Modelling at the interface of soil and plant

This session calls for contributions that focus on modelling approaches that balance processes in soil and plant towards a system’s view on plant nutrition, growth and development and related environmental issues, such as pollution, over-use of resources and depletion in ecosystem functions and services. Especially rhizosphere process modelling that engages with bridging of micro-meter processes to meter-scale ecosystem functioning are welcomed, but also modelling approaches that connect global-scale available soil information and data products to mechanistic, one-dimensional simulation models of soil processes and plant physiology.

Convener: Jan Vanderborght | Co-Convener: Claas Nendel
| Wed, 19 May, 11:00–12:30 (CEST)
| Wed, 19 May, 12:30–14:00 (CEST)

Oral: Wed, 19 May

Katherine Williams, Daniel McKay Fletcher, Chiara Petroselli, Siul Ruiz, Nancy Walker, and Tiina Roose

Phosphorus (P) is critical for plant growth and can limit crop yields, but rock phosphate (the primary source of agricultural P) is a finite resource which is predicted to run out within 50-250 years. However, since P is important for short-term yield gains, it is often over-applied, causing run-off and water pollution. It is crucial to apply the right fertilisers at the most efficient rate, time, and place to protect our food security and environment for the future.

Optimal application requires an understanding of the processes affecting P availability to plants. Fertilisers range from soluble in water (e.g TSP) to only slightly soluble (e.g. struvite). However, experiments testing the efficacy of fertilisers with different solubilities have reached variable results. Standard soil testing methods sample at fixed time points, while the dissolution, diffusion, sorption and uptake of P are dynamic processes, so to make predictions we must understand those dynamics.

We used image-based modelling to investigate the predicted effects of dissolution rate and soil buffer power on P uptake by spring wheat root systems taken from X-ray CT images. We added a P source to represent a fertiliser granule and modelled the predicted P uptake based on 1 day, 1 week, and 14 week dissolution of the same amount of P for two realistic soil buffer powers.

We demonstrated that rapid dissolution increased short-term root uptake, but dissolution over 1 week did not differ from dissolution over 1 day. We also found that root system architecture has a large effect on the efficiency of a P fertiliser pellet, highlighting the importance of application location. These results provide a starting point for predictive modelling of the efficacy of different P fertilisers in different soils, and our image-based approach gives the ability to add different root architectures for different species or varieties.

How to cite: Williams, K., McKay Fletcher, D., Petroselli, C., Ruiz, S., Walker, N., and Roose, T.: Modelling the effects of fertiliser solubility and soil buffer power on phosphorus uptake by spring wheat using an image-based approach, 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-12,, 2021.

Xia Pan, Zhenyi Wang, Yong Gao, and Xiaohong Dang

A better understanding of the distribution of the airflow field and wind velocity around the simulated shrubs is essential to provide optimized design and maximize the efficiency of the windbreak forests. In this study, a profiling set of Pitot Tube was used to measure the airflow field and wind velocity of simulated shrubs by wind tunnel simulation. The effects of form configurations and row spaces of simulated shrubs on windproof effectiveness were in-depth studied. We come to the following results: The weakening strength to wind velocities of hemisphere-shaped and broom-shaped shrubs at 26.25 cm was mainly concentrated below 2 cm near the root and 6-14 cm in the middle-upper part, while the spindle-shaped shrubs were at 0.2-14 cm above the canopy, which meant the windproof effect of spindle-shaped shrubs was was better than that of hemisphere-shaped and broom-shaped. With the improvement of row spaces, the weakening height to wind velocities of the hemisphere-shaped shrubs at 35 cm was only concentrated below 2 cm near the root exclude for the 6-14 cm at 26.25 cm, which presented the hemisphere-shaped shrubs were not suitable for the layout of wide row space. Further, the form configurations of simulated shrubs had a stronger influence on wind velocity than row spaces. Moreover, the designed windbreaks with Nitraria tangutorum, which more effectively reduced the wind velocity among the windbreaks compared to behind the windbreaks. In the wind control system, the hemisphere-shaped windbreaks should be applied as near-surface barriers, and the windbreaks of broom-shaped and spindle-shaped can be used as shelterbelts above the near-surface. These analytical findings offer theoretical guidelines on how to arrange the windbreak forests for preventing wind erosion in the most convenient and efficient ways.

