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  • 1
    Language: English
    In: Transport in Porous Media, 2013, Vol.96(2), pp.271-294
    Description: The 3D description of the soil structure at the pore scale level can help to elucidate the biological functioning of soil. The water–air distribution in the 3D-pore space is of particular interest because it determines the diffusion pathways of nutrients and the localisation of active soil microorganisms. We used the Shan–Chen interparticle-potential approach to simulate spontaneous phase separation in complex academic and real 3D-porous media using the advanced TRT lattice Boltzmann scheme. The equation of state and phase diagram were calculated and the model was verified using hydrostatic laws. The 3D pattern of water/air interface in two complex academic pore geometries was accurately computed. Finally, 3D maps of static liquid–gas distribution were simulated in a real 3D X-ray computed tomography image obtained from an undisturbed soil column sampled in a silty clay loam soil. The simulated soil sample of 1.7 cm 3 was described at a voxel-resolution of 60 μm. The range of the simulated saturations (from 0.5 to 0.9) was in a good agreement with the expected saturations calculated from the phase diagram.
    Keywords: Lattice Boltzmann method ; Water meniscus ; TRT ; Shan–Chen ; Porous media
    ISSN: 0169-3913
    E-ISSN: 1573-1634
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  • 2
    Language: English
    In: Science of the Total Environment, 15 November 2014, Vol.499, pp.546-559
    Description: Transport processes in soils are strongly affected by heterogeneity of soil hydraulic properties. Tillage practices and compost amendments can modify soil structure and create heterogeneity at the local scale within agricultural fields. The long-term field experiment QualiAgro (INRA–Veolia partnership 1998–2013) explores the impact of heterogeneity in soil structure created by tillage practices and compost application on transport processes. A modeling study was performed to evaluate how the presence of heterogeneity due to soil tillage and compost application affects water flow and pesticide dynamics in soil during a long-term period. The study was done on a plot receiving a co-compost of green wastes and sewage sludge (SGW) applied once every 2 years since 1998. The plot was cultivated with a biannual rotation of winter wheat–maize (except 1 year of barley) and a four-furrow moldboard plow was used for tillage. In each plot, wick lysimeter outflow and TDR probe data were collected at different depths from 2004, while tensiometer measurements were also conducted during 2007/2008. Isoproturon concentration was measured in lysimeter outflow since 2004. Detailed profile description was used to locate different soil structures in the profile, which was then implemented in the HYDRUS-2D model. Four zones were identified in the plowed layer: compacted clods with no visible macropores (Δ), non-compacted soil with visible macroporosity (Γ), interfurrows created by moldboard plowing containing crop residues and applied compost (IF), and the plow pan (PP) created by plowing repeatedly to the same depth. Isoproturon retention and degradation parameters were estimated from laboratory batch sorption and incubation experiments, respectively, for each structure independently. Water retention parameters were estimated from pressure plate laboratory measurements and hydraulic conductivity parameters were obtained from field tension infiltrometer experiments. Soil hydraulic properties were optimized on one calibration year (2007/08) using pressure head, water content and lysimeter outflow data, and then tested on the whole 2004/2010 period. Lysimeter outflow and water content dynamics in the soil profile were correctly described for the whole period (model efficiency coefficient: 0.99) after some correction of LAI estimates for wheat (2005/06) and barley (2006/07). Using laboratory-measured degradation rates and assuming degradation only in the liquid phase caused large overestimation of simulated isoproturon losses in lysimeter outflow. A proper order of magnitude of isoproturon losses was obtained after considering that degradation occurred in solid (sorbed) phase at a rate 75% of that in liquid phase. Isoproturon concentrations were found to be highly sensitive to degradation rates. Neither the laboratory-measured isoproturon fate parameters nor the independently-derived soil hydraulic parameters could describe the actual multiannual field dynamics of water and isoproturon without calibration. However, once calibrated on a limited period of time (9 months), HYDRUS-2D was able to simulate the whole 6-year time series with good accuracy.
