Search

© 2019 The Author(s). Roots are known to use biopores as preferential growth pathways to overcome hard soil layers and access subsoil water resources. This study evaluates root- biopore interactions at the root-system scale under different soil physical and environmental conditions using a mechanistic simulation model and extensive experimental field data. In a field experiment, spring wheat (Triticum aestivum L.) was grown on silt loam with a large biopore density. X-ray computed tomography scans of soil columns from the field site were used to provide a realistic biopore network as input for the three-dimensional numerical R-SWMS model, which was then applied to simulate root architecture as well as water flow in the root-biopore-soil continuum. The model was calibrated against observed root length densities in both the bulk soil and biopores by optimizing root growth model input parameters. By implementing known interactions between root growth and soil penetration resistance into our model, we could simulate root systems whose response to biopores in the soil corresponded well to experimental observations described in the literature, such as increased total root length and increased rooting depth. For all considered soil physical (soil texture and bulk density) and environmental conditions (years of varying dryness), we found biopores to substantially mitigate transpiration deficits in times of drought by allowing roots to take up water from wetter and deeper soil layers. This was even the case when assuming reduced root water uptake in biopores due to limited root-soil contact. The beneficial impact of biopores on root water uptake was larger for more compact and less conductive soils. ispartof: VADOSE ZONE JOURNAL vol:18 issue:1 status: published

The International Soil Modeling Consortium (ISMC) was established in 2016 with the aim to integrate and advance soil systems modeling, data collection, and observational capabilities. ISMC is a community effort accepting members from all fields (https://soil-modeling.org/). Its activities are organized around three science panels: data and observation model linking (DO-LINK), soil modeling development and intercomparison (Soil-MIP), and cross cutting activities (CROSS-Connect). ISMC fosters development of new soil models for quantifying soil functions and their changes with land use, climate and degradation. Recently, a number of model intercomparison studies have been initiated, focusing on specific processes such as root growth and water uptake, soil evaporation, soil freezing, soil heat fluxes, infiltration and runoff processes, and the coupling of soil preferential flow with groundwater. ISMC is coordinating efforts to form a global soil data meta-repository that will be openly available for soil systems research. The meta-repository will be a resource to analyze past and recent model- and data requirements for continuous standardization and harmonization of soil data. ISMC also seeks to identify soil related knowledge gaps between science communities, and to share this knowledge with neighbouring disciplines to better translate soil processes into functions for assessing sustainability and ecosystem services. Finally, ISMC is involved in creating exchange platforms with other international partners like AgMip/MACSUR, GEWEX, ISCN (International Soil Carbon Network), and GSBI (Global Soil Biodiversity Initiative). In this presentation, we will highlight recent developments and activities and present future plans for engaging young scientists and communicating soil modelling with other disciplines and the public.

The interaction between carbon and flows within the plant is at the center of most growth and developmental processes. Understanding how these fluxes influence each other, and how they respond to heterogeneous environmental conditions, is important to answer diverse questions in forest, agriculture and environmental sciences. However, due to the high complexity of the plant-environment system, specific tools are needed to perform such quantitative analyses.Here we present CPlantBox, full plant modelling framework based on the root system model CRootBox. CPlantbox is capable of simulating the growth and development of a variety of plant architectures (root and shoot). In addition, the flexibility of CPlantBox enables its coupling with external modeling tools. Here, we connected it to an existing mechanistic model of water and carbon flows in the plant, PiafMunch.The usefulness of the CPlantBox modelling framework is exemplified in four case studies. Firstly, we illustrate the range of plant structures that can be simulated using CPlantBox. In the second example, we simulated diurnal carbon and water flows, which corroborates published experimental data. In the third case study, we simulated impacts of heterogeneous environment on carbon and water flows. Finally, we showed that our modelling framework can be used to fit phloem pressure and flow speed to (published) experimental data.The CPlantBox modelling framework is open-source, highly accessible and flexible. Its aim is to provide a quantitative framework for the understanding of plant-environment interaction.

