Recent Developments and Applications of the HYDRUS Computer Software Packages

The HYDRUS-1D and HYDRUS (2D/3D) computer software packages are widely used finite-element models for simulating the one- and two- or three-dimensional movement of water, heat, and multiple solutes in variably saturated media, respectively. In 2008, Šimůnek et al. (2008b) described the entire history of the development of the various HYDRUS programs and related models and tools such as STANMOD, RETC, ROSETTA, UNSODA, UNSATCHEM, HP1, and others. The objective of this manuscript is to review selected capabilities of HYDRUS that have been implemented since 2008. Our review is not limited to listing additional processes that were implemented in the standard computational modules, but also describes many new standard and nonstandard specialized add-on modules that significantly expanded the capabilities of the two software packages. We also review additional capabilities that have been incorporated into the graphical user interface (GUI) that supports the use of HYDRUS (2D/3D). Another objective of this manuscript is to review selected applications of the HYDRUS models such as evaluation of various irrigation schemes, evaluation of the effects of plant water uptake on groundwater recharge, assessing the transport of particle-like substances in the subsurface, and using the models in conjunction with various geophysical methods

Root growth and crop performance of soybean under chemical, physical, and biological changes after subsoiling.

Chemical, physical and biological soil attributes can facilitate soybean root growth in greater volume and depth in the soil, which can minimize yield reduction caused by water deficit. Soil management can contribute positively or negatively to these soil attributes. The aim of this work was to evaluate the root growth and crop performance of soybean, in response to chemical, physical and biological changes after subsoiling at different depths. At the R5 phenological stage, trenches were made for sampling and soil collection for chemical, physical and biological analysis and root growth was carried out. At V5, V7, R2 and R5 stages, plants were collected to evaluate height, leaf area and dry mass. At V5, stage number and dry mass of the nodules were evaluated. Subsoiling increased pH and Ca, and decreased Al in the soil, resulted in higher relative density and did not affect in mechanical penetration resistance compared to non-subsoiled soil. Basal respiration and soybean nodulation were higher in the subsoiled soil. Up to 15 cm depth, there were 87.91% of the total root dry mass and 78.79% of the total root volume. Initial and final plant growth were the same in subsoiled and non-subsoiled soil. Number of nodules in the subsoiled soil was 28% higher than in the non-subsoiled soil. Under these study conditions, subsoiling provides lower root growth but benefits grain yield

Tracing root-felt sodium concentrations under different transpiration rates and salinity levels

© 2019, Springer Nature Switzerland AG. Aims: (1) Monitoring ‘root-felt’ salinity by using rhizoslides as a non-invasive method, (2) Studying how transpiration rate, salinity in irrigation water, and root water uptake affect sodium distribution around single roots, (3) Interpreting experimental results by using simulations with a 3-D root system architecture model coupled with water flow and solute transport models. Methods: Tomato plants were grown on rhizoslides under various salinity levels and two transpiration rates: high and low. Daily root images were processed with GIMP and incorporated into a 3-D numerical model. The experiments were simulated with R-SWMS, a 3-dimensional numerical model that simulates water flow and solute transport in soil, into the root and inside root systems. Results: Both experimental and simulation results displayed higher root-felt sodium concentrations compared with the bulk concentrations, and larger accumulation at higher transpiration rate. The simulations illustrated that the root-felt to bulk concentration ratio changed during the experiment depending both on the irrigation water salinity and transpiration rate. Conclusions: Changes in sodium concentrations with transpiration rates are most likely caused by root water uptake and ion exclusion. Simulation results indicate that root-scale process models are required to link root system architecture, environmental, and soil conditions with root-felt salinities.status: publishe

