy chlorophyll fluorescence with a low-cost light emitting diode platform.

Chlorophyll fluorescence measured at the leaf scale through pulse amplitude modulation (PAM) has provided valuable insight into photosynthesis. At the canopy- and satellite-scale, solar-induced fluorescence (SIF) provides a method to estimate the photosynthetic activity of plants across spatiotemporal scales. However, retrieving SIF signal remotely requires instruments with high spectral resolution, making it difficult and often expensive to measure canopy-level steady-state chlorophyll fluorescence under natural sunlight. Considering this, we built a novel low-cost photodiode system that retrieves far-red chlorophyll fluorescence emission induced by a blue light emitting diode (LED) light source, for 2 h at night, above the canopy. Our objective was to determine if an active remote sensing-based night-time photodiode method could track changes in canopy-scale LED-induced chlorophyll fluorescence (LEDIF) during an imposed drought on a broadleaf evergreen shrub, Polygala myrtifolia. Far-red LEDIF (720-740 nm) was retrieved using low-cost photodiodes (LEDIFphotodiode) and validated against measurements from a hyperspectral spectroradiometer (LEDIFhyperspectral). To link the LEDIF signal with physiological drought response, we tracked stomatal conductance (gsw) using a porometer, two leaf-level vegetation indices-photochemical reflectance index and normalized difference vegetation index-to represent xanthophyll and chlorophyll pigment dynamics, respectively, and a PAM fluorimeter to measure photochemical and non-photochemical dynamics. Our results demonstrate a similar performance between the photodiode and hyperspectral retrievals of LEDIF (R2 = 0.77). Furthermore, LEDIFphotodiode closely tracked drought responses associated with a decrease in photochemical quenching (R2 = 0.69), Fv/Fm (R2 = 0.59) and leaf-level photochemical reflectance index (R2 = 0.59). Therefore, the low-cost LEDIFphotodiode approach has the potential to be a meaningful indicator of photosynthetic activity at spatial scales greater than an individual leaf and over time.

Comparative Analysis on the Estimation of Diurnal Solar-Induced Chlorophyll Fluorescence Dynamics for a Subtropical Evergreen Coniferous Forest

Solar-induced chlorophyll fluorescence (SIF) is considered as a prospective indicator of vegetation photosynthetic activity and the ecosystem carbon cycle. The current coarse spatial-temporal resolutions of SIF data from satellite missions and ground measurements still cannot satisfy the corroboration of its correlation with photosynthesis and carbon flux. Practical approaches are needed to be explored for the supplementation of the SIF measurements. In our study, we clarified the diurnal variations of leaf and canopy chlorophyll fluorescence for a subtropical evergreen coniferous forest and evaluated the performance of the canopy chlorophyll concentration (CCC) approach and the backward approach from gross primary production (GPP) for estimating the diurnal variations of canopy SIF by comparing with the Soil Canopy Observation Photosynthesis Energy (SCOPE) model. The results showed that the canopy SIF had similar seasonal and diurnal variations with the incident photosynthetically active radiation (PAR) above the canopy, while the leaf steady-state fluorescence remained stable during the daytime. Neither the CCC nor the raw backward approach from GPP could capture the short temporal dynamics of canopy SIF. However, after improving the backward approach with a correction factor of normalized PAR incident on leaves, the variation of the estimated canopy SIF accounted for more than half of the diurnal variations in the canopy SIF (SIF687: R2 = 0.53, p < 0.001; SIF760: R2 = 0.72, p < 0.001) for the subtropical evergreen coniferous forest without water stress. Drought interfered with the utilization of the improved backward approach because of the decoupling of SIF and GPP due to stomatal closure. This new approach offers new insight into the estimation of diurnal canopy SIF and can help understand the photosynthesis of vegetation for future climate change studies.

