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Estimating vegetation traits of mediterranean open canopies using imaging spectroscopy
Abstract
Due to increasing climatic and anthropic pressures, the Mediterranean ecoregions, that are recognized plant biodiversity hotspots, are some of the most endangered ecosystems. Airborne and satellite remote sensing methods, which can provide information about large landscapes in a regular fashion, are most adapted for a future global monitoring. However, difficulties arise when retrieving information from open forests, largely distributed in the Mediterranean-climate regions, as the contribution of tree crowns to the measured radiative signal is limited. This thesis aims at developing method for the estimation of vegetation traits of open canopies, when field knowledge is insufficient to calibrate regression models. Initially, 18 m GSD airborne hyperspectral images were considered. First, using the DART model, a simplified modeling, with a flat lambertian ground and ellipsoidal tree crowns, was identified as suitable for physically-based estimations of LAI and leaf pigment contents. Then, exploratory works were undertaken to identify a method to estimate EWT and LMA with acceptable accuracy, first by considering refinements in the sampling schemes, then by assessing the effects of the 3D modeling on trees' radiative behavior. Finally, the findings were used to estimate all multiple vegetation traits (gap fraction, leaf chlorophyll and carotenoid contents, EWT, LMA) from synthetic hyperspectral satellite images at 8 an 30 m GSD using a hybrid method. This thesis had demonstrated that physically-based and hybrid methods were adequate for the estimation of multiple canopy and leaf traits from hyperspectral satellite images of open canopies in an operational context, using little if any a priori knowledge. To consolidate the results, efforts are required to test the methods over more various sites that would present a higher diversity in terms of traits, trait variation ranges, or species. Moreover, identifying methods that would work for periods during which the understory is photosynthetically active would be necessary to allow for a global monitoring over the complete annual phenological cycle.
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Equivalent water thickness (EWT) and leaf mass per area (LMA) are important indicators of plant processes, such as photosynthetic and potential growth rates and health status, and are also important variables for fire risk assessment. Retrieving these traits through remote sensing is challenging and often requires calibration with in situ measurements to provide acceptable results. However, calibration data cannot be expected to be available at the operational level when estimating EWT and LMA over large regions. In this study, we assessed the ability of a hybrid retrieval method, consisting of training a random forest regressor (RFR) over the outputs of the discrete anisotropic radiative transfer (DART) model, to yield accurate EWT and LMA estimates depending on the scene modeling within DART and the spectral interval considered. We show that canopy abstractions mostly affect crown reflectance over the 0.75–1.3 μm range. It was observed that excluding these wavelengths when training the RFR resulted in the abstraction level having no effect on the subsequent LMA estimates (RMSE of 0.0019 g/cm2 for both the detailed and abstract models), and EWT estimates were not affected by the level of abstraction. Over AVIRIS-Next Generation images, we showed that the hybrid method trained with a simplified scene obtained accuracies (RMSE of 0.0029 and 0.0028 g/cm2 for LMA and EWT) consistent with what had been obtained from the test dataset of the calibration phase (RMSE of 0.0031 and 0.0032 g/cm2 for LMA and EWT), and the result yielded spatially coherent maps. The results demonstrate that, provided an appropriate spectral domain is used, the uncertainties inherent to the abstract modeling of tree crowns within an RTM do not significantly affect EWT and LMA accuracy estimates when tree crowns can be identified in the images.
Forest extent mapping is required for climate modeling and monitoring changes in ecosystem state. Different global land cover (LC) products employ simple tree cover (referred also as “forest cover” or even “vegetation cover”) definitions to differentiate forests from non-forests. Since 1990, a large number of forest extent maps have become available. Although many studies have compared forest extent data, they often use old data (i.e., around the year 2000). In this study, we assessed tree cover representations of three different annual, global LC products (MODIS VCF (MOD44B, Collection 6 (C6)), MCD12Q1 (C6), and CCI LC (v.2.1.1)) using the Finnish Multi-Source National Forest Inventory (MS-NFI) data for the year 2017. In addition, we present an intercomparison approach for analyzing spatial representations of coniferous and deciduous species. Intercomparison of different LC products is often overlooked due to challenges involved in non-standard and overlapping LC class definitions. Global LC products are used for monitoring changes in land use and land cover and modeling of surface fluxes. Given that LC is a major driver of global change through modifiers such as land surface albedo, more attention should be paid to spatial mapping of coniferous and deciduous species. Our results show that tree cover was either overestimated or underestimated depending on the LC product, and classification accuracy varied between 42 and 75%. Intercomparison of the LC products showed large differences in conifer and deciduous species spatial distributions. Spatial mapping of coniferous and deciduous tree covers was the best represented by the CCI LC product as compared with the reference MS-NFI data.
The PROSPECT and PROSAIL family of radiative transfer models (RTMs) are among the most popular for simulating vegetation spectra and estimating vegetation properties at the leaf and canopy levels. However, the main limitation of the radiative transfer model approach is that model performance depends on the exhaustiveness of the calibration database(s). The PROSPECT model was calibrated mainly with photosynthetic leaves, and thus does not contain specific absorption coefficients of decay pigments responsible for the spectral behavior of non-photosynthetic vegetation. Hence, PROSPECT and PROSAIL may be ill-suited to mixed ecosystems (e.g., grasslands and wetlands), especially in the late growing season when the non-photosynthetic vegetation is likely to obfuscate the quantification of green vegetation. This study investigates the performance of different versions of PROSPECT/PROSAIL models for simulating spectra and estimating biophysical properties of photosynthetic and non-photosynthetic vegetation, and aims to better understand the limitations of these RTMs and identify possible ways to improve their performance. Results show that the PROSPECT-5 and PROSPECT-D had challenges in simulating spectra of non-photosynthetic leaves in a mixed grassland area, while a modified version (PROSPECT-5M) that considered the absorption effects of decay pigments achieved higher accuracy (e.g., mean Root Mean Square Error (RMSE) of 0.014 compared to 0.026 for the PROSPECT-5). In comparison, there is minimal difference in RMSE between models for simulating green photosynthetic leaves. At the canopy level, the original PROSAIL model simulated the spectra well for homogeneous green canopies (with mean RMSE around 0.012), while a modified PROSAIL model simulated the spectra more accurately for mixed canopies that have photosynthetic and non-photosynthetic leaves (e.g., with a mean RMSE of 0.010 compared to 0.020 of original PROSAIL). The original and modified PROSAIL were then inverted using helicopter-based high-spatial resolution hyperspectral imagery to estimate vegetation properties, and achieved higher accuracies for green and mixed canopies, respectively (e.g., estimating canopy chlorophyll with R² values over 0.75). Overall, different versions of PROSPECT/PROSAIL models have a varied performance for photosynthetic and non-photosynthetic vegetation. Understanding the limitations of the models and adopting corresponding measures to improve their performance is critical for successful applications of RTMs in the estimation of vegetation spectral and biophysical properties.
Models of radiative transfer (RT) are important tools for remote sensing of vegetation, allowing for forward simulations of remotely sensed data as well as inverse estimation of biophysical and biochemical traits from vegetation optical properties. Estimation of foliar protein content is the key to monitor the nitrogen cycle in terrestrial ecosystems, in particular to assess the photosynthetic capacity of plants and to improve nitrogen management in agriculture. However, until now physically based leaf RT models have not allowed for proper spectral decomposition and estimation of leaf dry matter as nitrogen-based proteins and other carbon-based constituents (CBC) from optical properties of fresh and dry foliage. Such an achievement is the key for subsequent upscaling to canopy level and for development of new Earth observation applications.
Therefore, we developed a new version of the PROSPECT model, named PROSPECT-PRO, which separates the nitrogen-based constituents (proteins) from CBC (including cellulose, lignin, hemicellulose, starch and sugars). PROSPECT-PRO was calibrated and validated on subsets of the LOPEX dataset, accounting for both fresh and dry broadleaf and grass samples. We applied an iterative model inversion optimization algorithm and identified the optimal spectral ranges for retrieval of proteins and CBC. When combining leaf reflectance and transmittance within the selected optimal spectral domains, PROSPECT-PRO inversions revealed similarly accurate CBC estimates of fresh and dry leaf samples (respective validation R2 = 0.96 and 0.95, NRMSE = 9.6% and 13.4%), whereas a better performance was obtained for fresh than for dry leaves when estimating proteins (respective validation R2 = 0.79 and 0.57, NRMSE = 15.1% and 26.1%). The accurate estimation of leaf constituents for fresh samples is attributed to the optimal spectral feature selection procedure.