Water flow and multicomponent solute transport in drip-irrigated lysimeters

Controlled experiments and modeling are crucial components in the evaluation of the fate of water and solutes in environmental and agricultural research. Lysimeters are commonly used to determine water and solute balances and assist in making sustainable decisions with respect to soil reclamation, fertilization, or irrigation with low-quality water. While models are cost-effective tools for estimating and preventing environmental damage by agricultural activities, their value is highly dependent on the accuracy of their parameterization, often determined by calibration. The main objective of this study was to use measured major ion concentrations collected from drip-irrigated lysimeters to calibrate the variably saturated water flow model HYDRUS (2D/3D) coupled with the reactive transport model UNSATCHEM. Irrigation alternated between desalinated and brackish waters. Lysimeter drainage and soil solution samples were collected for chemical analysis and used to calibrate the model. A second objective was to demonstrate the potential use of the calibrated model to evaluate lower boundary design options of lysimeters with respect to leaching fractions determined using drainage water fluxes, chloride concentrations, and overall salinity of drainage water, and exchangeable sodium percentage (ESP) in the profile. The model showed that, in the long term, leaching fractions calculated with electrical conductivity values would be affected by the lower boundary condition pressure head, while those calculated with chloride concentrations and water fluxes would not be affected. In addition, clear dissimilarities in ESP profiles were found between lysimeters with different lower boundary conditions, suggesting a potential influence on hydraulic conductivities and flow patterns

Application of a single root-scale model to improve macroscopic modeling of root water uptake: focus on osmotic stress

Application of a single root-scale model to improve macroscopic modelingof root water uptake: focus on osmotic stressHelena Jorda (1), Adi Perelman (2), Naftali Lazarovitch (2), and Jan Vanderborght (3)(1) Division of Soil and Water Management, KU Leuven, Leuven, Belgium ([email protected]), (2) FrenchAssociates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research,Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel, (3) Institute of Bio- and Geosciences, AgrosphereInstitute, IBG-3, ForschungszentrumJülich GmbH, Jülich, GermanyRoot water uptake is a fundamental process in the hydrological cycle and it largely regulates the water balancein the soil vadose zone. Macroscopic stress functions are currently used to estimate the effect of salinity on rootwater uptake. These functions commonly assume stress to be a function of bulk salinity and of the plant sensitivityto osmotic stress expressed as the salinity at which transpiration is reduced by half or so called tolerance value.However, they fail to integrate additional relevant factors such as atmospheric conditions or root architectural traits.We conducted a comprehensive simulation study on a single root using a 3-D physically-based model thatresolves flow and transport to individual root segments and that couples flow in the soil and root system. Theeffect of salt concentrations on root water uptake was accounted for by including osmotic water potential gradientsbetween the solution at the soil root interface and the root xylem sap in the hydraulic gradient between thesoil and root. A large set of factors were studied, namely, potential transpiration rate and dynamics, root lengthdensity (RLD), irrigation water quality and irrigation frequency, and leaching fraction. Results were fitted to themacroscopic function developed by van Genuchten and Hoffman (1984) and the dependency of osmotic stress andthe fitted macroscopic parameters on the studied factors was evaluated.Osmotic stress was found to be highly dependent on RLD. Low RLDs result in a larger stress to the plantdue to high evaporative demand per root length unit. In addition, osmotic stress was positively correlated topotential transpiration rate, and sinusoidal potential transpiration lead to larger stress than when imposed as aconstant boundary condition.Macroscopic parameters are usually computed as single values for each crop and used for the entire grow-ing season. However, our study shows that both tolerance value and shape parameter p from the van Genuchtenand Hoffman (1984) function were highly dependent on both potential transpiration and RLD. Plant salt tolerancewas lower under high evaporative demand and lower RLD. In addition, the shape of the stress curve, which isdefined by p, was found to be steeper under larger RLD and low transpiration rate. Time-variant macroscopicparameters based on knowledge of current potential transpiration rate per root unit length would be moreconvenient to accurately predict osmotic stress, and hence root water uptake, during a growing season. In a nextstep, simulations considering the whole root systems will be conducted to assess how macroscopic parameters arealso related to root architectural characteristics.van Genuchten, M.T., Hoffman, G., 1984. Analysis of crop production. Soil Salin. Irrig. Springer Berl.258–27

