Impact of Structural, Photochemical and Instrumental Effects on Leaf and Canopy Reflectance Variability in the 500-600 nm Range

Current rapid technological improvement in optical radiometric instrumentation provides an opportunity to develop innovative measurements protocols where the remote quantification of the plant physiological status can be determined with higher accuracy. In this study, the leaf and canopy reflectance variability in the PRI spectral region (i.e., 500-600 nm) is quantified using different laboratory protocols that consider both instrumental and experimental set-up aspects, as well as canopy structural effects and vegetation photoprotection dynamics. First, we studied how an incorrect characterization of the at-target incoming radiance translated into an erroneous vegetation reflectance spectrum and consequently in an incorrect quantification of reflectance indices such as PRI. The erroneous characterization of the at-target incoming radiance translated into a 2% overestimation and a 31% underestimation of estimated chlorophyll content and PRI-related vegetation indexes, respectively. Second, we investigated the dynamic xanthophyll pool and intrinsic Chl vs. Car long-term pool changes affecting the entire 500-600 nm spectral region. Consistent spectral behaviors were observed for leaf and canopy experiments. Sun-adapted plants showed a larger optical change in the PRI range and a higher capacity for photoprotection during the light transient time when compared to shade-adapted plants. Outcomes of this work highlight the importance of well-established spectroscopy sampling protocols to detect the subtle photochemical features which need to be disentangled from the structural and biological effects

Towards the quantitative and physically-based interpretation of solar-induced vegetation fluorescence retrieved from global imaging

Due to emerging high spectral resolution, remote sensing techniques and ongoing developments to retrieve the spectrally resolved vegetation fluorescence spectrum from several scales, the light reactions of photosynthesis are receiving a boost of attention for the monitoring of the Earth's carbon balance. Sensor-retrieved vegetation fluorescence (from leaf, tower, airborne or satellite scale) originating from the excited antenna chlorophyll a molecule has become a new quantitative biophysical vegetation parameter retrievable from space using global imaging techniques. However, to retrieve the actual quantum efficiencies, and hence a true photosynthetic status of the observed vegetation, all signal distortions must be accounted for, and a high-precision true vegetation reflectance must be resolved. ESA's upcoming Fluorescence Explorer aims to deliver such novel products thanks to technological and instrumental advances, and by sophisticated approaches that will enable a deeper understanding of the mechanics of energy transfer underlying the photosynthetic process in plant canopies and ecosystems

Chlorophyll Fluorescence Response to Water and Nitrogen Deficit

The increasing food demand as well as the need to predict the impact of warming climate on vegetation makes it critical to find the best tools to assess crop production and carbon dioxide (CO₂) exchange between the land and atmosphere. Photosynthesis is a good indicator of crop production and CO₂ exchange. Chlorophyll fluorescence (ChF) is directly related to photosynthesis. ChF can be measured at leaf-scale using active techniques and at field-scales using passive techniques. The measurement principles of both techniques are different. In this study, three overarching questions about ChF were addressed: Q1) How water, nutrient and ambient light conditions determine the relationships between photosynthesis and ChF? Which is the optimum irradiance level for detecting water and nutrient deficit conditions with ChF?; Q2) which are the limits within which active and passive techniques are comparable?; and Q3) What is the seasonal relationship between photosynthesis and ChF when nitrogen is the limiting factor? To address these questions, two main experiments were conducted: Exp1) Concurrent photosynthesis and ChF light-response curves were measured in camelina and wheat plants growing under (i) intermediate-light and (ii) high-light conditions respectively. Plant stress was induced by (i) withdrawing water, and (ii) applying different nitrogen levels; and Exp2) coincident active and passive ChF measurements were made in a wheat field under different nitrogen treatments. The results indicated ChF has a direct relationship with photosynthesis when water or nitrogen drives the relationship. This study demonstrates that the light level at which plants were grown was optimum for detecting water and nutrient deficit with ChF. Also, the results showed that for leaf-average-values, active measurements can be used to better understand the daily and seasonal behavior of passive ChF. Further, the seasonal relation between photosynthesis and ChF with nitrogen stress was not a simple linear function. Our study showed that at times in the season when nitrogen was sufficient and photosynthesis was highest, ChF decreased because these two processes compete for available energy. These results demonstrated that ChF is a reliable indicator of crop stress and has great potential for better understand the CO₂ exchange between the land and atmosphere

