Performance of Seven Land Surface Schemes in the WRFv4.3 Model for Simulating Precipitation in the Record-Breaking Meiyu Season Over the Yangtze-Huaihe River Valley in China.

In 2020, the Yangtze-Huai river valley (YHRV) experienced the highest record-breaking Meiyu season since 1961, which was mainly characterized by the longest duration of precipitation lasting from early-June to mid-July, with frequent heavy rainstorms that caused severe flooding and deaths in China. Many studies have investigated the causes of this Meiyu season and its evolution, but the accuracy of precipitation simulations has received little attention. It is important to provide more accurate precipitation forecasts to help prevent and reduce flood disasters, thereby facilitating the maintenance of a healthy and sustainable earth ecosystem. In this study, we determined the optimal scheme among seven land surface model (LSMs) schemes in the Weather Research and Forecasting model for simulating the precipitation in the Meiyu season during 2020 over the YHRV region. We also investigated the mechanisms in the different LSMs that might affect precipitation simulations in terms of water and energy cycling. The results showed that the simulated amounts of precipitation were higher under all LSMs than the observations. The main differences occurred in rainstorm areas (>12 mm/day), and the differences in low rainfall areas were not significant (<8 mm/day). Among all of the LSMs, the Simplified Simple Biosphere (SSiB) model obtained the best performance, with the lowest root mean square error and the highest correlation. The SSiB model even outperformed the Bayesian model averaging result. Finally, some factors responsible for the differences modeling results were investigated to understand the related physical mechanism.

Prediction of diffuse solar radiation by integrating radiative transfer model and machine-learning techniques.

Diffuse radiation is a major component of solar radiation that is important in carbon exchanges and material, energy, and information flows in agricultural ecosystems; however, measuring diffuse radiation is difficult and expensive, leaving only few stations in China that can record diffuse radiation. Therefore, five high-speed and highly accurate hybrid models were developed and compared to simulate diffuse radiation based on the aerosol optical properties and radiation parameters provided by the Aerosol Robotic Network (AERONET), Baseline Surface Radiation Network (BSRN), Wuhan University, Chinese Ecosystem Research Network (CERN), GLASS surface albedo data, and combined radiative transfer model (RTM) with machine learning (ML) models that include random forest (RF), extreme gradient boosting (XGBoost), multi-layer perceptron (MLP), deep neural networks (DNN), and convolutional neural network (CNN). Furthermore, the uncertainty in the simulated diffuse radiation due to the measurement uncertainties of aerosol optical properties and land surface albedo was quantified, and the relative contributions of multiple variables to diffuse radiation were analyzed. The results showed that RTM-RF was the most successful, with determination coefficients (R2) of 0.95, 0.94, and 0.98, and minimum root mean square errors (RMSE) of 9.56, 10.05, and 13.27 W m-2 at the Lulin, Wuhan, and Xianghe sites, respectively. The largest measurement uncertainty in the aerosol optical depth (AOD) was found at the Lulin site, while that of the single-scattering albedo led to the largest errors in Wuhan and Xianghe. AOD, solar zenith angle (SZA), and single-scattering albedo contributed significantly more than the asymmetry factor, land surface albedo, precipitable water vapor, and ozone. This was especially true for AOD, which was higher than 28 % at all sites. Overall, the proposed RTM-RF method exhibited superior performance, therefore we recommend it for estimating diffuse radiation in China.

Gaussian processes retrieval of crop traits in Google Earth Engine based on Sentinel-2 top-of-atmosphere data.