We further tested the ability of PROSPECT-PRO to estimate leaf mass per area (LMA) as the sum of proteins and CBC using independent datasets acquired for numerous plant species. Results showed that both PROSPECT-PRO and PROSPECT-D inversions were able to produce comparable LMA estimates across an independent dataset gathering 1685 leaf samples (validation R2 = 0.90 and NRMSE = 16.5% for PROSPECT-PRO, and R2 = 0.90 and NRMSE = 18.3% for PROSPECT-D). Findings also revealed that PROSPECT-PRO is capable of assessing the carbon-to-nitrogen ratio based on the retrieved CBC-to-proteins ratio (R2 = 0.87 and NRMSE = 15.7% for fresh leaves, and R2 = 0.65 and NRMSE = 28.1% for dry leaves). The performance assessment of newly designed PROSPECT-PRO demonstrates a promising potential for its involvement in precision agriculture and ecological applications aiming at estimation of leaf carbon and nitrogen contents from observations of current and forthcoming airborne and satellite imaging spectroscopy sensors.
Advances in high-performance computer resources and exploitation of high-density terrestrial laser scanning (TLS) data allow for reconstruction of close-to-reality 3D forest scenes for use in canopy radiative transfer models. Consequently, our main objectives were (i) to reconstruct 3D representation of Norway spruce (Picea abies) trees by deriving distribution of woody and foliage elements from TLS and field structure data and (ii) to use the reconstructed 3D spruce representations for evaluation of the effects of canopy structure on forest reflectance simulated in the Discrete Anisotropic Radiative Transfer (DART) model. Data for this study were combined from two spruce research sites located in the mountainous areas of the Czech Republic. The canopy structure effects on simulated top-of-canopy reflectance were evaluated for four scenarios (10 × 10 m scenes with 10 trees), ranging from geometrically simple to highly detailed architectures. First scenario A used predefined simple tree crown shapes filled with a turbid medium with simplified trunks and branches. Other three scenarios used the reconstructed 3D spruce representations with B detailed needle shoots transformed into turbid medium, C with simplified shoots retained as facets, and D with detailed needle shoots retained as facets D. For the first time, we demonstrated the capability of the DART model to simulate reflectance of complex coniferous forest scenes up to the level of a single needle (scenario D). Simulated bidirectional reflectance factors extracted for each scenario were compared with actual airborne hyperspectral and space-borne Sentinel-2 MSI reflectance data. Scenario A yielded the largest differences from the remote sensing observations, mainly in the visible and NIR regions, whereas scenarios B, C, and D produced similar results revealing a good agreement with the remote sensing data. When judging the computational requirements for reflectance simulations in DART, scenario B can be considered as most operational spruce forest representation, because the transformation of 3D shoots in turbid medium reduces considerably the simulation time and hardware requirements.
Gap Fraction, leaf pigment contents (content of chlorophylls a and b (Cab) and carotenoids content (Car)), Leaf Mass per Area (LMA), and Equivalent Water Thickness (EWT) are considered relevant indicators of forests’ health status, influencing many biological and physical processes. Various methods exist to estimate these variables, often relying on the extensive use of Radiation Transfer Models (RTMs). While 3D RTMs are more realistic to model open canopies, their complexity leads to important computation times that limit the number of simulations that can be considered; 1D RTMs, although less realistic, are also less computationally expensive. We investigated the possibility to approximate the outputs of a 3D RTM (DART) from a 1D RTM (PROSAIL) to generate in very short time numerous extensive Look-Up Tables (LUTs). The intrinsic error of the approximation model was evaluated through comparison with DART reference values. The model was then used to generate LUTs used to estimate Gap Fraction, Cab, Car, EWT, and LMA of Blue Oak-dominant stands in a woodland savanna from AVIRIS-C data. Performances of the approximation model for estimation purposes compared to DART were evaluated using Wilmott’s index of agreement (dr), and estimation accuracy was measured with coefficients of determination (R2) and Root Mean Squared Error (RMSE). The low approximation error of the proposed model demonstrated that the model could be considered for canopy covers as low as 30%. Gap Fraction estimations presented similar performances with either DART or the approximation (dr 0.78 and 0.77, respectively), while Cab and Car showed improved performances (dr increasing from 0.65 to 0.77 and 0.34 to 0.65, respectively). No satisfying estimation methods were found for LMA and EWT using either models, probably due to the high sensitivity of the scene’s reflectance to Gap Fraction and soil modeling at such low LAI. Overall, estimations using the approximated reflectances presented either similar or improved accuracy. Our findings show that it is possible to approximate DART reflectances from PROSAIL using a minimal number of DART outputs for calibration purposes, drastically reducing computation times to generate reflectance databases: 300,000 entries could be generated in 1.5 h, compared to the 12,666 total CPU hours necessary to generate the 21,840 calibration entries with DART.
The European Space Agency (ESA)’s Sentinel-2A (S2A) mission is providing time series that allow the characterisation of dynamic vegetation, especially when combined with the National Aeronautics and Space Administration (NASA)/United States Geological Survey (USGS) Landsat 7 (L7) and Landsat 8 (L8) missions. Hybrid retrieval workflows combining non-parametric Machine Learning Regression Algorithms (MLRAs) and vegetation Radiative Transfer Models (RTMs) were proposed as fast and accurate methods to infer biophysical parameters such as Leaf Area Index (LAI) from these data streams. However, the exact design of optimal retrieval workflows is rarely discussed. In this study, the impact of five retrieval workflow features on LAI prediction performance of MultiSpectral Instrument (MSI), Enhanced Thematic Mapper Plus (ETM+) and Operational Land Imager (OLI) observations was analysed over a Dutch beech forest site for a one-year period. The retrieval workflow features were the (1) addition of prior knowledge of leaf chemistry (two alternatives), (2) the choice of RTM (two alternatives), (3) the addition of Gaussian noise to RTM produced training data (four and five alternatives), (4) possibility of using Sun Zenith Angle (SZA) as an additional MLRA training feature (two alternatives), and (5) the choice of MLRA (six alternatives). The features were varied in a full grid resulting in 960 inversion models in order to find the overall impact on performance as well as possible interactions among the features. A combination of a Terrestrial Laser Scanning (TLS) time series with litter-trap derived LAI served as independent validation. The addition of absolute noise had the most significant impact on prediction performance. It improved the median prediction Root Mean Square Error (RMSE) by 1.08 m2 m−2 when 5% noise was added compared to inversions with 0% absolute noise. The choice of the MLRA was second most important in terms of median prediction performance, which differed by 0.52 m2 m−2 between the best and worst model. The best inversion model achieved an RMSE of 0.91 m2 m−2 and explained 84.9% of the variance of the reference time series. The results underline the need to explicitly describe the used noise model in future studies. Similar studies should be conducted in other study areas, both forest and crop systems, in order to test the noise model as an integral part of hybrid retrieval workflows.
Leaf pigment contents, such as chlorophylls a and b content (C a b ) or carotenoid content (Car), and the leaf area index (LAI) are recognized indicators of plants’ and forests’ health status that can be estimated through hyperspectral imagery. Their measurement on a seasonal and yearly basis is critical to monitor plant response and adaptation to stress, such as droughts. While extensively done over dense canopies, estimation of these variables over tree-grass ecosystems with very low overstory LAI (mean site LAI < 1 m 2 /m 2 ), such as woodland savannas, is lacking. We investigated the use of look-up table (LUT)-based inversion of a radiative transfer model to retrieve LAI and leaf C a b and Car from AVIRIS images at an 18 m spatial resolution at multiple dates over a broadleaved woodland savanna during the California drought. We compared the performances of different cost functions in the inversion step. We demonstrated the spatial consistency of our LAI, C a b , and Car estimations using validation data from low and high canopy cover parts of the site, and their temporal consistency by qualitatively confronting their variations over two years with those that would be expected. We concluded that LUT-based inversions of medium-resolution hyperspectral images, achieved with a simple geometric representation of the canopy within a 3D radiative transfer model (RTM), are a valid means of monitoring woodland savannas and more generally sparse forests, although for maximum applicability, the inversion cost functions should be selected using validation data from multiple dates. Validation revealed that for monitoring use: the normalized difference vegetation index (NDVI) outperformed other indices for LAI estimations (root mean square error (RMSE) = 0.22 m 2 /m 2 , R 2 = 0.81); the band ratio ρ 0 . 750 μ m ρ 0 . 550 μ m retrieved C a b more accurately than other chlorophylls indices (RMSE = 5.94 μ g/cm 2 , R 2 = 0.75); RMSE over the 0.5–0.55 μ m interval showed encouraging results for Car estimations.
