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.

Core Ideas: A 3D soil–root model was used to investigate root–biopore interactions. Known effects of biopores on root growth, i.e., increased root length and depth were reproduced. Despite reducing root–soil contact, biopores led to increased water uptake in dry periods. Biopores had a larger impact on water uptake for more compact and less conductive soils. 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.

In models of water flow in soil and roots, differences in the soil hydraulic properties of the rhizosphere and the bulk soil are usually neglected. There is, however, strong experimental evidence that rhizosphere and bulk soil hydraulic properties differ significantly from each other due to various root-soil interaction processes. Two such processes, which can also influence each other, are rhizosphere loosening or compaction and mucilage deposition. In this work, we identified realistic gradients in rhizosphere bulk density and mucilage concentration using X-ray CT imaging, respectively, model simulation for two different soil types and soil bulk densities and related them to soil hydraulic parameters. Using a 1D-single-root model, we then evaluated both the individual and combined effects of these gradients on soil water dynamics using scenario simulations. We showed that during soil drying, a lower rhizosphere bulk density leads to an earlier onset of water stress and to a reduced root water uptake that is sustained longer. The presence of mucilage led to a faster reduction of root water uptake. This is due to the stronger effect of mucilage viscosity on hydraulic conductivity compared to the mucilage- induced increase in water retention. Root water uptake was rapidly reduced when both mucilage and rhizosphere bulk density gradients were considered. The intensity of the effect of gradients in rhizosphere bulk density and mucilage concentration depended strongly on the interplay between initial soil hydraulic conditions, soil type and soil bulk densities. Both gradients in rhizosphere bulk density and mucilage concentration appear as a measure to sustain transpiration at a lower level and to avoid fast dehydration.

In this study, we developed a novel model approach to compute the spatio-temporal distribution patterns of rhizodeposits around growing root systems in three dimensions. This model approach allows us to study the evolution of rhizodeposition patterns around complex three-dimensional root systems. Root systems were generated using the root architecture model CPlantBox. The concentration of rhizodeposits at a given location in the soil domain was computed analytically. To simulate the spread of rhizodeposits in the soil, we considered rhizodeposit release from the roots, rhizodeposit diffusion into the soil, rhizodeposit sorption to soil particles and rhizodeposit degradation by microorganisms. To demonstrate the capabilities of our new model approach, we performed simulations for the two example rhizodeposits mucilage and citrate and the example root system Vicia faba. The rhizodeposition model was parameterized using values from the literature. Our simulations showed that the rhizosphere soil volume with rhizodeposit concentrations above a defined threshold value (i.e. the rhizodeposit hotspot volume) exhibited a maximum at intermediate root growth rates. Root branching allowed the rhizospheres of individual roots to overlap, resulting in a greater volume of rhizodeposit hotspots. This was particularly important in the case of citrate, where overlap of rhizodeposition zones accounted for more than half of the total rhizodeposit hotspot volumes. Coupling a root architecture model with a rhizodeposition model allowed us to get a better understanding of the influence of root architecture as well as rhizodeposit properties on the evolution of the spatio-temporal distribution patterns of rhizodeposits around growing root systems.