How to cite: Pan, X., Wang, Z., Gao, Y., and Dang, X.: A Wind Tunnel Simulation of Windproof Effectiveness of Simulated Shrubs with Different Spatial Configurations, 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-15,, 2021.

Jannis Groh and Horst H. Gerke and the crop-soil modelling initiative

Crop model comparisons have mostly been carried out to test predictive ability under previous climate conditions and for soils of the same location. However, the ability of individual agricultural models to predict the effects of changes in climatic conditions on soil-ecosystems beyond the range of site-specific variability is unknown. The objective of this study was to test the predictive ability of agroecosystem models using weighable lysimeter data for the same soil under changing climatic conditions and to compare simulated plant growth and soil-ecosystem response to climate change between these models. To achieve this, data from the TERENO-SOILCan lysimeters-network for a soil-ecosystem at the original site (Dedelow) and data from the lysimeters with Dedelow soil monoliths transferred to Bad Lauchstädt and Selhausen were analysed. The transfer of the soils took place to a drier and warmer location (Bad Lauchstädt) and to a warmer and wetter location (Selhausen) compared to the original location of the soils in Dedelow with the same crop rotation. After model calibration for data from the original Dedelow site, crop growth and soil water balances of transferred Dedelow soil monoliths were predicted using the site-specific boundary conditions and compared with the observations at Selhausen and Bad Lauchstädt. The overall simulation output of the models was separated into a plant-related part, ecosystem-productivity (grain yield, biomass, LAI) and an environmental part, ecosystem-fluxes (evapotranspiration, net-drainage, soil moisture). The results showed that when the soil was transferred to a drier region, the agronomic part of the crop models predicted well, and when the soil was moved to wetter regions, the environmental flow part of the models seemed to predict better. The results suggest that accounting for climate change scenarios, more consideration of soil properties and testing model performance for conditions outside the calibrated range and site-specific variability will help improve the models.

How to cite: Groh, J. and Gerke, H. H. and the crop-soil modelling initiative: Same soil - different climate: crop model inter-comparison with lysimeter data of translocated monoliths, 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-45,, 2021.

Marine Lacoste, Hocine Bourennane, Mathieu Lamandé, Clément Dupré, Annie Duparque, Damian Martin, Guillaume Brisset, Rémy Duval, Pierre Descazaux, Myriam El Adas, and Pascale Métais

Sustainable crop production implies high efficiency of field operations and protection of the soil as a natural resource. Soil physical fertility is threatened by compaction, especially deep soil horizons for which remediation is more critical. Increased soil compaction, linked to the increase of agricultural equipment weight, causes yield losses on spring and summer crops. To avoid soil compaction and ensure field operations efficiency, including satisfactory crop production in a cost-effective way, field readiness prediction is necessary. Field readiness is defined by the combination of soil workability (soil suitability for cultural operations) and soil trafficability (soil capacity to support machinery during traffic without soil physical degradation).

Available tools focused on one part of the problem, e.g. soil compaction risk in deep soil horizon, or possibility of efficient field operation ; each has usually been built for a specific pedoclimatic context, which questions its application in a broader context. Available tools also frequently need to be upgraded to better consider compaction risk according to machinery evolution.

The J-DISTAS project (2019-2022) aims at evaluating and improving these tools, and structuring them to create a prototype of interoperable tools to predict field readiness. The resulting tool will be based on the combination of two mechanistic models (Terranimo for soil compaction and the CHN crop model for soil water content), pedotransfer functions to estimate soil water potential and soil workability, and a decisional tool of field readiness build from expert knowledge. Its ability to predict field readiness and its sensibility to input data will be evaluated.