Canopy chlorophyll fluorescence applied to stress detection using an easy-to-build micro-lidar

LEDFLEX is a micro-lidar dedicated to the measurement of vegetation fluorescence. The light source consists of 4 blue Light-Emitting Diodes (LED) to illuminate part of the canopy in order to average the spatial variability of small crops. The fluorescence emitted in response to a 5-μs width pulse is separated from the ambient light through a synchronized detection. Both the reflectance and the fluorescence of the target are acquired simultaneously in exactly the same field of view, as well as the photosynthetic active radiation and air temperature. The footprint is about 1 m2 at a distance of 8 m. By increasing the number of LEDs longer ranges can be reached. The micro-lidar has been successfully applied under full sunlight conditions to establish the signature of water stress on pea (Pisum Sativum) canopy. Under well-watered conditions the diurnal cycle presents an M shape with a minimum (Fmin) at noon which is Fmin > Fo. After several days withholding watering, Fs decreases and Fmin < Fo. The same patterns were observed on mint (Menta Spicata) and sweet potatoes (Ipomoea batatas) canopies. Active fluorescence measurements with LEDFLEX produced robust fluorescence yield data as a result of the constancy of the excitation intensity and its geometry fixity. Passive methods based on Sun-Induced chlorophyll Fluorescence (SIF) that uses high-resolution spectrometers generate only flux data and are dependent on both the 3D structure of vegetation and variable irradiance conditions along the day. Parallel measurements with LEDFLEX should greatly improve the interpretation of SIF changes.

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.

Spatio-temporal patterns of chlorophyll fluorescence and physiological and structural indices acquired from hyperspectral imagery as compared with carbon fluxes measured with eddy covariance

This study provides insight into the assessment of the spatio-temporal trends of chlorophyll fluorescence, narrow-band physiological indices, and structural indices acquired with a hyperspectral imager flown over a flux tower in a canopy characterized by small seasonal structural changes and a heterogeneous architecture. A total of seven flights between summer and autumn were conducted with a hyperspectral camera that captured 30cm resolution imagery and 260 spectral bands in the 400-900nm region. This enabled the identification of pure-vegetation tree crown pixels around an eddy covariance flux tower without shadow components or background effects. The hyperspectral imagery was used to study the temporal patterns of canopy fluorescence and reflectance indices related to physiology and canopy structure. The seasonal trends observed in the airborne indices and fluorescence and their relationship with gross primary production (GPP) demonstrated that vegetation indices mostly related to structure such as the normalized difference vegetation index (NDVI) and the enhanced vegetation index (EVI) yielded non-significant relationships (r2=0.17; p>0.05) due to the small structural changes in the canopy through the season. By contrast, physiological indices related to chlorophyll content (TCARI/OSAVI), light use efficiency (PRI570), and canopy chlorophyll fluorescence calculated through the Fraunhofer Line Depth principle (FLD3) showed a similar seasonal trend to that of GPP measured at the same time of the flights (r2 in the range 0.75–0.84; p<0.01). These results are consistent with the physiological trend observed during summer and autumn, which showed that chlorophyll content increased by 17.9% while the NDVI and the estimated tree crown projected LAI (LAIp) remained almost constant during the experiment (3% variation). The time-series hyperspectral dataset demonstrated that the seasonal trajectories of the NDVI and EVI were weakly related (p>0.05) to the physiological indicators such as TCARI/OSAVI, PRI570 and fluorescence. The spatial variability of the hyperspectral indices investigated through the coefficient of variation (CV) showed that fluorescence around the tower varied up to 17% at the time of the maximum stress (summer), while LAIp showed little variation during that time (CV=1.8%). After the summer stress period, the CV for fluorescence and chlorophyll content decreased in autumn down to 9%. This study demonstrates that small physiological changes occurring in an evergreen canopy were still captured by remote sensing physiological indices and high-resolution airborne fluorescence. These indicators are required for GPP monitoring when the vegetation dynamics are not captured by remote sensing structural indices.

Near-distance imaging spectroscopy investigating chlorophyll fluorescence and photosynthetic activity of grassland in the daily course.