The scattering and re-absorption of red and near-infrared chlorophyll fluorescence in the models Fluspect and SCOPE

Scattering and re-absorption have been recognized as relevant aspects for the interpretation of solar induced chlorophyll fluorescence (SIF) in vegetation remote sensing. In an earlier study [Yang and Van der Tol, RSE 215, 97–108, 2018] we addressed the problem of scattering and re-absorption of near-infrared fluorescence in the vegetation canopy. In this study we analyse within-leaf re-absorption of both red and near-infrared fluorescence using the radiative transfer model Fluspect. The leaf scattering determines the ratio of backward to total leaf fluorescence emission Fb/(Fb + Ff). Fluspect reproduces this ratio with an RMSE of less than 0.1, and explains the observed dependence of the spectral shape of this ratio on chlorophyll content and other leaf properties. We further provide a theoretical evaluation of how asymmetric SIF emission affects the SIF of a whole canopy and explain why recent within-canopy scattering models for fluorescence are not valid for red SIF

Impact of Structural, Photochemical and Instrumental Effects on Leaf and Canopy Reflectance Variability in the 500–600 nm Range

Current rapid technological improvement in optical radiometric instrumentation provides an opportunity to develop innovative measurements protocols where the remote quantification of the plant physiological status can be determined with higher accuracy. In this study, the leaf and canopy reflectance variability in the PRI spectral region (i.e., 500–600 nm) is quantified using different laboratory protocols that consider both instrumental and experimental set-up aspects, as well as canopy structural effects and vegetation photoprotection dynamics. First, we studied how an incorrect characterization of the at-target incoming radiance translated into an erroneous vegetation reflectance spectrum and consequently in an incorrect quantification of reflectance indices such as PRI. The erroneous characterization of the at-target incoming radiance translated into a 2% overestimation and a 31% underestimation of estimated chlorophyll content and PRI-related vegetation indexes, respectively. Second, we investigated the dynamic xanthophyll pool and intrinsic Chl vs. Car long-term pool changes affecting the entire 500–600 nm spectral region. Consistent spectral behaviors were observed for leaf and canopy experiments. Sun-adapted plants showed a larger optical change in the PRI range and a higher capacity for photoprotection during the light transient time when compared to shade-adapted plants. Outcomes of this work highlight the importance of well-established spectroscopy sampling protocols to detect the subtle photochemical features which need to be disentangled from the structural and biological effects

A Method for Uncertainty Assessment of Passive Sun-Induced Chlorophyll Fluorescence Retrieval Using an Infrared Reference Light

Measurements of sun-induced chlorophyll fluorescence (SIF) over plant canopies provide a proxy for plant photosynthetic capacity and are of high interest for plant research. Together with spectral reflectance, SIF has the potential to act as a noninvasive approach to quantify photosynthetic plant traits from field to air and spaceborne scales. However, SIF is a small signal contribution to the reflected sunlight and often not distinguishable from sensor noise. SIF estimation is, therefore, affected by an unquantified uncertainty, making it difficult to estimate accurately how much SIF is truly emitted from the plant. To investigate and overcome this, we designed a device based on a spectrometer covering the visible range and equipped it with an LED emitting at the wavelength of SIF. Using this as a reference and applying thorough calibrations, we present consistent evidence of the instrument's capability of SIF retrieval and accuracy estimations. The LED's intensity was measured under sunlight with 1.27 ± 0.27 mW × sr-1m-2nm-1 stable over the day. The large increase of SIF due to the Kautsky effect was measured spectrally and temporally proving the biophysical origin of the signal. We propose rigorous tests for instruments intended to measure SIF and show ways to further improve the presented methods