Leaf mass per area (LMA) is a key plant trait, reflecting tradeoffs between leaf photosynthetic function, longevity, and structural investment. Capturing spatial and temporal variability in LMA has been a long‐standing goal of ecological research and is an essential component for advancing Earth system models. Despite the substantial variation in LMA within and across Earth's biomes, an efficient, globally generalizable approach to predict LMA is still lacking.
We explored the capacity to predict LMA from leaf spectra across much of the global LMA trait space, with values ranging from 17 to 393 g m⁻². Our dataset contained leaves from a wide range of biomes from the high Arctic to the tropics, included broad‐ and needleleaf species, and upper‐ and lower‐canopy (i.e. sun and shade) growth environments.
Here we demonstrate the capacity to rapidly estimate LMA using only spectral measurements across a wide range of species, leaf age and canopy position from diverse biomes. Our model captures LMA variability with high accuracy and low error (R² = 0.89; root mean square error (RMSE) = 15.45 g m⁻²).
Our finding highlights the fact that the leaf economics spectrum is mirrored by the leaf optical spectrum, paving the way for this technology to predict the diversity of LMA in ecosystems across global biomes.
One of the main problems in the Mediterranean area is the long dry season, and hence there is a need to individuate plants that are tolerant to low water availability. The mechanisms adopted by different plant species to overcome drought stress conditions and reduce water loss could allow the identification of tolerant species to drought stress, thereby increasing the sustainability of ornamental plant utilization in green areas. In this regard, the aim of this study was to investigate the morphological, physiological, and anatomical responses of Polygala myrtifolia L. and Viburnum tinus L. ‘Lucidum’ irrigated under different irrigation deficits. In pot plants, four water regimes were adopted (10%, 20%, 30% and 40% of water container capacity (WC)). Drought stress significantly reduced the biomass accumulation in both shrubs. In Viburnum, total dry biomass reduction was observed only in 10% WC with a reduction by 33%, while in Polygala, this was observed both in 20% WC and 10% WC (~48%). The higher deficit irrigation conditions improve the root-to-shoot ratio, which was increased in Polygala 20% WC (by 20%) but not in Viburnum ones. The latter species shows higher drought tolerance, as demonstrated by the gas exchange values, chlorophyll fluorescence, leaf structure, and water relationship.
Widespread episodes of recent forest die-off have been tied to the occurrence of anomalously warm droughts, although the underlying mechanisms remain inadequately understood. California’s 2012–2015 drought, with exceptionally low precipitation and warmth, and widespread conifer death, provides an opportunity to explore the chain of events leading to forest die-off. Here, we present the spatial and temporal patterns of die-off and moisture deficit during California’s drought, based on field and remote sensing observations. We found that die-off was closely tied to multi-year deep-rooting-zone drying, and that this relationship provides a framework with which to diagnose and predict mortality. Marked tree death in an intensively studied Sierra Nevada forest followed a four-year moisture overdraft, with cumulative 2012–2015 evapotranspiration exceeding precipitation by ~1,500 mm, and subsurface moisture exhaustion to 5–15-m depth. Observations across the entire Sierra Nevada further linked tree death to deep drying, with die-off and moisture overdraft covarying across latitude and elevation. Unusually dense vegetation and warm temperatures accelerated southern Sierran evapotranspiration in 2012–2015, intensifying overdraft and compounding die-off by an estimated 55%. Climate change is expected to further amplify evapotranspiration and moisture overdraft during drought, potentially increasing Sierran tree death during drought by ~15–20% °C⁻¹.
Spectroscopy is becoming an increasingly powerful tool to alleviate the challenges of traditional measurements of key plant traits at the leaf, canopy, and ecosystem scales. Spectroscopic methods often rely on statistical approaches to reduce data redundancy and enhance useful prediction of physiological traits. Given the mechanistic uncertainty of spectroscopic techniques, genetic modification of plant biochemical pathways may affect reflectance spectra causing predictive models to lose power. The objectives of this research were to assess over two separate years, whether a predictive model can represent natural and imposed variation in leaf photosynthetic potential for different crop cultivars and genetically modified plants, to assess the interannual capabilities of a partial least square regression (PLSR) model, and to determine whether leaf N is a dominant driver of photosynthesis in PLSR models. In 2016, a PLSR analysis of reflectance spectra coupled with gas exchange data was used to build predictive models for photosynthetic parameters including maximum carboxylation rate of Rubisco (Vc,max ), maximum electron transport rate (J
max
) and percentage leaf nitrogen ([N]). The model was developed for wild type and genetically modified plants that represent a wide range of photosynthetic capacities. Results show that hyperspectral reflectance accurately predicted Vc,max, J
max
and [N] for all plants measured in 2016. Applying these PLSR models to plants grown in 2017 resulted in a strong predictive ability relative to gas exchange measurements for Vc,max, but not for Jmax, and not for genotypes unique to 2017. Building a new model including data collected in 2017 resulted in more robust predictions, with R2 increases of 17% for Vc,max . and 13% J
max
. Plants generally have a positive correlation between leaf nitrogen and photosynthesis, however, tobacco with reduced Rubisco (SSuD) had significantly higher [N] despite much lower Vc,max. The PLSR model was able to accurately predict both lower Vc,max and higher leaf [N] for this genotype suggesting that the spectral based estimates of Vc,max and leaf nitrogen [N] are independent. These results suggest that the PLSR model can be applied across years, but only to genotypes used to build the model and that the actual mechanism measured with the PLSR technique is not directly related to leaf [N]. The success of the leaf-scale analysis suggests that similar approaches may be successful at the canopy and ecosystem scales but to use these methods across years and between genotypes at any scale, application of accurately populated physical based models based on radiative transfer principles may be required.
Leaf area index (LAI) is a critical vegetation structural variable and is essential in the feedback of vegetation to the climate system. The advancement of the global Earth Observation has enabled the development of global LAI products and boosted global Earth system modeling studies. This overview provides a comprehensive analysis of LAI field measurements and remote sensing estimation methods, the product validation methods and product uncertainties, and the application of LAI in global studies. First, the paper clarifies some definitions related to LAI and introduces methods to determine LAI from field measurements and remote sensing observations. After introducing some major global LAI products, progresses made in temporal compositing and prospects for future LAI estimation are analyzed. Subsequently, the overview discusses various LAI product validation schemes, uncertainties in global moderate resolution LAI products, and high resolution reference data. Finally, applications of LAI in global vegetation change, land surface modeling, and agricultural studies are presented. It is recommended that (1) continued efforts are taken to advance LAI estimation algorithms and provide high temporal and spatial resolution products from current and forthcoming missions; (2) further validation studies be conducted to address the inadequacy of current validation studies, especially for underrepresented regions and seasons; and (3) new research frontiers, such as machine learning algorithms, light detection and ranging technology, and unmanned aerial vehicles be pursued to broaden the production and application of LAI.
Species distributions and abundances are undergoing rapid changes worldwide. This highlights the significance of reliable, integrated information for guiding and assessing actions and policies aimed at managing and sustaining the many functions and benefits of species. Here we synthesize the types of data and approaches that are required to achieve such an integration and conceptualize ‘essential biodiversity variables’ (EBVs) for a unified global capture of species populations in space and time. The inherent heterogeneity and sparseness of raw biodiversity data are overcome by the use of models and remotely sensed covariates to inform predictions that are contiguous in space and time and global in extent. We define the species population EBVs as a space–time–species–gram (cube) that simultaneously addresses the distribution or abundance of multiple species, with its resolution adjusted to represent available evidence and acceptable levels of uncertainty. This essential information enables the monitoring of single or aggregate spatial or taxonomic units at scales relevant to research and decision-making. When combined with ancillary environmental or species data, this fundamental species population information directly underpins a range of biodiversity and ecosystem function indicators. The unified concept we present links disparate data to downstream uses and informs a vision for species population monitoring in which data collection is closely integrated with models and infrastructure to support effective biodiversity assessment.
