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

Simulating solar-induced chlorophyll fluorescence in a boreal forest stand reconstructed from terrestrial laser scanning measurements

Solar-induced chlorophyll fluorescence (SIF) has been shown to be a suitable remote sensing proxy of photosynthesis at multiple scales. However, the relationship between fluorescence and photosynthesis observed at the leaf level cannot be directly applied to the interpretation of retrieved SIF due to the impact of canopy structure. We carried out a SIF modelling study for a heterogeneous forest canopy considering the effect of canopy structure in the Discrete Anisotropic Radiative Transfer (DART) model. A 3D forest simulation scene consisting of realistic trees and understory, including multi-scale clumping at branch and canopy level, was constructed from terrestrial laser scanning data using the combined model TreeQSM and FaNNI for woody structure and leaf insertion, respectively. Next, using empirical data and a realistic range of leaf-level biochemical and physiological parameters, we conducted a local sensitivity analysis to demonstrate the potential of the approach for assessing the impact of structural, biochemical and physiological factors on top of canopy (TOC) SIF. The analysis gave insight into the factors that drive the intensity and spectral properties of TOC SIF in heterogeneous boreal forest canopies. DART simulated red TOC fluorescence was found to be less affected by biochemical factors such as chlorophyll and dry matter contents or the senescent factor than far-red fluorescence. In contrast, canopy structural factors such as overstory leaf area index (LAI), leaf angle distribution and fractional cover had a substantial and comparable impact across all SIF wavelengths, with the exception of understory LAI that affected predominantly far-red fluorescence. Finally, variations in the fluorescence quantum efficiency (Fqe) of photosystem II affected all TOC SIF wavelengths. Our results also revealed that not only canopy structural factors but also understory fluorescence should be considered in the interpretation of tower, airborne and satellite SIF datasets, especially when acquired in the (near-) nadir viewing direction and for forests with open canopies. We suggest that the modelling strategy introduced in this study, coupled with the increasing availability of TLS and other 3D data sources, can be applied to resolve the interplay between physiological, biochemical and structural factors affecting SIF across ecosystems and independently of canopy complexity, paving the way for future SIF-based 3D photosynthesis models.Peer reviewe

Stress detection in conifer forest with high resolution hyperspectral and thermal remote sensing and radiative transfer modeling

Recently, widespread forest mortality related to drought or temperature stress has been described for drought-prone forests throughout the world. Long-term exposure of water stress to a combination of high light levels and temperatures causes a depression of photosynthesis and photosystem II efficiency that is not easily reversed even for resistant Mediterranean pines. Several authors have demonstrated that declining physiological status is connected with decline in chlorophyll content and with decreasing rate of photosynthesis; whereas the ratio C a+b/C x+c shows a decreasing trend. This thesis evaluates different physiological vegetation indices (SVI) at the canopy level and methods for the estimation of chlorophyll (C a+b) and carotenes (C x+c) pigment content with high spatial resolution sensors and radiative transfer models in heterogeneous conifer canopies. The objective is the early detection of decline processes based on the analysis of the trees physiological status and mapping of the major pigments regulating photosynthesis efficiency. Relationships between spectral vegetation indices and pigment content have been widely analyzed at the leaf level in previous works. However, studies were lacking where these kind of relationships were explored at the canopy level and for heterogeneous forest canopies. The heterogeneous forest canopies are more structurally complex than other vegetation types, therefore previous relationships obtained at the leaf level or on homogeneous canopies might not be applicable in a general way. Consequently, modelling work at leaf and canopy scales is needed to enable an operational use of SVI to map stress levels in non-homogeneous canopies where structural variation plays the main role in the reflectance signature. New formulations of SVI related to Cx+c and xanthophylls cicle were formulated based on radiative transfer simulation and experiemtal data and demonstrated to be more robust at the canopy level. A new modelling method is presented in this thesis based on scalingup methods to estimate Ca+b and Cx+c pigment concentration. The methodology has been tested in two conifer species: Pinus sylvestris and Pinus nigra. This study required extensive field measurements of biophysical paremeters of the canopy, leaf optical and biochemistry laboratory analysis, as well as analysis of highperspectral airborne imagery acquired by a sensor on board and unmanned aerial vehicle (UAV). Moreover, the use of radiative transfer models allowed the evaluation of the influence of different biophysical paramenters; at the leaf level, such us Ca+b and Cx+c as well as the relation between them,and at the canopy level, such as Leaf Area Index (LAI) or tree density.En los últimos años se han descrito procesos de mortalidad en distintos tipos de bosques en todo el mundo, siendo una de las causas más importantes el estrés hídrico y térmico. La exposición a largo plazo de estrés hídrico combinado con altos niveles de radiación y altas temperaturas provoca una depresión de la fotosíntesis y la eficiencia del fotosistema II, que no es fácilmente reversible incluso para especies vegetales resistentes a este tipo de ambientes como las coníferas mediterráneas. Varios autores han demostrado que el estado de estrés fisiológico está relacionado con la disminución en el contenido de clorofila y de la fotosintésis, mientras que la proporción de C a+b / Cx +c muestra una tendencia decreciente. Esta tesis evalúa diferentes índices de vegetación fisiológicos (SVI) a nivel de la cubierta y para la estimación del contenido de clorofila (C a + b) y carotenos (C x + c) con sensores de alta resolución espacial y modelos de transferencia radiativa en bosques de coníferas. El objetivo es la detección temprana de los procesos de decaimiento basados en el análisis del estado fisiológico de los árboles y la cartografía del contenido de los principales pigmentos que regulan la eficiencia de la fotosíntesis. Las relaciones entre los índices espectrales de vegetación y contenido de pigmentos han sido ampliamente analizadas a nivel de hoja en trabajo anteriores. Sin embargo, existe una carencia de conocimiento de este tipo de relaciones a nivel de cubierta, y más concretamente aplicado a doseles de vegetación heterogéneos como los bosques de coníferas. Los doseles en este tipo de masas son estructuralmente más complejos que otros tipos de vegetación, por lo tanto, las relaciones derivadas a nivel de hoja o de cubierta homogénea no se pueden aplicar de una manera generalizada. En consecuencia, la modelización a escala de la hoja y de cubierta es necesaria para permitir un uso operativo de SVI que permitan determinar los niveles de estrés en cubiertas no homogéneos, donde la variación estructural tiene gran efecto sobre la firma espectral de la cubierta. Este trabajo presenta nuevas formulaciones de SVI relacionados con Cx+c y ciclo de las xantofilas (VAZ) obtenidas a partir de la simulación con modelos de transferencia radiativa y datos experimentales, demostrando la fiabilidad de dichas formulaciones a nivel de cubierta. La metodología ha sido probada en dos especies de coníferas mediterráneas: Pinus sylvestris y Pinus nigra. Este estudio ha requerido mediciones de parámentros biofísicos en campo, análisis ópticos y bioquímicos foliares de laboratorio, así como el análisis de imágenes hiperespectrales adquiridas en plataformas tripuladas y de vehículos aéreos no tripulados (UAV)

