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  • 1
    In: in silico Plants, Oxford University Press (OUP), Vol. 5, No. 2 ( 2023-07-01)
    Abstract: Plant growth and development involve the integration of numerous processes, influenced by both endogenous and exogenous factors. At any given time during a plant’s life cycle, the plant architecture is a readout of this continuous integration. However, untangling the individual factors and processes involved in the plant development and quantifying their influence on the plant developmental process is experimentally challenging. Here we used a combination of computational plant models (CPlantBox and PiafMunch) to help understand experimental findings about how local phloem anatomical features influence the root system architecture. Our hypothesis was that strong local phloem resistance would restrict local carbon flow and locally modify root growth patterns. To test this hypothesis, we simulated the mutual interplay between the root system architecture development and the carbohydrate distribution to provide a plausible mechanistic explanation for several experimental results. Our in silico experiments highlighted the strong influence of local phloem hydraulics on the root growth rates, growth duration and final length. The model result showed that a higher phloem resistivity leads to shorter roots due to the reduced flow of carbon within the root system. This effect was due to local properties of individual roots, and not linked to any of the pleiotropic effects at the root system level. Our results open a door to a better representation of growth processes in a plant computational model.
    Type of Medium: Online Resource
    ISSN: 2517-5025
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 3019806-9
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  • 2
    In: in silico Plants, Oxford University Press (OUP), Vol. 5, No. 2 ( 2023-07-01)
    Abstract: A plant’s development is strongly linked to the water and carbon flows in the soil–plant–atmosphere continuum. Expected climate shifts will alter the water and carbon cycles and will affect plant phenotypes. Comprehensive models that simulate mechanistically and dynamically the feedback loops between a plant’s three-dimensional development and the water and carbon flows are useful tools to evaluate the sustainability of genotype–environment–management combinations which do not yet exist. In this study, we present the latest version of the open-source three-dimensional Functional–Structural Plant Model CPlantBox with PiafMunch and DuMu${}^{\text{x}}$ coupling. This new implementation can be used to study the interactions between known or hypothetical processes at the plant scale. We simulated semi-mechanistically the development of generic C3 monocots from 10 to 25 days after sowing and undergoing an atmospheric dry spell of 1 week (no precipitation). We compared the results for dry spells starting on different days (Day 11 or 18) against a wetter and colder baseline scenario. Compared with the baseline, the dry spells led to a lower instantaneous water-use efficiency. Moreover, the temperature-induced increased enzymatic activity led to a higher maintenance respiration which diminished the amount of sucrose available for growth. Both of these effects were stronger for the later dry spell compared with the early dry spell. We could thus use CPlantBox to simulate diverging emerging processes (like carbon partitioning) defining the plants’ phenotypic plasticity response to their environment. The model remains to be validated against independent observations of the soil–plant–atmosphere continuum.
    Type of Medium: Online Resource
    ISSN: 2517-5025
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 3019806-9
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  • 3
    In: Annals of Botany, Oxford University Press (OUP), Vol. 121, No. 5 ( 2018-04-18), p. 1033-1053
    Type of Medium: Online Resource
    ISSN: 0305-7364 , 1095-8290
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 1461328-1
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2013
    In:  Geophysical Journal International Vol. 195, No. 2 ( 2013-11-01), p. 932-944
    In: Geophysical Journal International, Oxford University Press (OUP), Vol. 195, No. 2 ( 2013-11-01), p. 932-944
    Type of Medium: Online Resource
    ISSN: 1365-246X , 0956-540X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2013
    detail.hit.zdb_id: 3042-9
    detail.hit.zdb_id: 2006420-2
    detail.hit.zdb_id: 1002799-3
    SSG: 16,13
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  • 5
    In: Geophysical Journal International, Oxford University Press (OUP)
    Abstract: Spectral electrical impedance tomography (sEIT) is a promising method to image the subsurface complex resistivity distribution in a broad frequency range (i.e. mHz to kHz). However, inductive coupling between cables is known to affect measurement accuracy for frequencies above 50 Hz. Previous studies have proposed correction methods, but these have not been widely adopted yet. In this study, we evaluated the influence of inductive coupling on the measured complex impedance for different electrode and cable configurations. We propose a novel index to evaluate the inductive coupling strength and use it to develop a filter that selects data with limited inductive coupling. In a first step, the inductive coupling strength of a fan-shaped and parallel cable layout were evaluated. It was found that the fan-shaped layout provided more measurements with low inductive coupling strength. Using a synthetic modeling study with a fan-shaped cable layout, we then showed that it is possible to achieve good inversion results without data correction if measurements with high inductive coupling strength are filtered out before inversion. In a final step, we use the novel filtering approach based on inductive coupling strength with actual surface sEIT measurements. The EIT inversion results based on the filtered data corresponded well with inversion results using data corrected for inductive coupling and also showed good spectral consistency. It was concluded that it is possible to achieve reliable inversion results without data correction for inductive coupling when a fan-shaped layout and configurations with sufficiently low inductive coupling strength are used.