The unprecedented availability of optical satellite data in cloud-based computing platforms, such as Google Earth Engine (GEE), opens new possibilities to develop crop trait retrieval models from the local to the planetary scale. Hybrid retrieval models are of interest to run in these platforms as they combine the advantages of physically- based radiative transfer models (RTM) with the flexibility of machine learning regression algorithms. Previous research with GEE primarily relied on processing bottom-of-atmosphere (BOA) reflectance data, which requires atmospheric correction. In the present study, we implemented hybrid models directly into GEE for processing Sentinel-2 (S2) Level-1C (L1C) top-of-atmosphere (TOA) reflectance data into crop traits. To achieve this, a training dataset was generated using the leaf-canopy RTM PROSAIL in combination with the atmospheric model 6SV. Gaussian process regression (GPR) retrieval models were then established for eight essential crop traits namely leaf chlorophyll content, leaf water content, leaf dry matter content, fractional vegetation cover, leaf area index (LAI), and upscaled leaf variables (i.e., canopy chlorophyll content, canopy water content and canopy dry matter content). An important pre-requisite for implementation into GEE is that the models are sufficiently light in order to facilitate efficient and fast processing. Successful reduction of the training dataset by 78% was achieved using the active learning technique Euclidean distance-based diversity (EBD). With the EBD-GPR models, highly accurate validation results of LAI and upscaled leaf variables were obtained against in situ field data from the validation study site Munich-North-Isar (MNI), with normalized root mean square errors (NRMSE) from 6% to 13%. Using an independent validation dataset of similar crop types (Italian Grosseto test site), the retrieval models showed moderate to good performances for canopy-level variables, with NRMSE ranging from 14% to 50%, but failed for the leaf-level estimates. Obtained maps over the MNI site were further compared against Sentinel-2 Level 2 Prototype Processor (SL2P) vegetation estimates generated from the ESA Sentinels' Application Platform (SNAP) Biophysical Processor, proving high consistency of both retrievals (R 2 from 0.80 to 0.94). Finally, thanks to the seamless GEE processing capability, the TOA-based mapping was applied over the entirety of Germany at 20 m spatial resolution including information about prediction uncertainty. The obtained maps provided confidence of the developed EBD-GPR retrieval models for integration in the GEE framework and national scale mapping from S2-L1C imagery. In summary, the proposed retrieval workflow demonstrates the possibility of routine processing of S2 TOA data into crop traits maps at any place on Earth as required for operational agricultural applications.

Retrieval of Crop Variables from Proximal Multispectral UAV Image Data Using PROSAIL in Maize Canopy.

Mapping crop variables at different growth stages is crucial to inform farmers and plant breeders about the crop status. For mapping purposes, inversion of canopy radiative transfer models (RTMs) is a viable alternative to parametric and non-parametric regression models, which often lack transferability in time and space. Due to the physical nature of RTMs, inversion outputs can be delivered in sound physical units that reflect the underlying processes in the canopy. In this study, we explored the capabilities of the coupled leaf-canopy RTM PROSAIL applied to high-spatial-resolution (0.015 m) multispectral unmanned aerial vehicle (UAV) data to retrieve the leaf chlorophyll content (LCC), leaf area index (LAI) and canopy chlorophyll content (CCC) of sweet and silage maize throughout one growing season. Two different retrieval methods were tested: (i) applying the RTM inversion scheme to mean reflectance data derived from single breeding plots (mean reflectance approach) and (ii) applying the same inversion scheme to an orthomosaic to separately retrieve the target variables for each pixel of the breeding plots (pixel-based approach). For LCC retrieval, soil and shaded pixels were removed by applying simple vegetation index thresholding. Retrieval of LCC from UAV data yielded promising results compared to ground measurements (sweet maize RMSE = 4.92 µg/cm2, silage maize RMSE = 3.74 µg/cm2) when using the mean reflectance approach. LAI retrieval was more challenging due to the blending of sunlit and shaded pixels present in the UAV data, but worked well at the early developmental stages (sweet maize RMSE = 0.70m2/m2, silage RMSE = 0.61m2/m2 across all dates). CCC retrieval significantly benefited from the pixel-based approach compared to the mean reflectance approach (RMSEs decreased from 45.6 to 33.1 µg/m2). We argue that high-resolution UAV imagery is well suited for LCC retrieval, as shadows and background soil can be precisely removed, leaving only green plant pixels for the analysis. As for retrieving LAI, it proved to be challenging for two distinct varieties of maize that were characterized by contrasting canopy geometry.

QUantitative and Automatic Atmospheric Correction (QUAAC): Application and Validation.

The difficulty of atmospheric correction based on a radiative transfer model lies in the acquisition of synchronized atmospheric parameters, especially the aerosol optical depth (AOD). At the moment, there is no fully automatic and high-efficiency atmospheric correction method to make full use of the advantages of geostationary meteorological satellites in large-scale and efficient atmospheric monitoring. Therefore, a QUantitative and Automatic Atmospheric Correction (QUAAC) method is proposed which can efficiently correct high-spatial-resolution (HSR) satellite images. QUAAC uses the atmospheric aerosol products of geostationary satellites to match the synchronized AOD according to the temporal and spatial information of HSR satellite images. This method solves the problem that the AOD is difficult to obtain or the accuracy is not high enough to meet the demand of atmospheric correction. By using the obtained atmospheric parameters, atmospheric correction is performed to obtain the surface reflectance (SR). The whole process can achieve fully automatic operation without manual intervention. After QUAAC applied to Gaofen-2 (GF-2) HSR satellite and Himawari-8 (H-8) geostationary satellite, the results show that the effect of QUAAC correction is slightly better than that of the Fast Line-of-sight Atmospheric Analysis of Spectral Hypercubes (FLAASH) correction, and the QUAAC-corrected surface spectral curves have good coherence to that of the synchronously measured by field experiments.

