Sergio Cogliati

Sun-induced fluorescence - a new probe of photosynthesis: First maps from the imaging spectrometer HyPlant

Variations in photosynthesis still cause substantial uncertainties in predicting photosynthetic CO2 uptake rates and monitoring plant stress. Changes in actual photosynthesis that are not related to greenness of vegetation are difficult to measure by reflectance based optical remote sensing techniques. Several activities are underway to evaluate the sun-induced fluorescence signal on the ground and on a coarse spatial scale using space-borne imaging spectrometers. Intermediate-scale observations using airborne-based imaging spectroscopy, which are critical to bridge the existing gap between small-scale field studies and global observations, are still insufficient. Here we present the first validated maps of sun-induced fluorescence in that critical, intermediate spatial resolution, employing the novel airborne imaging spectrometer HyPlant. HyPlant has an unprecedented spectral resolution, which allows for the first time quantifying sun-induced fluorescence fluxes in physical units according to the Fraunhofer Line Depth Principle that exploits solar and atmospheric absorption bands. Maps of sun-induced fluorescence show a large spatial variability between different vegetation types, which complement classical remote sensing approaches. Different crop types largely differ in emitting fluorescence that additionally changes within the seasonal cycle and thus may be related to the seasonal activation and deactivation of the photosynthetic machinery. We argue that sun-induced fluorescence emission is related to two processes: (i) the total absorbed radiation by photosynthetically active chlorophyll; and (ii) the functional status of actual photosynthesis and vegetation stress.

Red and far red Sun‐induced chlorophyll fluorescence as a measure of plant photosynthesis

Remote estimation of Sun-induced chlorophyll fluorescence emitted by terrestrial vegetation can provide an unparalleled opportunity to track spatiotemporal variations of photosynthetic efficiency. Here we provide the first direct experimental evidence that the two peaks of the chlorophyll fluorescence spectrum can be accurately mapped from high-resolution radiance spectra and that the signal is linked to variations in actual photosynthetic efficiency. Red and far red fluorescence measured using a novel airborne imaging spectrometer over a grass carpet treated with an herbicide known to inhibit photosynthesis was significantly higher than the corresponding signal from an equivalent untreated grass carpet. The reflectance signal of the two grass carpets was indistinguishable, confirming that the fast dynamic changes in fluorescence emission were related to variations in the functional status of actual photosynthesis induced by herbicide application. Our results from a controlled experiment at the local scale illustrate the potential for the global mapping of terrestrial photosynthesis through space-borne measurements of chlorophyll fluorescence.

Ground-Based Optical Measurements at European Flux Sites: A Review of Methods, Instruments and Current Controversies

This paper reviews the currently available optical sensors, their limitations and opportunities for deployment at Eddy Covariance (EC) sites in Europe. This review is based on the results obtained from an online survey designed and disseminated by the Co-cooperation in Science and Technology (COST) Action ESO903—“Spectral Sampling Tools for Vegetation Biophysical Parameters and Flux Measurements in Europe” that provided a complete view on spectral sampling activities carried out within the different research teams in European countries. The results have highlighted that a wide variety of optical sensors are in use at flux sites across Europe, and responses further demonstrated that users were not always fully aware of the key issues underpinning repeatability and the reproducibility of their spectral measurements. The key findings of this survey point towards the need for greater awareness of the need for standardisation and development of a common protocol of optical sampling at the European EC sites.

Leaf level early assessment of ozone injuries by passive fluorescence and photochemical reflectance index

Excess energy dissipation pathways (heat and fluorescence) were monitored, at leaf level as indicators of plant physiological status, with field spectroscopy techniques on poplar clones subjected to ozone fumigation. Measurements of spectral radiance emerging from a leaf provide a fast, non‐destructive method for the assessment of excess energy dissipation: xanthophyll‐related heat dissipation was estimated with the photochemical reflectance index (PRI) calculated from a traditional field spectrometer, and steady‐state fluorescence (Fs) under natural illumination conditions was estimated by exploiting a variation of the Fraunhofer line‐depth principle, where the radiance collected with very high resolution spectrometers (FWHM = 0.13 nm) was spectrally modelled. Both remotely‐sensed dissipation pathways responded to fumigation. During a 26‐day fumigation experiment, four diurnal cycles of spectral measurements were collected in parallel to meteorological and key physiological variables (active fluorescence, net photosynthesis) and leaf sample collection for pigment extraction. We outline evidence of a link between the remotely‐sensed Fs and PRI and leaf physiological status. These results open up new possibilities for assessment of plant stress by means of hyperspectral remote sensing.