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

Optické vlastnosti listu ve vztahu k anatomickým vlastnostem listu

K předpovědi reakcí ekosystémů na faktory prostředí se běžně používají funkční znaky rostlin na úrovni listu, popisující projevy globálních změn klimatu na úrovni ekosystémů. Mezi funkční znaky rostlin řadíme jak biofyzikální vlastnosti listu (např. obsah fotosyntetických pigmentů a obsahu vody) tak jeho strukturní vlastnosti (např. tloušťka listu a poměr fotosyntetických a nefotosyntetických pletiv listu). Biofyzikální a strukturní vlastnosti listu je možné zjišťovat buď destruktivně v laboratoři, nebo nedestruktivně s využitím optických vlastností listu. Ačkoli je odhadování obsahu chlorofylu na základě optických vlastností listů dobře zavedenou metodou, vliv struktury a vnitřní anatomie listů na jejich optické vlastnosti je důkladně studován teprve v posledních dvou dekádách. Publikace zahrnuté v mé práci a většina práce je věnována evropským opadavým dřevinám, typickým pro temperátní a hemiboreální lesy s listy vykazujícími podobnou dorziventrální strukturu, (tj. mezofyl je diferencován na palisádový a houbovitý parenchym). Dále má disertační práce zahrnuje studii vlivu strukturních znaků povrchu listů dvou skupin bylin na jejich optické vlastnosti. V této studii byly použity dvě skupiny fylogeneticky blízkých bylin se srovnatelnou vnitřní strukturou listů (mutanty Arabidopsis thaliana L. a...Plant functional traits at the leaf level are commonly used to predict ecosystem responses to environmental factors and describe global climate change processes at the ecosystem level. Plant functional traits include both leaf biophysical traits (e.g., photosynthetic pigment content and water content) and structural traits (e.g., leaf thickness and proportion of photosynthetic and non-photosynthetic tissues). Leaf biophysical and structural traits can be detected either destructively in the laboratory or non-destructively using leaf optical properties. Although estimating chlorophyll content from leaf optical properties is a well-established methodology, the influence of leaf structure and internal anatomy on leaf optical properties has only been thoroughly studied in the last two decades. The papers included in my thesis and my thesis itself are mostly focused on the study of typical European deciduous trees of temperate and hemiboreal forests with leaves having a dorsiventral structure (i.e., the mesophyll is differentiated into palisade and spongy parenchyma). Furthermore, my thesis includes a study on the effect of leaf surface structural traits on optical properties. In this study, two groups of phylogenetically close herbs with comparable internal leaf structure were used (mutants of...Department of Experimental Plant BiologyKatedra experimentální biologie rostlinFaculty of SciencePřírodovědecká fakult