The developed inter-operable tools could be used as a decision support tool that includes field readiness in strategic decisions, conception of cropping systems in the context of global changes, or optimization of mechanical cost for equipment in agricultural machinery, and will help to soil physical quality protection.

How to cite: Lacoste, M., Bourennane, H., Lamandé, M., Dupré, C., Duparque, A., Martin, D., Brisset, G., Duval, R., Descazaux, P., El Adas, M., and Métais, P.: J-DISTAS: predict field readiness to ensure efficiency of field operations and avoid soil compaction., 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-56,, 2021.

Alexander Prechtel, Simon Zech, Alice Lieu, Raphael Schulz, and Nadja Ray

Key functions of soils, such as permeability or habitat for microorganisms, are determined by structures at the microaggregate scale. The evolution of elemental distributions and dynamic processes can often not be assessed experimentally. So mechanistic models operating at the pore scale are needed.
We consider the complex coupling of biological, chemical, and physical processes in a hybrid discrete-continuum modeling approach. It integrates dynamic wetting (liquid) and non-wetting (gas) phases including biofilms, diffusive processes for solutes, mobile bacteria transforming into immobile biomass, and ions which are prescribed by means of partial differential equations. Furthermore the growth of biofilms as, e.g., mucilage exuded by roots, or the distribution of particulate organic matter in the system, is incorporated in a cellular automaton framework (CAM) presented in [1, 2]. It also allows for structural changes of the porous medium itself (see, e.g. [3]). As the evolving computational domain leads to discrete discontinuities, we apply the local discontinuous Galerkin (LDG) method for the transport part. Mathematical upscaling techniques incorporate the information from the pore to the macroscale [1,4].
The model is applied for two research questions: We model the incorporation and turnover of particulate OM influencing soil aggregation, including ‘gluing’ hotspots, and show scenarios varying of OM input, turnover, or particle size distribution.
Second, we quantify the effective diffusivity on 3D geometries from CT scans of a loamy and a sandy soil. Conventional models cannot account for natural pore geometries and varying phase properties. Upscaling allows also to quantify how root exudates (mucilage) can significantly alter the macroscopic soil hydraulic properties.

[1]  Ray, Rupp, Prechtel (2017). AWR (107), 393-404.
[2] Rupp, Totsche, Prechtel, Ray (2018). Front. Env. Sci. (6) 96.
[3] Zech, Dultz, Guggenberger, Prechtel, Ray (2020). Appl. Clay Sci. 198, 105845.
[4] Ray, Rupp, Schulz, Knabner (2018). TPM 124(3), 803-824.

How to cite: Prechtel, A., Zech, S., Lieu, A., Schulz, R., and Ray, N.: Evaluating the interaction of biofilms, organic matter and soil structures at the pore scale, 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-59,, 2021.

Fabian Bernhard and Katrin Meusburger

The water balance in forest soils is strongly affected by vertical distribution of root water uptake. Our objective is to constrain the parametrization of root water uptake in the field by using the naturally occurring, seasonal variability in stable isotope signatures in precipitation to trace water fluxes through the soil and into the trees.

The 1D soil hydrologic model LWFBrook90.jl contains the necessary processes to accurately reproduce hydrometric observations of volumetric soil moisture content and soil matric potential at forest sites in Switzerland. Root water uptake is described with a gradient-driven model using vertically varying root density and moisture-dependent rhizosphere resistivities. The hydrologic model will be extended with transport and fractionation processes to enable the modeling of isotopic signatures in soil and tree water.

We present a planned field sampling campaign over two subsequent vegetation seasons at 10 long-term monitoring forest sites. Soil water is sampled with lysimeters at four soil depths, and tree water is sampled from the xylem with increment corers. Both types of samples are taken bi-weekly. First results from an ongoing multi-year soil water sampling campaign show that the signal can be traced along the soil profile and are presented to illustrate the approach.

How to cite: Bernhard, F. and Meusburger, K.: Using natural abundances of stable water isotopes to constrain vertically distributed root water uptake of forest trees, 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-101,, 2021.

