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  • Otten, Wilfred  (15)
  • Baveye, Philippe C  (15)
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Year
  • 1
    Language: English
    In: PLoS ONE, 01 January 2015, Vol.10(9), p.e0137205
    Description: There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 2
    Language: English
    In: Geoderma, Sept 15, 2011, Vol.164(3-4), p.146(9)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.geoderma.2011.05.018 Byline: Simona M. Hapca, Zi X. Wang, Wilfred Otten, Clare Wilson, Philippe C. Baveye Keywords: X-ray CT; SEM-EDX; Segmentation techniques; Spatial correlation; 3D soil images; 2D chemical maps Abstract: Recent 2-dimensional measurements reveal that soils are chemically very heterogeneous at nanometric and micrometric scales. Direct measurement techniques are still lacking to extend these observations to 3 dimensions. Sequential sectioning of soils, followed by 2-dimensional mapping of chemical elements and geometric interpolation to 3D, appears to be the only available alternative. Unfortunately, sectioning of soil samples suffers from geometric distortions that are difficult to avoid in practise. In this regard, the objective of the research described in this article was to develop a procedure enabling one to locate, in a 3D X-ray microtomographic image of a soil sample, a physical surface that is obtained by sectioning and for which a number of chemical maps are available. This procedure involves three steps: (1) the reconstitution of the physical structure of the soil layer surface, (2) the alignment of the chemical maps with the reconstituted soil surface image, and (3) the 3D alignment of the 2D chemical maps with the internal structure of the soil cube. Visual comparison of the C and Si maps and of the reconstituted CT images of the layer surfaces suggests a good correspondence between them, which is supported by Pearson correlation coefficients of -0.57, -0.58, 0.45, and 0.43 for the different surfaces and elements considered. Relative to the original 3D X-ray CT image of the soil sample, the planes associated with the C and Si maps, respectively, are nearly superposed, which further confirms the validity of the alignment procedure. Article History: Received 16 November 2010; Revised 27 May 2011; Accepted 28 May 2011
    Keywords: Soil Structure -- Analysis ; Soil Structure -- Methods ; Soils -- Analysis ; Soils -- Methods
    ISSN: 0016-7061
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: Water, Air, & Soil Pollution, 2014, Vol.225(6), pp.1-5
    Keywords: Inter-disciplinary ; Multi-disciplinary ; Pluri-disciplinary ; Cross-disciplinary ; Trans-disciplinary
    ISSN: 0049-6979
    E-ISSN: 1573-2932
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  • 4
    Language: English
    In: Soil Science Society of America journal, 2011, Vol.75(6), pp.2037-2048
    Description: When the Soil Science Society of America was created, 75 yr ago, the USA was suffering from major dust storms, causing the loss of enormous amounts of topsoil as well as human lives. These catastrophic events reminded public officials that soils are essential to society's well-being. The Soil Conservation Service was founded and farmers were encouraged to implement erosion mitigation practices. Still, many questions about soil processes remained poorly understood and controversial. In this article, we argue that the current status of soils worldwide parallels that in the USA at the beginning of the 20th century. Dust bowls and large-scale soil degradation occur over vast regions in a number of countries. Perhaps more so even than in the past, soils currently have the potential to affect populations critically in several other ways as well, from their effect on global climate change, to the toxicity of brownfield soils in urban settings. Even though our collective understanding of soil processes has experienced significant advances since 1936, many basic questions still remain unanswered, for example whether or not a switch to no-till agriculture promotes C sequestration in soils, or how to account for microscale heterogeneity in the modeling of soil organic matter transformation. Given the enormity of the challenges raised by our (ab)uses of soils, one may consider that if we do not address them rapidly, and in the process heed the example of U.S. public officials in the 1930s who took swift action, humanity may not get a chance to explore other frontiers of science in the future. From this perspective, insistence on the fact that soils are critical to life on earth, and indeed to the survival of humans, may again stimulate interest in soils among the public, generate support for soil research, and attract new generations of students to study soils. ; p. 2037-2048.
    Keywords: Dust Storms ; Students ; Carbon Sequestration ; Topsoil ; Urban Soils ; Society ; No-Tillage ; Soil Organic Matter ; Humans ; Climate Change ; Models ; Farmers ; Soil Degradation ; Toxicity ; Soil Conservation
    ISSN: 0361-5995
    E-ISSN: 14350661
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  • 5
    In: Soil Science, 2012, Vol.177(2), pp.111-119
    Description: ABSTRACT: Macroscopic measurements and observations in two-dimensional soil-thin sections indicate that fungal hyphae invade preferentially the larger, air-filled pores in soils. This suggests that the architecture of soils and the microscale distribution of water are likely to influence significantly the dynamics of fungal growth. Unfortunately, techniques are lacking at present to verify this hypothesis experimentally, and as a result, factors that control fungal growth in soils remain poorly understood. Nevertheless, to design appropriate experiments later on, it is useful to indirectly obtain estimates of the effects involved. Such estimates can be obtained via simulation, based on detailed micron-scale X-ray computed tomography information about the soil pore geometry. In this context, this article reports on a series of simulations resulting from the combination of an individual-based fungal growth model, describing in detail the physiological processes involved in fungal growth, and of a Lattice Boltzmann model used to predict the distribution of air-liquid interfaces in soils. Three soil samples with contrasting properties were used as test cases. Several quantitative parameters, including Minkowski functionals, were used to characterize the geometry of pores, air-water interfaces, and fungal hyphae. Simulation results show that the water distribution in the soils is affected more by the pore size distribution than by the porosity of the soils. The presence of water decreased the colonization efficiency of the fungi, as evinced by a decline in the magnitude of all fungal biomass functional measures, in all three samples. The architecture of the soils and water distribution had an effect on the general morphology of the hyphal network, with a “looped” configuration in one soil, due to growing around water droplets. These morphologic differences are satisfactorily discriminated by the Minkowski functionals, applied to the fungal biomass.
