Sun-induced chlorophyll fluorescence II: Review of passive measurement setups, protocols, and their application at the leaf to canopy level

Imaging and non-imaging spectroscopy employed in the field and from aircraft is frequently used to assess biochemical, structural, and functional plant traits, as well as their dynamics in an environmental matrix. With the increasing availability of high-resolution spectroradiometers, it has become feasible to measure fine spectral features, such as those needed to estimate sun-induced chlorophyll fluorescence (F), which is a signal related to the photosynthetic process of plants. The measurement of F requires highly accurate and precise radiance measurements in combination with very sophisticated measurement protocols. Additionally, because F has a highly dynamic nature (compared with othe…

Mapping productivity and essential biophysical parameters of cultivated tropical grasslands from sentinel-2 imagery.

Nitrogen (N) is the main nutrient element that maintains productivity in forages

Diurnal Cycle Relationships between Passive Fluorescence, PRI and NPQ of Vegetation in a Controlled Stress Experiment

In order to estimate vegetation photosynthesis from remote sensing observations; some critical parameters need to be quantified. From all absorbed light; the plant needs to release any excess that is not used for photosynthesis; by non-photochemical quenching; by fluorescence emission and unregulated thermal dissipation. Non-photochemical quenching (NPQ) processes are controlled photoprotective mechanisms which; once activated; strongly control the dynamics of photochemical efficiency. With illumination conditions increasing and decreasing during a diurnal cycle; photoprotection mechanisms needs to change accordingly. The goal of this work is to quantify dynamic NPQ; measured from active fl…

Beyond APAR and NPQ: Factors Coupling and Decoupling SIF and GPP Across Scales

The connection between solar-induced fluorescence (SIF) and vegetation gross primary productivity is being widely investigated across spatial, temporal, and biological scales, including: a) studies at the leaf [1], [2], plant canopy [2]–[4] or satellite pixel scale [5], [6], b) temporally with studies spanning from diurnal [7] to seasonal scales [1], [3], [5], and b) biologically with studies covering various plant functional types (PFTs), e.g., crops [4], [7], deciduous [8] or evergreen forests [1], [3], in response to different sources of stress.

Multi-sensor spectral synergies for crop stress detection and monitoring in the optical domain: A review

Combined dynamics of the 500–600 nm leaf absorption and chlorophyll fluorescence changes in vivo: Evidence for the multifunctional energy quenching role of xanthophylls

Carotenoids (Cars) regulate the energy flow towards the reaction centres in a versatile way whereby the switch between energy harvesting and dissipation is strongly modulated by the operation of the xanthophyll cycles. However, the cascade of molecular mechanisms during the change from light harvesting to energy dissipation remains spectrally poorly understood. By characterizing the in vivo absorbance changes (Delta A) of leaves from four species in the 500-600 nm range through a Gaussian decomposition, while measuring passively simultaneous Chla fluorescence (F) changes, we present a direct observation of the quick antenna adjustments during a 3-min dark-to-high-light induction. Underlying…

Gaussian processes retrieval of leaf parameters from a multi-species reflectance, absorbance and fluorescence dataset.

Abstract: Biochemical and structural leaf properties such as chlorophyll content (Chl), nitrogen content (N), leaf water content (LWC), and specific leaf area (SLA) have the benefit to be estimated through nondestructive spectral measurements. Current practices, however, mainly focus on a limited amount of wavelength bands while more information could be extracted from other wavelengths in the full range (400-2500 nm) spectrum. In this research, leaf characteristics were estimated from a field-based multi-species dataset, covering a wide range in leaf structures and Chl concentrations. The dataset contains leaves with extremely high Chl concentrations (>100 mu g cm(-2)), which are seldom es…

Retrieval of canopy water content of different crop types with two new hyperspectral indices: Water Absorption Area Index and Depth Water Index