Interactive: Wed, 19 May, 12:30–14:00<

Siul Ruiz, Katherine Williams, Chiara Petroselli, Nancy Walker, Daniel McKay Fletcher, Giuseppe Pileio, and Tiina Roose

Plant roots secrete polymeric gels during root growth known as mucilage, which aid in root growth, nutrient acquisition, and water retention. Mucilage plays an important role in augmenting many soil physical and biogeochemical processes local to the root zone. However, most studies infer the effects of mucilage by reporting changes in the bulk soil. This investigation quantifies the isolated physical behaviour of plant mucilage in a highly simplified soil-analogous environment. We placed drops of hydrated mucilage between two flat surfaces to form liquid bridges and monitored their evolution under drying conditions considering different mucilage mass fractions. We used this information to develop a multi-phase model that characterises the mucilage-water interactions based on a polymeric description of the mucilage volume fraction. Unlike pure water liquid bridges that rupture, the hydrated mucilage liquid bridges collapsed under drying, but maintain connection between the surfaces. NMR imaging shows loss of water from the liquid bridge, particularly from the regions furthest from the surface contacts. Model of drying liquid bridges quantifies mucilage accumulation near the corners of the boundary where the adherence to surfaces is likely to occur. The modelled accumulation times overlapped with monitored bridge collapse for the different mass fractions. Consistency with the model and measurement results highlight the model’s ability to predict a transition when the hydrated mucilage mixture no longer behaves like a liquid. Results suggest that diffusion type models are not adequate for describing pore scale mucilage transport processes, indicating that mucilage’s zone of influence is local to the root, and the transition out of this zone is spatially sharp.

How to cite: Ruiz, S., Williams, K., Petroselli, C., Walker, N., McKay Fletcher, D., Pileio, G., and Roose, T.: A Pore Scale Characterisation of Plant Mucilage - Integrating Imaging, NMR, and Polymer Modelling  , 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-7,, 2021.

Nancy Walker, Kathryn Rankin, Siul Ruiz, Daniel McKay Fletcher, Katherine Williams, Chiara Petroselli, Pasquale Saldarelli, Maria Saponari, Steven White, and Tiina Roose

Photosynthesis relies on the transport of water and sugars from roots to leaves facilitated by two key tissues: xylem and phloem. Blockages in the xylem/phloem, either by structures formed by the pathogen itself or those formed by the plant as a defence mechanism, disrupt the soil-plant-atmosphere continuum and cause many vascular plant disease symptoms. Xylella fastidiosa (X. fastidiosa) is a bacterium that colonises internal plant vascular networks causing pathogenic effects on several commercially important crops, including those associated with the olive quick decline syndrome causing devastating olive decline in Apulia, Southern Italy. Despite a growing research effort since the recent detection of X. fastidiosa in Europe, the exact processes leading to X. fastidiosa disease symptoms are not fully understood due to difficulties in observing internal plant structures.

Our goal is to utilise models to elucidate fundamental processes that lead to olive quick decline syndrome. We are developing a mathematical model describing within-host biofilm development that predicts water-stresses that ultimately inhibit plant functionality. Our approach is centred on the assumption that the biofilm structure is determined by the arrangement of extracellular polysaccharide (EPS) molecules, and as such, our model contains a polymer-physical description of X. fastidiosa biofilm formation dynamics. We used our model, requiring minimal empirical assumptions, to replicate biofilm aggregation observed by microfluidics. We have also produced X-ray Computed Tomography (XCT) images of vascular networks in both resistant and susceptible olive cultivars. We are using these images to test whether susceptibility is correlated with morphological differences that might influence fluid flow through the plant. This work improves the understanding of possible cultivar resistance mechanisms to aid informed breeding and orchard management, and model simulations will provide insights for understanding xylem blockages and their relation to observed symptom severity.