Detection of Xylella fastidiosa in almond orchards by synergic use of an epidemic spread model and remotely sensed plant traits.

The early detection of Xylella fastidiosa (Xf) infections is critical to the management of this dangerous plan pathogen across the world. Recent studies with remote sensing (RS) sensors at different scales have shown that Xf-infected olive trees have distinct spectral features in the visible and infrared regions (VNIR). However, further work is needed to integrate remote sensing in the management of plant disease epidemics. Here, we research how the spectral changes picked up by different sets of RS plant traits (i.e., pigments, structural or leaf protein content), can help capture the spatial dynamics of Xf spread. We coupled a spatial spread model with the probability of Xf-infection predicted by a RS-driven support vector machine (RS-SVM) model. Furthermore, we analyzed which RS plant traits contribute most to the output of the prediction models. For that, in almond orchards affected by Xf (n = 1426 trees), we conducted a field campaign simultaneously with an airborne campaign to collect high-resolution thermal images and hyperspectral images in the visible-near-infrared (VNIR, 400-850 nm) and short-wave infrared regions (SWIR, 950-1700 nm). The best performing RS-SVM model (OA = 75%; kappa = 0.50) included as predictors leaf protein content, nitrogen indices (NIs), fluorescence and a thermal indicator (Tc), alongside pigments and structural parameters. Leaf protein content together with NIs contributed 28% to the explanatory power of the model, followed by chlorophyll (22%), structural parameters (LAI and LIDFa), and chlorophyll indicators of photosynthetic efficiency. Coupling the RS model with an epidemic spread model increased the accuracy (OA = 80%; kappa = 0.48). In the almond trees where the presence of Xf was assayed by qPCR (n = 318 trees), the combined RS-spread model yielded an OA of 71% and kappa = 0.33, which is higher than the RS-only model and visual inspections (both OA = 64-65% and kappa = 0.26-31). Our work demonstrates how combining spatial epidemiological models and remote sensing can lead to highly accurate predictions of plant disease spatial distribution.

TLSLeAF: automatic leaf angle estimates from single-scan terrestrial laser scanning.

Leaf angle distribution (LAD) in forest canopies affects estimates of leaf area, light interception, and global-scale photosynthesis, but is often simplified to a single theoretical value. Here, we present TLSLeAF (Terrestrial Laser Scanning Leaf Angle Function), an automated open-source method of deriving LADs from terrestrial laser scanning. TLSLeAF produces canopy-scale leaf angle and LADs by relying on gridded laser scanning data. The approach increases processing speed, improves angle estimates, and requires minimal user input. Key features are automation, leaf-wood classification, beta parameter output, and implementation in R to increase accessibility for the ecology community. TLSLeAF precisely estimates leaf angle with minimal distance effects on angular estimates while rapidly producing LADs on a consumer-grade machine. We challenge the popular spherical LAD assumption, showing sensitivity to ecosystem type in plant area index and foliage profile estimates that translate to c. 25% and c. 11% increases in canopy net photosynthesis (c. 25%) and solar-induced chlorophyll fluorescence (c. 11%). TLSLeAF can now be applied to the vast catalog of laser scanning data already available from ecosystems around the globe. The ease of use will enable widespread adoption of the method outside of remote-sensing experts, allowing greater accessibility for addressing ecological hypotheses and large-scale ecosystem modeling efforts.

Plant ecophysiological processes in spectral profiles: perspective from a deciduous broadleaf forest.

The need for progress in satellite remote sensing of terrestrial ecosystems is intensifying under climate change. Further progress in Earth observations of photosynthetic activity and primary production from local to global scales is fundamental to the analysis of the current status and changes in the photosynthetic productivity of terrestrial ecosystems. In this paper, we review plant ecophysiological processes affecting optical properties of the forest canopy which can be measured with optical remote sensing by Earth-observation satellites. Spectral reflectance measured by optical remote sensing is utilized to estimate the temporal and spatial variations in the canopy structure and primary productivity. Optical information reflects the physical characteristics of the targeted vegetation; to use this information efficiently, mechanistic understanding of the basic consequences of plant ecophysiological and optical properties is essential over broad scales, from single leaf to canopy and landscape. In theory, canopy spectral reflectance is regulated by leaf optical properties (reflectance and transmittance spectra) and canopy structure (geometrical distributions of leaf area and angle). In a deciduous broadleaf forest, our measurements and modeling analysis of leaf-level characteristics showed that seasonal changes in chlorophyll content and mesophyll structure of deciduous tree species lead to a seasonal change in leaf optical properties. The canopy reflectance spectrum of the deciduous forest also changes with season. In particular, canopy reflectance in the green region showed a unique pattern in the early growing season: green reflectance increased rapidly after leaf emergence and decreased rapidly after canopy closure. Our model simulation showed that the seasonal change in the leaf optical properties and leaf area index caused this pattern. Based on this understanding we discuss how we can gain ecophysiological information from satellite images at the landscape level. Finally, we discuss the challenges and opportunities of ecophysiological remote sensing by satellites.

