Andrea Schnepf
Daniel Leitner
Gernot Bodner
Mathieu Javaux- 1Institute of Bio-Geosciences (IBG-3, Agrosphere), Forschungszentrum Jülich GmbH, Jülich, Germany
- 2Simulationswerkstatt – Services in Computational Sciences, Linz, Austria
- 3Department of Crop Sciences, Division of Agronomy, University of Natural Resources and Life Sciences BOKU Vienna, Tulln an der Donau, Austria
- 4Earth and Life Institute, Université Catholique de Louvain, Ottignies-Louvain-la-Neuve, Belgium
Editorial on the Research Topic
Benchmarking 3D-Models of Root Growth, Architecture and Functioning
Three-dimensional models of root system development and functioning have evolved as important tools that aid designing agricultural management schemes for improved resource use efficiency and selecting root traits for optimizing plant performance in specific environments (Benes et al., 2020). For their reliable application, benchmarking of such so-called functional-structural root architecture models (FSRM) is urgently needed. Similar relevant benchmarking initiatives have been performed for crop models (AgMIP), reactive transport models (Steefel et al., 2015), or models of water flow and solute transport in soils (Vanderborght et al., 2005). FSRMs generally solve flow and transport equations in the soil and in root system, and couple them via different approaches. Differences between different models' outputs might arise from differences in mathematical formulation of the processes and their coupling, in the numerical scheme, but also from coding errors. Consequently, potential errors might propagate into the plant and soil interaction simulations relying on an accurate simulation of root architecture development for describing root water and solute uptake processes. This Research Topic set out to shed some light on the extent of potential uncertainty due to these different factors.
Benchmarking is an emerging procedure to measure performance of models against a set of defined standards (Luo et al., 2012). In this issue, Schnepf et al. announced a “Call for Participation: Collaborative Benchmarking of Functional-Structural Root Architecture Models. The Case of Root Water Uptake”. They designed benchmark problems for root growth models, soil water flow models, root water flow models, and for water flow in the coupled soil-root system. All the benchmarks and corresponding reference solutions were published in the form of Jupyter Notebooks on the GitHub repository https://github.com/RSA-benchmarks/collaborative-comparison. Several groups that develop such functional-structural root architecture models have contributed with their solutions to the benchmark problems on this GitHub repository, and it may provide orientation for future model developments as well. The benchmarks follow a multi-step approach with growing level of complexity regarding both the number of processes accounted for and the dimension of the system. The first set of benchmarks is about individual modules only. The scenarios are simple, potentially solvable with analytical solutions, and the goal is to build trust in accuracy of the individual models. The second set of benchmarks is about the fully coupled models, with a focus on comparison of numerical representation of agreed-upon equations and process representations. In the third set of benchmarks, models do not have to have the same process representations. Evaluations of those are only possible against available data sets and by comparing the different model outputs.
In this issue, Khare et al. further extended the benchmark problem Schnepf et al. which is about root water uptake from a drying soil. They showed in a grid convergence study that the additional resistance to water flow toward the root surface caused by a dry rhizosphere must be considered for dry soil or else root water uptake is significantly overestimated. Simulations were performed with dumux-rosi. Solutions to the problem of dry rhizosphere are presented in Khare et al., but also in (Schröder et al., 2009a,b; Beudez et al., 2013; Mai et al., 2019; Koch et al., 2021). All of those solutions include a way to determine sub-resolution scale (with respect to the soil grid) rhizosphere water potential gradients in a computationally efficient way. The alternative is grid refinement but this comes at high computational costs as also discussed in Khare et al..
As part of this issue, soil compaction due to agricultural traffic and resulting mechanical and hydric stresses and their effect on root water uptake were simulated by de Moraes et al. using CRootBox (Schnepf et al., 2018) coupled with a 1-dimension soil water flow model. The model simulations could elucidate the feedback between root function and local soil stresses at the field scale for a Brazilian Oxisol. Here, the reference is not a mathematical reference solution but a reference data set. For field-scale simulations, FSRMs are often coupled to models that have 1-dimensional soil modules, e.g., crop models (Wu et al., 2015; Seidel et al., 2022). From a known 3D root hydraulic architecture, 1-dimensional sink terms can be derived (e.g. as shown in Vanderborght et al., 2021).
Model simulations may elucidate the contributions of different root types to overall plant nutrient uptake. Using OpenSimRoot (Postma et al., 2017), Gonzalez et al. indicated in this issue that nodal roots contribute most to P uptake by rice plants, followed by L-type lateral roots, S-type laterals and root hairs, but these strategies have different carbon costs. Implications for improving adaption to P deficiency in rice breeding are discussed. These results have to be also seen in light of the respective soil P and water content (De Bauw et al., 2020).
The longitudinal pattern of root aerenchyma formation modeled by the Ti-Gompertz model helped to deeply understand the relationship between the anatomical traits and physiological function in rice adventitious roots (Chen et al., as part of this issue). Such data will help to further develop models that include information on the root anatomy such as MECHA (Heymans et al., 2021) and GRANAR (Heymans et al., 2019).
Through this Research Topic, we continue to provide the opportunity to participate in the development and application of suitable benchmarks. This exercise allows us to point out sources of inaccuracies, knowledge gaps and to pin-point current challenges in mathematical model development of FSRM's.
Author Contributions
All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.
Conflict of Interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher's Note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Acknowledgments
This study was partially funded by the German Research Foundation (DFG) under Germany's Excellence Strategy, EXC-2070 – 390732324 – PhenoRob.
