The retrieval of plant functional traits from canopy spectra through RTM-inversions and statistical models are both critically affected by plant phenology

Plant functional traits play a key role in the assessment of ecosystem processes and properties. Optical remote sensing is ascribed a high potential in capturing those traits and their spatiotemporal patterns. In vegetation remote sensing, reflectance-based retrieval methods are either statistical (relying on empirical observations) or physically-based (based on inversions of a radiative transfer model, RTM). Both trait retrieval approaches remain poorly investigated regarding phenology. However, within the phenology of a plant, its leaf constituents, canopy structure, and the presence of phenology-related organs (i.e., flowers or inflorescence) vary considerably – and so does its reflectance. We, therefore, addressed the question of how plant phenology affects the predictive performance of both statistical and RTM-based methods and how this effect differs between traits. For a complete growing season, we weekly measured traits of 45 herbaceous plant species together with hyperspectral canopy reflectance (ASD FieldSpec III). Plants were grown in an experimental setup. The investigated traits comprised Leaf Area Index (LAI) and the leaf traits chlorophyll, anthocyanins, carotenoids, equivalent water thickness, and leaf mass per area. We compared the predictive performances of PLSR models and three variants of PROSAIL inversions based on (1) all observations and based on (2) a phenological subset where flowering plants were excluded and only those observations most suitable for modeling were kept. Our results show that both statistical and RTM-based trait retrievals were largely affected by phenology. For carotenoids for example, R$^{2}$ decreased from 0.58 at non-flowering canopies to 0.25 at 100% flowering canopies. Temporal trends were diverse. LAI and equivalent water thickness were best estimated earlier in the growing season; chlorophyll and carotenoids towards senescence. PLSR models showed generally higher bias than the PROSAIL-based retrieval approaches. Lookup-table inversion of PROSAIL in combination with a continuous wavelet transformation of reflectance showed highest accuracies. We found RTM-based retrieval not to be as accurate and transferable as previously indicated. Our results suggest that phenology is essential for accurate retrieval of plant functional traits and varies depending on the studied species and functional traits, respectively

Estimation of essential vegetation variables in a dehesa ecosystem using reflectance factors simulated at different phenological stages

[ES] Los pastos arbolados y arbustivos son vitales para la producción ganadera extensiva y sostenible, la conservación de la biodiversidad y la provisión de servicios ecosistémicos y se localizan en áreas que serán previsiblemente más afectadas por el cambio climático. Sin embargo, las características estructurales, fenológicas, y las propiedades ópticas de la vegetación en estos ecosistemas mixtos, como los ecosistemas adehesados en la Península Ibérica que combinan un estrato herbáceo y/o arbustivo con un dosel arbóreo disperso, constituyen un serio desafío para su estudio mediante teledetección. Este trabajo combina métodos físicos y empíricos para la estimación de variables de la vegetación esenciales para la modelización de su funcionamiento: índice de área foliar (LAI, m2 /m2 ), contenido en clorofila a nivel de hoja (Cab,leaf, μg/cm2 ) y dosel (Cab,canopy, g/m2 ) y contenido en materia seca a nivel de hoja (Cm,leaf, g/cm2 ) y dosel (Cm,canopy, g/m2), en un ecosistema de dehesa. Para este propósito se construyó una base de datos espectral simulada considerando las cuatro principales etapas fenológicas del estrato herbáceo, el más dinámico del ecosistema, (rebrote otoñal, máximo verdor, inicio de la senescencia y senescencia estival) mediante la combinación de los modelos de transferencia radiativa PROSAIL y FLIGHT. Esta base de datos se empleó para ajustar diferentes modelos predictivos basados en índices de vegetación (IV) propuestos en la literatura y en Partial Least Squares Regression (PLSR). PLSR permitió obtener los modelos con mayor poder de predicción (R2  ≥ 0,93, RRMSE ≤ 10,77 %), tanto para las variables a nivel de hoja como a nivel de dosel. Los resultados sugieren que los efectos direccionales y geométricos controlan las relaciones entre los factores de reflectividad (R) simulados y los parámetros foliares. Se observa una alta variabilidad estacional en la relación entre variables biofísicas e IVs, especialmente para LAI y Cab que se confirma en el análisis PLSR. Los modelos desarrollados deben ser aún validados con datos espectrales medidos con sensores próximos o remotos.