Remote Sensing of Plant Biodiversity

This Open Access volume aims to methodologically improve our understanding of biodiversity by linking disciplines that incorporate remote sensing, and uniting data and perspectives in the fields of biology, landscape ecology, and geography. The book provides a framework for how biodiversity can be detected and evaluated—focusing particularly on plants—using proximal and remotely sensed hyperspectral data and other tools such as LiDAR. The volume, whose chapters bring together a large cross-section of the biodiversity community engaged in these methods, attempts to establish a common language across disciplines for understanding and implementing remote sensing of biodiversity across scales. The first part of the book offers a potential basis for remote detection of biodiversity. An overview of the nature of biodiversity is described, along with ways for determining traits of plant biodiversity through spectral analyses across spatial scales and linking spectral data to the tree of life. The second part details what can be detected spectrally and remotely. Specific instrumentation and technologies are described, as well as the technical challenges of detection and data synthesis, collection and processing. The third part discusses spatial resolution and integration across scales and ends with a vision for developing a global biodiversity monitoring system. Topics include spectral and functional variation across habitats and biomes, biodiversity variables for global scale assessment, and the prospects and pitfalls in remote sensing of biodiversity at the global scale

Remote Sensing of Plant Biodiversity

At last, here it is. For some time now, the world has needed a text providing both a new theoretical foundation and practical guidance on how to approach the challenge of biodiversity decline in the Anthropocene. This is a global challenge demanding global approaches to understand its scope and implications. Until recently, we have simply lacked the tools to do so. We are now entering an era in which we can realistically begin to understand and monitor the multidimensional phenomenon of biodiversity at a planetary scale. This era builds upon three centuries of scientific research on biodiversity at site to landscape levels, augmented over the past two decades by airborne research platforms carrying spectrometers, lidars, and radars for larger-scale observations. Emerging international networks of fine-grain in-situ biodiversity observations complemented by space-based sensors offering coarser-grain imagery—but global coverage—of ecosystem composition, function, and structure together provide the information necessary to monitor and track change in biodiversity globally. This book is a road map on how to observe and interpret terrestrial biodiversity across scales through plants—primary producers and the foundation of the trophic pyramid. It honors the fact that biodiversity exists across different dimensions, including both phylogenetic and functional. Then, it relates these aspects of biodiversity to another dimension, the spectral diversity captured by remote sensing instruments operating at scales from leaf to canopy to biome. The biodiversity community has needed a Rosetta Stone to translate between the language of satellite remote sensing and its resulting spectral diversity and the languages of those exploring the phylogenetic diversity and functional trait diversity of life on Earth. By assembling the vital translation, this volume has globalized our ability to track biodiversity state and change. Thus, a global problem meets a key component of the global solution. The editors have cleverly built the book in three parts. Part 1 addresses the theory behind the remote sensing of terrestrial plant biodiversity: why spectral diversity relates to plant functional traits and phylogenetic diversity. Starting with first principles, it connects plant biochemistry, physiology, and macroecology to remotely sensed spectra and explores the processes behind the patterns we observe. Examples from the field demonstrate the rising synthesis of multiple disciplines to create a new cross-spatial and spectral science of biodiversity. Part 2 discusses how to implement this evolving science. It focuses on the plethora of novel in-situ, airborne, and spaceborne Earth observation tools currently and soon to be available while also incorporating the ways of actually making biodiversity measurements with these tools. It includes instructions for organizing and conducting a field campaign. Throughout, there is a focus on the burgeoning field of imaging spectroscopy, which is revolutionizing our ability to characterize life remotely. Part 3 takes on an overarching issue for any effort to globalize biodiversity observations, the issue of scale. It addresses scale from two perspectives. The first is that of combining observations across varying spatial, temporal, and spectral resolutions for better understanding—that is, what scales and how. This is an area of ongoing research driven by a confluence of innovations in observation systems and rising computational capacity. The second is the organizational side of the scaling challenge. It explores existing frameworks for integrating multi-scale observations within global networks. The focus here is on what practical steps can be taken to organize multi-scale data and what is already happening in this regard. These frameworks include essential biodiversity variables and the Group on Earth Observations Biodiversity Observation Network (GEO BON). This book constitutes an end-to-end guide uniting the latest in research and techniques to cover the theory and practice of the remote sensing of plant biodiversity. In putting it together, the editors and their coauthors, all preeminent in their fields, have done a great service for those seeking to understand and conserve life on Earth—just when we need it most. For if the world is ever to construct a coordinated response to the planetwide crisis of biodiversity loss, it must first assemble adequate—and global—measures of what we are losing