    Keywords: Soil Heterogeneity ; Water Flow ; Isoproturon ; Numerical Modeling ; Hydrus-2d ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 3
    Language: English
    In: Journal of Hydrology, December 2017, Vol.555, pp.253-256
    Description: In the last decade, X-ray computed tomography (CT) has become widely used to characterize the geometry and topology of the pore space of soils and natural porous media. Regardless of the resolution of CT images, a fundamental problem associated with their use, for example as a starting point in simulation efforts, is that sub-resolution pores are not detected. Over the last few years, a particular type of modeling method, known as "Grey" or "Partial Bounce Back" Lattice-Boltzmann (LB), has been adopted by increasing numbers of researchers to try to account for sub-resolution pores in the modeling of water and solute transport in natural porous media. In this short paper, we assess the extent to which Grey LB methods indeed offer a workable solution to the problem at hand. We conclude that, in spite of significant computational advances, a major experimental hurdle related to the evaluation of the penetrability of sub-resolution pores, is blocking the way ahead. This hurdle will need to be cleared before Grey LB can become a credible option in the microscale modeling of soils and sediments. A necessarily interdisciplinary effort, involving both modelers and experimentalists, is needed to clear the path forward.
    Keywords: Computer Modeling ; Transport Processes ; Image Resolution ; Measurement ; Interdisciplinary Research ; Geography
    ISSN: 0022-1694
    E-ISSN: 1879-2707
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  • 4
    Language: English
    In: Journal of Hydrology, 2011, Vol.403(1), pp.141-156
    Description: ► A surface-subsurface flow model with multi-objective global optimization is presented. ► The model performance was evaluated using bench-scale flow experiments. ► Inverse parameter estimation required observations at different spatial positions. ► The Pareto trade-off and model mismatch suggest lateral flow in soil layers. ► The model system is versatile for studying soil water and overland flow. A comprehensive description of water flow in environmental and agricultural systems requires an account of both surface and subsurface pathways. We present a new model which combines a 1D overland flow model and the 2D subsurface flow HYDRUS-2D model, and uses the multi-objective global search method AMALGAM for inverse parameter estimation. Furthermore, we present data from bench-scale flow experiments which were conducted with two 5-m long replicate soil channels. While rainfall was applied, surface runoff was recorded at the downstream end of the soil channel, subsurface drainage waters were sampled at three positions equally spaced along the channels, and pressure heads were recorded at five depths. The experimental observations were used to evaluate the performance of our modeling system. The complexity of the modeling approach was increased in three steps. First, only runoff and total drainage were simulated, then drainage flows from individual compartments were additionally evaluated, and finally a surface crust and immobile soil water were also considered. The results showed that a good match between measured and observed surface runoff and total drainage does not guarantee accurate representation of the flow process. An inspection of the Pareto results of different multiobjective calibration runs revealed a significant trade-off between individual objectives, showing that no single solution existed to match spatial variability in the flow. In spite of the observed crust formation, its consideration in the more complex model structure did not significantly improve the fit between the model and measurements. Accounting for immobile water regions only slightly improved the fit for one of the two replicate soil channels. Discrepancies between relatively complex model simulations and seemingly simple soil channel experiments suggest the presence of additional unknowns, such as heterogeneity of the soil hydraulic properties. Nevertheless, with its versatile subsurface options and powerful inverse method, the model system shows promise for studying hillslope flow problems involving both surface runoff and subsurface flow.