The hyperspectral irradiometer, a new instrument for long-term and unattended field spectroscopy measurements

Reliable time series of vegetation optical properties are needed to improve the modeling of the terrestrial carbon budget with remote sensing data. This paper describes the development of an automatic spectral system able to collect continuous long-term in-field spectral measurements of spectral down-welling and surface reflected irradiance. The paper addresses the development of the system, named hyperspectral irradiometer (HSI), describes its optical design, the acquisition, and processing operations. Measurements gathered on a vegetated surface by the HSI are shown, discussed and compared with experimental outcomes with independent instruments.

Characterization of fine resolution field spectrometers using solar Fraunhofer lines and atmospheric absorption features

The accurate spectral characterization of high-resolution spectrometers is required for correctly computing, interpreting, and comparing radiance and reflectance spectra acquired at different times or by different instruments. In this paper, we describe an algorithm for the spectral characterization of field spectrometer data using sharp atmospheric or solar absorption features present in the measured data. The algorithm retrieves systematic shifts in channel position and actual full width at half-maximum (FWHM) of the instrument by comparing data acquired during standard field spectroscopy measurement operations with a reference irradiance spectrum modeled with the MODTRAN4 radiative transfer code. Measurements from four different field spectrometers with spectral resolutions ranging from 0.05 to 3.5nm are processed and the results validated against laboratory calibration. An accurate retrieval of channel position and FWHM has been achieved, with an average error smaller than the instrument spectral sampling interval.

Sun-induced chlorophyll fluorescence from high-resolution imaging spectroscopy data to quantify spatio-temporal patterns of photosynthetic function in crop canopies

Passive detection of sun-induced chlorophyll fluorescence (SIF) using spectroscopy has been proposed as a proxy to quantify changes in photochemical efficiency at canopy level under natural light conditions. In this study, we explored the use of imaging spectroscopy to quantify spatio-temporal dynamics of SIF within crop canopies and its sensitivity to track patterns of photosynthetic activity originating from the interaction between vegetation structure and incoming radiation as well as variations in plant function. SIF was retrieved using the Fraunhofer Line Depth (FLD) principle from imaging spectroscopy data acquired at different time scales a few metres above several crop canopies growing under natural illumination. We report the first maps of canopy SIF in high spatial resolution. Changes of SIF were monitored at different time scales ranging from quick variations under induced stress conditions to seasonal dynamics. Natural changes were primarily determined by varying levels and distribution of photosynthetic active radiation (PAR). However, this relationship changed throughout the day demonstrating an additional physiological component modulating spatio-temporal patterns of SIF emission. We successfully used detailed SIF maps to track changes in the canopys photochemical activity under field conditions, providing a new tool to evaluate complex patterns of photosynthesis within the canopy.

Remote estimation of grassland gross primary production during extreme meteorological seasons

a b s t r a c t Different models driven by remotely sensed vegetation indexes (VIs) and incident photosynthetically active radiation (PAR) were developed to estimate gross primary production (GPP) in a subalpine grass- land equipped with an eddy covariance flux tower. Hyperspectral reflectance was collected using an automatic system designed for high temporal frequency acquisitions for three consecutive years, includ- ing one (2011) characterized by a strong reduction of the carbon sequestration rate during the vegetative season. Models based on remotely sensed and meteorological data were used to estimate GPP, and a cross-validation approach was used to compare the predictive capabilities of different model formula- tions. Vegetation indexes designed to be more sensitive to chlorophyll content explained most of the variability in GPP in the ecosystem investigated, characterized by a strong seasonal dynamic. Model performances improved when including also PARpotential defined as the maximal value of incident PAR under clear sky conditions in model formulations. Best performing models are based entirely on remotely sensed data. This finding could contribute to the development of methods for quantifying the temporal variation of GPP also on a broader scale using current and future satellite sensors.

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.

Comparison of Sun-Induced Chlorophyll Fluorescence Estimates Obtained from Four Portable Field Spectroradiometers

Remote Sensing of Sun-Induced Chlorophyll Fluorescence (SIF) is a research field of growing interest because it offers the potential to quantify actual photosynthesis and to monitor plant status. New satellite missions from the European Space Agency, such as the Earth Explorer 8 FLuorescence EXplorer (FLEX) mission—scheduled to launch in 2022 and aiming at SIF mapping—and from the National Aeronautics and Space Administration (NASA) such as the Orbiting Carbon Observatory-2 (OCO-2) sampling mission launched in July 2014, provide the capability to estimate SIF from space. The detection of the SIF signal from airborne and satellite platform is difficult and reliable ground level data are needed for calibration/validation. Several commercially available spectroradiometers are currently used to retrieve SIF in the field. This study presents a comparison exercise for evaluating the capability of four spectroradiometers to retrieve SIF. The results show that an accurate far-red SIF estimation can be achieved using spectroradiometers with an ultrafine resolution (less than 1 nm), while the red SIF estimation requires even higher spectral resolution (less than 0.5 nm). Moreover, it is shown that the Signal to Noise Ratio (SNR) plays a significant role in the precision of the far-red SIF measurements.