The International Soil Modeling Consortium (ISMC) was established in 2016 with the aim to integrate andadvance soil systems modeling, data collection, and observational capabilities. ISMC is a community effort. Itfollows a bottom-up approach, is based on scientific principles, voluntary contributions, and open to anybodywho wants to become a member of the consortium (https://soil-modeling.org/). Its activities are organized intothree science panels, organized around a broad workflow from data collection and observation (DO-LINK)to model development and intercomparison (Soil-MIP) to engagement with different scientific communities(CROSS-Connect). ISMC has an executive board and a scientific advisory board that guides ISMC in pursuing itsobjectives.The mission of the Soil-MIP science panel is to foster the further development of soil models that can predictsoil functions and their changes due to soil use and land management, as well as climate change and pollution.A number of model intercomparison studies were recently initiated, focusing on specific processes like soilhydraulic properties, soil thermal properties and related soil heat fluxes, root growth and root water uptake,soil evaporation, soil freezing, infiltration and runoff processes, and coupling between preferential flow in soilsand groundwater. From these comparisons, lessons can be learned about how process controls at small scalespropagate to larger scales and how this leads to effective process representations at larger scales. The missionof DO-Link is to assist with the development of a global soil data meta-repository that is openly availablefor soil system research. Data and data requirements are as diverse as the various disciplines developing andapplying soil models. The soil data meta-repository will be a resource to analyze past and recent model- anddata requirements for continuous standardization and harmonization of soil data. The CROSS-connect sciencepanel identifies soil related knowledge gaps between science communities, and shares this knowledge with otherISMC science panels to push forward development of new tools to better translate soil processes into functionsfor assessing sustainability and ecosystem services. CROSS-connect develops an exchange platform with otherinternational partners like AgMip/MACSUR, GEWEX, ISCN (International Soil Carbon Network), GSBI (GlobalSoil Biodiversity initiative) and CSDMS (Community Surface Dynamics Modeling System). In this presentation,we will highlight the most recent developments and activities that are currently underway as well as future projectsthat are under preparation.

The root system is the plant’s organ that has the important function of taking up water and plant nutrients from the soil. Root system functioning depends on its multiscale structure: the size and structure of cells in the conductive tissues, the development and spatial organization of tissues, and the network of root segments that make up the root system. Breeders select for these structural properties of roots and root systems to develop crop varieties with high water and nutrient efficiencies that give a high or stable yield under non-controllable adverse environmental conditions(droughts, nutrient poor soils, soil salinity, …). But, a direct relation between the functioning of a root system and its structure is not at hand. Functional-structural root system models that simulate the relations between root architectural and hydraulic properties, and the spatio-temporal patterns of water and solute fluxes in the root zone can therefore play an important role in this selection process. However, it must be first demonstrated that these models accurately reproduce the processes they intend to describe but this is a challenging task for two reasons. First, the root system is the so-called ‘hidden halve’ of the plant so that its structure and the flow and transport processes in the soil towards individual roots are hard to observe. Secondly, the properties that control water flow in root segments and that are required as input parameters in structural-functional root models vary with age and root order and quantitative information about these relations is scarce. In this paper, we demonstrate how this deadlock could be broken by combining co-registered root structure and tracer distributions obtained from magnetic resonance imaging, a functional-structural root system model, and inverse modeling. The main features in the tracer patterns were well reproduced by the model using root hydraulic parameters that were obtained using inverse modeling and that were found to correspond with available information about these parameters in the literature. The simulation results further demonstrated that water uptake location and intensity cannot be directly derived from neither observations of tracer accumulation nor water depletion. This proves that functionalstructural root system model simulations, combined with observations, are required to translate the observed variables (tracer accumulation and water depletion) into information about local processes and root system properties.

Many important functions of the soil and the land surface are related to processes that take place in the root zone at the interface between the soil and the vegetation. Jan Hopmans has made significant contributions that provided new insights in these processes and that inspired new research. Of special notice is his pioneering work on imaging root systems and on soil-root process simulations that resolve 3D root architectures. In this presentation, we present insights that we derived from imaging and simulation of soil-root processes. We developed the R_SWMS and CROOTBox codes that link features of 3D root systems to their functions with respect to water and nutrient uptake. 3D representations of root systems in simulation models can effectively valorize information obtained with novel measurements techniques which allow functional structural imaging and monitoring of root processes. These models allow for functional phenotyping of root systems. Finally, these models were used to couple soil conditions (water content and salinity) to crop and vegetation stresses and to derive mechanistic representations of these relations in larger scale soil, crop and land surface models. The importance of the root system for the interaction of the crop or vegetation with its environment calls for a better mechanistic understanding of the development and plasticity of root systems. Currently, we are developing CPLANTBOX, a functional-structural soil-plant model which simulates the distribution of assimilates and plant growth in function of environmental conditions by coupling carbon assimilates and water fluxes in 3D whole-plant architectures.