    Keywords: Overland Flow ; Surface Runoff ; Multi-Objective Global Parameter Optimization ; Mobile–Immobile Model ; Simulation ; Flow Channel Experiment ; Geography
    ISSN: 0022-1694
    E-ISSN: 1879-2707
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  • 5
    Language: English
    In: Science of the Total Environment, 15 November 2014, Vol.499, pp.560-573
    Description: Recycling composted organic residues in agriculture can reduce the need of mineral fertilizers and improve the physicochemical and biological properties of cultivated soils. However, some trace elements may accumulate in soils following repeated applications and impact other compartments of the agrosystems. This study aims at evaluating the long-term impact of such practices on the composition of soil leaching water, especially on trace metal concentrations. The field experiment QualiAgro started in 1998 on typical loess Luvisol of the Paris Basin, with a maize–wheat crop succession and five modalities: spreading of three different urban waste composts, farmyard manure (FYM), and no organic amendment (CTR). Inputs of trace metals have been close to regulatory limits, but supplies of organic matter and nitrogen overpassed common practices. Soil solutions were collected from wick lysimeters at 45 and 100 cm in one plot for each modality, during two drainage periods after the last spreading. Despite wide temporal variations, a significant effect of treatments on major solutes appears at 45 cm: DOC, Ca, K, Mg, Na, nitrate, sulphate and chloride concentrations were higher in most amended plots compared to CTR. Cu concentrations were also significantly higher in leachates of amended plots compared to CTR, whereas no clear effect emerged for Zn. The influence of amendments on solute concentrations appeared weaker at 1 m than at 45 cm, but still significant and positive for major anions and DOC. Average concentrations of Cu and Zn at 1 m depth lied in the ranges [2.5; 3.8] and [2.5; 10.5 μg/L], respectively, with values slightly higher for plots amended with sewage sludge compost or FYM than for CTR. However, leaching of both metals was less than 1% of their respective inputs through organic amendments. For Cd, most values were 〈 0.05 μg/L. So, metals added through spreading of compost or manure during 14 years may have increased metal concentrations in leachates of amended plots, in spite of increased soil organic matter, factor of metal retention. Indeed, DOC, also increased by amendments, favours the mobility of Cu; whereas pH variations, depending on treatments, influence negatively the solubility of Zn. Generic adsorption functions of these variables partly explain the variations of trace metal concentrations and helped to unravel the numerous processes induced by regular amendments with organic waste products.
    Keywords: Heavy Metal ; Trace Element ; Organic Waste ; Organic Amendment ; Cultivated Soil ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 6
    Language: English
    In: Science of the Total Environment, 01 July 2018, Vol.628-629, pp.1508-1517
    Description: Conservation tillage practices mainly based on cover crops and no-tillage with accumulation of crop residues at the soil surface (mulch) modify the environmental fate of pesticides. However, only few pesticide fate models are able to consider mulch of crop residues as well as the effect of intermediate cover crops. Thus, the objective was to develop an approach to model the effects of crop residues left at the soil surface and cover crops on the fate of pesticides. This approach consisted in (1) considering the crop residues as a soil layer with specific physical, hydrodynamic and pesticide-reactivity properties close to that of a high organic content soil layer, and (2) introducing a correction factor of the potential evapotranspiration, estimated through a calibration step, to take into account the reduction of soil evaporation by the presence of a mulch. This approach was developed using MACRO as support pesticide model. To assess the model performances, we used the data from a field experiment designed in an irrigated maize monoculture under conservation tillage. Soil water content, water percolates, soil temperature and S-metolachlor herbicide concentrations in the leachate at 1 m depth were measured during two years. The approach chosen to simulate the mulch effects allowed MACRO to make acceptable predictions of the observed water percolation, soil temperature and to a less extent herbicide leaching. However, it showed a poor performance to simulate the soil water content. Results are discussed in terms of further modelling options to better assess the environmental risks of pesticides under conservation tillage. This approach remains to be tested against various soils, crops, pesticides and types of mulch.
    Keywords: Pesticide Fate Model ; Macro ; Crop Residue ; Cover Crop ; Field Experiment ; Pesticide ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 7
    Language: English
    In: Ecological Modelling, 2018, Vol.383, pp.10-22
    Description: Soil respiration causes the second largest C flux between ecosystems and the atmosphere. Emerging soil carbon dynamics models consider the complex interplay of microscale interactions between the physical and biological drivers of soil organic...
    Keywords: Life Sciences ; Uncertainty Analysis ; Sensitivity Analysis ; Lattice–Boltzmann Model ; Soil Architecture ; Carbon ; Bacteria ; Environmental Sciences ; Ecology
    ISSN: 0304-3800
    E-ISSN: 1872-7026
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  • 8
    Language: English
    In: Soil Biology and Biochemistry, November 2014, Vol.78, pp.189-194
    Description: Modelling carbon mineralisation in natural soils is a major topic in soil and climate research. Current models need to be improved to include soil structure as an influencing factor to better predict C fluxes between pedosphere and atmosphere and to estimate carbon sequestration potentials. Geometry-based mechanistic modelling approaches have recently been developed to systematically study the effect of soil structure on carbon decomposition. Such models require spatially explicit input parameters describing the architecture of the pore space and the heterogeneous distribution of microbes and organic matter as decomposable substrate. The latter is very difficult to determine , resulting in increased uncertainty in the models. To obtain more realistic input data, we have developed a novel approach to locate soil organic matter (SOM) in undisturbed aggregates of soil using a combination of synchrotron-based X-ray microtomography and osmium as a staining agent for SOM. Here, we present the first results using 5 mm sized soil aggregate samples with contrasting C-contents in which we obtained maps of organic matter distributions in relation to the pore networks at the aggregate scale.