HyScreen: A Ground-Based Imaging System for High-Resolution Red and Far-Red Solar-Induced Chlorophyll Fluorescence

Solar-induced chlorophyll fluorescence (SIF) is used as a proxy of photosynthetic efficiency. However, interpreting top-of-canopy (TOC) SIF in relation to photosynthesis remains challenging due to the distortion introduced by the canopy’s structural effects (i.e., fluorescence re-absorption, sunlit-shaded leaves, etc.) and sun–canopy–sensor geometry (i.e., direct radiation infilling). Therefore, ground-based, high-spatial-resolution data sets are needed to characterize the described effects and to be able to downscale TOC SIF to the leafs where the photosynthetic processes are taking place. We herein introduce HyScreen, a ground-based push-broom hyperspectral imaging system designed to measure red ([Formula: see text]) and far-red ([Formula: see text]) SIF and vegetation indices from TOC with single-leaf spatial resolution. This paper presents measurement protocols, the data processing chain and a case study of SIF retrieval. Raw data from two imaging sensors were processed to top-of-canopy radiance by dark-current correction, radiometric calibration, and empirical line correction. In the next step, the improved Fraunhofer line descrimination (iFLD) and spectral-fitting method (SFM) were used for SIF retrieval, and vegetation indices were calculated. With the developed protocol and data processing chain, we estimated a signal-to-noise ratio (SNR) between 50 and 200 from reference panels with reflectance from 5% to 95% and noise equivalent radiance (NER) of 0.04 (5%) to 0.18 (95%) mW m [Formula: see text] sr [Formula: see text] nm [Formula: see text]. The results from the case study showed that non-vegetation targets had SIF values close to 0 mW m [Formula: see text] sr [Formula: see text] nm [Formula: see text] , whereas vegetation targets had a mean [Formula: see text] of 1.13 and [Formula: see text] of 1.96 mW m [Formula: see text] sr [Formula: see text] nm [Formula: see text] from the SFM method. HyScreen showed good performance for SIF retrievals at both [Formula: see text] and [Formula: see text]; nevertheless, we recommend further adaptations to correct for the effects of noise, varying illumination and sensor optics. In conclusion, due to its high spatial resolution, Hyscreen is a promising tool for investigating the relationship between leafs and TOC SIF as well as their relationship with plants’ photosynthetic capacity

FluoCat: A cable-suspended multi-sensor system for the vegetation SIF Cal/Val monitoring and estimation of effective sunlit surface fluorescence

With the upcoming Fluorescence Explorer (FLEX) satellite mission from the European Space Agency, vegetation fluorescence (650–780 nm) will become available at 300x300 m resolution. Calibration and validation strategies of the fluorescence (F) signal remain however challenging, due to (1) the radiometric subtlety of the signal, (2) the multiple entangled drivers of the signal in space and in time, and (3) the need of a spatially representative acquisition, considering the previous two points. To tackle these challenges, the present work introduces the FluoCat, a cable-suspended system for the proximal sensing indirect measurement of solar-induced fluorescence, mounted across an agricultural field, covering a 60-m transect. On board the FluoCat are mounted: a high-spectral resolution Piccolo Doppio dual spectrometer system, a MAIA-S2 multispectral camera and a TeAx Thermal Capture Fusion camera, which can be triggered simultaneously according to a pre-set protocol.In order to test the system, two protocols were evaluated, a point-wise protocol, stopping at a pre-determined points to acquire the measurements, and the swiping protocol, acquiring measurements while in movement along the transect. Taking as a reference the values obtained with the swiping protocol, which captures the higher spatial variability, it was found that to achieve an averaged mean absolute percentage error (MAPE) below 2 % within between the spectral range of 500–800 nm, it is required a minimum of 6 sampling points to characterize the spectral variability of the 40-m melon crop transect.Further, by combining the fluorescence products of the Piccolo system normalized by PAR (NormF687, NormF760) and the fractional cover of sunlit vegetation (FVC Sunlit) obtained from the MAIA, we developed a multi-sensor product, i.e., the ‘sunlit green F’ for both retrieved bands. This synergy product improved the estimation of the effective surface fluorescence flux, with the leaf fluorescence emission as reference, by reducing the errors from 36 % to 18 % (band 687 nm); and from 24 % to 6 % (band 760 nm)