Estimating the phenological dynamics of irrigated rice leaf area index using the combination of PROSAIL and Gaussian Process Regression.

The growth of rice is a sequence of three different phenological phases. This sequence of change in rice phenology implies that the condition of the plant during the vegetative phase relates directly to the health of leaves functioning during the reproductive and ripening phases. As such, accurate monitoring is important towards understanding rice growth dynamics. Leaf Area Index (LAI) is an important indicator of rice yields and the availability of this information during key phenological phases can support more informed farming decisions. Satellite remote sensing has been adopted as a proxy to field measurements of LAI and with the launch of freely available high resolution Satellite images such as Sentinel-2, it is imperative that accurate retrieval methods are adopted towards monitoring LAI at irrigated rice fields. Here, we evaluate the potential of a hybrid radiative transfer model (i.e., PROSAIL - Gaussian Process Regression (GPR), for estimating the phenological dynamics of irrigated rice LAI using imager derived from the Sentinel-2 multispectral instrument. LAI field measurements were obtained from an experimental rice field in Nasarawa state, Nigeria during the dry season. We used the PROSAIL radiative transfer model to create a look up table (LUT) that was subsequently used to train a GPR model. Afterwards, we evaluated the potential of the hybrid modelling approach by assessing the overall model accuracy and the extent to which LAI was able to accurately predict LAI during key rice phenological phases. We compared the predicted hybrid GPR LAI values with LAI values generated from the SNAP toolbox, based on a hybrid Artificial Neural Network (ANN) modelling approach. Our results show that the overall predictive accuracy of the hybrid GPR model (R2 = 0.82, RMSE = 1.65) was more accurate than that of the hybrid ANN model (R2 = 0.66, RMSE = 3.89) for retrieving LAI values from Sentinel-2 imagery. Both models underestimated LAI values during the reproductive and ripening phases . However, the accuracy during the phenological phases were more significant when using the hybrid GPR model (P < 0.05). During the different phenological phases, the hybrid GPR model predicted LAI more accurately during the reproductive (R2 = 0.7) and ripening (R2 = 0.59) phases compared to the hybrid ANN reproductive and ripening phases. When monitoring LAI phenological profiles of both hybrid models, the hybrid GPR and ANN models underestimated LAI during the reproductive and ripening phases. However, the ANN model underestimations were statistically significantly greater than those for the hybrid GPR model (P < 0.05). Our results highlight the potential of hybrid GPR models for estimating the phenological dynamics of irrigated rice LAI from Sentinel-2 data. They provided more accurate estimation of LAI patterns from varying nitrogen and water applications than hybrid ANN models.

Unique contributions of chlorophyll and nitrogen to predict crop photosynthetic capacity from leaf spectroscopy.

The photosynthetic capacity or the CO2-saturated photosynthetic rate (Vmax), chlorophyll, and nitrogen are closely linked leaf traits that determine C4 crop photosynthesis and yield. Accurate, timely, rapid, and non-destructive approaches to predict leaf photosynthetic traits from hyperspectral reflectance are urgently needed for high-throughput crop monitoring to ensure food and bioenergy security. Therefore, this study thoroughly evaluated the state-of-the-art physically based radiative transfer models (RTMs), data-driven partial least squares regression (PLSR), and generalized PLSR (gPLSR) models to estimate leaf traits from leaf-clip hyperspectral reflectance, which was collected from maize (Zea mays L.) bioenergy plots with diverse genotypes, growth stages, treatments with nitrogen fertilizers, and ozone stresses in three growing seasons. The results show that leaf RTMs considering bidirectional effects can give accurate estimates of chlorophyll content (Pearson correlation r=0.95), while gPLSR enabled retrieval of leaf nitrogen concentration (r=0.85). Using PLSR with field measurements for training, the cross-validation indicates that Vmax can be well predicted from spectra (r=0.81). The integration of chlorophyll content (strongly related to visible spectra) and nitrogen concentration (linked to shortwave infrared signals) can provide better predictions of Vmax (r=0.71) than only using either chlorophyll or nitrogen individually. This study highlights that leaf chlorophyll content and nitrogen concentration have key and unique contributions to Vmax prediction.

