Uncovering the hidden half of plants using new advances in root phenotyping

Major increases in crop yield are required to keep pace with population growth and climate change. Improvements to the architecture of crop roots promise to deliver increases in water and nutrient use efficiency but profiling the root phenome (i.e., its structure and function) represents a major bottleneck. We describe how advances in imaging and sensor technologies are making root phenomic studies possible. However, methodological advances in acquisition, handling and processing of the resulting ‘big-data’ is becoming increasingly important. Advances in automated image analysis approaches such as Deep Learning promise to transform the root phenotyping landscape. Collectively, these innovations are helping drive the selection of the next-generation of crops to deliver real world impact for ongoing global food security efforts

Drought and water stress of crops: a look at the soil-root system interplay.

International audienc

Transferts hydriques sol-plante et extraction racinaire (une approche de la spatialisation des prélèvements hydriques par tomographie de résistivité électrique)

Une meilleure connaissance du fonctionnement du prélèvement hydrique par les racines des plantes est nécessaire pour améliorer les stratégies de gestion de la ressource en eau et, à ce titre, comprendre l acquisition de l eau du sol par les systèmes racinaires reste un objectif important de la recherche agronomique. Cependant, la caractérisation du fonctionnement du transfert hydrique sol-plante et la spatialisation des prélèvements à l échelle parcellaire reste problématique. Le milieu sol-plante est un système complexe, variable dans l espace et dans le temps. La réduction et l épuisement de l eau dans la zone racinaire sont contrôlés par le sol, la plante et les facteurs climatiques. Pour pouvoir spatialiser l extraction hydrique à l échelle de la population de plantes (échelle parcellaire), il est nécessaire de posséder un moyen permettant d estimer l extraction hydrique et sa variabilité reflétant à la fois l hétérogénéité globale et spatiale de la population et celle du milieu. Dans ce contexte, nous avons utilisé la Tomographie de Résistivité Electrique (ERT) comme approche alternative aux méthodes classiques de mesures hydriques (bilan hydrique) pour estimer les prélèvements hydriques des racines. Cette méthode est basée sur une mesure spatialisée de la résistivité électrique du sol, qui est elle-même reliée à la variabilité spatio-temporelle de la teneur en eau. La cartographie 2D ou 3D de la résistivité et ses variations dans le temps seront alors reliées aux variations de teneur en eau et aux prélèvements hydriques distribués dans l espace. Les objectifs de cette étude expérimentale sont d évaluer les apports de la tomographie de résistivité électrique pour spatialiser les prélèvements hydriques à l échelle parcellaire et pour analyser les transferts d eau dans le système sol-plante, avec des plantes diverses et une disponibilité en eau variable. Pour cela, nous avons travaillé avec trois types de plante (Maïs, Sorgho, Féverole) présentant des systèmes racinaires et des capacités de prélèvement d eau différents. Ces plantes ont été soumises à trois conditions de disponibilité en eau allant de bien irrigué à sec. Nous avons pu estimer l extraction hydrique à l échelle parcellaire par une approche directe utilisant la variation temporelle de la résistivité électrique du sol ou par une calibration entre résistivité électrique et teneur en eau établie in situ. Les cartes de prélèvements hydriques issues de cette estimation montrent la variation des prélèvements dans l espace et le temps. L estimation des prélèvements hydriques racinaires est donc réalisable à l échelle parcellaire. Cependant, l estimations spatiale des ces prélèvements par ERT présente des limites plus ou moins fortes liées à la sensibilité de mesure (sensibilité décroissante en profondeur, erreur RMS de la calibration teneur en eau-résistivité de l ordre de 0.03 cm3.cm-3), au dispositif de mesures (résolution décroissante en profondeur avec une disposition d électrodes en surface) et aux conditions expérimentales (problèmes de mesures dans les sol secs et argileux: problème de contact sol électrodes et hétérogénéité induite par la fissuration). Ce travail présente donc une première étape méthodologique, montrant la faisabilité de l utilisation de l ERT dans une quantification spatiale du prélèvement si des données hydriques sont disponibles conjointement, et s inscrit dans une démarche plus générale de compréhension de l hétérogénéité spatiale de l extraction en relation avec les propriétés du sol et le développement du système racinaireA better knowledge of the functioning of water uptake by plant roots is necessary in order to optimize agricultural water resources management. To this respect, the understanding of the acquisition of soil water by root systems is an important objective of agronomical research. However, characterization of water transfer in the soil-plant system and the spatialization of water uptake at the field scale are still problematic and challenging.Soil - plant environment is a complex system, varying in time and space. The depletion of soil water in the rooted zone is controlled by soil, plant and climatic factors. In order to spatialize the water uptake at the plant s population scale, methodologies and proxy variable allowing an estimation of water extraction and its variability are highly needed. This would reflect simultaneously the overall and spatial heterogeneity of the population and its growing medium. To this aim, we used the Electrical Resistivity Tomography (ERT) as an alternative approach to the classical methods of water measurements (local soil water balance) for estimating root water uptake. ERT results in a spatial estimation of soil electrical resistivity, the latter being related to the variability of soil water content. 2D or 3D imaging of soil electrical resistivity and its variations with time are related to water content variations as well as water extraction distribution in soil. This experimental study aims at evaluating ERT for spatializing water uptake at the field scale with various plants and different levels of water availability. Three types of plant (Maize, Sorghum and Broad bean) were selected because they exhibit different root systems morphologies and /or and water extraction capacities. These crops were subjected in the field to three levels of water availability ranging from rain fed to full irrigation. Water extraction and its variability, at the field scale, was estimated firstly by a direct approach which empirically links the temporal difference in soil electrical resistivity and the uptake. Secondly, an indirect more general approach, using in situ calibration between soil electrical resistivity and water content into a spatialized water balance calculation has been used. The water uptake images resulting from these estimations show high spatial and temporal variation of water uptake. The estimation of root water uptake at field scale by ERT is thus possible. However, this spatial estimation can be more or less severely restricted by different constraints which are related to: ERT sensitivity (decrease of ERT sensitivity with depth, accuracy of the in situ water content-resistivity calibration relationship: RMSE ~ 0.03 cm3.cm-3), the type of ERT measurement setup (decrease of resolution with depth with a surface array) and to the environmental conditions (problems for ERT measurements in dry and clay soil: decrease of soil-electrode contact and increase of soil heterogeneity due to soil cracking). This work contributes to a first methodological step, showing the possible use of ERT for spatializing and quantifying the spatial variations of root water uptake, if soil hydrodynamic data are available. More globally, this work traces new developments in the understanding of the spatial heterogeneity of root water uptake in relation with soil properties and root system growthAVIGNON-BU Centrale (840072102) / SudocSudocFranceF