    Keywords: Soil Organic Matter ; Soil Structure ; Carbon Sequestration ; Synchrotron Microtomography ; Staining ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 9
    Language: English
    In: Ecological Modelling, 2008, Vol.216(3), pp.291-302
    Description: During the past 10 years, soil scientists have started to use 3D Computed Tomography in order to gain a clearer understanding of the geometry of soil structure and its relationships with soil properties. We propose a geometric model for the 3D representation of pore space and a practical method for its computation. Our basic idea consists in representing pore space using a minimal set of maximal balls (Delaunay spheres) recovering the shape skeleton. In this representation, each ball could be considered as a maximal local cavity corresponding to the “intuitive” notion of a pore as described in the literature. The space segmentation induced by the network of balls (pores) was then used to spatialize biological dynamics. Organic matter and microbial decomposers were distributed within the balls (pores). A valuated graph representing the pore network, organic matter and distribution of micro-organisms was then defined. Microbial soil organic matter decomposition was simulated by updating this valuated graph. The method was implemented and tested using real CT images. The model produced realistic simulated results when compared with data in the literature in terms of the water retention curve and carbon mineralization. A decrease in water pressure decreased carbon mineralization, which is also in accordance with findings in the literature. From our results we showed that the influence of water pressure on decomposition is a function of organic matter distribution in the pore space. As far as we know, this is the approach to have linked pore space geometry and biological dynamics in a formal way. Our next goal will be to compare the model with experimental data of decomposition using different soil structures, and to define geometric typologies of pore space shape that can be attached to specific biological and dynamic properties.
    Keywords: Computational Geometry ; Soil Science ; Pore Space Modelling ; Microbial Decomposition Simulation ; 3d Computer Vision ; Environmental Sciences ; Ecology
    ISSN: 0304-3800
    E-ISSN: 1872-7026
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  • 10
    Language: English
    In: Geoderma, 15 April 2016, Vol.268, pp.29-40
    Description: Compost amendments and tillage practices can modify soil structure and create heterogeneities at the local scale. Tillage affects soil physical properties and consequently water and solute transport in soil, while compost addition to soil influences pesticide sorption and degradation processes. Based on the long-term field experiment QualiAgro (a INRA–Veolia partnership), a modeling study was carried out using HYDRUS-2D to evaluate how two different compost types combined with the presence of heterogeneities due to tillage affect water and isoproturon dynamics in soil compared to a control plot. A municipal solid waste compost (MSW) and a co-compost of sewage sludge and green wastes (SGW) have been applied to experimental plots. In each plot, wick lysimeters, TDR probes, and tensiometers were installed to monitor water and solute dynamics. In the plowed layer, four zones differing in their structure were identified: compacted clods, non-compacted soil, interfurrows, and the plow pan. From 2004 to 2010, the unamended control (CONT) plot had the largest cumulative water outflow (1388 mm) compared to the MSW plot (962 mm) and SGW plot (979 mm). After calibration, the model was able to describe cumulative water outflow for the whole 2004–2010 period with a model efficiency value of 0.99 for all three plots. The CONT plot had the largest isoproturon cumulated leaching (21.31 μg) while similar cumulated isoproturon leaching was measured in the SGW (0.663 μg) and MSW (0.245 μg) plots. The model was able to simulate isoproturon leaching patterns except for the large preferential flow events that were observed in the MSW and CONT plots. The timing of these preferential flow events could be reproduced by the model but not their magnitude. Modeling results indicate that spatial and temporal variations in pesticide degradation rate due to tillage and compost application play a major role in the dynamics of isoproturon leaching. Both types of compost were found to reduce isoproturon leaching on the 6 year duration of the experiment.
    Keywords: Soil Heterogeneity ; Compost Amendments ; Conventional Tillage ; Water Flow ; Isoproturon ; Hydrus-2d ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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