Assessment of the radiation effect of aerosols on maize production in China.

With the recent increases in atmosphere aerosol concentration, its impact on agriculture in China is of considerable concern for scientific community. In this study, the effects that aerosols have on radiation and consequently the production of maize in China were investigated from 2002 to 2014 using the AErosol RObotic NETwork (AERONET) data, Second Simulation of a Satellite Signal in the Solar Spectrum radiative transfer (6S) model, and Agricultural Production Systems sIMulator (APSIM) model. Ten stations in the maize planting areas including Beijing, Xianghe, Taihu, Nanjing, Shanghai, Hefei, Baotou, Lanzhou, Qinghaihu, and Xuzhou stations were selected. The results showed that the APSIM-maize model, which was further calibrated, was able to simulate the interactions between maize and the climatic constraints in the maize planting areas of China. Our results indicated that aerosols obviously reduced the amount of solar radiation reaching the surface during the maize growing season in China. We also found that the aerosols have negative effects on both biomass and yield of maize in China at ten stations. The average annual maize biomass during the maize growing season from 2002 to 2014 decreased by 23.70%. The average yield of maize from 2002 to 2014 decreased by 15.10%. However, the influence of aerosol on different varieties of maize varied. We found the aerosols had greater negative impacts on summer maize than on spring maize. For spring maize, the average biomass and yield from 2002 to 2014 decreased by 10.36% and 5.16%, respectively. However, as for the summer maize, the average biomass and yield from 2002 to 2014 were reduced by 19.72% and 20.56%, respectively. Our findings can provide a useful method for estimating the effect of aerosols on crops at the national level, supporting local agricultural production in coping with the ongoing climate change.

Effect of Structural Uncertainty in Passive Microwave Soil Moisture Retrieval Algorithm.

Passive microwave sensors use a radiative transfer model (RTM) to retrieve soil moisture (SM) using brightness temperatures (TB) at low microwave frequencies. Vegetation optical depth (VOD) is a key input to the RTM. Retrieval algorithms can analytically invert the RTM using dual-polarized TB measurements to retrieve the VOD and SM concurrently. Algorithms in this regard typically use the τ-ω types of models, which consist of two third-order polynomial equations and, thus, can have multiple solutions. Through this work, we find that uncertainty occurs due to the structural indeterminacy that is inherent in all τ-ω types of models in passive microwave SM retrieval algorithms. In the process, a new analytical solution for concurrent VOD and SM retrieval is presented, along with two widely used existing analytical solutions. All three solutions are applied to a fixed framework of RTM to retrieve VOD and SM on a global scale, using X-band Advanced Microwave Scanning Radiometer-Earth Observing System (AMSR-E) TB data. Results indicate that, with structural uncertainty, there ensues a noticeable impact on the VOD and SM retrievals. In an era where the sensitivity of retrieval algorithms is still being researched, we believe the structural indeterminacy of RTM identified here would contribute to uncertainty in the soil moisture retrievals.

Assessment of Workflow Feature Selection on Forest LAI Prediction with Sentinel-2A MSI, Landsat 7 ETM+ and Landsat 8 OLI.

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.

Estimation of leaf area index using PROSAIL based LUT inversion, MLRA-GPR and empirical models: Case study of tropical deciduous forest plantation, North India.

Forests play a vital role in biological cycles and environmental regulation. To understand the key processes of forest canopies (e.g., photosynthesis, respiration and transpiration), reliable and accurate information on spatial variability of Leaf Area Index (LAI), and its seasonal dynamics is essential. In the present study, we assessed the performance of biophysical parameter (LAI) retrieval methods viz. Look-Up Table (LUT)-inversion, MLRA-GPR (Machine Learning Regression Algorithm-Gaussian Processes Regression) and empirical models, for estimating the LAI of tropical deciduous plantation using ARTMO (Automated Radiative Transfer Models Operator) tool and Sentinel-2 satellite images. The study was conducted in Central Tarai Forest Division, Haldwani, located in the Uttarakhand state, India. A total of 49 ESUs (Elementary Sampling Unit) of 30m×30m size were established based on variability in composition and age of plantation stands. In-situ LAI was recorded using plant canopy imager during the leaf growing, peak and senescence seasons. The PROSAIL model was calibrated with site-specific biophysical and biochemical parameters before used to the predicted LAI. The plantation LAI was also predicted by an empirical approach using optimally chosen Sentinel-2 vegetation indices. In addition, Sentinel-2 and MODIS LAI products were evaluated with respect to LAI measurements. MLRA-GPR offered best results for predicting LAI of leaf growing (R2 = 0.9, RMSE = 0.14), peak (R2 = 0.87, RMSE = 0.21) and senescence (R2 = 0.86, RMSE = 0.31) seasons while LUT inverted model outperformed VI's based parametric regression model. Vegetation indices (VIs) derived from 740 nm, 783 nm and 2190 nm band combinations of Sentinel-2 offered the best prediction of LAI.

