Mathieu Javaux

Modelling root–soil interactions using three–dimensional models of root growth, architecture and function

BackgroundThree–dimensional root architectural models emerged in the late 1980s, providing an opportunity to conceptualise and investigate that all important part of plants that is typically hidden and difficult to measure and study. These models have progressed from representing pre–defined root architectural arrangements, to simulating root growth in response to heterogeneous soil environments. This was done through incorporating soil properties and more complete descriptions of plant function, moving into the realm of functional-structural plant modelling. Modelling studies are often designed to investigate the relationship between root architectural traits and root distribution in soil, and the spatio–temporal variability of resource supply. Modelling root systems presents an opportunity to investigate functional tradeoffs between foraging strategies (i.e. shallow vs deep rooting) for contrasting resources (immobile versus mobile resources), and their dependence on soil type, rainfall and other environmental conditions. The complexity of the interactions between root traits and environment emphasises the need for models in which traits and environmental conditions can be independently manipulated, unlike in the real world.ScopeWe provide an overview of the development of three–dimensional root architectural models from their origins, to their place today in the world of functional–structural plant modelling. The uses and capability of root architectural models to represent virtual plants and soil environment are addressed. We compare features of six current models, RootTyp, SimRoot, ROOTMAP, SPACSYS, R-SWMS, and RootBox, and discuss the future development of functional-structural root architectural modelling.ConclusionFunctional-structural root architectural models are being used to investigate numerous root–soil interactions, over a range of spatial scales. They are not only providing insights into the relationships between architecture, morphology and functional efficiency, but are also developing into tools that aid in the design of agricultural management schemes and in the selection of root traits for improving plant performance in specific environments.

Model-assisted integration of physiological and environmental constraints affecting the dynamic and spatial patterns of root water uptake from soils

Due in part to recent progress in root genetics and genomics, increasing attention is being devoted to root system architecture (RSA) for the improvement of drought tolerance. The focus is generally set on deep roots, expected to improve access to soil water resources during water deficit episodes. Surprisingly, our quantitative understanding of the role of RSA in the uptake of soil water remains extremely limited, which is mainly due to the inherent complexity of the soil-plant continuum. Evidently, there is a need for plant biologists and hydrologists to develop together their understanding of water movement in the soil-plant system. Using recent quantitative models coupling the hydraulic behaviour of soil and roots in an explicit 3D framework, this paper illustrates that the contribution of RSA to root water uptake is hardly separable from the hydraulic properties of the roots and of the soil. It is also argued that the traditional view that either the plant or the soil should be dominating the patterns of water extraction is not generally appropriate for crops growing with a sub-optimal water supply. Hopefully, in silico experiments using this type of model will help explore how water fluxes driven by soil and plant processes affect soil water availability and uptake throughout a growth cycle and will embed the study of RSA within the domains of root hydraulic architecture and sub-surface hydrology.

A global multilevel coordinate search procedure for estimating the unsaturated soil hydraulic properties

We present a new inverse modeling procedure to characterize the hydraulic properties of partially saturated soils from soil moisture measurements during a natural transient flow experiment. The inversion of the governing one-dimensional Richards equation is carried out using the Global Multilevel Coordinate Search optimization algorithm in sequential combination with the local Nelder-Mead Simplex algorithm (GMCS-NMS). We introduce this optimization method in the area of unsaturated zone hydrology since it is adapted for solving accurately and efficiently complex nonlinear problems. Several numerical experiments have been conducted to evaluate the proposed inversion method using synthetic error-free and error-contaminated data for different textured soils. Inversion of the simulated error-free data and examination of the related response surfaces demonstrated the uniqueness of the inverse solution and the suitability of the GMCS-NMS strategy when identifying four key parameters of the hydraulic functions described by the Mualem-van Genuchten model. Inversion of the error-contaminated data proved further the good stability of the inverse solution that is consistent with the needs required by real experiments.