    Type of Medium: Online Resource
    ISSN: 0956-540X , 1365-246X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 3042-9
    detail.hit.zdb_id: 2006420-2
    detail.hit.zdb_id: 1002799-3
    SSG: 16,13
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  • 6
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  Geophysical Journal International Vol. 220, No. 2 ( 2020-02-01), p. 1187-1196
    In: Geophysical Journal International, Oxford University Press (OUP), Vol. 220, No. 2 ( 2020-02-01), p. 1187-1196
    Abstract: Induced calcite precipitation is used in geotechnics to modify the mechanical and hydrological properties of the underground. Laboratory experiments have shown that spectral induced polarization (SIP) measurements can detect calcite precipitation. However, the results of previous studies investigating the SIP response of calcite precipitation were not fully consistent. This study aims to investigate how the SIP response of calcite depends on solute concentration to explain the differences in SIP response observed in previous studies. A four-phase experiment with SIP measurements on a column filled with sand was performed. In phase I, calcite precipitation was generated for a period of 12 d by co-injecting Na2CO3 and CaCl2 solutions through two different ports. This resulted in a well-defined calcite precipitation front, which was associated with an increase in the imaginary part of the conductivity ($\sigma ^{\prime\prime}$). In phase II, diluted solutions were injected into the column. This resulted in a clear decrease in $\sigma ^{\prime\prime}$. In phase III, the injection of the two solutions was stopped while calcite precipitation continued and solute concentrations in the mixing zone decreased. Again, this decreased $\sigma ^{\prime\prime}$. Finally, the injection rate of the Na2CO3 solution was reduced relative to that of the CaCl2 solution in phase IV. This resulted in a shift of the mixing zone away from the calcite precipitation front established in phase I and an associated decrease of $\sigma ^{\prime\prime}$. These results imply that the SIP response of calcite is highly sensitive to the solute concentration near the precipitates, which may explain previously reported conflicting results.
    Type of Medium: Online Resource
    ISSN: 0956-540X , 1365-246X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 3042-9
    detail.hit.zdb_id: 2006420-2
    detail.hit.zdb_id: 1002799-3
    SSG: 16,13
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  • 7
    In: in silico Plants, Oxford University Press (OUP), Vol. 3, No. 2 ( 2021-07-01)
    Abstract: In 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 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 citrate 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.
    Type of Medium: Online Resource
    ISSN: 2517-5025
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 3019806-9
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  • 8
    In: in silico Plants, Oxford University Press (OUP), Vol. 5, No. 1 ( 2023-01-01)
    Abstract: Functional-structural root architecture models have evolved as tools for the design of improved agricultural management practices and for the selection of optimal root traits. In order to test their accuracy and reliability, we present the first benchmarking of root water uptake from soil using five well-established functional-structural root architecture models: DuMux, CPlantBox, R-SWMS, OpenSimRoot and SRI. The benchmark scenarios include basic tests for water flow in soil and roots as well as advanced tests for the coupled soil-root system. The reference solutions and the solutions of the different simulators are available through Jupyter Notebooks on a GitHub repository. All of the simulators were able to pass the basic tests and continued to perform well in the benchmarks for the coupled soil-plant system. For the advanced tests, we created an overview of the different ways of coupling the soil and the root domains as well as the different methods used to account for rhizosphere resistance to water flow. Although the methods used for coupling and modelling rhizosphere resistance were quite different, all simulators were in reasonably good agreement with the reference solution. During this benchmarking effort, individual simulators were able to learn about their strengths and challenges, while some were even able to improve their code. Some now include the benchmarks as standard tests within their codes. Additional model results may be added to the GitHub repository at any point in the future and will be automatically included in the comparison.
    Type of Medium: Online Resource
    ISSN: 2517-5025
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 3019806-9
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  • 9
    In: in silico Plants, Oxford University Press (OUP), Vol. 2, No. 1 ( 2020-01-01)
    Abstract: The interaction between carbon and flows within the vasculature is at the centre of most growth and developmental processes. Understanding how these fluxes influence each other, and how they respond to heterogeneous environmental conditions, is important to answer diverse questions in agricultural and natural ecosystem sciences. However, due to the high complexity of the plant–environment system, specific tools are needed to perform such quantitative analyses. Here, we present CPlantBox, a whole-plant modelling framework based on the root system model CRootBox. CPlantBox is capable of simulating the growth and development of a variety of plant architectures (root and shoot). In addition, the flexibility of CPlantBox enables its coupling with external modelling tools. Here, we connected the model to an existing mechanistic model of water and carbon flows in the plant, PiafMunch. The usefulness of the CPlantBox modelling framework is exemplified in five case studies. Firstly, we illustrate the range of plant structures that can be simulated using CPlantBox. In the second example, we simulated diurnal carbon and water flows, which corroborates published experimental data. In the third case study, we simulated impacts of heterogeneous environment on carbon and water flows. Finally, we showed that our modelling framework can be used to fit phloem pressure and flow speed to (published) experimental data. The CPlantBox modelling framework is open source, highly accessible and flexible. Its aim is to provide a quantitative framework for the understanding of plant–environment interaction.
    Type of Medium: Online Resource
    ISSN: 2517-5025
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 3019806-9
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