Assessment of chlorophyll fluorescence yields at canopy level by active and passive methods. Application to water stress detection

La fluorescence de la chlorophylle (ChlF) est directement liée au processus photosynthétique. Cependant, au niveau de la canopée, ce lien physiologique entre la fluorescence et la photosynthèse peut être brouillé par les changements structurels de la végétation et les interactions entre la lumière du soleil et la structure 3D de la canopée. De plus, une grande partie de nos connaissances sur la relation entre la fluorescence et l'état physiologique des plantes provient d'études au niveau des feuilles réalisées dans des conditions de laboratoire. La signification physiologique de la ChlF au niveau de la canopée et dans des conditions naturelles est toujours un sujet de recherche majeur. Ce projet doctoral avait pour objectifs : 1. Etude du rendement de fluorescence de la chlorophylle au niveau de la canopée: nous décrivons un nouvel instrument, Ledflex, qui est un micro-LIDAR dédié à effectuer des mesures continues du rendement de fluorescence de la végétation. Ledflex a été appliqué avec succès dans des conditions de plein soleil pour établir la signature du stress hydrique sur la canopée du pois (Pisum Sativum). Dans des conditions bien irriguées, le cycle diurne du rendement de fluorescence observé (Fs) présente une forme en M avec un minimum (Fmin) vers midi supérieur au niveau observé à l’obscurité (Fo). Après plusieurs jours sans irrigation, Fs diminue et Fmin<Fo. Cette méthodologie s'est révélée être un indice à distance efficace pour détecter le stress hydrique dans la végétation. 2. Mesures actives et passives de la fluorescence de la chlorophylle au niveau de la canopée des cultures de pomme de terre et étude comparative des cycles diurnes des rendements de fluorescence apparents: nous avons présenté pour la première fois des mesures parallèles actives et passives des cycles diurnes de ChlF de cultures de pommes de terre au niveau de la canopée. Les mesures de fluorescence actives ont été réalisées à l'aide de Ledflex. Des mesures passives de fluorescence induite par le soleil (SIF) ont été effectuées avec Spectroflex, un instrument basé sur la méthode du comblement des bandes d'absorption A et B de l'oxygène à 760 nm et 687 nm, respectivement. Les mesures actives ont montré des variations significatives tout au long du cycle diurne, directement attribuées aux changements du rendement photosynthétique du photosystème II. Les flux de fluorescence acquis par Spectroflex à 687 et 760 nm ont montré des différences qualitatives et quantitatives expliquées par l'importance relative des émissions des photosystèmes I et II entre ces deux bandes. Nous avons défini une nouvelle approche pour dériver un proxy du rendement de fluorescence de SIF à partir d'une combinaison linéaire des flux à 687 nm et 760 nm. 3. Mesures de fluorescence actives in situ et passives aéroportées pour la détection du stress hydrique sur un champ de fétuque: nous avons utilisé Ledflex pour déterminer l'effet du stress hydrique sur la fluorescence d'un champ de fétuque. En plus des données de fluorescence, la température de surface a également été mesurée à l'aide de radiomètres infrarouges. Enfin, Airflex, un fluorimètre passif mesurant le comblement de la bande d'absorption d'oxygène atmosphérique à 760 nm a été installé dans un avion ultra-léger et a survolé les parcelles étudiées pendant les jours les plus critiques de la campagne. Ledflex a détecté le stress hydrique et sa récupération, bien corrélés avec la différence de température de surface entre la parcelle stressée et une parcelle témoin. Bien que les mesures de fluorescence actives et passives de la chlorophylle soient qualitativement en accord, la précision et la sensibilité de la méthode active étaient bien meilleures.The chlorophyll fluorescence (ChlF) is directly related to the photosynthetic process. However, at canopy level this physiological link between fluorescence and photosynthesis may be blurred by structural vegetation changes and geometrical effects linked to interactions between sunlight and the three-dimensional structure of the canopy. Furthermore, much of our knowledge about the relationship between fluorescence and the physiological status of plants come from leaf level studies carried out under laboratory conditions. The physiological significance of ChlF at canopy level and under natural conditions is still a major subject of research and a source of uncertainties in the interpretation of SIF. This doctoral project aims were: 1. To study chlorophyll fluorescence yield at canopy level: we describe a new instrument, Ledflex, which is a micro-LIDAR dedicated to perform continuous measurements of vegetation fluorescence yield. Ledflex has been successfully applied under full sunlight conditions to establish the signature of water-stress on a pea (Pisum Sativum) canopy. Under well-watered conditions the Fs diurnal cycle present an M shape with a minimum (Fmin) at noon which is higher than the fluorescence level observed at predawn (Fo). After several days withholding watering, Fs decreases and Fmin<Fo. This methodology was successfully validated on different crops. This has shown to be an efficient remote index to detect water stress in vegetation. 2. Active and passive chlorophyll fluorescence measurements at canopy level on potato crops and comparison of diurnal cycles of apparent fluorescence yields: we presented by the first time parallel active and passive outdoors measurements of diurnal cycles of ChlF of potato crops at canopy level. Active fluorescence measurements were performed using Ledflex. Passive solar-induced fluorescence (SIF) measurements were done with Spectroflex, an instrument based on the method of filling-in in the A and B oxygen absorption bands at 760 nm and 687 nm, respectively. Active measurements showed significant variations throughout the day, directly attributed to changes in photosystem II (PS II) photosynthetic yield. The fluorescence fluxes recovered by Spectroflex at 687 nm and 760 nm showed qualitative and quantitative differences accounted for by the relative importance of photosystems I and II emissions between these two bands. We defined a new approach to derive a proxy of fluorescence yield from SIF from a linear combination of fluxes at 687 nm and 760 nm. 3. Active in situ and passive airborne fluorescence measurements for water stress detection on a fescue field: we used Ledflex to determine the water stress effect on fluorescence of a fescue field. In addition to fluorescence data, surface temperature was also measured using infrared radiometers. Last but not least, Airflex, a passive fluorometer measuring the filling-in of the atmospheric oxygen absorption band at 760 nm, was installed in an ultralight plane and flown during the most critical days of the campaign. Ledflex detected the water stress and posterior recovery of stressed plot, well correlated with the surface temperature difference between the stressed and a control plot. Although active and passive chlorophyll fluorescence measurements are qualitatively in agreement, the accuracy and sensitivity of the active method was much better