Crop canopy water content (CWC) is an essential indicator of the crop’s physiological state. While a diverse range of vegetation indices have earlier been developed for the remote estimation of CWC, most of them are defined for specific crop types and areas, making them less universally applicable. We propose two new water content indices applicable to a wide variety of crop types, allowing to derive CWC maps at a large spatial scale. These indices were developed based on PROSAIL simulations and then optimized with an experimental dataset (SPARC03; Barrax, Spain). This dataset consists of water content and other biophysical variables for five common crop types (lucerne, corn, potato, sugar …

Upward and downward solar-induced chlorophyll fluorescence yield indices of four tree species as indicators of traffic pollution in Valencia

Abstract: Passive steady-state chlorophyll fluorescence (Fs) provides a direct diagnosis of the functional status of vegetation photosynthesis. With the prospect of mapping Fs using remote sensing techniques, field measurements are mandatory to understand to which extent Fs allows detecting plant stress in different environments. Trees of four common species in Valencia were classified in either a low or a high local traffic exposure class based on their leaf magnetic value. Upward and downward hyperspectral fluorescence yield (FY) and indices based on the two Fs peaks (at 687 and 741 nm) were calculated. FY indices of P. canariensis and P. x acerifolia were significantly different between …

Chlorophyll content mapping of urban vegetation in the city of Valencia based on the hyperspectral NAOC index

Abstract: Spatially distributed chlorophyll content of urban vegetation provides an important indicator of a plant's health status, which might depend on the habitat quality of the specific urban environment. Recent advances in optical remote sensing led to improved methodologies to monitor vegetation properties. The hyperspectral index NAOC (Normalized Area Over reflectance Curve) is one of these new tools that can be used for mapping chlorophyll content. In this paper we present the work done to quantify vegetation chlorophyll content over the city of Valencia (Spain) based on chlorophyll measurements of four representative tree species: the London plane tree (Platanus x. acerifolia), the…

Bidirectional sun-induced chlorophyll fluorescence emission is influenced by leaf structure and light scattering properties : a bottom-up approach

Abstract Sun-induced chlorophyll fluorescence (SIF) at leaf level is emitted in both upward and downward directions in the red and far-red part of the spectrum (650–850 nm) when a leaf is illuminated from the upper leaf surface. Hence, total SIF is represented by the sum of the upward and downward emission components. Nevertheless, the downward component of leaf SIF is often not considered despite that downward fluorescence yield (↓FY) can amount up to 40% of the total fluorescence yield (FYtot). Downward SIF is mainly emitted in the far-red, since this part of fluoresced light is highly scattered within leaves, unlike red Chl fluorescence, which is mostly reabsorbed. While total FY can be …

Photoprotection dynamics observed at leaf level from fast temporal reflectance changes

Vegetation dynamically reacts to the available photosynthetically active radiation (PAR) by adjusting the photosynthetic apparatus to either a light harvesting or a photoprotective modus. When activating the photoprotection mechanism, either minor or major pigment-protein interactions may occur at the leaf level, resulting in different light absorption and consequently reflectance intensities. The reflectance changes were measured during sudden illumination transients designed to provoke fast adaptation to high irradiance. Different spectral reflectance change features were observed during different stages of photoprotection activation, extending over part of the visible spectral range (i.e…

Remote Estimation of Canopy Water Content in Different Crop Types with New Hyperspectral Indices

A diverse range of vegetation indices have earlier been developed for the remote estimation of canopy water content (CWC), but most of them are not universally applicable. The aim of this study is to define new indices valid for a wide variety of crop types, that allow to obtain CWC maps at a large spatial scale. These indices were developed based on PROSAIL simulations and then optimized with an experimental dataset (SPARC03; Barrax, Spain), which consists of field data including water content and other biophysical parameters collected for 6 different crops (lucerne, corn, potato, sugar beet, garlic and onion) and associated TOC reflectance spectra acquired by the HyMap airborne sensor. Sp…

