scholarly journals CRootBox: A structural-functional modelling framework for root systems

2017 ◽  
Author(s):  
Andrea Schnepf ◽  
Daniel Leitner ◽  
Magdalena Landl ◽  
Guillaume Lobet ◽  
Trung Hieu Mai ◽  
...  
Keyword(s):  
Water Flow ◽  
Web Application ◽  
Root Architecture ◽  
Root Systems ◽  
Root Water Uptake ◽  
Soil Conditions ◽  
Soil Physics ◽  
Architecture Model ◽  
Single Root ◽  
The Impact

ABSTRACTBackground 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.MethodsCRootBox 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.Key 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.ConclusionsIn 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.

scholarly journals MARSHAL, a novel tool for virtual phenotyping of maize root system hydraulic architectures

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Félicien Meunier ◽  
Adrien Heymans ◽  
Xavier Draye ◽  
Valentin Couvreur ◽  
Mathieu Javaux ◽  
...  
Keyword(s):  
Root System ◽  
Web Application ◽  
Root Traits ◽  
Root Systems ◽  
R Package ◽  
Maize Root ◽  
Model Parameters ◽  
System Modelling ◽  
Architecture Model ◽  
System Models

Abstract Functional-structural root system models combine functional and structural root traits to represent the growth and development of root systems. In general, they are characterized by a large number of growth, architectural and functional root parameters, generating contrasted root systems evolving in a highly non-linear environment (soil, atmosphere), which makes the link between local traits and functioning unclear. On the other end of the root system modelling continuum, macroscopic root system models associate to each root system a set of plant-scale, easily interpretable parameters. However, as of today, it is unclear how these macroscopic parameters relate to root-scale traits and whether the upscaling of local root traits is compatible with macroscopic parameter measurements. The aim of this study was to bridge the gap between these two modelling approaches. We describe here the MAize Root System Hydraulic Architecture soLver (MARSHAL), a new efficient and user-friendly computational tool that couples a root architecture model (CRootBox) with fast and accurate algorithms of water flow through hydraulic architectures and plant-scale parameter calculations. To illustrate the tool’s potential, we generated contrasted maize hydraulic architectures that we compared with root system architectural and hydraulic observations. Observed variability of these traits was well captured by model ensemble runs. We also analysed the multivariate sensitivity of mature root system conductance, mean depth of uptake, root system volume and convex hull to the input parameters to highlight the key model parameters to vary for virtual breeding. It is available as an R package, an RMarkdown pipeline and a web application.

scholarly journals Toward Marker-assisted Breeding for Root Architecture Traits in Southern Highbush Blueberry

2016 ◽  
Vol 141 (5) ◽  
pp. 414-424 ◽  
Author(s):  
Gerardo H. Nunez ◽  
Hilda Patricia Rodríguez-Armenta ◽  
Rebecca L. Darnell ◽  
James W. Olmstead
Keyword(s):  
Root Growth ◽  
Root Architecture ◽  
Root Systems ◽  
Vaccinium Corymbosum ◽  
Lower Percentage ◽  
Soil Conditions ◽  
Growth Substrate ◽  
Family Pedigree ◽  
Southern Highbush ◽  
Trait Associations

Root growth and root system architecture (RSA) are affected by edaphic and genetic factors and they can impact plant growth and farm profitability. Southern highbush blueberries [SHBs (Vaccinium corymbosum hybrids)] develop shallow, fibrous root systems, and exhibit a preference for acidic soils where water and ammonium are readily available. The amendments used to create these soil conditions negatively affect the profitability of SHB plantations. Hence, breeding for RSA traits has been suggested as an alternative to soil amendments. Vaccinium arboreum is a wild species that is used in SHB breeding. V. arboreum exhibits greater drought tolerance and broader soil pH adaptation than SHB, and—according to anecdotal evidence—it develops deep, taproot-like root systems. The present study constitutes the first in-depth study of the RSA of Vaccinium species with the intention of facilitating breeding for RSA traits. Root systems were studied in rhizotron-grown seedling families. In separate experiments, we tested the effect that growth substrate and family pedigree can have on root growth and RSA. Subsequently, a genotyping by sequence approach was used to develop single nucleotide polymorphism (SNP) markers that could be used along with the phenotyping method to investigate the heritability of RSA traits and look for marker-trait associations. We found that RSA is affected by growth substrate and family pedigree. In addition, we found that V. arboreum exhibited greater maximum root depth and a lower percentage of roots in the top 8 cm of soil than SHB, and interspecific hybrids generally exhibited intermediate phenotypes. Also, we found that RSA traits exhibit moderate to low heritability and genetic correlations among them. Finally, we found 59 marker-trait associations. Among these markers, 37 were found to be located in exons, and 16 of them were annotated based on protein homology with entries in National Center for Biotechnology Information (NCBI) GenBank. Altogether, the present study provides tools that can be used to breed for root architecture traits in SHB.