Healthy vegetation function supports diverse biological communities and ecosystem processes, and provides crops, forest products, forage, and countless other benefits. Vegetation function can be assessed by examining dynamic processes and by evaluating plant traits, which themselves are dynamic. Using both trait-based and process-based approaches, spectroscopy can assess vegetation function at multiple scales using a variety of sensors and platforms ranging from proximal to airborne and satellite measurements. Since spectroscopic data are defined by the instruments and platforms available, along with their corresponding spatial, temporal and spectral scales, and since these scales may not always match those of the function of interest, consideration of scale is a necessary focus. For a full understanding of vegetation processes, combined (multi-scale) sampling methods using empirical and theoretical approaches are required, along with improved informatics.
With the advent of Sentinel-2, it is now possible to generate large-scale chlorophyll content maps with unprecedented spatial and temporal resolution, suitable for monitoring ecological processes such as vegetative stress and/or decline. However methodological gaps exist for adapting this technology to heterogeneous natural vegetation and for transferring it among vegetation species or plan functional types. In this study, we investigated the use of Sentinel-2A imagery for estimating needle chlorophyll (Ca+b) in a sparse pine forest undergoing significant needle loss and tree mortality. Sentinel-2A scenes were acquired under two extreme viewing geometries (June vs. December 2016) coincident with the acquisition of high-spatial resolution hyperspectral imagery, and field measurements of needle chlorophyll content and crown leaf area index. Using the high-resolution hyperspectral scenes acquired over 61 validation sites we found the CI chlorophyll index R750/R710 and Macc index (which uses spectral bands centered at 680 nm, 710 nm and 780 nm) had the strongest relationship with needle chlorophyll content from individual tree crowns (r² = 0.61 and r² = 0.59, respectively; p < 0.001), while TCARI and TCARI/OSAVI, originally designed for uniform agricultural canopies, did not perform as well (r² = 0.21 and r² = 0.01, respectively). Using lower-resolution Sentinel-2A data validated against hyperspectral estimates and ground truth needle chlorophyll content, the red-edge index CI and the Sentinel-specific chlorophyll indices CI-Gitelson, NDRE1 and NDRE2 had the highest accuracy (with r² values >0.7 for June and >0.4 for December; p < 0.001). The retrieval of needle chlorophyll content from the entire Sentinel-2A bandset using the radiative transfer model INFORM yielded r² = 0.71 (RMSE = 8.1 μg/cm²) for June, r² = 0.42 (RMSE = 12.2 μg/cm²) for December, and r² = 0.6 (RMSE = 10.5 μg/cm²) as overall performance using the June and December datasets together. This study demonstrates the retrieval of leaf Ca+b with Sentinel-2A imagery by red-edge indices and by an inversion method based on a hybrid canopy reflectance model that accounts for tree density, background and shadow components common in sparse forest canopies.
The emerging challenges in preserving and managing forest ecosystems are multiscale in terms of space and time, and therefore require spatially and temporally contiguous information sources. Imaging spectroscopy has the potential to contribute information that cannot be raised by other Earth Observation Systems. In particular, the spectral capacity to monitor the distributions of chemical traits, such as canopy foliar nitrogen distribution, and to track changes in water content or the percentage water in plants, has already opened novel pathways toward assessing the global variability of ecosystem functions and services. However, there is an ongoing debate on how to best extract this type of information from the spectral measurements. Empirical approaches have demonstrated their efficiency in a multitude of local studies, but are criticized with respect to poor generalization capacities. Alternative strategies, such as the use of physically based models of leaf or canopy reflectance, or hybrid approaches, have the potential advantage to be more widely applicable. This paper attempts to assess achievements and shortcomings of these strategies and finds that the often-cited disadvantages of using empirical approaches are becoming less pronounced in the light of recent research results. While retrievals based on physically based models on leaf/needle level are close to laboratory quality, results on canopy level available to date still have considerable deficits. Owing to improved instrumental designs, better data calibration, new approaches for compensating canopy effects, and the use of increasingly efficient methods for establishing data-driven models, the scope of empirical approaches has considerably widened and they have been successfully applied to large areas. The future availability of regularly acquired hyperspectral imagery from Earth orbits will substantially contribute to their generalizability.
Imaging spectroscopy, also known as hyperspectral remote sensing, is based on the characterization of Earth surface materials and processes through spectrally-resolved measurements of the light interacting with matter. The potential of imaging spectroscopy for Earth remote sensing has been demonstrated since the 1980s. However, most of the developments and applications in imaging spectroscopy have largely relied on airborne spectrometers, as the amount and quality of space-based imaging spectroscopy data remain relatively low to date. The upcoming Environmental Mapping and Analysis Program (EnMAP) German imaging spectroscopy mission is intended to fill this gap. An overview of the main characteristics and current status of the mission is provided in this contribution. The core payload of EnMAP consists of a dual-spectrometer instrument measuring in the optical spectral range between 420 and 2450 nm with a spectral sampling distance varying between 5 and 12 nm and a reference signal-to-noise ratio of 400:1 in the visible and near-infrared and 180:1 in the shortwave-infrared parts of the spectrum. EnMAP images will cover a 30 km-wide area in the across-track direction with a ground sampling distance of 30 m. An across-track tilted observation capability will enable a target revisit time of up to four days at the Equator and better at high latitudes. EnMAP will contribute to the development and exploitation of spaceborne imaging spectroscopy applications by making high-quality data freely available to scientific users worldwide.
Quantitative equivalent water thickness on canopy level (EWTcanopy) is an important land surface variable and retrieving EWTcanopy from remote sensing has been targeted by many studies. However, the effect of radiative penetration into the canopy has not been fully understood. Therefore, in this study the Beer-Lambert law is applied to inversely determine water content information in the 930 to 1060 nm range of canopy reflectance from measured winter wheat and corn spectra collected in 2015, 2017, and 2018. The spectral model was calibrated using a look-up-table (LUT) of 50,000 PROSPECT spectra. Internal model validation was performed using two leaf optical properties datasets (LOPEX93 and ANGERS). Destructive in-situ measurements of water content were collected separately for leaves, stalks, and fruits. Correlation between measured and modelled water content was most promising for leaves and ears in case of wheat, reaching coefficients of determination (R2) up to 0.72 and relative RMSE (rRMSE) of 26% and in case of corn for the leaf fraction only (R2 = 0.86, rRMSE = 23%). These findings indicate that, depending on the crop type and its structure, different parts of the canopy are observed by optical sensors. The results from the Munich-North-Isar test sites indicated that plant compartment specific EWTcanopy allows us to deduce more information about the physical meaning of model results than from equivalent water thickness on leaf level (EWT) which is upscaled to canopy water content (CWC) by multiplication of the leaf area index (LAI). Therefore, it is suggested to collect EWTcanopy data and corresponding reflectance for different crop types over the entire growing cycle. Nevertheless, the calibrated model proved to be transferable in time and space and thus can be applied for fast and effective retrieval of EWTcanopy in the scope of future hyperspectral satellite missions.
Leaf mass per area (LMA) and leaf equivalent water thickness (EWT) are key leaf functional traits providing information for many applications including ecosystem functioning modeling and fire risk management. In this paper, we investigate two common conclusions generally made for LMA and EWT estimation based on leaf optical properties in the near-infrared (NIR) and shortwave infrared (SWIR) domains: (1) physically-based approaches estimate EWT accurately and LMA poorly, while (2) statistically-based and machine learning (ML) methods provide accurate estimates of both LMA and EWT.
Using six experimental datasets including broadleaf species samples of >150 species collected over tropical, temperate and boreal ecosystems, we compared the performances of a physically-based method (PROSPECT model inversion) and a ML algorithm (support vector machine regression, SVM) to infer EWT and LMA based on leaf reflectance and transmittance. We assessed several merit functions to invert PROSPECT based on iterative optimization and investigated the spectral domain to be used for optimal estimation of LMA and EWT. We also tested several strategies to select the training samples used by the SVM, in order to investigate the generalization ability of the derived regression models.
We evidenced that using spectral information from 1700 to 2400 nm leads to strong improvement in the estimation of EWT and LMA when performing a PROSPECT inversion, decreasing the LMA and EWT estimation errors by 55% and 33%, respectively.
The comparison of various sampling strategies for the training set used with SVM suggests that regression models show limited generalization ability, particularly when the regression model is applied on data fully independent from the training set. Finally, our results demonstrate that, when using an appropriate spectral domain, the PROSPECT inversion outperforms SVM trained with experimental data for the estimation of EWT and LMA. Thus we recommend that estimation of LMA and EWT based on leaf optical properties should be physically-based using inversion of reflectance and transmittance measurements on the 1700 to 2400 nm spectral range.