    Keywords: Agriculture;
    ISSN: 0038-075X
    E-ISSN: 15389243
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  • 6
    In: Vadose Zone Journal, August 2013, Vol.12(3), pp.1-13
    Description: Recent advances in imaging techniques offer the possibility of visualizing the three‐dimensional structure of soils at very fine scales. To make use of such information, a thresholding process is commonly implemented to separate the image into solid particles...
    Keywords: Soils ; Algorithms ; Applications ; Complexity ; Computed Tomography Data ; Data Processing ; Dundee Scotland ; Europe ; Experimental Studies ; Great Britain ; Greyscale Imagery ; Imagery ; Mapping ; Matlab ; Micro-Tomography ; Microstructure ; Particulate Materials ; Porosity ; Scotland ; Segmentation ; Soils ; Statistical Analysis ; Synthetic Imagery ; Three-Dimensional Models ; Thresholding Method ; United Kingdom ; Values ; Variance Analysis ; Visualization ; Western Europe ; X-Ray Data;
    ISSN: 1539-1663
    E-ISSN: 1539-1663
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  • 7
    Language: English
    In: Frontiers in Microbiology, 01 July 2018, Vol.9
    Description: There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic matter, in addition to the spatial connectivity...
    Keywords: Soil ; Pore Scale ; Organic Matter ; Resource Allocation ; Bacteria ; Biodiversity ; Biology
    E-ISSN: 1664-302X
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  • 8
    Language: English
    In: Geoderma, 2011, Vol.164(3), pp.146-154
    Description: Recent 2-dimensional measurements reveal that soils are chemically very heterogeneous at nanometric and micrometric scales. Direct measurement techniques are still lacking to extend these observations to 3 dimensions. Sequential sectioning of soils, followed by 2-dimensional mapping of chemical elements and geometric interpolation to 3D, appears to be the only available alternative. Unfortunately, sectioning of soil samples suffers from geometric distortions that are difficult to avoid in practise. In this regard, the objective of the research described in this article was to develop a procedure enabling one to locate, in a 3D X-ray microtomographic image of a soil sample, a physical surface that is obtained by sectioning and for which a number of chemical maps are available. This procedure involves three steps: (1) the reconstitution of the physical structure of the soil layer surface, (2) the alignment of the chemical maps with the reconstituted soil surface image, and (3) the 3D alignment of the 2D chemical maps with the internal structure of the soil cube. Visual comparison of the C and Si maps and of the reconstituted CT images of the layer surfaces suggests a good correspondence between them, which is supported by Pearson correlation coefficients of − 0.57, − 0.58, 0.45, and 0.43 for the different surfaces and elements considered. Relative to the original 3D X-ray CT image of the soil sample, the planes associated with the C and Si maps, respectively, are nearly superposed, which further confirms the validity of the alignment procedure. ► A procedure is developed to locate physical planes in 3D X-ray CT images of soils. ► This procedure allows alignment of 2D chemical maps with the soil structure. ► Measured C and Si maps and reconstituted CT images correspond well with each other. ► Planes associated with the C and Si maps are nearly superposed.
    Keywords: X-Ray CT ; SEM–Edx ; Segmentation Techniques ; Spatial Correlation ; 3d Soil Images ; 2d Chemical Maps ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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  • 9
    Language: English
    In: Frontiers in Environmental Science, 01 July 2018, Vol.6
    Description: Simplified experimental systems, often referred to as microcosms, have played a central role in the development of modern ecological thinking on issues ranging from competitive exclusion to examination of spatial resources and competition mechanisms, with important model-driven insights to...
    Keywords: X-Ray CT Scanning ; Bacterial Growth ; Bacterial Spread ; CARD-FISH ; Microcosm Experiment ; Pseudomonas ; Environmental Sciences
    E-ISSN: 2296-665X
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  • 10
    Language: English
    In: Frontiers in Environmental Science, 01 July 2018, Vol.6
    Description: In spite of the very significant role that fungi are called to play in agricultural production and climate change over the next two decades, very little is known at this point about the parameters that control the spread of fungal hyphae in the pore space of soils. Monitoring of this process...
    Keywords: Hyphae ; Spread ; Microfluidics ; Fungal Highway ; Microscale ; Environmental Sciences
    E-ISSN: 2296-665X
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