scholarly journals Effects of large macropores on soil evaporation in salt marshes

2020 ◽  
Author(s):  
Tingzhang Zhou ◽  
Pei Xin ◽  
Jirka Jirka Šimůnek
Keyword(s):  
Water Flow ◽  
Salt Marshes ◽  
Evaporation Rate ◽  
Preferential Flow ◽  
Soil Surface ◽  
Soil Evaporation ◽  
Infrared Light ◽  
Soil Conditions ◽  
Set Up ◽  
The Impact

<p>The occurrence of macropores in salt marsh sediments is a natural and ubiquitous phenomenon. Although they are widely assumed to significantly affect water flow in salt marshes, the effects are not well understood. We conducted physical laboratory experiments and numerical simulations to examine the impact of macropores on soil evaporation. Soil columns packed with either sand or clay and with or without macropores were set up with water tables in the columns set at different levels. A high potential evaporation rate was induced by infrared light and a fan. The results showed that in the soil with a low saturated hydraulic conductivity (and thus a low transport capacity), macropores behaved as preferential flow paths, delivering water from the groundwater towards the soil surface and maintaining a high evaporation rate in comparison with the soil without macropores. This effect was more pronounced for sediments with lower hydraulic conductivities and shallower groundwater tables. These results not only improve our understanding of water flow and soil conditions in salt marshes but also shed light on soil evaporation in other hydrological systems.</p>

scholarly journals Simulating rhizodeposition patterns around growing and exuding root systems

2021 ◽  
Author(s):  
Magdalena Landl ◽  
Adrian Haupenthal ◽  
Daniel Leitner ◽  
Eva Kroener ◽  
Doris Vetterlein ◽  
...  
Keyword(s):  
Root Architecture ◽  
Three Dimensional ◽  
Temporal Distribution ◽  
Root Systems ◽  
Distribution Patterns ◽  
Three Dimensions ◽  
Root Branching ◽  
Architecture Model ◽  
Spatio Temporal ◽  
Model Approach

1AbstractIn 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.

scholarly journals An approach to modelling tree root architecture in virtual urban growing conditions

2021 ◽  
Author(s):  
Justin Miron
Keyword(s):  
Root Growth ◽  
Root System ◽  
Root Architecture ◽  
Root Systems ◽  
System Structure ◽  
Tree Roots ◽  
System Architectures ◽  
Architecture Model ◽  
Investigation Methods ◽  
Urban Conditions

Understanding the architecture of tree roots is an important component of urban forestry management practice. Tree roots are structurally and functionally important to the survival of trees, and this can be even more so in urban environments where underground space for roots is limited. Tree root architecture models can provide a complementary approach to traditional on-site field investigation methods. Root architecture models are unique in that they can simulate the spatial arrangements of root system structure explicitly, and allow investigators to create hypothetical simulations to test their assumptions about what may be driving root growth. The use of root architecture models in the literature is extensive and may be applied in diverse streams of investigation, but their application to tree root systems is less common. This research demonstrates a root architecture model, Rootbox, as a case study in the application of plant architecture models to simulate tree root growth in urban conditions. Model parameterization was based on conformity of root simulations to tree root architecture reported in the literature. The model is deployed in four hypothetical urban soil scenarios, which are representative of planting sites commonly observed in urban settings. The analysis demonstrates that plausible tree root system architectures – specifically, commonly observed growth attributes - can be produced by Rootbox, but only after several adaptive changes to both the source code/model design are made. Custom soil models can integrate with the simulation to represent urban conditions by modifying both the growth direction and elongation of portions of the root architecture, and thus offer greater control over the output architecture. Rootbox offers a flexible method of simulating the architecture of tree root systems, but further research should focus on optimizing the model’s parameters and functions to enable greater user control over model output.

scholarly journals Parameterizing complex root water uptake models – the arrangement of root hydraulic properties within the root architecture affects dynamics and efficiency of root water uptake

2014 ◽  
Vol 11 (1) ◽  
pp. 757-805 ◽  
Author(s):  
M. Bechmann ◽  
C. Schneider ◽  
A. Carminati ◽  
D. Vetterlein ◽  
S. Attinger ◽  
...  
Keyword(s):  
Root System ◽  
Water Uptake ◽  
Plant Resistance ◽  
Hydraulic Properties ◽  
Three Dimensional ◽  
Root Systems ◽  
Root Water Uptake ◽  
Hydraulic Lift ◽  
Excessive Bleeding ◽  
Single Root