Suivi expérimental du rendement de fluorescence des couverts végétaux par des techniques actives et passives. Application à la détection du stress hydrique

The chlorophyll fluorescence (ChlF) is directly related to the photosynthetic process. However, at canopy level this physiological link between fluorescence and photosynthesis may be blurred by structural vegetation changes and geometrical effects linked to interactions between sunlight and the three-dimensional structure of the canopy. Furthermore, much of our knowledge about the relationship between fluorescence and the physiological status of plants come from leaf level studies carried out under laboratory conditions. The physiological significance of ChlF at canopy level and under natural conditions is still a major subject of research and a source of uncertainties in the interpretation of SIF. This doctoral project aims were: 1. To study chlorophyll fluorescence yield at canopy level: we describe a new instrument, Ledflex, which is a micro-LIDAR dedicated to perform continuous measurements of vegetation fluorescence yield. Ledflex has been successfully applied under full sunlight conditions to establish the signature of water-stress on a pea (Pisum Sativum) canopy. Under well-watered conditions the Fs diurnal cycle present an M shape with a minimum (Fmin) at noon which is higher than the fluorescence level observed at predawn (Fo). After several days withholding watering, Fs decreases and Fmin<Fo. This methodology was successfully validated on different crops. This has shown to be an efficient remote index to detect water stress in vegetation. 2. Active and passive chlorophyll fluorescence measurements at canopy level on potato crops and comparison of diurnal cycles of apparent fluorescence yields: we presented by the first time parallel active and passive outdoors measurements of diurnal cycles of ChlF of potato crops at canopy level. Active fluorescence measurements were performed using Ledflex. Passive solar-induced fluorescence (SIF) measurements were done with Spectroflex, an instrument based on the method of filling-in in the A and B oxygen absorption bands at 760 nm and 687 nm, respectively. Active measurements showed significant variations throughout the day, directly attributed to changes in photosystem II (PS II) photosynthetic yield. The fluorescence fluxes recovered by Spectroflex at 687 nm and 760 nm showed qualitative and quantitative differences accounted for by the relative importance of photosystems I and II emissions between these two bands. We defined a new approach to derive a proxy of fluorescence yield from SIF from a linear combination of fluxes at 687 nm and 760 nm. 3. Active in situ and passive airborne fluorescence measurements for water stress detection on a fescue field: we used Ledflex to determine the water stress effect on fluorescence of a fescue field. In addition to fluorescence data, surface temperature was also measured using infrared radiometers. Last but not least, Airflex, a passive fluorometer measuring the filling-in of the atmospheric oxygen absorption band at 760 nm, was installed in an ultralight plane and flown during the most critical days of the campaign. Ledflex detected the water stress and posterior recovery of stressed plot, well correlated with the surface temperature difference between the stressed and a control plot. Although active and passive chlorophyll fluorescence measurements are qualitatively in agreement, the accuracy and sensitivity of the active method was much better.La fluorescence de la chlorophylle (ChlF) est directement liée au processus