How to cite: Walker, N., Rankin, K., Ruiz, S., McKay Fletcher, D., Williams, K., Petroselli, C., Saldarelli, P., Saponari, M., White, S., and Roose, T.: A Model and Image Based Investigation of X. fastidiosa Within Host Dynamics  , 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-14,, 2021.

Luis Alfredo Pires Barbosa and Horst H. Gerke

Biopore surface is often characterized by finer particles and increased concentration of polysaccharides from root and earthworm exudates, presenting physico-chemical properties different from those of the soil matrix. Such exudates controls not only the wettability or sorption properties but also the adhesive forces of the surrounding soil particles. Thus, increased mechanical stability may be expected on biopore-matrix interface affecting preferential flow and transport processes, as well.

However, it is still unknown (i) to what extent the particle cohesion in the coated region is able to increase the resilience of the biopore to an external loading and (ii) how it affects the permeability of the biopore-matrix pore region.

We created a discrete element model (DEM) model of a hollow cylindrical soil sample with a coated biopore in the center (i.e., 1 cm height, 1 cm outer and 0.6 cm inner diameter). The spherical particles in the model presented diameter of 0.13 mm for the coated material and 0.22 mm for the soil matrix. The cohesion among particles in the soil matrix was set to a constant value of 10.9 MPa while the cohesion among particles in the coated region varied between 10.9 and 50.9 MPa. The sample was subjected to axial compression and the force and cracks recorded. The permeability in the radial direction from the biopore to soil matrix was calculated using ImageJ and a 3D stokes solver (FDMMS).

The increment in the coating cohesion increased the overall soil stiffness in terms of the Young’s modulus. Before axial compression, the calculated hydraulic permeability for the interface coating and matrix was 182 μm2. After compression, although the lower coating cohesion resulted in a larger number of cracks, permeability increased with coating cohesion. This suggests that with increasing soil stiffness, the cracks decrease in number but increase in length (i.e. improved connectivity).

How to cite: Pires Barbosa, L. A. and Gerke, H. H.: Modelling coating cohesion effect on soil mechanical stability and permeability of the biopore - matrix interface pore region, 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-38,, 2021.

Responses of bacterial communities to spatial distribution and biogeochemical migration in Panzhihua mining tailing
Ying Yang and Yi Huang
Jan Vanderborght, Andrea Schnepf, Mathieu Javaux, and Guillaume Lobet

We developed root scale models that simulate water and nutrient uptake by crops. Water flow in the soil and root systems was linked in order to describe root water uptake as a function of root properties and distributions, soil and leaf water potentials. One of the underlying motivations is to predict the crop water stress level and its impact on transpiration and growth. The mechanistic description of water fluxes resulted in models that were sensitive to hydraulic properties of the root system, including root density, and root distribution with depth. These sensitivities improved predictions of crop water uptake and water stress in different soils and for different water treatments. Crucial was the correct representation of the root system and its response to different ‘treatments’. Thus, in order to predict the impact of water stress on growth, the growth response to the water stress must be predicted. So far, these response functions and especially the distribution of carbon within the plant to the different plant organs are empirical functions. A coupled carbon and water flow model within the plant is a way forward to more mechanistic descriptions of these responses. A similar storyline can be developed for nutrient uptake. Mechanistic nutrient uptake models do not consider nutrient transport within the root system but focus on transport towards the root surface. Multi-scale flow and transport simulations demonstrated that small scale transport towards growing root tips and root system scale water and nutrient distributions controlled nutrient uptake. These simulations predicted the observed interaction between water and phosphate uptake of an upland rice crop. However, here again, simulated uptake depended on the root development in response to nutrient and water stress. Mechanistic descriptions of root growth response to nutrients require a further understanding of plant physiological processes that cause these responses. 

How to cite: Vanderborght, J., Schnepf, A., Javaux, M., and Lobet, G.: Modeling water and nutrient uptake by crops: simulate uptake to predict growth or simulate growth to predict uptake?, 3rd ISMC Conference ─ Advances in Modeling Soil Systems, online, 18–22 May 2021, ISMC2021-98,, 2021.