Abstract. Detailed three-dimensional models of root water uptake have become increasingly popular for investigating the process of root water uptake. However they suffer from a lack of information in important parameters, especially distribution of root hydraulic properties. In this paper we explore the role that arrangement of root hydraulic properties and root system topology play for modelled uptake dynamics. We apply microscopic models of single root structures to investigate the mechanisms shaping uptake dynamics and demonstrate the effects in a complex three dimensional root water uptake model. We introduce two efficiency indices, for (a) overall plant resistance and (b) water stress and show that an appropriate arrangement of root hydraulic properties can increase modelled efficiency of root water uptake in single roots, branched roots and entire root systems. The average uptake depth of the complete root system was not influenced by parameterization. However, other factors such as evolution of collar potential, which is related to the plant resistance, root bleeding and redistribution patterns were strongly affected by the parameterization. Root systems are more efficient when they are assembled of different root types, allowing for separation of root function in uptake (short young) roots and transport (longer mature) roots. Results become similar, as soon as this composition is accounted for to some degree (between 40 and 80% of young uptake roots). Overall resistance to root water uptake was decreased up to 40% and total transpiration was increased up to 25% in these composed root systems, compared to homogenous root systems. Also, one parameterization (homogenous young root system) was characterized by excessive bleeding (hydraulic lift), which was accompanied by lowest efficiency. We conclude that heterogeneity of root hydraulic properties is a critical component of complex three dimensional uptake models. Efficiency measures together with information on critical xylem potentials may be useful in parameterizing root property distribution.

scholarly journals An approach to modelling tree root architecture in virtual urban growing conditions

2021 ◽  
Author(s):  
Justin Miron
Keyword(s):  
Root Growth ◽  
Root System ◽  
Root Architecture ◽  
Root Systems ◽  
System Structure ◽  
Tree Roots ◽  
System Architectures ◽  
Architecture Model ◽  
Investigation Methods ◽  
Urban Conditions

Understanding the architecture of tree roots is an important component of urban forestry management practice. Tree roots are structurally and functionally important to the survival of trees, and this can be even more so in urban environments where underground space for roots is limited. Tree root architecture models can provide a complementary approach to traditional on-site field investigation methods. Root architecture models are unique in that they can simulate the spatial arrangements of root system structure explicitly, and allow investigators to create hypothetical simulations to test their assumptions about what may be driving root growth. The use of root architecture models in the literature is extensive and may be applied in diverse streams of investigation, but their application to tree root systems is less common. This research demonstrates a root architecture model, Rootbox, as a case study in the application of plant architecture models to simulate tree root growth in urban conditions. Model parameterization was based on conformity of root simulations to tree root architecture reported in the literature. The model is deployed in four hypothetical urban soil scenarios, which are representative of planting sites commonly observed in urban settings. The analysis demonstrates that plausible tree root system architectures – specifically, commonly observed growth attributes - can be produced by Rootbox, but only after several adaptive changes to both the source code/model design are made. Custom soil models can integrate with the simulation to represent urban conditions by modifying both the growth direction and elongation of portions of the root architecture, and thus offer greater control over the output architecture. Rootbox offers a flexible method of simulating the architecture of tree root systems, but further research should focus on optimizing the model’s parameters and functions to enable greater user control over model output.

scholarly journals From hydraulic root architecture models to macroscopic representations of root hydraulics in soil water flow and land surface models

2021 ◽  
Author(s):  
Jan Vanderborght ◽  
Valentin Couvreur ◽  
Felicien Meunier ◽  
Andrea Schnepf ◽  
Harry Vereecken ◽  
...  
Keyword(s):  
Soil Water ◽  
Water Flow ◽  
Water Uptake ◽  
Land Surface ◽  
Root Architecture ◽  
Root Water Uptake ◽  
Land Surface Models ◽  
Surface Models ◽  
Root Model ◽  
Soil Water Flow

Abstract. Root water uptake is an important process in the terrestrial water cycle. How this process depends on soil water content, root distributions, and root properties is a soil-root hydraulic problem. We compare different approaches to implement root hydraulics in macroscopic soil water flow and land surface models. By upscaling a three dimensional hydraulic root architecture model, we derived an exact macroscopic root hydraulic model. The macroscopic model uses three characteristics: the root system conductance, Krs, the standard uptake fraction, SUF, that represents the uptake from a soil profile with a uniform hydraulic head, and a compensatory matrix that describes the redistribution of water uptake in a non-uniform hydraulic head profile. Two characteristics, Krs and SUF, are sufficient to describe the total uptake as a function of the collar and soil water potential; and water uptake redistribution does not depend on the total uptake or collar water potential. We compared the exact model with two hydraulic root models that make a-priori simplifications of the hydraulic root architecture: the parallel and big root model. The parallel root model uses only two characteristics, Krs and SUF, that can be calculated directly following a bottom up approach from the 3D hydraulic root architecture. The big root model uses more parameters than the parallel root model but these parameters cannot be obtained straightforwardly with a bottom up approach. The big root model was parameterized using a top down approach, i.e. directly from root segment hydraulic properties assuming a-priori a single big root architecture. This simplification of the hydraulic root architecture led to less accurate descriptions of root water uptake than by the parallel root model. To compute root water uptake in macroscopic soil water flow and land surface models, we recommend the use of the parallel root model with Krs and SUF computed in a bottom up approach from a known 3D root hydraulic architecture.