A new opportunity for biomagnetic monitoring of particulate pollution in an urban environment using tree branches

Abstract: Environmental magnetism, and the magnetic leaf signal in particular, is amply investigated and applied as proxy for atmospheric particulate matter pollution. In this study, we investigated the magnetic signal of annual segments of tree branches, and the composition of particles deposited hereon. Branches are, contrary to leaves of deciduous trees, available during leaf-off seasons and exposed to air pollution year-round. We examined the intra- and inter-tree variation in saturation isothermal remanent magnetization (SIRM) of branch internodes of London plane (Platanus x aeerifolia Willd.) trees in an urban environment. The branch SIRM, normalized by surface area, ranged from 18 to…

Evaluation of Soil Organic Carbon Storage of Atillo in the Ecuadorian Andean Wetlands

Identifying the SOC levels and revealing the potential of SOC storage of ecosystems difficult to sample and study are necessary contributions to the understanding of the global reserves of SOC. Wetlands store large amounts of SOC within their soils. They have an important role in water regulation and have great biological and floristic diversity. Therefore, this study aimed to assess the SOC stock in Atillo micro-watershed in the Ecuadorian Andean wetlands at two soil depths (0–30 cm and 30–60 cm below ground) and to assess the importance of the ecosystem and its conservation in favor of reducing emissions due to degradation processes. For that, we sampled the study zone with 10…

Chlorophyll a fluorescence illuminates a path connecting plant molecular biology to Earth-system science

Remote sensing methods enable detection of solar-induced chlorophyll a fluorescence. However, to unleash the full potential of this signal, intensive cross-disciplinary work is required to harmonize biophysical and ecophysiological studies. For decades, the dynamic nature of chlorophyll a fluorescence (ChlaF) has provided insight into the biophysics and ecophysiology of the light reactions of photosynthesis from the subcellular to leaf scales. Recent advances in remote sensing methods enable detection of ChlaF induced by sunlight across a range of larger scales, from using instruments mounted on towers above plant canopies to Earth-orbiting satellites. This signal is referred to as solar-in…

In vivo photoprotection mechanisms observed from leaf spectral absorbance changes showing VIS–NIR slow-induced conformational pigment bed changes

Abstract Regulated heat dissipation under excessive light comprises a complexity of mechanisms, whereby the supramolecular light-harvesting pigment–protein complex (LHC) shifts state from light harvesting towards heat dissipation, quenching the excess of photo-induced excitation energy in a non-photochemical way. Based on whole-leaf spectroscopy measuring upward and downward spectral radiance fluxes, we studied spectrally contiguous (hyperspectral) transient time series of absorbance A(λ,t) and passively induced chlorophyll fluorescence F(λ,t) dynamics of intact leaves in the visible and near-infrared wavelengths (VIS–NIR, 400–800 nm) after sudden strong natural-like illumination exposure. …

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

Multi-sensor spectral synergies for crop stress detection and monitoring in the optical domain: A review

Remote detection and monitoring of the vegetation responses to stress became relevant for sustainable agriculture. Ongoing developments in optical remote sensing technologies have provided tools to increase our understanding of stress-related physiological processes. Therefore, this study aimed to provide an overview of the main spectral technologies and retrieval approaches for detecting crop stress in agriculture. Firstly, we present integrated views on: i) biotic and abiotic stress factors, the phases of stress, and respective plant responses, and ii) the affected traits, appropriate spectral domains and corresponding methods for measuring traits remotely. Secondly, representative result…

Leaf reflectance variation along a vertical crown gradient of two deciduous tree species in a Belgian industrial habitat

Abstract: The reflectometry of leaf asymmetry is a novel approach in the bio-monitoring of tree health in urban or industrial habitats. Leaf asymmetry responds to the degree of environmental pollution and reflects structural changes in a leaf due to environmental pollution. This paper describes the boundary conditions to scale up from leaf to canopy level reflectance, by describing the variability of adaxial and abaxial leaf reflectance, hence leaf asymmetry, along the crown height gradients of two tree species. Our findings open a research pathway towards bio-monitoring based on the airborne remote sensing of tree canopies and their leaf asymmetric properties. (C) 2015 Elsevier Ltd. All ri…