A one-dimensional model of water flow in soil-plant systems based on plant architecture

The estimation of root water uptake and water flow in plants is crucial to quantify transpiration and hence the water exchange between land surface and atmosphere. In particular the soil water extraction by plant roots which provides the water supply of plants is a highly dynamic and non-linear process interacting with soil transport processes that are mainly determined by the natural soil variability at different scales. To better consider this root-soil interaction we extended and further developed a finite element tree hydro-dynamics model based on the one-dimensional (1D) porous media equation. This is achieved by including in addition to the explicit three-dimensional (3D) architectural representation of the tree crown a corresponding 3D characterisation of the root system. This 1D xylem water flow model was then coupled to a soil water flow model derived also from the 1D porous media equation. We apply the new model to conduct sensitivity analysis of root water uptake and transpiration dynamics and compare the results to simulation results obtained by using a 3D model of soil water flow and root water uptake. Based on data from lysimeter experiments with young European beech trees (Fagus silvatica L.) is shown, that the model is able to correctly describe transpiration and soil water flow. In conclusion, compared to a fully 3D model the 1D porous media approach provides a computationally efficient alternative, able to reproduce the main mechanisms of plant hydro-dynamics including root water uptake from soil.

Water stress drastically reduces root growth and inulin yield in Cichorium intybus (var. sativum) independently of photosynthesis

Root chicory (Cichorium intybus var. sativum) is a cash crop cultivated for inulin production in Western Europe. This plant can be exposed to severe water stress during the last 3 months of its 6-month growing period. The aim of this study was to quantify the effect of a progressive decline in water availability on plant growth, photosynthesis, and sugar metabolism and to determine its impact on inulin production. Water stress drastically decreased fresh and dry root weight, leaf number, total leaf area, and stomatal conductance. Stressed plants, however, increased their water-use efficiency and leaf soluble sugar concentration, decreased the shoot-to-root ratio and lowered their osmotic potential. Despite a decrease in photosynthetic pigments, the photosynthesis light phase remained unaffected under water stress. Water stress increased sucrose phosphate synthase activity in the leaves but not in the roots. Water stress inhibited sucrose:sucrose 1-fructosyltransferase and fructan:fructan 1 fructosyltransferase after 19 weeks of culture and slightly increased fructan 1-exohydrolase activity. The root inulin concentration, expressed on a dry-weight basis, and the mean degree of polymerization of the inulin chain remained unaffected by water stress. Root chicory displayed resistance to water stress, but that resistance was obtained at the expense of growth, which in turn led to a significant decrease in inulin production.

Plant Water Uptake in Drying Soils

Integrative soil-plant system approaches are needed to understand plant water uptake dynamics. Over the last decade, investigations on root water uptake have evolved toward a deeper integration of the soil and roots compartment properties, with the goal of improving our understanding of water acquisition from drying soils. This evolution parallels the increasing attention of agronomists to suboptimal crop production environments. Recent results have led to the description of root system architectures that might contribute to deep-water extraction or to water-saving strategies. In addition, the manipulation of root hydraulic properties would provide further opportunities to improve water uptake. However, modeling studies highlight the role of soil hydraulics in the control of water uptake in drying soil and call for integrative soil-plant system approaches.

Soil hydrology: Recent methodological advances, challenges, and perspectives

Technological and methodological progress is essential to improve our understanding of fundamental processes in natural and engineering sciences. In this paper, we will address the potential of new technological and methodological advancements in soil hydrology to move forward our understanding of soil water related processes across a broad range of scales. We will focus on advancements made in quantifying root water uptake processes, subsurface lateral flow, and deep drainage at the field and catchment scale, respectively. We will elaborate on the value of establishing a science-driven network of hydrological observatories to test fundamental hypotheses, to study organizational principles of soil hydrologic processes at catchment scale, and to provide data for the development and validation of models. Finally, we discuss recent developments in data assimilation methods, which provide new opportunities to better integrate observations and models and to improve predictions of the short-term evolution of hydrological processes.