Plant transpiration and root water uptake are dependent on multiple traits that interact with site soil characteristics and environmental factors such as radiation, atmospheric temperature, relative humidity, and soil-moisture content. Models of root architecture and functions are increasingly employed to simulate root-soil interactions. Root water uptake is thereby affected by the root hydraulic architecture, the soil moisture conditions, soil hydraulic properties and the transpiration demand as controlled by atmospheric conditions. Stomatal conductance plays a vital role in regulating transpiration in plants. Isohydric plants follow the strategy to close their stomata in order to maintain the leaf water potential at a constant level, while anisohydric plants leave their stomata open when leaf water potentials fall due to drought stress. Modeling the stomatal regulation effectively will result in a more reliable model that will regulate the excessive loss of water. We performed the simulations of plant water uptake and transpiration on a DUNE-based simulator DuMux. It simulates the flow and transport processes in porous media that can represent the porous medium (including soil) with embedded hierarchical biological networks (in this case, root system). We implemented hydraulic and chemical stomatal control of root water uptake in DuMux following the current approach where stomatal control is regulated by simulated water potential and/or chemical signal concentration. We then performed a mesh convergence study in order to verify the accuracy of our results. Finally, we conducted the simulations for different scenarios to study the effect of hydraulic and chemical regulation on root system performance under drought stress. Future work will include incorporating further modeling capabilities into DuMux which will facilitate the consideration of further soil and rhizosphere processes in the simulations, such as nutrients, root exudes or soil microorganisms.

This manuscript to the proceedings of the ExtremeData – Demands, Technologies, and Services – Workshop1,gives an overview on the characteristics, components, steps andmethods of a complex data flow path around a fully coupledregional Earth system model and highlights the challenges weface working with very large data, as well as the concepts andstrategies towards a big data-enabled modeling chain.

Ground penetrating radar (GPR) has shown a high potential to derive soil water content (SWC) at different scales. In this study, we combined multiple horizontal GPR measurements at different depths to investigate the spatial and temporal variability of the SWC under cropped plots. The SWC data were analyzed for four growing seasons between 2014 and 2017, two soil types (gravelly and clayey–silty), two crops (wheat [Triticum aestivum L.] and maize [Zea mays L.]), and three different water treatments. We acquired more than 150 time-lapse GPR datasets along 6-m-long horizontal crossholes at six depths. The GPR SWC distributions are distinct both horizontally and vertically for both soil types. A clear change in SWC can be observed at both sites between the surface layer (>0.3 m) and subsoil. Alternating patches of higher and lower SWC, probably caused by the soil heterogeneity, were observed along the horizontal SWC profiles. To investigate the changes in SWC with time, GPR and time-domain reflectometry (TDR) data were averaged for each depth and compared with changes in precipitation, treatment, and soil type. The high-temporal-resolution TDR and the large-sampling-volume GPR show similar trends in SWC for both sites, but because of the different sensing volumes, different responses were obtained due to the spatial heterogeneity. A difference in spatial variation of the crosshole GPR SWC data was detected between maize and wheat. The results for this 4-yr period indicate the potential of this novel experimental setup to monitor spatial and temporal SWC changes that can be used to study soil–plant–atmosphere interactions.