Availability of soil cadmium using stable and radioactive isotope dilution

The aim of this research was (i) to compare the use of stable (111Cd) and radioactive (109Cd) isotopes for assessing the isotopically exchangeable pool of Cd (ECd), (ii) to evaluate a simpler alternative method, the extraction by 1 M CaCl2, (iii) to determine ECd in a wide range of soil and contamination types and (iv) to assess how ECd can be affected by the soil characteristics. Measurement with 111Cd gave equivalent but more repeatable results than those of 109Cd. Increasing the acidity of the spike solution led to an overestimation of ECd. Extraction by 1 M CaCl2 generally gave similar values to isotope dilution. Measured on 29 soil samples, ECd was on average 44% of the total Cd (CdT). The cultivated soils showed the highest relative cadmium availability (ECd/CdT = 46% on average) and the geochemically enriched soils the lowest (20%). For the whole sample set, ECd variance was mainly explained by the correlation with CdT (r = 0.86), while ECd/CdT was negatively correlated with pH (r = − 0.73). In the cultivated soils, ECd increased with CEC (r = 0.94), while ECd/CdT decreased with increasing iron content (r = − 0.91)

Non-invasive monitoring of soil water dynamics in mixed cropping systems: A case-study in Ratchaburi province, Thailand

Agriculture on shallow or steep soils in the humid tropics often leads to low resource use efficiency. Contour hedgerow intercropping systems have been proposed to reduce run-off and control soil erosion. However, competition for water and nutrients between crops and associated hedgerows may reduce the overall performance of contour hedgerow systems. Electrical resistivity tomography (ERT) is a valuable technique used to assess the distribution and dynamics of soil moisture noninvasively. In this study, we demonstrated its potential to measure soil water depletion in the field in distinct cropping patterns in Ratchaburi province, Thailand. The measurements showed that the soils of our experimental plots were very heterogeneous both along the slope as with depth. This observation highlighted some constraints of the ERT method for soil moisture monitoring in the field, such as the difficulty of defining a relationship between electrical conductivity and soil moisture in very heterogeneous soils. Nevertheless, spatial analysis of the data revealed contrasting water depletion patterns under monocropping and intercropping systems. In this way, ERT provides access to information about the vadose zone moisture dynamics that would be unavailable with classical soil moisture measurements

Evaluating experimental design of ERT for soil moisture monitoring in contour hedgerow intercropping systems

Contour hedgerow intercropping systems have been proposed as an alternative to traditional agricultural practice with a single crop, as they are effective in reducing run-off and soil erosion. However, competition for water and nutrients between crops and associated hedgerows may reduce the overall performance of these systems. To get a more detailed understanding of the competition for water, spatially resolved monitoring of soil water contents in the soil-plant-atmosphere system is necessary. Electrical resistivity tomography (ERT) is potentially a valuable technique to monitor changes in soil moisture in space and time. In this study, the performance of different ERT electrode arrays to detect the soil moisture dynamics in a mono- and an intercropping system was tested. Their performance was analyzed based on a synthetic study using geophysical measures, such as data recovery and resolution, and using spatial statistics of retrieved water content, such as an adjusted coefficient of variation and semivariances. The synthetic ERT measurements detected differences between the cropping systems and retrieved spatial structure of the soil moisture distribution, but the variance and semivariance were underestimated. Sharp water content contrasts between horizons or in the neighborhood of a root water uptake bulb were smoothened. The addition of electrodes deeper in the soil improved the performance, but sometimes only marginally. ERT is therefore a valuable tool for soil moisture monitoring in the field under different cropping systems if an electrode array is used which can resolve the patterns expected to be present in the medium. The use of spatial statistics allowed to not only identify the overall model recovery, but also to quantify the recovery of spatial structures