Implementation and application of a root growth module in HYDRUS

A root growth module was adapted and implemented into the HYDRUS software packages to model root growth as a function of different environmental stresses. The model assumes that various environmental factors, as well as soil hydraulic properties, can influence root development under suboptimal conditions. The implementation of growth and stress functions in the HYDRUS software opens the opportunity to derive parameters of these functions from laboratory or field experimental data using inverse modeling. One of the most important environmental factors influencing root growth is soil temperature. The effects of temperature in the root growth module was the first part of the newly developed HYDRUS add-on to be validated by comparing modeling results with measured rooting depths in an aeroponic experimental system with bell pepper (Capsicum annuum L.). The experiment was conducted at root zone temperatures of 7, 17, and 27°C. Inverse optimization was used to estimate a single set of parameters that was found to well reproduce measured time series of rooting depths for all temperature treatments. A sensitivity analysis showed that parameters such as the maximum rooting depth and cardinal temperatures had only a small impact on the model output and can thus be specified using values from the literature without significantly increasing prediction uncertainties. On the other hand, parameters that define the growth rate or the shape of the temperature stress function had a high influence. The root growth module that considers temperature stress only slightly increased the complexity of the standard HYDRUS models

Application of a single root-scale model to improve macroscopic modeling of root water uptake: focus on osmotic stress

status: publishe

Properties of anthropogenic soils in ancient run-off capturing agricultural terraces in the Central Negev desert (Israel) and related effects of biochar and ash on crop growth

In the Central Negev hills (Israel) many ancient terraced wadis exist, which captured run-off and caused gradual soil aggradation, which enabled agricultural practices. In these terraces, dark colored soil horizons were observed, containing charcoal, as can be found in Terra Preta soils, suggesting higher fertility compared to natural soils. The aim of our investigation was to investigate these anthropogenic soils and to study the effects of charcoal and ash addition on soil properties and crop growth. We investigated 12 soil profiles, focusing on possible differences between light and dark colored soil horizons. We also investigated the effects of amendment of charcoal and ash on the growth of wheat (Triticum Aestivum L.) in a 40-day pot experiment involving two water regimes. Results show that charcoal content in light and dark horizons were both low (<0.2 %), but significantly lower bulk densities were found in dark colored horizons. In the crop experiment, charcoal addition resulted in decreased crop growth, while, in the water deficit regime, ash addition resulted in increased crop growth. Considering the observed charcoal and the results from the crop experiment, we hypothesize that, in ancient run-off capturing agricultural systems, ash was purposefully added as fertilizer

From experiments to simulations: tracing Na+ distribution around roots under different transpiration rates and salinity levels

From experiments to simulations: tracing Na+ distribution around rootsunder different transpiration rates and salinity levelsAdi Perelman (1), Helena Jorda (2), Jan Vanderborght (2,3), Andreas Pohlmeier (2), and Naftali Lazarovitch (1)(1) French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research,Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel ([email protected]), (2) Institute of Bio- andGeoscience, Agrosphere Institute, IBG-3, Forschungszentrum Jülich GmbH Jülich, Germany, (3) Department of Earth andEnvironmental Sciences, Faculty of Bioscience Engineering, KU Leuven,Leuven, BelgiumWhen salinity increases beyond a certain threshold it will result in reduced crop yield at a fixed rate, according toMaas and Hoffman model (1976). Thus, there is a great importance of predicting salinization and its impact oncrops. Current models do not consider the impact of environmental conditions on plants salt tolerance, even thoughthese conditions are affecting plant water uptake and therefore salt accumulation around the roots. Different fac-tors, such as transpiration rates, can influence the plant sensitivity to salinity by influencing salt concentrationsaround the roots. Better parametrization of a model can help improving predicting the real effects of salinity oncrop growth and yield. The aim of this research is to study Na+ distribution around roots at different scales usingdifferent non-invasive methods, and study how this distribution is being affected by transpiration rate and plantwater uptake. Results from tomato plants growing on Rhizoslides (capillary paper growth system), show that Na+concentration is higher at the root- substrate interface, compared with the bulk. Also, Na+ accumulation around theroots decreased under low transpiration rate, which is supporting our hypothesis. Additionally, Rhizoslides enableto study roots’ growth rate and architecture under different salinity levels. Root system architecture was retrievedfrom photos taken during the experiment and enabled us to incorporate real root systems into a simulation. Toobserve the correlation of root system architectures and Na+ distribution in three dimensions, we used magneticresonance imaging (MRI). MRI provides fine resolution of Na+ accumulation around a single root without disturb-ing the root system. With time, Na+ was accumulating only where roots were found in the soil and later on aroundspecific roots. These data are being used for model calibration, which is expected to predict root water uptake insaline soils for different climatic conditions and different soil water availabilities