Evaporation from bare soil surfaces can be restrained to a great extent with the development of a dry layer at the soil surface where capillary hydraulic conductance ceases and water flow proceeds only by gas phase transport. Model calculations and preliminary experiments with model porous media have shown that this surface layer can be very thin. An accurate characterization of these processes is required, which is provided by noninvasive magnetic resonance (MR) methods. The evaporative drying of a silt loam and a sandy loam was monitored at high spatial resolution in laboratory experiments. The MR data were used to assess the performance of two numerical models: (i) the Richards equation, which considers isothermal liquid water flow, and (ii) a coupled soil water, heat, and vapor flow numerical model. The experimental results reveal two distinct drying regimes for both soil types where, at the onset of the second evaporation stage, a dry surface zone developed with increasing thickness over time. This layer revealed that water loss inside the soil coincided with a relatively low evaporation rate as the liquid continuity to the soil surface vanished. The modeling results clearly demonstrated the need to consider heat and vapor flow. It was shown, as a proof of principle, that MR relaxation time spectra may serve as a proxy to follow desaturation processes where spatially resolved transverse relaxation can reveal a secondary evaporation front.

This special section of Vadose Zone Journal (VZJ) contains 15 contributions focusing on the physical, biological, and chemical aspects of water and solute transport into and through the soil root zone, including root water and solute uptake. The papers stem from presentations at the 2016 Kirkham Conference, “The Root Zone: Soil Physics and Beyond,” which took place at the Sede Boqer campus of Ben-Gurion University of the Negev, Israel, during 10 to 14 April (https://www.soils.org/membership/divisions/soil-physics-and-hydrology/kirkham-conferences). Much consensus existed at the conference for a special VZJ section to reflect the importance of the soil root zone from many disciplinary perspectives (soil, environmental, agricultural, hydrologic, and atmospheric) and the complexity of the basic processes involved. The contributions deal with root zone processes at different scales and from different disciplinary viewpoints, while covering a broad range of topics from the very theoretical to important practical applications. Special emphasis is on novel measurement and modeling tools at various scales and the need for interdisciplinary research.

Worldwide ecosystems primary production and survival are largely limited by soil water availability, and affected by plant traits that control water uptake, transport, and release in the atmosphere. In order to understand how these complex systems will react to future climates, and optimally adjust their management, the development of experimental and modelling approaches is crucial. In particular, integrating process-based representations plant hydraulics and stomatal closure in land surface models (LSMs) is a major challenge as the limited computational resources necessitate the use of simplified descriptions of these processes. We present methods used to identify scale consistent emergent principles governing water flow in plants. We show that simplistic mechanistic expressions arise from the cell to the root system scale, and along stems whose geometry, saturated conductivity, sensitivity to cavitation, and leaf area vary continuously with height. Our results support that cavitation is a whole-stem emergent property; in which compounding effects of gravity and vertical traits variations reported experimentally all substantially contribute to the occurrence of hydraulic failure in tall trees, and need to be accounted for in LSMs. Furthermore, a macroscopic solution of water flow in plant hydraulic architectures was implemented in the Terrestrial Systems Modeling Platform. As compared to the standard approach, this new model of water capture characteristically exhibits a different sensitivity of the onset of water stress to root distribution and soil properties.

Existing literature about maize root system hydraulic and architectural properties is abundant and can serve as input for contrasted root system hydraulic architecture generation tools. Therefore observations of root hydraulic and architectural phenes in and/or laboratory experiments must be first converted into parameters for feeding root growth model and water flow algorithms. MARSHAL aims at gathering the existing information about the maize plant and at making it available for the community. Existing maize root system architecture parameterizations as well as measured hydraulic functions were gathered in a common database and linked with the state-of-art model of the water transfer in the soil-plantatmosphere continuum. MARSHAL is as an online and flexible tool that generates contrasted root system hydraulic architectures using this database, calculates the water flow within the root system under user-provided boundary conditions (transpiration and soil water potential distribution) and calculates plant-scale macroscopic parameters. The generated root systems hydraulic architectures can be saved in common formats such as RSML to be easily imported in other models. Finally, MARSHAL is coupled with sensitivity and optimization algorithms in order to investigate the sensitive input parameters for a used-defined! objective function or to provide an optimal set of parameters that minimizes an error function, alongside with parameter uncertainty. As illustration of the model potentiality, we used MARSHAL to generate maize contrasted hydraulic architectures and we compared them with plant-scale observations of both architecture (root length density profile field measurements) and hydraulics (root system conductance measurements). The macroscopic parameters could be easily fitted with the model and the observed local variability of root phenes determined. The hydraulic architectures were then used as contrasted genotypes in a water flow model of the soil-plant-atmosphere continuum to highlight G x E interactions and they indeed performed differently in contrasted pedo-climatic conditions.