Gaussian processes retrieval of LAI from Sentinel-2 top-of-atmosphere radiance data.

Retrieval of vegetation properties from satellite and airborne optical data usually takes place after atmospheric correction, yet it is also possible to develop retrieval algorithms directly from top-of-atmosphere (TOA) radiance data. One of the key vegetation variables that can be retrieved from at-sensor TOA radiance data is leaf area index (LAI) if algorithms account for variability in atmosphere. We demonstrate the feasibility of LAI retrieval from Sentinel-2 (S2) TOA radiance data (L1C product) in a hybrid machine learning framework. To achieve this, the coupled leaf-canopy-atmosphere radiative transfer models PROSAIL-6SV were used to simulate a look-up table (LUT) of TOA radiance data and associated input variables. This LUT was then used to train the Bayesian machine learning algorithms Gaussian processes regression (GPR) and variational heteroscedastic GPR (VHGPR). PROSAIL simulations were also used to train GPR and VHGPR models for LAI retrieval from S2 images at bottom-of-atmosphere (BOA) level (L2A product) for comparison purposes. The BOA and TOA LAI products were consistently validated against a field dataset with GPR (R2 of 0.78) and with VHGPR (R 2 of 0.80) and for both cases a slightly lower RMSE for the TOA LAI product (about 10% reduction). Because of delivering superior accuracies and lower uncertainties, the VHGPR models were further applied for LAI mapping using S2 acquisitions over the agricultural sites Marchfeld (Austria) and Barrax (Spain). The models led to consistent LAI maps at BOA and TOA scale. The LAI maps were also compared against LAI maps as generated by the SNAP toolbox, which is based on a neural network (NN). Maps were again consistent, however the SNAP NN model tends to overestimate over dense vegetation cover. Overall, this study demonstrated that hybrid LAI retrieval algorithms can be developed from TOA radiance data given a cloud-free sky, thus without the need of atmospheric correction. To the benefit of the community, the development of such hybrid models for the retrieval vegetation properties from BOA or TOA images has been streamlined in the freely downloadable ALG-ARTMO software framework.

Quantifying vegetation biophysical variables from the Sentinel-3/FLEX tandem mission: Evaluation of the synergy of OLCI and FLORIS data sources.

The ESA's forthcoming FLuorescence EXplorer (FLEX) mission is dedicated to the global monitoring of the vegetation's chlorophyll fluorescence by means of an imaging spectrometer, FLORIS. In order to properly interpret the fluorescence signal in relation to photosynthetic activity, essential vegetation variables need to be retrieved concomitantly. FLEX will fly in tandem with Sentinel-3 (S3), which conveys the Ocean and Land Colour Instrument (OLCI) that is designed to characterize the atmosphere and the terrestrial vegetation at a spatial resolution of 300 m. In this work we present the retrieval models of four essential biophysical variables: (1) Leaf Area Index (LAI), (2) leaf chlorophyll content (Cab), (3) fraction of absorbed photosynthetically active radiation (fAPAR), and (4) fractional vegetation cover (FCover). These variables can be operationally inferred by hybrid retrieval approaches, which combine the generalization capabilities offered by radiative transfer models (RTMs) with the flexibility and computational efficiency of machine learning methods. The RTM SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes) was used to generate a database of reflectance spectra corresponding to a large variety of canopy realizations, which served subsequently as input to train a Gaussian Process Regression (GPR) algorithm for each targeted variable. Three sets of GPR models were developed, based on different spectral band settings: (1) OLCI (21 bands between 400 and 1040 nm), (2) FLORIS (281 bands between 500 and 780 nm), and (3) their synergy. Their respective performances were assessed based on simulated reflectance scenes. Regarding the retrieval of Cab, the OLCI model gave good model performances (R2: 0.91; RMSE: 7.6 µg. cm -2), yet superior accuracies were achieved as a result of FLORIS' higher spectral resolution (R2: 0.96; RMSE: 4.8 µg. cm -2). The synergy of both datasets did not further enhance the variable retrieval. Regarding LAI, the improvement of the model performances by using only FLORIS spectra (R2: 0.87; RMSE: 1.05 m2.m-2) rather than only OLCI spectra (R2: 0.86; RMSE: 1.12 m2.m-2) was less evident but merging both data sets was more beneficial (R2: 0.88; RMSE: 1.01 m2.m-2). Finally, the three data sources gave good model performances for the retrieval of fAPAR and Fcover, with the best performing model being the Synergy model (fAPAR: R2: 0.99; RMSE: 0.02 and FCover: R2: 0.98; RMSE: 0.04). The ability of the models to process real data was subsequently demonstrated by applying the OLCI models to S3 surface reflectance products acquired over Western Europe and Argentina. Obtained maps showed consistent patterns and variable ranges, and comparison against corresponding Sentinel-2 products (coarsened to a 300 m spatial resolution) led to reasonable matches (R2: 0.5-0.7). Altogether, given the availability of the multiple data sources, the FLEX tandem mission will foster unique opportunities to quantify essential vegetation properties, and hence facilitate the interpretation of the measured fluorescence levels.

