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Purpose Simultaneously interacting rhizosphere processes determine emergent plant behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. However, these processes occur on multiple scales, challenging modelling of rhizosphere and plant behaviour. Current advances in modelling and experimental methods open the path to unravel the importance and interconnectedness of those processes across scales. Methods We present a series of case studies of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images. Results Each case study includes a model that links scales and experimental data to explain and predict spatial and temporal distribution of rhizosphere components. We exemplify the state-of-the-art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling, and functional-structural plant modelling. We show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties. Furthermore, we demonstrate ways of modelling the links between rhizodeposition and plant nutrient uptake or soil microbial activity. Conclusion Modelling allows to integrate new experimental data across different rhizosphere processes and scales and to explore more variables than is possible with experiments. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes including the dynamics of root growth is the logical next step for future research.

Wettability is an important parameter that significantly determines hydrology in porous media, and it especially controls the flow of water across the rhizosphere—the soil-plant interface. However, the influence of spatially heterogeneous distributions on the soil particles surfaces is scarcely known. Therefore, this study investigates the influence of spatially heterogeneous wettability distributions on infiltration into porous media. For this purpose, we utilize a two-phase flow model based on Lattice-Boltzmann to numerically simulate the infiltration in porous media with a simplified geometry and for various selected heterogeneous wettability coatings. Additionally, we simulated the rewetting of the dry rhizosphere of a sandy soil where dry hydrophobic mucilage depositions on the particle surface are represented via a locally increased contact angle. In particular, we can show that hydraulic dynamics and water repellency are determined by the specific location of wettability patterns within the pore space. When present at certain locations, tiny hydrophobic depositions can cause water repellency in an otherwise well-wettable soil. In this case, averaged, effective contact angle parameterizations such as the Cassie equation are unsuitable. At critical conditions, when the rhizosphere limits root water uptake, consideration of the specific microscale locations of exudate depositions may improve models of root water uptake.

PurposeSimultaneously interacting small-scale rhizosphere processes determine emergent plant-scale behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. Current advances in modelling and experimental methods open the path to unravel and link those processes.MethodsWe present a series of examples of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images.ResultsEach example includes a model that links scales and experimental data to set-up simulations that explain and predict spatial and temporal distribution of rhizodeposition as driven by root architecture development, soil structure, presence of root hairs, soil water content and distribution of soil water. Furthermore, two models explicitly simulate the impact of the rhizodeposits on plant nutrient uptake and soil microbial activity, respectively. This exemplifies the currently available state of the art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling and functional-structural plant modelling. We further show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties.ConclusionModelling allows to integrate and make use of new experimental data across different rhizosphere processes (and thus across different disciplines) and scales. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes is the logical next step for future research.

Background: Gaseous matter exchanges in soil are determined by the connectivity of the pore system which is easily clogged by fresh root exudates. However, it remains unclear how a hydrogel (e.g., mucilage) affects soil pore tortuosity and gas diffusion properties when drying. Aims: The aim of this viewpoint study is to extend the understanding of gas exchange processes in the rhizosphere by (a) relating it to the patterns formed by drying mucilage within pore space and (b) to give a concept of the effect of drying mucilage on soil gas diffusivity using the combination of experimental evidence and simulations. Methods: To describe the effect of mucilage on soil gas exchanges, we performed gas diffusion experiments on dry soil–mucilage samples and took images of glass beads mixed with mucilage to visualize the formation of mucilage after drying, using Environmental Scanning Electron Microscopy. Finally, we set up simulations to characterize the geometric distribution of mucilage within soil during the drying process. Results: Experiments of gas diffusion show that mucilage decreases gas diffusion coefficient in dry soil without significantly altering bulk density and porosity. Electron microscopy indicates that during drying mucilage forms filaments and interconnected structures throughout the pore space reducing gas phase connectivity. The evolution of these geometric structures is explained via pore scale modelling based on identifying the elastic strength of rhizodeposition during soil drying. Conclusion: Our results suggest that releasing mucilage may be a plant adaption strategy to actively alter gas diffusion in soil.

<p>A central component of the rhizosphere is root mucilage, a hydrogel exuded by plants that dramatically alters chemical and physical properties of the soil. It is characterized by its large water holding capacity and is hydrophilic or hydrophobic depending on its hydration status: when swollen, mucilage is hydrophilic but becomes hydrophobic when dry, forming local hydrophobic spots on the surface of soil particles. The morphology of these hydrophobic regions formed by dried mucilage is affected by the type of mucilage and microorganisms and can vary from isolated local spots, to networks spanning across larger areas of the soil particle surface. However, until now the understanding on how this heterogeneous distribution and its morphology affect water retention and water repellency in soil is limited.</p><p>Therefore, the goal of this study is to investigate the impact of the spatially heterogeneous interfacial tension distributions on the capillary rise in soil. We utilize a two phase flow model based on the Lattice-Boltzmann to numerically simulate capillary rise between parallel slides having a heterogeneous distribution of interfacial tension during imbibition and drainage.</p><p>The simulations allow us to quantitatively evaluate how heterogeneous micro-scale distributions of interfacial tension affect the macro-scale water retention behavior. This we could approximately explain with three hypotheses: The equilibrium capillary rise volume (i) is a measure for the hydrophilicity of a field, (ii) capillary rise is affected by the standard deviation of the interfacial tension field, (iii) hysteresis is induced by the heterogeneous field and depends on the correlation length of the patterns.</p><p>In future, simulations will be extended also to the geometry of real soil.</p>

<p>Gaseous matter exchanges in soil are determined by the connectivity of the pore system which is easily clogged by fresh root exudates. However, it remains unclear how a hydrogel (e.g. mucilage) affects soil pore tortuosity when drying. The aim of this study is to obtain a better understanding of gas diffusion processes in the rhizosphere by explaining patterns formed by drying mucilage.</p><p>We measured oxygen diffusion through a soil-mucilage mixture after drying using a diffusion chamber experiment. Therefore we mixed soil with different particle size with various amounts of mucilage. Afterwards we saturated the soil and measured the gas diffusion coefficient during drying.</p><p>We found that mucilage decreases gas diffusion coefficient in dry soil without significantly altering bulk density and porosity. Electron microscopy indicate that during drying mucilage forms filaments and interconnected structures throughout the pore space. Exudation of mucilage may be a plant possibility to actively alter gas diffusion in soil.</p>

<p>Compared to bulk soil, rhizosphere has different properties because of the existence of root mucilage which affects the physical, chemical and also microbial processes. Hydraulic phenomena like limiting water flow at certain dry soil conditions, modulating extreme water contents by slow response to water potential changes; and also influencing solute transport and gas diffusion by varying the connectivity of liquid and gas phases are all classified under the set of the physical processes which are affected by mucilage in the rhizosphere.</p><p>Overview of the literature and previous models shows the lack of a three-dimensional pore-scale dynamic model for a better understanding of the connectivity between different phases during imbibition and drainage processes. A major challenge is that mucilage shows a complex behavior which at low concentrations is more like a liquid while at higher concentration when it is almost dry, it becomes a solid.</p><p>In particular, this study will use the Lattice Boltzmann method as a powerful tool for fluid dynamics study and the discrete element method for describing solids to present a pore-scale model for more accurate simulation and study of physical processes in the rhizosphere.</p>