A field study on solar-induced chlorophyll fluorescence and pigment parameters along a vertical canopy gradient of four tree species in an urban environment

Abstract: To better understand the potential uses of vegetation indices based on the sun-induced upward and downward chlorophyll fluorescence at leaf and at canopy scales, a field study was carried out in the city of Valencia (Spain). Fluorescence yield (FY) indices were derived for trees at different traffic intensity locations and at three canopy heights. This allowed investigating within-tree and between-tree variations of FY indices for four tree species. Several FY indices showed a significant (p < 0.05) and important effect of tree location for the species Morus alba (white mulberry) and Phoenix canariensis (Canary Island date palm). The upward FY parameters of M. alba, and the upward…

Challenges in the atmospheric characterization for the retrieval of spectrally resolved fluorescence and PRI region dynamics from space

Abstract In the coming years, Earth Observation missions like the FLuorescence EXplorer (FLEX) will acquire the radiance signal from the visible to the near-infrared at a very high spectral resolution, enabling exciting prospects for new insights in satellite-based photosynthetic studies. In this context, the process of de-coupling atmospheric and vegetation-related spectral signatures will become essential to guarantee a reliable estimation of the vegetation photosynthetic activity from space. Dynamic changes related to the vegetation photosynthetic status result in subtle contributions to the top of atmosphere radiance signal, e.g. due to the emission of the solar-induced chlorophyll fluo…

A New Algorithm for the Retrieval of Sun Induced Chlorophyll Fluorescence of Water Bodies Exploiting the Detailed Spectral Shape of Water-Leaving Radiance

Sun induced chlorophyll fluorescence (SICF) emitted by phytoplankton provides considerable insights into the vital role of the carbon productivity of the earth’s aquatic ecosystems. However, the SICF signal leaving a water body is highly affected by the high spectral variability of its optically active constituents. To disentangle the SICF emission from the water-leaving radiance, a new high spectral resolution retrieval algorithm is presented, which significantly improves the fluorescence line height (FLH) method commonly used so far. The proposed algorithm retrieves the reflectance without SICF contribution by the extrapolation of the reflectance from the adjacent regions. Then, the SICF …

Improving the remote estimation of soil organic carbon in complex ecosystems with Sentinel-2 and GIS using Gaussian processes regression

Abstract Background and aims The quantitative retrieval of soil organic carbon (SOC) storage, particularly for soils with a large potential for carbon sequestration, is of global interest due to its link with the carbon cycle and the mitigation of climate change. However, complex ecosystems with good soil qualities for SOC storage are poorly studied. Methods The interrelation between SOC and various vegetation remote sensing drivers is understood to demonstrate the link between the carbon stored in the vegetation layer and SOC of the top soil layers. Based on the mapping of SOC in two horizons (0–30 cm and 30–60 cm) we predict SOC with high accuracy in the complex and mountainous heterogene…

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 spectru…

Multi-Crop Green LAI Estimation with a New Simple Sentinel-2 LAI Index (SeLI)

The spatial quantification of green leaf area index (LAIgreen), the total green photosynthetically active leaf area per ground area, is a crucial biophysical variable for agroecosystem monitoring. The Sentinel-2 mission is with (1) a temporal resolution lower than a week, (2) a spatial resolution of up to 10 m, and (3) narrow bands in the red and red-edge region, a highly promising mission for agricultural monitoring. The aim of this work is to define an easy implementable LAIgreen index for the Sentinel-2 mission. Two large and independent multi-crop datasets of in situ collected LAIgreen measurements were used. Commonly used LAIgreen indices applied on the Sentinel-2 10 m &times