In the last few decades, researchers have developed a plethora of hyperspectral Earth Observation (EO) remote sensing techniques, analysis and applications. While hyperspectral exploratory sensors are demonstrating their potential, Sentinel-2 multispectral satellite remote sensing is now providing free, open, global and systematic high resolution visible and infrared imagery at a short revisit time. Its recent launch suggests potential synergies between multi- and hyper-spectral data. This study, therefore, reviews 20 years of research and applications in satellite hyperspectral remote sensing through the analysis of Earth observation hyperspectral sensors’ publications that cover the Sentinel-2 spectrum range: Hyperion, TianGong-1, PRISMA, HISUI, EnMAP, Shalom, HyspIRI and HypXIM. More specifically, this study (i) brings face to face past and future hyperspectral sensors’ applications with Sentinel-2’s and (ii) analyzes the applications’ requirements in terms of spatial and temporal resolutions. Eight main application topics were analyzed including vegetation, agriculture, soil, geology, urban, land use, water resources and disaster. Medium spatial resolution, long revisit time and low signal-to-noise ratio in the short-wave infrared of some hyperspectral sensors were highlighted as major limitations for some applications compared to the Sentinel-2 system. However, these constraints mainly concerned past hyperspectral sensors, while they will probably be overcome by forthcoming instruments. Therefore, this study is putting forward the compatibility of hyperspectral sensors and Sentinel-2 systems for resolution enhancement techniques in order to increase the panel of hyperspectral uses.
Upcoming satellite hyperspectral sensors require powerful and robust methodologies for making optimum use of the rich spectral data. This paper reviews the widely applied coupled PROSPECT and SAIL radiative transfer models (PROSAIL), regarding their suitability for the retrieval of biophysical and biochemical variables in the context of agricultural crop monitoring. Evaluation was carried out using a systematic literature review of 281 scientific publications with regard to their (i) spectral exploitation, (ii) vegetation type analyzed, (iii) variables retrieved, and (iv) choice of retrieval methods. From the analysis, current trends were derived, and problems identified and discussed. Our analysis clearly shows that the PROSAIL model is well suited for the analysis of imaging spectrometer data from future satellite missions and that the model should be integrated in appropriate software tools that are being developed in this context for agricultural applications. The review supports the decision of potential users to employ PROSAIL for their specific data analysis and provides guidelines for choosing between the diverse retrieval techniques.
Thin cirrus clouds frequently contaminate images acquired with either Landsat 7 ETM+ or the earlier generation of Landsat series satellite instruments. The situation has changed since the launch of the Landsat 8 Operational Land Imager (OLI) into space in 2013. OLI implemented a cirrus detecting channel (Band 9) centered within a strong atmospheric water vapor absorption band near 1.375 µm with a width of 30 nm. The specifications for this channel were the same as those specified for the NASA Moderate Resolution Imaging Spectroradiometer (MODIS) in the early 1990s. The OLI Band 9 has been proven to be very effective in detecting and masking thin cirrus-contaminated pixels at the high spatial resolution of 30 m. However, this channel has not yet been routinely used for the correction of thin cirrus effects in other OLI band images. In this article, we describe an empirical technique for the removal of thin cirrus scattering effects in OLI visible near infrared (IR) and shortwave IR (SWIR) spectral regions. We present results from applications of the technique to three OLI data sets. We also discuss issues associated with parallax anomalies in OLI data.
Plants provide the productive basis for all other life, and their diversity is critical for the Earth’s life support systems. Many plant species are at risk for extinction due to global change factors, including drought stress, exotic species invasions, pathogens, land-use change combined with altered disturbance regimes (e.g., fire), application of chemicals, and overexploitation. One in five species within the Plant Kingdom is thought to be threatened with extinction (Kew Royal Botanic Gardens, 2016). Given the multifaceted consequences of plant biodiversity for providing the ecosystem services on which humans depend, including the food we grow, the regulating services that maintain our fresh water supply and provision the multitude of organisms we care about, plant biodiversity is important to understand and to monitor across scales from genetic variation at local scales to the entire plant tree of life. Here we argue that deeper understanding and wider application of plant electromagnetic spectra—the patterns of light absorbed, trans- mitted, and reflected at different wavelengths from plants—can inte- grate previously disparate sectors of biodiversity science and the remote sensing community at multiple biological and spatial scales.
In March 2012 the Italy Space Agency (ASI) and Israeli Space Agency (ISA) have agreed to support space industries from both countries, in order to perform a joint study of the feasibility of development, launch and operation of a commercial hyperspectral remote sensing (HRS) satellite in orbit. Soon after, the mission was named as the Space-borne Hyperspectral Applicative Land and Ocean Mission (SHALOM). Several organizations in both countries were incorporated in the mission, including in Israel: Israel Aerospace Industry (IAI) - MBT, Elbit Systems, elOP, and in Italy: Selex, Telespazio and Thales Alenia Space Italy (TASI). The main idea is to make this hyperspectral instrument fully commercialized and to provide innovative applications to a wide range of end users worldwide. In November 2013 the feasibility stage (Phase A) has been accomplished and the project is waiting for an approval to go for Phase B.
The numerous Mediterranean islands (>10,000) are very important from a biodiversity point of view, both in term of plant species (numerous endemics, presence of ‘climate relicts’) and of ecosystems’ assemblage. These patterns can be explained by complex interactions between a highly heterogeneous historical biogeography and ecological processes related to diverse island conditions. Furthermore, most of the ups and downs of this biodiversity were closely linked with human pressures which have changed many times through the long socio-ecological history of these island landscapes since the Neolithic period. At present, insular plant biodiversity and rural landscapes are threatened by diverse global environmental changes related to urbanization, habitat fragmentation, unsustainable tourism and other practices (e.g. overgrazing, forest fires), and by other more recent drivers such as climate warming and aridification, sea-level rise and biological invasions. Some of these impacts will be exacerbated on islands because of no (or highly limited) adjacent areas of expansion, notably on the smallest ones (i.e. size < ca. 1000 ha). With regards to the biome crisis facing the Mediterranean basin and induced by human activities, islands constitute key ecological systems and ‘current refugia’ to ensure the long-term preservation of coastal plant biodiversity. They also represent fascinating ecological systems to disentangle the role of environmental versus human pressures on spatially simplified communities of the Mediterranean coastal areas. Future detailed studies of these ‘natural island microcosms’ could greatly improve our knowledge of the functional and evolutionary processes induced by rapid environmental changes in this region.
Leaf pigments provide valuable information about plant physiology. High resolution monitoring of their dynamics will give access to better understanding of processes occurring at different scales, and will be particularly important for ecologists, farmers, and decision makers to assess the influence of climate change on plant functions, and the adaptation of forest, crop, and other plant canopies. In this article, we present a new version of the widely-used PROSPECT model, hereafter named PROSPECT-D for dynamic, which adds anthocyanins to chlorophylls and carotenoids, the two plant pigments in the current version. We describe the evolution and improvements of PROSPECT-D compared to the previous versions, and perform a validation on various experimental datasets. Our results show that PROSPECT-D outperforms all the previous versions. Model prediction uncertainty is decreased and photosynthetic pigments are better retrieved. This is particularly the case for leaf carotenoids, the estimation of which is particularly challenging. PROSPECT-D is also able to simulate realistic leaf optical properties with minimal error in the visible domain, and similar performances to other versions in the near infrared and shortwave infrared domains.
In this white paper we develop ideas for a NASA Terrestrial Ecology (TE) field activity that will
enhance remote sensing and earth system modeling capabilities in ecosystems characterized by
mixtures of woody and herbaceous species (‘tree-grass’ systems). The “Tree-Grass” (TG) project will
transform our ability to use satellite data and earth system models to assess the current and future
role of tree-grass systems in the earth system, and their future in the face of changing climate,
changing land use and human population growth. In so doing we will enhance our ability to manage
tree-grass ecosystems for sustainability, food security and human wellbeing.