Accurate estimates of soil hydraulic parameters and dispersivities are crucial to simulate water flow and solute transport in terrestrial systems, particularly in the vadose zone. However, parameters obtained from inverse modeling can be ambiguous when identifying multiple parameters simultaneously and when boundary conditions are not well known. Here, we performed an inverse modeling study in which we estimated soil hydraulic parameters and dispersivities of layered soils from soil water content, matric potential, and stable water isotope ( d 18O) measurements in weighable lysimeter systems. We used different optimization strategies to investigate which observation types are necessary for simultaneously estimating soil hydraulic and solute transport parameters. Combining water content, matric potential, and tracer (e.g., d 18O) data in one objective function (OF) was found to be the best strategy for estimating parameters that can simulate all observed water flow and solute transport variables. A sequential optimization, in which first an OF with only water flow variables and subsequently an OF with transport variables was optimized, performed slightly worse indicating that transport variables contained additional information for estimating soil hydraulic parameters. Hydraulic parameters that were obtained from optimizing OFs that used either water contents or matric potential could not predict non-measured water flow variables. When a bromide (Br−) tracer experiment was simulated using the optimized parameters, the arrival time of the bromide pulse was underestimated. This suggested that Br− sorbed onto clay minerals and amorphous oxides under the prevailing geochemical conditions with low pH values. When accounting for anion adsorption in the simulation, Br− concentrations were well predicted, which validated the dispersivity parameterization.

3D models of root growth, architecture and function are evolving as they become important tools that aid the design of agricultural management schemes and the selection of beneficial root traits. However, while benchmarking is common for water and solute transport models in soil, 3D root-soil interaction models have never been systematically analysed. Several interacting processes might induce disagreement between models: root growth, sink term definitions of root water and solute uptake and representation of the rhizosphere. The extent of discrepancies is currently unknown. Thus, a framework for quantitatively comparing such models is required. We propose, in a first step, to define benchmarking scenarios that test individual components of the complex models: root architecture, water flow in soil and roots, solute transport in soil and roots. While the latter will focus mainly on comparing numerical aspects, the root architectural models have to be compared at a conceptual level as they generally differ in process representation. Therefore defining common inputs that recreate reference root systems in all models will be a key challenge. In a second step, benchmarking scenarios for the coupled root-rhizosphere-soil models can be defined. We expect that the results of step 1 will enable us to better interpret differences found in step 2. We expect that this benchmarking will result in improved models, with which we can simulate various scenarios with greater confidence, avoiding that future work is based on accidental results caused by bugs, numerical errors or conceptual misunderstandings and will set a standard for future model development.

Geophysical methods are increasingly being used in hydrogeological studies, allowing to characterize the structure and the heterogeneity of the subsurface in a noninvasive way. Transport processes could be monitored using these methods when the tracer changes the geophysical properties of the aquifer (e.g. electrical conductivity, permittivity) and when these changes can be resolved in space and time. Ground penetration radar (GPR) measurements processed by the full-waveform inversion (FWI) method allow mapping the subsurface with a decimeter scale resolution. Time-lapse GPR imaging of saline tracer in fractured rock demonstrated the potential to monitor transport processes (e.g. Shakas et al., 2016). In the current research, a time-lapse GPR imaging of a saline tracer test is planned in an alluvial aquifer, to test the potential of GPR to detect transport processes.The experiment will be performed in a sand-gravel aquifer at the Krauthausen test site, nearby Jülich where we will inject a saline tracer into the aquifer through a borehole and transported by natural groundwater flow. Time-lapse GPR data will be acquired in a crosshole setup to monitor the tracer distribution. To optimize the imaging and detection of the tracer plume, a numerical test simulating the field experiment in a hydrogeological model of the aquifer was applied using a flow and transport model and a GPR wave propagation forward model. The numerical experiment simulates the plume spread in time and space, and the signals that are measured with GPR. An appraisal of the spatial resolution of the tracer distribution that can be obtained with GPR is derived from a comparison between the simulated tracer distributions and the tracer distributions obtained after a full waveform inversion of the GPR signals. Preliminary results of the transport simulation show a narrow plume with high salinity gradients at the decimeter scale, which performs the importance of the prediction for optimizing geophysical imaging and interpretation. At the next steps of the simulation, GPR forward modeling followed by FWI will be applied while adjusting the tracer concentrations, radar frequencies, and crosshole locations to optimize imaging of the field experiment.