References
Benes, B., Guan, K., Lang, M., Long, S. P., Lynch, J. P., Marshall-Colon, A., et al. (2020). Multiscale computational models can guide experimentation and targeted measurements for crop improvement. Plant J. 103, 21–31. doi: 10.1111/tpj.14722
Beudez, N., Doussan, C., Lefeuve-Mesgouez, G., and Mesgouez, A. (2013). Influence of Three Root Spatial Arrangement on Soil Water Flow and Uptake. Results from an Explicit and an Equivalent, Upscaled, Model. Proc. Environ. Sci. 19, 37–46. doi: 10.1016/j.proenv.2013.06.005
De Bauw, P., Mai, T. H., Schnepf, A., Merckx, R., Smolders, E., and Vanderborght, J. (2020). A functional-structural model of upland rice root systems reveals the importance of laterals and growing root tips for phosphate uptake from wet and dry soils. Ann. Bot. 126, 789–806. doi: 10.1093/aob/mcaa120
Heymans, A., Couvreur, V., LaRue, T., Paez-Garcia, A., and Lobet, G. (2019). GRANAR, a Computational Tool to Better Understand the Functional Importance of Monocotyledon Root Anatomy1 [OPEN]. Plant Physiol. 182, 707–720. doi: 10.1104/pp.19.00617
Heymans, A., Couvreur, V., and Lobet, G. (2021). Combining cross-section images and modeling tools to create high-resolution root system hydraulic atlases in Zea mays. Plant Direct. 5. doi: 10.1002/pld3.334
Koch, T., Wu, H., and Schneider, M. (2021). Nonlinear mixed-dimension model for embedded tubular networks with application to root water uptake. J. Comput. Phys. 450, 110823. doi: 10.1016/j.jcp.2021.110823
Luo, Y. Q., Randerson, J. T., Abramowitz, G., Bacour, C., Blyth, E., Carvalhais, N., et al. (2012). A framework for benchmarking land models. Biogeosciences 9, 3857–3874. doi: 10.5194/bg-9-3857-2012
Mai, T. H., Schnepf, A., Vereecken, H., and Vanderborght, J. (2019). Continuum multiscale model of root water and nutrient uptake from soil with explicit consideration of the 3D root architecture and the rhizosphere gradients. Plant Soil. 439, 273–292. doi: 10.1007/s11104-018-3890-4
Postma, J. A., Kuppe, C., Owen, M. R., Mellor, N., Griffiths, M., Bennett, M. J., et al. (2017). OpenSimRoot: widening the scope and application of root architectural models. New Phytol. 215, 1274–1286. doi: 10.1111/nph.14641
Schnepf, A., Leitner, D., Landl, M., Lobet, G., Mai, T. H., Morandage, S., et al. (2018). CRootBox: a structural–functional modelling framework for root systems. Ann. Botany. 121, 1033–1053. doi: 10.1093/aob/mcx221
Schröder, T., Javaux, M., Vanderborght, J., Korfgen, B., and Vereecken, H. (2009a). Implementation of a Microscopic Soil-Root Hydraulic Conductivity Drop Function in a Three-Dimensional Soil-Root Architecture Water Transfer Model. Vadose Zone J. 8, 783–792. doi: 10.2136/vzj2008.0116
Schröder, T., Tang, L., Javaux, M., Vanderborght, J., Körfgen, B., and Vereecken, H. (2009b). A grid refinement approach for a three-dimensional soil-root water transfer model. Water Resour. Res. 45. doi: 10.1029/2009WR007873
Seidel, S. J., Gaiser, T., Kumar, A. S., Leitner, D., Schmittmann, O., Athmann, M., et al. (2022). Simulating root growth as a function of soil strength and yield with a field-scale crop model coupled with a 3D architectural root model. Front. Plant Sci.
Steefel, C. I., Yabusaki, S. B., and Mayer, K. U. (2015). Reactive transport benchmarks for subsurface environmental simulation. Comput. Geosci. 19, 439–443. doi: 10.1007/s10596-015-9499-2
Vanderborght, J., Couvreur, V., Meunier, F., Schnepf, A., Vereecken, H., Bouda, M., et al. (2021). From hydraulic root architecture models to macroscopic representations of root hydraulics in soil water flow and land surface models. Hydrol. Earth Syst. Sci. 25, 4835–4860. doi: 10.5194/hess-25-4835-2021
Vanderborght, J., Kasteel, R., Herbst, M., Javaux, M., Thiéry, D., Vanclooster, M., et al. (2005). A Set of Analytical Benchmarks to Test Numerical Models of Flow and Transport in Soils. Vadose Zone J. 4, 206–221. doi: 10.2136/vzj2005.0206
Keywords: root architecture modeling, benchmarking, root hydrology, plant-soil interaction, mathematical modeling, simulation
Citation: Schnepf A, Leitner D, Bodner G and Javaux M (2022) Editorial: Benchmarking 3D-Models of Root Growth, Architecture and Functioning. Front. Plant Sci. 13:902587. doi: 10.3389/fpls.2022.902587
Received: 23 March 2022; Accepted: 13 April 2022;
Published: 26 May 2022.
Edited and reviewed by: Sebastian Leuzinger, Auckland University of Technology, New Zealand
Copyright © 2022 Schnepf, Leitner, Bodner and Javaux. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Andrea Schnepf, YS5zY2huZXBmJiN4MDAwNDA7ZnotanVlbGljaC5kZQ==