photosynthétique. Cependant, au niveau de la canopée, ce lien physiologique entre la fluorescence et la photosynthèse peut être brouillé par les changements structurels de la végétation et les interactions entre la lumière du soleil et la structure 3D de la canopée. De plus, une grande partie de nos connaissances sur la relation entre la fluorescence et l'état physiologique des plantes provient d'études au niveau des feuilles réalisées dans des conditions de laboratoire. La signification physiologique de la ChlF au niveau de la canopée et dans des conditions naturelles est toujours un sujet de recherche majeur. Ce projet doctoral avait pour objectifs : 1. Etude du rendement de fluorescence de la chlorophylle au niveau de la canopée: nous décrivons un nouvel instrument, Ledflex, qui est un micro-LIDAR dédié à effectuer des mesures continues du rendement de fluorescence de la végétation. Ledflex a été appliqué avec succès dans des conditions de plein soleil pour établir la signature du stress hydrique sur la canopée du pois (Pisum Sativum). Dans des conditions bien irriguées, le cycle diurne du rendement de fluorescence observé (Fs) présente une forme en M avec un minimum (Fmin) vers midi supérieur au niveau observé à l’obscurité (Fo). Après plusieurs jours sans irrigation, Fs diminue et Fmin<Fo. Cette méthodologie s'est révélée être un indice à distance efficace pour détecter le stress hydrique dans la végétation. 2. Mesures actives et passives de la fluorescence de la chlorophylle au niveau de la canopée des cultures de pomme de terre et étude comparative des cycles diurnes des rendements de fluorescence apparents: nous avons présenté pour la première fois des mesures parallèles actives et passives des cycles diurnes de ChlF de cultures de pommes de terre au niveau de la canopée. Les mesures de fluorescence actives ont été réalisées à l'aide de Ledflex. Des mesures passives de fluorescence induite par le soleil (SIF) ont été effectuées avec Spectroflex, un instrument basé sur la méthode du comblement des bandes d'absorption A et B de l'oxygène à 760 nm et 687 nm, respectivement. Les mesures actives ont montré des variations significatives tout au long du cycle diurne, directement attribuées aux changements du rendement photosynthétique du photosystème II. Les flux de fluorescence acquis par Spectroflex à 687 et 760 nm ont montré des différences qualitatives et quantitatives expliquées par l'importance relative des émissions des photosystèmes I et II entre ces deux bandes. Nous avons défini une nouvelle approche pour dériver un proxy du rendement de fluorescence de SIF à partir d'une combinaison linéaire des flux à 687 nm et 760 nm. 3. Mesures de fluorescence actives in situ et passives aéroportées pour la détection du stress hydrique sur un champ de fétuque: nous avons utilisé Ledflex pour déterminer l'effet du stress hydrique sur la fluorescence d'un champ de fétuque. En plus des données de fluorescence, la température de surface a également été mesurée à l'aide de radiomètres infrarouges. Enfin, Airflex, un fluorimètre passif mesurant le comblement de la bande d'absorption d'oxygène atmosphérique à 760 nm a été installé dans un avion ultra-léger et a survolé les parcelles étudiées pendant les jours les plus critiques de la campagne. Ledflex a détecté le stress hydrique et sa récupération, bien corrélés avec la différence de température de surface entre la parcelle stressée et une parcelle témoin. Bien que les mesures de fluorescence actives et passives de la chlorophylle soient qualitativement en accord, la précision et la sensibilité de la méthode active étaient bien meilleures