Detection of grassland canopy chlorophyll fluorescence (Chl-F) conducted with an imaging spectroradiometer provided evidence of potential remote sensing estimation of steady-state Chl-F (Chl-Fs). Daily near-nadir views of extremely high spatial resolution hyperspectral images were acquired from a distance of 4 m for temperate montane grassland in the Czech Republic. Simultaneously, measurements of Chl-F and total chlorophyll content (Chla + b) were made on a single leaf at ground level were collected. A specifically designed 'shade removal' experiment revealed the influence of dynamic physiological plant processes on hyperspectral reflectance of three wavelengths: 532, 686 and 740 nm. Based on this information, the vegetation indexes R686/R630, R740/R800 and PRI calculated as (R532-R570)/(R532+R570) were tested for statistical significance with directly measured Chl-F parameters (maximum fluorescence yield, Fv/Fm; steady-state chlorophyll fluorescence, Chl-Fs and actual quantum yield, ФII). The grassland species under investigation were: Festuca rubra agg. (L.), Hieracium sp., Plantago sp., Nardus stricta (L.) and Jacea pseudophrygia (C.A. Meyer). The coefficients of determination (R2) for best-fit relationships between PRI-ФII and PRI-Chl-Fs, measured in the daily course, show a high variability of 0.23-0.78 and 0.20-0.65, respectively. Similarly, R2 for the R686/R630-ФII and R686/R630-Chl-Fs relationships varied between 0.20-0.73 and 0.41-0.70, respectively. The highest average R2 values were found between PRI and Chla + b (0.63) and R686/R630 and Chla + b (0.72). The ratio R740/R800 did not yield a statistically significant relation with Chl-F parameters.

FluorMODgui V3.0: A graphic user interface for the spectral simulation of leaf and canopy chlorophyll fluorescence

The FluorMODgui Graphic User Interface (GUI) software package developed within the frame of the FluorMOD project Development of a Vegetation Fluorescence Canopy Model is presented in this manuscript. The FluorMOD project was launched in 2002 by the European Space Agency (ESA) to advance the science of vegetation fluorescence simulation through the development and integration of leaf and canopy fluorescence models based on physical methods. The design of airborne or space missions dedicated to the measurement of solar-induced chlorophyll fluorescence using remote-sensing instruments require physical methods for quantitative feasibility analysis and sensor specification studies. The FluorMODgui model developed as part of this project is designed to simulate the effects of chlorophyll fluorescence at leaf and canopy levels using atmospheric inputs, running the leaf model, FluorMODleaf, and the canopy model, FluorSAIL, independently, through a coupling scheme, and by a multiple iteration protocol to simulate changes in the viewing geometry and atmospheric characteristics. Inputs for the FluorMODleaf model are the number of leaf layers, chlorophyll a+ b content, water equivalent thickness, dry matter content, fluorescence quantum efficiency, temperature, species type, and stoichiometry. Inputs for the FluorSAIL canopy model are a MODTRAN-4 6-parameter spectra or measured direct horizontal irradiance and diffuse irradiance spectra, a soil reflectance spectrum, leaf reflectance & transmittance spectra and a excitation-fluorescence response matrix in upward and downward directions (all from FluorMODleaf), 2 PAR-dependent coefficients for the fluorescence response to light level, relative azimuth angle and viewing zenith angle, canopy leaf area index, leaf inclination distribution function, and a hot spot parameter. Outputs available in the 400–1000 nm spectral range from the graphical user interface, FluorMODgui, are the leaf spectral reflectance and transmittance, and the canopy reflectance, with and without fluorescence effects. In addition, solar and sky irradiance on the ground, radiance with and without fluorescence on the ground, and top-of-atmosphere (TOA) radiances for bare soil and surroundings same as target are also produced. The models and documentation regarding the FluorMOD project can be downloaded at http://www.ias.csic.es/fluormod.

Simulation of canopy fluorescence as a function of canopy structure and leaf fluorescence

Canopy chlorophyll fluorescence depends on the variation of individual leaf response inside the canopy, the attenuation of incident exciting radiation, and the scattering of emitted radiation toward the sensor. A simple model is presented which takes into account leaf fluorescence profile inside the canopy, structural variations of the canopy, and background reflection. Analysis shows that canopy fluorescence is strongly affected by these parameters. However, the use of the fluorescence ratio F 690 F 730 can limit these effects.