The overarching TG science questions are:
1) How are climate change and land-use change altering the structure, function and productivity of
tree-grass systems at landscape, regional and global scales? (“Global Change Processes”)
2) How will changes in tree-grass structure, function and productivity interact in the earth system
and feed-back on the major cycles of carbon, water and nutrients and energy flows? (“Biophysical
and Ecological Interactions”)
3) How will global change and biophysical interactions in tree-grass systems impact human wellbeing,
food security and sustainability into the future? Conversely, what is the potential for global change
mitigation, and can human populations in tree-grass regions benefit from this potential? (“Goods and
Services”)
The coordinated TG research activity will focus on a) remote sensing science to realize the potential
of airborne and satellite assets to retrieve key parameters describing tree-grass ecosystem state and
function; b) development and testing of earth system modeling capabilities suited to the structural
and functional characteristics of savannas; c) model-data synthesis (data-assimilation) to integrate
new remote sensing and modeling capabilities, and d) extensive education and outreach programs.
TG field activities will adopt a hierarchical sampling approach, with locally intensive field components
in North America, linked to globally distributed activities deployed in partnership with international
collaborators. We propose a phased implementation for TG, with Phase 1 (“Synthesis and
Evaluation”) concentrating on synthesis and evaluation of existing remote sensing and modeling
capabilities in tree-grass systems, Phase 2 (“Field Campaigns’) implementing major field, remote
sensing and model development activities, and Phase 3 (‘Applications’) focusing on regional-global
scale applications relevant to understanding and management of tree-grass systems.
TG seeks to revolutionize earth observation science through improved consideration of woody and
herbaceous functional groups in remote sensing and modeling of terrestrial ecosystems. The TG
program will entrain and inspire the next generation of earth system scientists and enhance public
appreciation of the crucial role NASA remote sensing technologies can play in understanding and
managing the earth system.
A new wave of terrestrial lidar scanners, optimized for rapid scanning and portability, such as the Compact Biomass Lidar (CBL), enable and improve observations of structure across a range of important ecosystems. We performed studies with the CBL in temperate and tropical forests, caves, salt marshes and coastal areas subject to erosion. By facilitating additional scanning points, and therefore view angles, this new class of terrestrial lidar alters observation coverage within samples, potentially reducing uncertainty in estimates of ecosystem properties. The CBL has proved competent at reconstructing trees and mangrove roots using the same cylinder-based Quantitative Structure Models commonly utilized for data from more capable instruments (Raumonen et al. 2013). For tropical trees with morphologies that challenge standard reconstruction techniques, such as the buttressed roots of Ceiba trees and the multiple stems of strangler figs, the CBL was able to provide the versatility and the speed of deployment needed to fully characterize their unique features. For geomorphological features, the deployment flexibility of the CBL enabled sampling from optimal view-angles, including from a novel suspension system for sampling salt marsh creeks. Overall, the practical aspects of these instruments, which improve deployment logistics, and therefore data acquisition rate, are shown to be emerging capabilities, greatly increasing the potential for observation, particularly in highly temporally dynamic, inaccessible and geometrically complex ecosystems. In order to better analyze information quality across these diverse and challenging ecosystems, we also provide a novel and much-needed conceptual framework, the microstate model, to characterize and mitigate uncertainties in terrestrial lidar observations.
Remote sensing (RS) approaches commonly applied to constrain estimates of gross primary production (GPP) employ greenness-based vegetation indices derived from surface reflectance data. Such approaches cannot capture dynamic changes of photosynthesis rates as caused by environmental stress. Further, applied vegetation indices are often affected by background reflectance or saturation effects. Sun. induced chlorophyll fluorescence (F) provides the most direct measure of photosynthesis and has been recently proposed as a new RS approach to improve estimates of GPP and tracing plant stress reactions. This work aims to provide further evidence on the complementary information content of F and its relation to changes in photosynthetic activity compared to traditional RS approaches. We use the airborne imaging spectrometer HyPlant to obtain several F products including red fluorescence (F687), far-red fluorescence (F760), F760 yield (F760yield) and the ration between F687 and F760 (Fratio). We calculate several vegetation indices indicative for vegetation greenness. We apply a recently proposed F-based semi-mechanistic approach to improve the forward modeling of GPP using F760 and compare this approach with a traditional one based on vegetation greenness and ground measurements of GPP derived from chamber measurements. In addition, we assess the sensitivity of F760yield and Fratio for environmental stress. Our results show an improved predictive capability of GPP when using F760 compared to greenness-based vegetation indices. F760yield and Fratio show a strong variability in time and between different crop types suffering from different levels of water shortage, indicating a strong sensitivity of F products for plant stress reactions. We conclude that the new RS approach of F provides complements to the set of commonly applies RS: The use of F760 improves constraining estimates of GPP while the ratio of red and far-red F shows large potential for tracking spatio-temporal plant adaptation in response to environmental stress conditions.
Forest inventory and management requirements are changing rapidly in the context of an increasingly complex set of economic, environmental, and social policy objectives. Advanced remote sensing technologies provide data to assist in addressing these escalating information needs and to support the subsequent development and parameterization of models for an even broader range of information needs. This special issue contains papers that use a variety of remote sensing technologies to derive forest inventory or inventory-related information. Herein, we review the potential of 4 advanced remote sensing technologies, which we posit as having the greatest potential to influence forest inventories designed to characterize forest resource information for strategic, tactical, and operational planning: airborne laser scanning (ALS), terrestrial laser scanning (TLS), digital aerial photogrammetry (DAP), and high spatial resolution (HSR)/very high spatial resolution (VHSR) satellite optical imagery. ALS, in particular, has proven to be a transformative technology, offering forest inventories the required spatial detail and accuracy across large areas and a diverse range of forest types. The coupling of DAP with ALS technologies will likely have the greatest impact on forest inventory practices in the next decade, providing capacity for a broader suite of attributes, as well as for monitoring growth over time.
In this study we evaluated various spectral inputs for retrieval of forest chlorophyll content (Cab) and leaf area index (LAI) from high spectral and spatial resolution airborne imaging spectroscopy data collected for two forest study sites in the Czech Republic (beech forest at Štítná nad Vláří and spruce forest at Bílý Kříž). The retrieval algorithm was based on a machine learning method – support vector regression (SVR). Performance of the four spectral inputs used to train SVR was evaluated: a) all available hyperspectral bands, b) continuum removal (CR) 645 – 710 nm, c) CR 705 – 780 nm, and d) CR 680 – 800 nm. Spectral inputs and corresponding SVR models were first assessed at the level of spectral databases simulated by combined leaf-canopy radiative transfer models PROSPECT and DART. At this stage, SVR models using all spectral inputs provided good performance (RMSE for Cab < 10 μg cm−2 and for LAI < 1.5), with consistently better performance for beech over spruce site. Since application of trained SVRs on airborne hyperspectral images of the spruce site produced unacceptably overestimated values, only the beech site results were analysed. The best performance for the Cab estimation was found for CR bands in range of 645 – 710 nm, whereas CR bands in range of 680 – 800 nm were the most suitable for LAI retrieval. The CR transformation reduced the across-track bidirectional reflectance effect present in airborne images due to large sensor field of view.
Although satellite-based variables have for long been expected to be key components to a unified and global biodiversity monitoring strategy, a definitive and agreed list of these variables still remains elusive. The growth of interest in biodiversity variables observable from space has been partly underpinned by the development of the essential biodiversity variable (EBV) framework by the Group on Earth Observations – Biodiversity Observation Network, which itself was guided by the process of identifying essential climate variables. This contribution aims to advance the development of a global biodiversity monitoring strategy by updating the previously published definition of EBV, providing a definition of satellite remote sensing (SRS) EBVs and introducing a set of principles that are believed to be necessary if ecologists and space agencies are to agree on a list of EBVs that can be routinely monitored from space. Progress toward the identification of SRS-EBVs will require a clear understanding of what makes a biodiversity variable essential, as well as agreement on who the users of the SRS-EBVs are. Technological and algorithmic developments are rapidly expanding the set of opportunities for SRS in monitoring biodiversity, and so the list of SRS-EBVs is likely to evolve over time. This means that a clear and common platform for data providers, ecologists, environmental managers, policy makers and remote sensing experts to interact and share ideas needs to be identified to support long-term coordinated actions.
Forests and trees throughout the world are increasingly affected by factors related to global change. Expanding international
trade has facilitated invasions of numerous insects and pathogens into new regions. Many of these invasions have caused substantial
forest damage, economic impacts and losses of ecosystem goods and services provided by trees. Climate change is already affecting
the geographic distribution of host trees and their associated insects and pathogens, with anticipated increases in pest impacts
by both native and invasive pests. Although climate change will benefit many forest insects, changes in thermal conditions
may disrupt evolved life history traits and cause phenological mismatches. Individually, the threats posed to forest ecosystems
by invasive pests and climate change are serious. Although interactions between these two drivers and their outcomes are poorly
understood and hence difficult to predict, it is clear that the cumulative impacts on forest ecosystems will be exacerbated.