Root System Markup Language: toward a unified root architecture description language

Portability of root architecture data with the Root System Markup Language paves the way for central root phenotype repositories. The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow.

On the identification of macroscopic root water uptake parameters from soil water content observations

[1] In this paper, we analyze the identification problem of macroscopic root water uptake parameters from soil water content observations. For this study, the macroscopic root water uptake is considered to be linearly decreasing with depth with A and B parameters conditioning, respectively, the maximum root water uptake at the surface and the decreasing rate with depth. For identification of parameter A and B, two different identification approaches are tested using a detailed soil moisture data set consisting of vertical profiles measured with time domain reflectometry (TDR) and neutron probe on 28 locations within a small maize cropped field during a dry period of 26 days. The first approach is based on a simplified water balance, while the second one uses an integrated soil-vegetation-atmosphere transfer (SVAT) model in an inverse mode. Results of the simplified water balance show first that the root water uptake measured within the field is quite variable with CV ranging from 22 to 34% for the root uptake parameters A and B, respectively. Furthermore, positive correlation between A and B suggests that low superficial root water uptake could be compensated by high deep root water uptake. Second, numerical simulations used to test the validity of this simplified approach show that the method is quite robust, at least for a certain range of A parameter values (0.008 < A < 0.013), for B, and for all investigated differently textured soils, except the coarse sand. To investigate the feasibility and the robustness of the second approach, we address the problems of insensitivity, instability, and nonuniqueness by means of numerical simulations. Results show, for soils with different textures, that the soil water content and, to a lesser extent, the time derivative of soil water content are quite insensitive to root water uptake parameters, at least compared to soil hydraulic parameters. Furthermore, instability analysis clearly illustrates that root water uptake parameters are quite and even very instable with respect to small uncertainties on the apparently known parameters (e. g., soil parameters). Finally, results show that if root water uptake plus additional other parameters (e. g., soil parameters) are simultaneously optimized, nonuniqueness of parameter sets must be expected. Therefore a robust identification of root water uptake parameters by means of a full SVAT inversion is unlikely to be achieved during a dry period with soil water content observations at least when some other parameters driving the system, like soil hydraulic properties, are not error free. In this context, further in depth research is needed to investigate if the use of longer periods characterized by both drying and redistribution events may increase the success of a full SVAT inversion. Finally, to extend the results of this study, we recommend applying a similar analysis to other macroscopic conceptual root water uptake models.

Dynamic aspects of soil water availability for isohydric plants: Focus on root hydraulic resistances

Soil water availability for plant transpiration is a key concept in agronomy. The objective of this study is to revisit this concept and discuss how it may be affected by processes locally influencing root hydraulic properties. A physical limitation to soil water availability in terms of maximal flow rate available to plant leaves (Qavail) is defined. It is expressed for isohydric plants, in terms of plant-centered variables and properties (the equivalent soil water potential sensed by the plant, ws eq; the root system equivalent conductance, Krs; and a threshold leaf water potential, wleaf lim). The resulting limitation to plant transpiration is compared to commonly used empirical stress functions. Similarities suggest that the slope of empirical functions might correspond to the ratio of Krs to the plant potential transpiration rate. The sensitivity of Qavail to local changes of root hydraulic conductances in response to soil matric potential is investigated using model simulations. A decrease of radial conductances when the soil dries induces earlier water stress, but allows maintaining higher night plant water potentials and higher Qavail during the last week of a simulated 1 month drought. In opposition, an increase of radial conductances during soil drying provokes an increase of hydraulic redistribution and Qavail at short term. This study offers a first insight on the effect of dynamic local root hydraulic properties on soil water availability. By better understanding complex interactions between hydraulic processes involved in soil-plant hydrodynamics, better prospects on how root hydraulic traits mitigate plant water stress might be achieved.