[EN] Mixed vegetation systems such as wood pastures and shrubby pastures are vital for extensive and sustainable livestock production as well as for the conservation of biodiversity and provision of ecosystem services, and are mostly located in areas that are expected to be more strongly affected by climate change. However, the structural characteristics, phenology, and the optical properties of the vegetation in these mixed -ecosystems such as savanna-like ecosystems in the Iberian Peninsula which combines herbaceous and/or shrubby understory with a low density tree cover, constitute a serious challenge for the remote sensing studies. This work combines physical and empirical methods to improve the estimation of essential vegetation variables: leaf area index (LAI, m2 / m2 ), leaf (Cab,leaf, μg / cm2 ) and canopy(Cab,canopy, g / m2 ) chlorophyll content, and leaf (Cm, leaf, g / cm2 ) and canopy (Cm,canopy, g / m2 ) dry matter content in a dehesa ecosystem. For this purpose, a spectral simulated database for the four main phenological stages of the highly dynamic herbaceous layer (summer senescence, autumn regrowth, greenness peak and beginning of senescence), was built by coupling PROSAIL and FLIGHT radiative transfer models. This database was used to calibrate different predictive models based on vegetation indices (VI) proposed in the literature which combine different spectral bands; as well as Partial Least Squares Regression (PLSR) using all bands in the simulated spectral range (400-2500 nm). PLSR models offered greater predictive power (R2 ≥ 0.93, RRMSE ≤ 10.77 %) both for the leaf and canopy- level variables. The results suggest that directional and geometric effects control the relationships between simulated reflectance factors and the foliar parameters. High seasonal variability is observed in the relationship between biophysical variables and IVs, especially for LAI and Cab, which is confirmed in the PLSR analysis. The models developed need to be validated with spectral data obtained either with proximal or remote sensors.ste estudio se ha llevado a cabo en el contexto de los proyectos FLUXPEC (CGL2012-34383) y SynerTGE (CGL2015-69095-R, MINECO/FEDER,UE) financiados por el Ministerio de Economía y Competitividad. Agradecemos el apoyo de los proyectos IB16185 de la Junta de Extremadura, MoReDEHESHyReS (No. 50EE1621, Agencia Espacial Alemana (DLR) y Ministerio Alemán de Asuntos Económicos y Energía) y el premio de la fundación Alexander von Humboldt vía Premio Max-Planck a Markus ReichsteinMartín, MP.; Pacheco-Labrador, J.; González-Cascón, R.; Moreno, G.; Migliavacca, M.; García, M.; Yebra, M.... (2020). Estimación de variables esenciales de la vegetación en un ecosistema de dehesa utilizando factores de reflectividad simulados estacionalmente. Revista de Teledetección. 0(55):31-48. https://doi.org/10.4995/raet.2020.13394OJS3148055Alonso, M., Rozados, M.J., Vega, J.A., Pérez- Gorostiaga, P., Cuiñas, P., Fontúrbel, M.T., Fernández, C. 2002. Biochemical Responses of Pinus pinaster Trees to Fire-Induced Trunk Girdling and Crown Scorch: Secondary Metabolites and Pigments as Needle Chemical Indicators. 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Remote sensing tools for monitoring grassland plant leaf traits and biodiversity

Rocchini, Duccio1This project has received funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant No. 721995 (project Trustee).openGrasslands are one of the most important ecosystems on Earth, covering approximately onethird of the Earth’s surface. Grassland biodiversity is important as many services provided by such ecosystems are crucial for the human economy and well-being. Given the importance of grasslands ecosystems, in recent years research has been carried out on the potential to monitor them with novel remote sensing techniques. Improved detectors technology and novel sensors providing finescale hyperspectral imagery have been enabling new methods to monitor plant traits (PTs) and biodiversity. The aims of the work were to study different approaches to monitor key grassland PTs such as Leaf Area Index (LAI) and biodiversity-related traits. The thesis consists of 3 parts: 1) Evaluating the performance of remote sensing methods to estimate LAI in grassland ecosystems, 2) Estimating plant biodiversity by using the optical diversity approach in grassland ecosystems, and 3) Investigating the relationship between PTs variability with alpha and beta diversity for the applicability of the optical diversity approach in a subalpine grassland of the Italian Alps To evaluate the performance of remote sensing methods to estimate LAI, temporal