Here we introduce and synthesize the information in this special issue of Forestry with articles that illustrate the impacts of invasions of insects and pathogens, climate change, forest management and their
interactions, as well as methods to predict, assess and mitigate these impacts. Most of these contributions were presented
at the XXIV IUFRO World Congress in 2014.
Airborne high fidelity imaging spectroscopy (HiFIS) holds great promise for bridging the gap between field studies of functional diversity, which are spatially limited, and satellite detection of ecosystem properties, which lacks resolution to understand within landscape dynamics. We use Carnegie Airborne Observatory HiFIS data combined with field collected foliar trait data to develop quantitative prediction models of foliar traits at the tree-crown level across over 1000 ha of humid tropical forest. We predicted foliar leaf mass per area (LMA) as well as foliar concentrations of nitrogen, phosphorus, calcium, magnesium and potassium for canopy emergent trees (R2: 0.45-0.67, relative RMSE: 11%-14%). Correlations between remotely sensed model coefficients for these foliar traits are similar to those found in laboratory studies, suggesting that the detection of these mineral nutrients is possible through their biochemical stoichiometry. Maps derived from HiFIS provide quantitative foliar trait information across a tropical forest landscape at fine spatial resolution, and along environmental gradients. Multi-nutrient maps implemented at the fine organismic scale will subsequently provide new insight to the functional biogeography and biological diversity of tropical forest ecosystems.
Cambridge Core - Plant Sciences - Leaf Optical Properties - by Stéphane Jacquemoud
Leaf traits and subsequently leaf spectral properties depend on the leaf phenological stage and light conditions within a canopy. The PROSPECT radiative transfer model has been extensively and successfully used to retrieve leaf traits for mature, sunlit leaves at peak vegetation growth, i.e. summer. However, research on the quanti-fication of leaf traits using PROSPECT across the canopy vertical profile throughout the growing season is still lacking. Therefore, this study aims at examining the effect of leaf position on the performance of the PROSPECT model in modelling leaf optical properties and retrieving leaf chlorophyll content (C ab), equivalent water thickness (EWT), and leaf mass per area (LMA) throughout the growing season. To achieve this objective, we collected 588 leaf samples from the upper and lower canopies of deciduous stands over three seasons (i.e., spring, summer and autumn) in Bavaria Forest National Park, Germany. Leaf traits including C ab , EWT and LMA, were measured for all the samples, and their reflectance spectra were obtained using an ASD FieldSpec-3 Pro FR spectroradiometer coupled with an Integrating Sphere. We initially assessed the performance of the PROSPECT model by comparing reflectance spectra generated in forward mode against reflectance spectra measured on leaf samples collected in the field. We subsequently inverted the PROSPECT model to retrieve C ab , EWT and LMA using the look-up-table (LUT) approach. Our results consistently demonstrated that the measured reflectance of leaf samples collected from the lower canopy had a stronger match with PROSPECT simulated reflectance spectra, especially in the NIR spectrum compared to leaf samples collected from the upper canopy throughout the growing season. This observation concurred with the pattern of C ab and EWT retrieval accuracies across the canopy i.e. the retrieval accuracy for the lower canopy was consistently higher (NRMSE = 0.1-0.2 for C ab ; NRMSE = 0.125-0.16 for EWT) when compared to the upper canopy (NRMSE = 0.122-0.269 for C ab ; NRMSE = 0.162-0.0.258 for EWT) across all seasons. In contrast, LMA retrieval accuracies for the upper canopy (NRMSE = 0.146-0.184) were higher compared to the lower canopy (NRMSE = 0.162-0.239) for all seasons except for the spring season. For all the leaf traits examined in this study, the range in retrieval accuracy between the upper and lower canopy was greater in summer (compared to other seasons). We report for the first time that although the PROSPECT model provides reasonable retrieval accuracy of C ab , EWT and LMA, variations in leaf biochemistry and morphology through the vertical canopy profile affects the performance of the model over the growing season. Findings of this study have important implications on field sampling protocols and upscaling leaf traits to canopy and landscape level using multi-layered physical models coupled with PROSPECT.
Leaf chlorophyll plays an essential role in controlling photosynthesis, physiological activities and forest health. In this study, the performance of Sentinel-2 and RapidEye satellite data and the Invertible Forest Reflectance Model (INFORM) radiative transfer model (RTM) for retrieving and mapping of leaf chlorophyll content in the Norway spruce (Picea abies) stands of a temperate forest was evaluated. Biochemical properties of leaf samples as well as stand structural characteristics were collected in two subsequent field campaigns during July 2015 and 2016 in the Bavarian Forest National Park (BFNP), Germany, parallel with the timing of the RapidEye and Sentinel-2 images. Leaf chlorophyll was measured both destructively and nondestructively using wet chemical spectrophotometry analysis and a hand-held chlorophyll content meter. The INFORM was utilised in the forward mode to generate two lookup tables (LUTs) in the spectral band settings of RapidEye and Sentinel-2 data using information obtained from the field campaigns. Before generating the LUTs, the sensitivity of the model input parameters to the spectral data from RapidEye and Sentinel-2 were examined. The canopy reflectance of the studied plots were obtained from the satellite images and used as input for the inversion of LUTs. The coefficient of determination (R2), root mean square errors (RMSE), and the normalised root mean square errors (NRMSE), between the retrieved and measured leaf chlorophyll, were then used to examine the attained results from RapidEye and Sentinel-2 data, respectively. The use of multiple solutions and spectral subsets for the inversion process were further investigated to enhance the retrieval accuracy of foliar chlorophyll. The result of the sensitivity analysis demonstrated that the simulated canopy reflectance of Sentinel-2 is sensitive to the alternation of all INFORM input parameters, while the simulated canopy reflectance from RapidEye did not show sensitivity to leaf water content variations. In general, there was agreement between the simulated and measured reflectance spectra from RapidEye and Sentinel-2, particularly in the visible and red-edge regions. However, examining the average absolute error from the simulated and measured reflectance revealed a large discrepancy in spectral bands around the near-infrared shoulder. The relationship between retrieved and measured leaf chlorophyll content from the Sentinel-2 data had a higher coefficient of determination with a higher NRMSE (NRMSE = 0.36 μg/cm2, R2 = 0.45) compared to those obtained using the RapidEye data (NRMSE = 0.31 μg/cm2 and R2 = 0.39). Using the mean of the ten best solutions (retrieved chlorophyll) the retrieval error for both Sentinel-2 and RapidEye data decreased (NRMSE = 0.34, NRMSE = 0.26, respectively), as compared to only selecting the single best solution. When the Sentinel-2 red edge bands were used as the spectral subset, the retrieval error of leaf chlorophyll decreased indicating the importance of red edge, as well as properly located spectral bands, for leaf chlorophyll estimation. The chlorophyll maps produced by the inversion of the two LUTs effectively represented the variation of foliar chlorophyll in BFNP and confirmed our earlier findings on the observed stress pattern caused by insect infestation. Our findings emphasise the importance of multispectral satellites which benefits from red edge spectral bands such as Sentinel-2 as well as RapidEye for regional mapping of vegetation foliar properties, particularly, chlorophyll using RTMs such as INFORM.
Leaf inclination angle and leaf angle distribution (LAD) are important plant structural traits, influencing the flux of radiation, carbon and water. Although leaf angle distribution may vary spatially and temporally, its variation is often neglected in ecological models, due to difficulty in quantification. In this study, terrestrial LiDAR (TLS) was used to quantify the LAD variation in natural European beech (Fagus Sylvatica) forests. After extracting leaf points and reconstructing leaf surface, leaf inclination angle was calculated automatically. The mapping accuracy when discriminating between leaves and woody material was very high across all beech stands (overall accuracy = 87.59%). The calculation accuracy of leaf angles was evaluated using simulated point cloud and proved accurate generally (R 2 = 0.88, p < 0.001; RMSE = 8.37°; nRMSE = 0.16). Then the mean (mean), mode (mode), and skewness of LAD were calculated to quantify LAD variation. Moderate variation of LAD was found in different successional status stands (mean [36.91°, 46.14°], mode [17°, 43°], skewness [0.07, 0.48]). Rather than the previously assumed spherical distribution or reported planophile distribution, here we find that LAD tended towards a uniform distribution in young and medium stands, and a planophile distribution in mature stands. A strong negative correlation was also found between plot mean and plot median canopy height, making it possible to estimate plot specific LAD from canopy height data. Larger variation of LAD was found on different canopy layers (mean [33.64°, 52.97°], mode [14°, 64°], skewness [−0.30, 0.71]). Beech leaves grow more vertically in the top layer, while more obliquely or horizontally in the middle and bottom layer. LAD variation quantified by TLS can be used to improve leaf area index mapping and canopy photosynthesis modelling.