Developing a New Spectral Index for Detecting Cadmium-Induced Stress in Rice on a Regional Scale.

In natural farmland ecosystems, cadmium (Cd) pollution in rice has attracted increasing attention because of its high toxicity, relative mobility, and high water solubility. This study aims to develop a spectral index for detecting Cd stress in rice on a regional scale. Three experimental sites are selected in Zhuzhou City, Hunan Province. The hyperspectral data, chlorophyll (Chl) content, leaf area index, average leaf angle, Cd concentration in soil, and Sentinel-2A images from 2017 and 2018 are collected. A new spectral index sensitive to Cd stress in rice is established based on the global sensitivity analysis of the radiative transfer model PROSPECT + SAIL (commonly called PROSAIL) model with the auxiliary of the field-measured data. The heavy metal Cd stress-sensitive spectral index (HCSI) is devised as an indicator of the degree of Cd stress in rice. Results indicate that (1) the HCSI developed based on Chl is a good indicator of rice damage caused by Cd stress, that is, low values of HCSI occur in rice subject to relatively high pollution; (2) compared with common spectral indices, such as red-edge position and red-edge Chl index, HCSI is more sensitive to Chl content with higher Pearson correlation coefficients with respect to Chl content, ranging from 0.85 to 0.95; (3) HCSI is successfully applied in Sentinel-2A images from the two different years of monitoring rice Cd stress on a regional scale. Cd stress levels in rice stabilized, and the largest area percentage of each pollution levels of Cd decreased in the following order: No pollution (i.e., 40%), low pollution (i.e., 35%), and high pollution (i.e., 25%). This study indicates that a combination of simulation data from the PROSAIL model and measured data appears to be a promising method for establishing a sensitivity spectral index to heavy metal stress, which can accurately detect regional Cd stress in crops.

Uncertainty in Soil Moisture Retrievals: an Ensemble Approach using SMOS L-Band Microwave Data.

The uncertainty of surface soil moisture (SM) retrievals from satellite brightness temperature (TB) observations depends primarily on the choice of radiative transfer model (RTM) parameters, prior SM information and TB inputs. This paper studies the sensitivity of several established and experimental SM retrieval products from the Soil Moisture Ocean Salinity (SMOS) mission to these choices at 11 reference sites, located in 7 watersheds across the United States (US). Different RTM parameter sets cause large biases between retrievals. Whereas typical RTM parameter sets are calibrated for SM retrievals, it is shown that a parameter set carefully optimized for TB forward modeling can also be used for retrieving SM. It is also shown that the inclusion of dynamic prior SM estimates in a Bayesian retrieval scheme can strongly improve SM retrievals, regardless of the choice of RTM parameters. The second part of this paper evaluates the ensemble uncertainty metrics for SM retrievals obtained by propagating a wide range of RTM parameters through the RTM, and the relationship with time series metrics obtained by comparing SM retrievals with in situ data. As expected for bounded variables, the total spread in the ensemble SM retrievals is smallest for wet and dry SM values and highest for intermediate SM values. After removal of the strong long-term SM bias associated with the RTM parameter values for individual ensemble members, the remaining anomaly ensemble SM spread shows higher values when SM deviates further from its long-term mean SM. This reveals higher-order biases (e.g. differences in variances) in the retrieval error, which should be considered when characterizing retrieval error. The time-average anomaly ensemble SM spread of 0.037 m3/m3 approximates the actual time series unbiased root-mean-square-difference of 0.042 m3/m3 between ensemble mean retrievals and in situ data across the reference sites.