Estudio de la posibilidad de utilizar una cámara CCD chaeleon para obtener imágenes de la fluorescencia de la vegetación a nivel de campo

La agricultura es una actividad económica esencial para el desarrollo humano y es el sustento de millones de personas fomentando la seguridad alimentaria e impulsando la economía de países en desarrollo. Sin embargo la producción agrícola es afectada por diferentes factores abióticos (cambio climático) y bióticos (plagas y enfermedades) que disminuyen drásticamente su eficiencia. La fotosíntesis es el único mecanismo de entrada de energía de la biosfera y agentes estresantes como, por ejemplo, la escasez de agua limitan la conductancia estomática en las hojas disminuyendo la entrada de CO2 en las plantas lo que conlleva a una reducción de la fotosíntesis (Flexas et al., 2002a; Flexas y Medrano 2002a). Por estos motivos, resulta importante detectar el estrés antes que los síntomas visuales sean evidentes.Tesi

Active and passive chlorophyll fluorescence measurements at canopy level on potato crops. Evidence of similitude of diurnal cycles of apparent fluorescence yields

International audienceAbstract We performed active and passive measurements of diurnal cycles of chlorophyll fluorescence on potato crops at canopy level in outdoors conditions for 26 days. Active measurements of the stationary fluorescence yield (Fs) were performed using Ledflex, a fluorescence micro-LIDAR described in Moya et al. (Photosynth Res 142:1–15, 2019), capable of remote measurements of chlorophyll fluorescence under full sun-light in the wavelength range from 650 to 800 nm. Passive measurements of solar-induced fluorescence (SIF) fluxes were performed with Spectroflex, an instrument based on the method of filling-in in the O 2 A and O 2 B absorption bands at 760 nm (F760) and 687 nm (F687), respectively. Diurnal cycles of Fs showed significant variations throughout the day, directly attributed to changes in photosystem II yield. Contrasting patterns were observed according to illumination conditions. Under cloudy sky, Fs varied in parallel with photosynthetically active radiation (PAR). By contrast, during clear sky days, the diurnal cycle of Fs showed a “M” shape pattern with a minimum around noon. F687 and F760 showed different patterns, according to illumination conditions. Under low irradiance associated with cloudy conditions, F687 and F760 followed similar diurnal patterns, in parallel with PAR. Under high irradiance associated with clear sky we observed an increase of the F760/F687 ratio, which we attributed to the contributions in the 760 nm emission of photosystem I fluorescence from deeper layers of the leaves, on one end, and by the decrease of 687 nm emission as a result of red fluorescence re-absorption, on the other end. We defined an approach to derive a proxy of fluorescence yield (FYSIF) from SIF measurements as a linear combination of F687 and F760 normalized by vegetation radiance, where the coefficients of the linear combination were derived from the spectral transmittance of Ledflex. We demonstrated a close relationship between diurnal cycles of FYSIF and Fs, which outperformed other approaches based on normalization by incident light

Canopy chlorophyll fluorescence applied to stress detection using an easy-to-build micro-lidar

International audienceLEDFLEX is a micro-lidar dedicated to the measurement of vegetation fluorescence. The light source consists of 4 blue Light-Emitting Diodes (LED) to illuminate part of the canopy in order to average the spatial variability of small crops. The fluorescence emitted in response to a 5-μs width pulse is separated from the ambient light through a synchronized detection. Both the reflectance and the fluorescence of the target are acquired simultaneously in exactly the same field of view, as well as the photosynthetic active radiation and air temperature. The footprint is about 1 m 2 at a distance of 8 m. By increasing the number of LEDs longer ranges can be reached. The micro-lidar has been successfully applied under full sunlight conditions to establish the signature of water stress on pea (Pisum Sativum) canopy. Under well-watered conditions the diurnal cycle presents an M shape with a minimum (Fmin) at noon which is Fmin > Fo. After several days withholding watering, Fs decreases and Fmin < Fo. The same patterns were observed on mint (Menta Spicata) and sweet potatoes (Ipomoea batatas) canopies. Active fluorescence measurements with LEDFLEX produced robust fluorescence yield data as a result of the constancy of the excitation intensity and its geometry fixity. Passive methods based on Sun-Induced chlorophyll Fluores-cence (SIF) that uses high-resolution spectrometers generate only flux data and are dependent on both the 3D structure of vegetation and variable irradiance conditions along the day. Parallel measurements with LEDFLEX should greatly improve the interpretation of SIF changes