Knowledge about leaf inclination angle distribution is essential for determining the radiation transmission within vegetation canopies and to indirectly quantify canopy attributes such as leaf area index and G-function. For this purpose, we measured and compiled an extensive dataset of leaf inclination angles for 138 deciduous broadleaf woody species commonly found in temperate and boreal ecoclimatic regions. We released an R routine to calculate leaf inclination angle statistics, leaf inclination angle distribution type, and G-function from measured leaf inclination angles, which can be used to parametrize optical measurements of light transmittance and for radiative transfer modeling purposes. The leaf inclination angle distribution type can be also used as a plant functional trait to understand light use and photosynthetic plant strategies and to perform functional diversity analyses. Dataset access is at https://doi.org/10.17632/4rmc7r8zvy.2 Associated metadata is available at https://metadata-afs.nancy.inra.fr/geonetwork/srv/eng/catalog.search#/metadata/c1197b55-a582-4ed4-82bc-7008ce9294d9.
Radiation processes in vegetation canopies can be analyzed using methods based on the equation of radiative transfer (RT) or by computer simulations. RT equation-based models describe RT in homogeneous vegetation canopies (grass, dense crops, dense broadleaf forests). RT models link measurable canopy structure parameters to the coefficients of the RT equation. Models of RT in discontinuous canopies are complex models which describe the canopy structure at different scales (leaf, conifer needle, shoot, branch, tree crown, forest stand) and analyze RT in such structures. Computer simulation models follow traveling of photons in a vegetation canopy or use some computer graphics methods to simulate scene radiance.
We present the Airborne Prism Experiment (APEX), its calibration and subsequent radiometric measurements as well as Earth science applications derived from this data. APEX is a dispersive pushbroom imaging spectrometer covering the solar reflected wavelength range between 372 and 2540 nm with nominal 312 (max. 532) spectral bands. APEX is calibrated using a combination of laboratory, in-flight and vicarious calibration approaches. These are complemented by using a forward and inverse radiative transfer modeling approach, suitable to further validate APEX data. We establish traceability of APEX radiances to a primary calibration standard, including uncertainty analysis. We also discuss the instrument simulation process ranging from initial specifications to performance validation. In a second part, we present Earth science applications using APEX. They include geometric and atmospheric compensated as well as reflectance anisotropy minimized Level 2 data. Further, we discuss retrieval of aerosol optical depth as well as vertical column density of NOx, a radiance data-based coupled canopy–atmosphere model, and finally measuring sun-induced chlorophyll fluorescence (Fs) and infer plant pigment content. The results report on all APEX specifications including validation. APEX radiances are traceable to a primary standard with < 4% uncertainty and with an average SNR of > 625 for all spectral bands. Radiance based vicarious calibration is traceable to a secondary standard with ≤ 6.5% uncertainty. Except for inferring plant pigment content, all applications are validated using in-situ measurement approaches and modeling. Even relatively broad APEX bands (FWHM of 6 nm at 760 nm) can assess Fs with modeling agreements as high as R2 = 0.87 (relative RMSE = 27.76%). We conclude on the use of high resolution imaging spectrometers and suggest further development of imaging spectrometers supporting science grade spectroscopy measurements.
Spectral reflectance of maple, chestnut and beech leaves in a wide range of pigment content and composition was investigated to devise a nondestructive technique for total carotenoid (Car) content estimation in higher plant leaves. Reciprocal reflectance in the range 510 to 550 nm was found to be closely related to the total pigment content in leaves. The sensitivity of reciprocal reflectance to Car content was maximal in a spectral range around 510 nm; however, chlorophylls (Chl) also affect reflectance in this spectral range. To remove the Chl effect on the reciprocal reflectance at 510 nm, a reciprocal reflectance at either 550 or 700 nm was used, which was linearly proportional to the Chl content. Indices for nondestructive estimation of Car content in leaves were devised and validated. Reflectances in three spectral bands, 510 ± 5 nm, either 550 ± 15 nm or 700 ± 7.5 nm and the near infrared range above 750 nm are sufficient to estimate total Car content in plant leaves nondestructively with a root mean square error of less than 1.75 nmol/cm².
Estimating the proportion of woody-to-total plant material ‘α’ is an essential step to convert Plant Area Index ‘PAI’ estimates into Leaf Area Index ‘LAI’. α has also been shown to have a significant impact on the passive optical remote sensing signal for retrieval of biophysical parameters in forests, woodlands, and savannas. However, benchmarked indirect α retrieval methods are lacking and thus it is common for this pivotal correction to be ignored. In this paper we validate an α retrieval method using a 3D radiative transfer simulation framework, enabling the retrieval method to be benchmarked against a known and precise model truth. The 3D framework consists of a representative and highly detailed 3D explicit Eucalypt forest reconstructed from field measurements. The 3D structure is coupled with a 3D scattering model to enable simulation of remote sensing instruments. The retrieval method utilises classified hemispherical photography ‘HP’, but is applicable to all ground-based optical instruments that can separate leaf and woody elements. The method is applicable to evergreen forests and thus independent of the estimation of PAI or LAI. The unknown degree of mutual shading or occlusion of leaf and woody elements was traditionally a key impediment to the operational use of this method and was therefore closely examined. The indirect α method utilising classified HP imagery agreed on average to within 0.01 α of the reference (αref = 0.37). In addition, the method demonstrated robustness to a range of LAI, stem density, and stem distribution values, matching to within ±0.05 α of the reference. Angular dependence on indirect α retrieval was also found; where the entire HP image (180° FOV) was needed to produce the most accurate estimate. Conversely, the classified narrow view zenith angle range around 55−60° zenith also provided an α estimate matching the reference. At this narrow zenith angle the method is insensitive to leaf angle distribution. As such, careful consideration of zenith angle range utilised from the instrument is recommended. The results demonstrate the method’s applicability for accurate indirect estimation of α in single-storey forest types. The simple and efficient method can be used to convert estimates of PAI into LAI from a variety of optical ground-based instruments. Quantitative α estimates can and should be used to aid interpretation of the remote sensing signal from satellite imagery, which has been shown to be sensitive to the proportion and spatial distribution of woody canopy materials.
The ability of plants to sequester carbon is highly variable over the course of the year and reflects seasonal variation in photosynthetic efficiency. This seasonal variation is most prominent during autumn, when leaves of deciduous tree species such as sugar maple (Acer saccharum Marsh.) undergo senescence, which is associated with downregulation of photosynthesis and a change of leaf color. The remote sensing of leaf color by spectral reflectance measurements and digital repeat images is increasingly used to improve models of growing season length and seasonal variation in carbon sequestration. Vegetation indices derived from spectral reflectance measurements and digital repeat images might not adequately reflect photosynthetic efficiency of red-senescing tree species during autumn due to the changes in foliar pigment content associated with autumn phenology. In this study, we aimed to assess how effectively several widely used vegetation indices capture autumn phenology and reflect the changes in physiology and photosynthetic pigments during autumn. Chlorophyll fluorescence and pigment content of green, yellow, orange and red leaves were measured to represent leaf senescence during autumn and used as a reference to validate and compare vegetation indices derived from leaf-level spectral reflectance measurements and color analysis of digital images. Vegetation indices varied in their suitability to track the decrease of photosynthetic efficiency and chlorophyll content despite increasing anthocyanin content. Commonly used spectral reflectance indices such as the normalized difference vegetation index and photochemical reflectance index showed major constraints arising from a limited representation of gradual decreases in chlorophyll content and an influence of high foliar anthocyanin levels. The excess green index and green-red vegetation index were more suitable to assess the process of senescence. Similarly, digital image analysis revealed that vegetation indices such as Hue and normalized difference index are superior compared with the often-used green chromatic coordinate. We conclude that indices based on red and green color information generally represent autumn phenology most efficiently.