scholarly journals From hydraulic root architecture models to macroscopic representations of root hydraulics in soil water flow and land surface models

2021 ◽  
Vol 25 (9) ◽  
pp. 4835-4860
Author(s):  
Jan Vanderborght ◽  
Valentin Couvreur ◽  
Felicien Meunier ◽  
Andrea Schnepf ◽  
Harry Vereecken ◽  
...  
Keyword(s):  
Soil Water ◽  
Water Flow ◽  
Water Uptake ◽  
Land Surface ◽  
Root Architecture ◽  
Root Water Uptake ◽  
Land Surface Models ◽  
Surface Models ◽  
Root Model ◽  
Soil Water Flow

Abstract. Root water uptake is an important process in the terrestrial water cycle. How this process depends on soil water content, root distributions, and root properties is a soil–root hydraulic problem. We compare different approaches to implement root hydraulics in macroscopic soil water flow and land surface models. By upscaling a three-dimensional hydraulic root architecture model, we derived an exact macroscopic root hydraulic model. The macroscopic model uses the following three characteristics: the root system conductance, Krs, the standard uptake fraction, SUF, which represents the uptake from a soil profile with a uniform hydraulic head, and a compensatory matrix that describes the redistribution of water uptake in a non-uniform hydraulic head profile. The two characteristics, Krs and SUF, are sufficient to describe the total uptake as a function of the collar and soil water potential, and water uptake redistribution does not depend on the total uptake or collar water potential. We compared the exact model with two hydraulic root models that make a priori simplifications of the hydraulic root architecture, i.e., the parallel and big root model. The parallel root model uses only two characteristics, Krs and SUF, which can be calculated directly following a bottom-up approach from the 3D hydraulic root architecture. The big root model uses more parameters than the parallel root model, but these parameters cannot be obtained straightforwardly with a bottom-up approach. The big root model was parameterized using a top-down approach, i.e., directly from root segment hydraulic properties, assuming a priori a single big root architecture. This simplification of the hydraulic root architecture led to less accurate descriptions of root water uptake than by the parallel root model. To compute root water uptake in macroscopic soil water flow and land surface models, we recommend the use of the parallel root model with Krs and SUF computed in a bottom-up approach from a known 3D root hydraulic architecture.

scholarly journals Implementing small scale processes at the soil-plant interface – the role of root architectures for calculating root water uptake profiles

2010 ◽  
Vol 14 (2) ◽  
pp. 279-289 ◽  
Author(s):  
C. L. Schneider ◽  
S. Attinger ◽  
J.-O. Delfs ◽  
A. Hildebrandt
Keyword(s):  
Soil Water ◽  
Water Flow ◽  
Water Uptake ◽  
Soil Water Potential ◽  
Root Systems ◽  
Root Water Uptake ◽  
Bulk Soil ◽  
Small Scale ◽  
Sink Term

Abstract. In this paper, we present a stand alone root water uptake model called aRoot, which calculates the sink term for any bulk soil water flow model taking into account water flow within and around a root network. The boundary conditions for the model are the atmospheric water demand and the bulk soil water content. The variable determining the plant regulation for water uptake is the soil water potential at the soil-root interface. In the current version, we present an implementation of aRoot coupled to a 3-D Richards model. The coupled model is applied to investigate the role of root architecture on the spatial distribution of root water uptake. For this, we modeled root water uptake for an ensemble (50 realizations) of root systems generated for the same species (one month old Sorghum). The investigation was divided into two Scenarios for aRoot, one with comparatively high (A) and one with low (B) root radial resistance. We compared the results of both aRoot Scenarios with root water uptake calculated using the traditional Feddes model. The vertical rooting density profiles of the generated root systems were similar. In contrast the vertical water uptake profiles differed considerably between individuals, and more so for Scenario B than A. Also, limitation of water uptake occurred at different bulk soil moisture for different modeled individuals, in particular for Scenario A. Moreover, the aRoot model simulations show a redistribution of water uptake from more densely to less densely rooted layers with time. This behavior is in agreement with observation, but was not reproduced by the Feddes model.

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