Biology subjects

Landl, M.

Publications and source records attributed to Landl, M..

4 recordsLinked to original sources

bioRxiv2021

Linking rhizosphere processes across scales: Opinion

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.

bioengineering↗

bioRxiv2021

Simulating rhizodeposition patterns around growing and exuding root systems

1In 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 for the first time 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 cit-rate 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.

plant biology↗

bioRxiv2019

Call for participation: Collaborative benchmarking of functional-structural root architecture models. The case of root water uptake.

Three-dimensional models of root growth, architecture and function are becoming important tools that aid the design of agricultural management schemes and the selection of beneficial root traits. However, while benchmarking is common in many disciplines that use numerical models such as natural and engineering sciences, functional-structural root architecture models have never been systematically compared. The following reasons might induce disagreement between the simulation results of different models: different representation of root growth, sink term of root water and solute uptake and representation of the rhizosphere. Presently, the extent of discrepancies is unknown, and a framework for quantitatively comparing functional-structural root architecture models is required. We propose, in a first step, to define benchmarking scenarios that test individual components of complex models: root architecture, water flow in soil and water flow in roots. While the latter two 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 allow recreating reference root systems in all models will be a key challenge. In a second step, benchmarking scenarios for the coupled problems are defined. We expect that the results of step 1 will enable us to better interpret differences found in step 2. This benchmarking will result in a better understanding of the different models and contribute towards improving them. Improved models will allow us to simulate various scenarios with greater confidence and avoid bugs, numerical errors or conceptual misunderstandings. This work will set a standard for future model development.

plant biology↗

bioRxiv2017

CRootBox: A Structural-Functional Modelling Framework For Root Systems

Background and AimsRoot architecture development determines the sites in soil where roots provide input of carbon and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architectural models have been widely used and been further developed into functional-structural models that simulate the fate of water and solutes in the soil-root system. We present a root architectural model, CRootBox, as a flexible framework to model architecture and its interactions with static and dynamic soil environments.\n\nMethodsCRootBox is a C++ -based root architecture model with Python binding, so that CRootBox can be included via a shared library into any Python code. Output formats include VTP, DGF, RSML and CSV. We further created a database of published root architectural parameters. The capabilities of CRootBox for the unconfined growth of single root systems, as well as the different parameter sets, are highlighted into a freely available web application.\n\nKey resultsWe demonstrate the use of CRootBox for 5 different cases (1) free growth of individual root systems (2) growth of root systems in containers as a way to mimic experimental setups, (3), field scale simulation, (4) root growth as affected by heterogeneous, static soil conditions, and (5) coupling CRootBox with Soil Physics with Python code to dynamically compute water flow in soil, root water uptake, and water flow inside roots.\n\nConclusionsIn conclusion, we present a fast and flexible functional-structural root model which is based on state-of-the-art computational science methods. Its aim is to facilitate modelling of root responses to environmental conditions as well as the impact of root on soil. In the future, we plan to extend this approach to the aboveground part of the plant.

plant biology↗