and spatial observations of hyperspectral reflectance and LAI were analyzed at a grassland site in Monte Bondone, Italy (IT-MBo). In 2018, ground temporal observations of hyperspectral reflectance and LAI were carried out at a grassland site in Neustift, Austria (AT-NEU). To estimate biodiversity, in 2018 and 2019 a floristics survey was conducted to determine species composition and hyperspectral data were acquired at two grassland sites: IT-MBo and University of Padova’s Experimental Farm, Legnaro, Padua, Italy (IT-PD) respectively. Furthermore, in 2018, biochemistry analysis of the biomass samples collected from the grassland site IT-MBo was carried out to determine the foliar biochemical PTs variability. The results of the thesis demonstrated that the grassland spectral response across different spectral regions (Visible: VIS, red-edge: RE, Near-infrared: NIR) showed to be both site-specific and scale-dependent. In the first part of the thesis, the performance of spectral vegetation indices (SVIs) based on visible, red-edge (RE), and NIR bands alongside SVIs solely based or NIRshoulder bands (wavelengths 750 - 900 nm) was evaluated. A strong correlation (R2 > 0.8) was observed between grassland LAI and both RE and NIR-shoulder SVIs on a temporal basis, but not on a spatial basis. Using the PROSAIL Radiative Transfer Model (RTM), it was demonstrated that grassland structural heterogeneity strongly affects the ability to retrieve LAI, with high uncertainties due to structural and biochemical PTs co-variation. In the second part, the applicability of the spectral variability hypothesis (SVH) was questioned and highlighted the challenges to use high-resolution hyperspectral images to estimate biodiversity in complex grassland ecosystems. It was reported that the relationship between biodiversity (Shannon, Richness, Simpson, and Evenness) and optical diversity metrics (Coefficient of variation (CV) and Standard deviation (SD)) is not consistent across plant communities. The results of the second part suggested that biodiversity in terms of species richness could be estimated by optical diversity metrics with an R2 = 0.4 at the IT-PD site where the grassland plots were artificially established and are showing a lower structure and complexity from the natural grassland plant communities. On the other hand, in the natural ecosystems at IT-MBo, it was more difficult to estimate biodiversity indices, probably due to structural and biochemical PTs co-variation. The 18 effects of canopy non-vegetative elements (flowers and dead material), shadow pixels, and overexposed pixels on the relationship between optical diversity metrics and biodiversity indices were highlighted. In the third part, we examined the relationship between PTs variability (at both local and community scales, measured by standard deviation and by the Euclidean distances of the biochemical and biophysical PTs respectively) and taxonomic diversity (both α-diversity and βdiversity, measured by Shannon’s index and by Jaccard dissimilarity index of the species, families, and functional groups percent cover respectively) in Monte Bondone, Trentino province, Italy. The results of the study showed that the PTs variability metrics at alpha scale were not correlated with α-diversity. However, the results at the community scale (β-diversity) showed that some of the investigated biochemical and biophysical PTs variations metrics were associated with β-diversity. The SVH approach was also tested to estimate β-diversity and we found that spectral diversity calculated by spectral angular mapper (SAM) showed to be a better proxy of biodiversity in the same ecosystem where the spectral diversity failed to estimate alpha diversity, this leading to the conclusion that the link between functional and species diversity may be an indicator of the applicability of optical sampling methods to estimate biodiversity. The findings of the thesis highlighted that grassland structural heterogeneity strongly affects the ability to retrieve both LAI and biodiversity, with high uncertainties due to structural and biochemical PTs co-variation at complex grassland ecosystems. In this context, the uncertainties of satellite-based products (e.g., LAI) in monitoring grassland canopies characterized by either spatially or temporally varying structure need to be carefully taken into account. The results of the study highlighted that the poor performance of optical diversity proxies in estimating biodiversity in structurally heterogeneous grasslands might be due to the complex relationships between functional diversity and biodiversity, rather than the impossibility to detect functional diversity with spectral proxiesopenImran, H.A