Vanderborght, J. | bioRxiv Science

bioRxiv2018

Connecting the dots between computational tools to analyse soil-root water relations

In the recent years, many computational tools, such as image analysis, data management, process-based simulation and upscaling tools, were developed to help quantify and understand water flow in the soil-root system, at multiple scales (tissue, organ, plant and population). Several of these tools work together or, at least, are compatible. However, for the un-informed researcher, they might seem disconnected, forming a unclear and disorganised succession of tools.\n\nIn this article, we present how different pieces of work can be further developed by connecting them to analyse soil-root-water relations in a comprehensive and structured network. This \"explicit network of soil-root computational tools\" informs the reader about existing tools and help them understand how their data (past and future) might fit within the network. We also demonstrate the novel possibilities of scale-consistent parameterizations made possible by the network with a set of case studies from the literature. Finally, we discuss existing gaps in the network and how we can move forward to fill them.\n\nHighlightsMany computational tools exist to quantify water flow in the soil-root system. These tools can be arranged in a comprehensive network that can be leveraged to better interpret experimental data.

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↗