Applying Multifractal Analysis to Remotely Sensed Data for Assessing PYVV Infection in Potato (Solanum tuberosum L.) Crops

Multispectral reflectance imagery and spectroradiometry can be used to detect stresses affecting crops. Previously, we have shown that changes in spectral reflectance and vegetation indices detected viral infection 14 days before visual symptoms were noticed by the trained eye. Herein we present evidence that shows that the application of multifractal analysis and wavelet transform to spectroradiometrical data improves the diagnostic power of the remote sensing-based methodology proposed in our previous work. The diagnosis of viral infection was effectively enhanced, providing the earliest detection ever reported, as anomalies were detected 29 and 33 days before appearance of visual symptoms in two experiments

Phenotyping of productivity and resilience in sweetpotato under water stress through UAV‐based multispectral and thermal imagery in Mozambique

International audienc

Implementing Cloud Computing for the Digital Mapping of Agricultural Soil Properties from High Resolution UAV Multispectral Imagery

The spatial heterogeneity of soil properties has a significant impact on crop growth, making it difficult to adopt site-specific crop management practices. Traditional laboratory-based analyses are costly, and data extrapolation for mapping soil properties using high-resolution imagery becomes a computationally expensive procedure, taking days or weeks to obtain accurate results using a desktop workstation. To overcome these challenges, cloud-based solutions such as Google Earth Engine (GEE) have been used to analyze complex data with machine learning algorithms. In this study, we explored the feasibility of designing and implementing a digital soil mapping approach in the GEE platform using high-resolution reflectance imagery derived from a thermal infrared and multispectral camera Altum (MicaSense, Seattle, WA, USA). We compared a suite of multispectral-derived soil and vegetation indices with in situ measurements of physical-chemical soil properties in agricultural lands in the Peruvian Mantaro Valley. The prediction ability of several machine learning algorithms (CART, XGBoost, and Random Forest) was evaluated using R2, to select the best predicted maps (R2 > 0.80), for ten soil properties, including Lime, Clay, Sand, N, P, K, OM, Al, EC, and pH, using multispectral imagery and derived products such as spectral indices and a digital surface model (DSM). Our results indicate that the predictions based on spectral indices, most notably, SRI, GNDWI, NDWI, and ExG, in combination with CART and RF algorithms are superior to those based on individual spectral bands. Additionally, the DSM improves the model prediction accuracy, especially for K and Al. We demonstrate that high-resolution multispectral imagery processed in the GEE platform has the potential to develop soil properties prediction models essential in establishing adaptive soil monitoring programs for agricultural regions

High-throughput characterization and phenotyping of resistance and tolerance to virus infection in sweetpotato

Breeders have made important efforts to develop genotypes able to resist virus attacks in sweetpotato, a major crop providing food security and poverty alleviation to smallholder farmers in many regions of Sub-Saharan Africa, Asia and Latin America. However, a lack of accurate objective quantitative methods for this selection target in sweetpotato prevents a consistent and extensive assessment of large breeding populations. In this study, an approach to characterize and classify resistance in sweetpotato was established by assessing total yield loss and virus load after the infection of the three most common viruses (SPFMV, SPCSV, SPLCV). Twelve sweetpotato genotypes with contrasting reactions to virus infection were grown in the field under three different treatments: pre-infected by the three viruses, un-infected and protected from re-infection, and un-infected but exposed to natural infection. Virus loads were assessed using ELISA, (RT-)qPCR, and loop-mediated isothermal amplification (LAMP) methods, and also through multispectral reflectance and canopy temperature collected using an unmanned aerial vehicle. Total yield reduction compared to control and the arithmetic sum of (RT-)qPCR relative expression ratios were used to classify genotypes into four categories: resistant, tolerant, susceptible, and sensitives. Using 14 remote sensing predictors, machine learning algorithms were trained to classify all plots under the said categories. The study found that remotely sensed predictors were effective in discriminating the different virus response categories. The results suggest that using machine learning and remotely sensed data, further complemented by fast and sensitive LAMP assays to confirm results of predicted classifications could be used as a high throughput approach to support virus resistance phenotyping in sweetpotato breeding