Downscaling of far-red solar-induced chlorophyll fluorescence of different crops from canopy to leaf level using a diurnal data set acquired by the airborne imaging spectrometer HyPlant

Remote sensing-based measurements of solar-induced chlorophyll fluorescence (SIF) are useful for assessing plant functioning at different spatial and temporal scales. SIF is the most direct measure of photosynthesis and is therefore considered important to advance capacity for the monitoring of gross primary production (GPP) while it has also been suggested that its yield facilitates the early detection of vegetation stress. However, due to the influence of different confounding effects, the apparent SIF signal measured at canopy level differs from the fluorescence emitted at leaf level, which makes its physiological interpretation challenging. One of these effects is the scattering of SIF emitted from leaves on its way through the canopy. The escape fraction () describes the scattering of SIF within the canopy and corresponds to the ratio of apparent SIF at canopy level to SIF at leaf level. In the present study, the fluorescence correction vegetation index (FCVI) was used to determine of far-red SIF for three structurally different crops (sugar beet, winter wheat, and fruit trees) from a diurnal data set recorded by the airborne imaging spectrometer HyPlant. This unique data set, for the first time, allowed a joint analysis of spatial and temporal dynamics of structural effects and thus the downscaling of far-red SIF from canopy () to leaf level (). For a homogeneous crop such as winter wheat, it seems to be sufficient to determine once a day to reliably scale SIF760 from canopy to leaf level. In contrast, for more complex canopies such as fruit trees, calculating for each observation time throughout the day is strongly recommended. The compensation for structural effects, in combination with normalizing SIF760 to remove the effect of incoming radiation, further allowed the estimation of SIF emission efficiency (ε) at leaf level, a parameter directly related to the diurnal variations of plant photosynthetic efficiency

Downscaling of far-red solar-induced chlorophyll fluorescence of different crops from canopy to leaf level using a diurnal data set acquired by the airborne imaging spectrometer HyPlant

Remote sensing-based measurements of solar-induced chlorophyll fluorescence (SIF) are useful for assessing plant functioning at different spatial and temporal scales. SIF is the most direct measure of photosynthesis and is therefore considered important to advance capacity for the monitoring of gross primary production (GPP) while it has also been suggested that its yield facilitates the early detection of vegetation stress. However, due to the influence of different confounding effects, the apparent SIF signal measured at canopy level differs from the fluorescence emitted at leaf level, which makes its physiological interpretation challenging. One of these effects is the scattering of SIF emitted from leaves on its way through the canopy. The escape fraction (f esc) describes the scattering of SIF within the canopy and corresponds to the ratio of apparent SIF at canopy level to SIF at leaf level. In the present study, the fluorescence correction vegetation index (FCVI) was used to determine f esc of far-red SIF for three structurally different crops (sugar beet, winter wheat, and fruit trees) from a diurnal data set recorded by the airborne imaging spectrometer HyPlant. This unique data set, for the first time, allowed a joint analysis of spatial and temporal dynamics of structural effects and thus the downscaling of far-red SIF from canopy (SIF 760 canopy) to leaf level (SIF 760 leaf). For a homogeneous crop such as winter wheat, it seems to be sufficient to determine f esc once a day to reliably scale SIF 760 from canopy to leaf level. In contrast, for more complex canopies such as fruit trees, calculating f esc for each observation time throughout the day is strongly recommended. The compensation for structural effects, in combination with normalizing SIF 760 to remove the effect of incoming radiation, further allowed the estimation of SIF emission efficiency (ε SIF) at leaf level, a parameter directly related to the diurnal variations of plant photosynthetic efficiency