Existing literature about maize root system hydraulic and architectural properties is abundant and can serve as input for contrasted root system hydraulic architecture generation tools. Therefore observations of root hydraulic and architectural phenes in field and/or laboratory experiments must be first converted into parameters for feeding root growth model and water flow algorithms. MARSHAL aims at gathering the existing information about the maize plant and at making it available for the community. Existing maize root system architecture parameterizations as well as measured hydraulic functions were gathered in a common database and linked with the state-of-art model of the water transfer in the soil-plant-atmosphere continuum. MARSHAL is as an online and flexible tool that generates contrasted root system hydraulic architectures using this database, calculates the water flow within the root system under user-provided boundary conditions (transpiration and soil water potential distribution) and calculates plant-scale macroscopic parameters. The generated root systems hydraulic architectures can be saved in common formats such as RSML to be easily imported in other models. Finally, MARSHAL is coupled with sensitivity and optimization algorithms in order to investigate the sensitive input parameters for a used-defined objective function or to provide an optimal set of parameters that minimizes an error function, alongside with parameter uncertainty. As illustration of the model potentiality, we used MARSHAL to generate maize contrasted hydraulic architectures and we compared them with plant-scale observations of both architecture (root length density profile field measurements) and hydraulics (root system conductance measurements). The macroscopic parameters could be easily fitted with the model and the observed local variability of root phenes determined. The hydraulic architectures were then used as contrasted genotypes in a water flow model of the soil-plant-atmosphere continuum to highlight G x E interactions and they indeed performed differently in contrasted pedo-climatic conditions. Finally, MARSHAL served to validate a fully analytical model of the root system hydraulic architecture and to calculate the sensitivity of mature root system conductance, depth of standard uptake, volume and convex hull volume to the input parameters.

Poster used in PMA2018 conference

Time-lapse geophysical imaging of tracer tests is essential to infer channelized transport properties. Cross-hole ground-penetrating radar (GPR) tomography is a high resolution imaging method to characterize the near-surface. We present preliminary results of crosshole GPR full-waveform inversion of time-lapse synthetic data during a saline tracer test. The tracer movement was obtained from a 3D transport simulation in a hydrogeological model representing the Krauthausen aquifer where in future also field tests will be performed. The full-waveform inversion accurately resolved the infiltrated tracer distribution in the plane within decimeter scale. The results indicate the potential of GPR full-waveform inversion for saline tracer detection and high-resolution time-lapse transport characterization.

Soil, through its various functions, plays a vital role in the Earth's ecosystems and provides multiple ecosystem services to humanity. Pedotransfer functions (PTFs) are simple to complex knowledge rules that relate available soil information to soil properties and variables that are needed to parameterize soil processes. In this paper, we review the existing PTFs and document the new generation of PTFs developed in the different disciplines of Earth system science. To meet the methodological challenges for a successful application in Earth system modeling, we emphasize that PTF development has to go hand in hand with suitable extrapolation and upscaling techniques such that the PTFs correctly represent the spatial heterogeneity of soils. PTFs should encompass the variability of the estimated soil property or process, in such a way that the estimation of parameters allows for validation and can also confidently provide for extrapolation and upscaling purposes capturing the spatial variation in soils. Most actively pursued recent developments are related to parameterizations of solute transport, heat exchange, soil respiration, and organic carbon content, root density, and vegetation water uptake. Further challenges are to be addressed in parameterization of soil erosivity and land use change impacts at multiple scales. We argue that a comprehensive set of PTFs can be applied throughout a wide range of disciplines of Earth system science, with emphasis on land surface models. Novel sensing techniques provide a true breakthrough for this, yet further improvements are necessary for methods to deal with uncertainty and to validate applications at global scale.