Estimation of leaf traits from reflectance measurements: comparison between methods based on vegetation indices and several versions of the PROSPECT model.

BACKGROUND: Leaf biochemical composition corresponds to traits related to the plant state and its functioning. This study puts the emphasis on the main leaf absorbers: chlorophyll a and b ([Formula: see text]), carotenoids ([Formula: see text]), water ([Formula: see text]) and dry mater ([Formula: see text]) contents. Two main approaches were used to estimate [[Formula: see text] [Formula: see text], [Formula: see text], [Formula: see text]] in a non-destructive way using spectral measurements. The first one consists in building empirical relationships from experimental datasets using either the raw reflectances or their combination into vegetation indices (VI). The second one relies on the inversion of physically based models of leaf optical properties. Although the first approach is commonly used, the calibration of the empirical relationships is generally conducted over a limited dataset. Consequently, poor predictions may be observed when applying them on cases that are not represented in the training dataset, i.e. when dealing with different species, genotypes or under contrasted environmental conditions. The retrieval performances of the selected VIs were thus compared to the ones of four PROSPECT model versions based on reflectance data acquired at two phenological stages, over six wheat genotypes grown under three different nitrogen fertilizations and two sowing density modalities. Leaf reflectance was measured in the lab with a spectrophotometer equipped with an integrating sphere, the leaf being placed in front of a white Teflon background to increase the sensitivity to leaf biochemical composition. Destructive measurements of [[Formula: see text] [Formula: see text], [Formula: see text], [Formula: see text]] were performed concurrently. RESULTS: The destructive measurements demonstrated that the carotenoid, [Formula: see text], and chlorophyll, [Formula: see text], contents were strongly correlated (r2 = 0.91). The sum of [Formula: see text] and [Formula: see text], i.e. the total chlorophyllian pigment content, [Formula: see text], was therefore used in this study. When inverting the PROSPECT model, accounting for the brown pigment content, [Formula: see text], was necessary when leaves started to senesce. The values of [Formula: see text] and [Formula: see text] were well estimated (r2 = 0.81 and r2 = 0.88 respectively) while the dry matter content, [Formula: see text], was poorly estimated (r2 = 0.00). Retrieval of [Formula: see text] from PROSPECT versions was only slightly biased, while substantial overestimation of [Formula: see text] was observed. The ranking between estimated values of [Formula: see text] and [Formula: see text] from the several PROSPECT versions and that derived using the VIs were similar to the ranking observed over the destructively measured values of [Formula: see text] and [Formula: see text]. CONCLUSIONS: PROSPECT model inversion and empirical VI approach provide similar retrieval performances and are useful methods to estimate leaf biochemical composition from spectral measurements. However, the PROSPECT model inversion gives potential access to additional traits on surface reflectivity and leaf internal structure. This study suggests that non-destructive estimation of leaf chlorophyll and water contents is a relevant method to provide leaf traits with relatively high throughput.

SCOPE model applied for rapeseed in Spain.

The integrated SCOPE (Soil, Canopy Observation, Photochemistry and Energy balance) model, coupling radiative transfer theory and biochemistry, was applied to a biodiesel crop grown in a Spanish agricultural area. Energy fluxes and CO2 exchange were simulated with this model for the period spanning January 2008 to October 2008. Results were compared to experimental measurements performed using eddy covariance and meteorological instrumentation. The reliability of the model was proven by simulating latent (LE) and sensible (H) heat fluxes, soil heat flux (G), and CO2 exchanges (NEE and GPP). LAI data used as input in the model were retrieved from the MODIS and MERIS sensors. SCOPE was able to reproduce similar seasonal trends to those measured for NEE, GPP and LE. When considering H, the modelled values were underestimated for the period covering July 2008 to mid-September 2008. The modelled fluxes reproduced the observed seasonal evolution with determination coefficients of over 0.77 when LE and H were evaluated. The modelled results offered good agreement with observed data for NEE and GPP, regardless of whether LAI data belonged to MODIS or MERIS, showing slopes of 0.87 and 0.91 for NEE-MODIS and NEE-MERIS, and 0.91 and 0.94 for GPP-MODIS and GPP-MERIS, respectively. Moreover, SCOPE was able to reproduce similar seasonal behaviours to those observed for the experimental carbon fluxes, clearly showing the CO2 sink/source behaviour for the whole period studied.