{"type": "FeatureCollection", "features": [{"id": "10.1007/s11356-017-8823-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:15:29Z", "type": "Journal Article", "created": "2017-03-24", "title": "Quantitative characterization of pore structure of several biochars with 3D imaging", "description": "Open Access16 pages, 4 figures. The final publication is available at Springer via http://dx.doi.org/10.1007/s11356-017-8823-x", "keywords": ["x-ray tomography", "Condensed Matter - Materials Science", "soil amendment", "pore structure", "ta1171", "ta1182", "Water", "Materials Science (cond-mat.mtrl-sci)", "FOS: Physical sciences", "04 agricultural and veterinary sciences", "01 natural sciences", "6. Clean water", "Diffusion", "Imaging", " Three-Dimensional", "image analysis", "Charcoal", "Image Processing", " Computer-Assisted", "0401 agriculture", " forestry", " and fisheries", "biochar", "Porosity", "soil amendments", "ta218", "water retention", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11356-017-8823-x.pdf"}, {"href": "https://doi.org/10.1007/s11356-017-8823-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20and%20Pollution%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11356-017-8823-x", "name": "item", "description": "10.1007/s11356-017-8823-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11356-017-8823-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-24T00:00:00Z"}}, {"id": "10.1007/s11538-017-0350-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:15:31Z", "type": "Journal Article", "created": "2017-10-13", "title": "An Explicit Structural Model of Root Hair and Soil Interactions Parameterised by Synchrotron X-ray Computed Tomography", "description": "The rhizosphere is a zone of fundamental importance for understanding the dynamics of nutrient acquisition by plant roots. The canonical difficulty of experimentally investigating the rhizosphere led long ago to the adoption of mathematical models, the most sophisticated of which now incorporate explicit representations of root hairs and rhizosphere soil. Mathematical upscaling regimes, such as homogenisation, offer the possibility of incorporating into larger-scale models the important mechanistic processes occurring at the rhizosphere scale. However, we lack concrete descriptions of all the features required to fully parameterise models at the rhizosphere scale. By combining synchrotron X-ray computed tomography (SRXCT) and a novel root growth assay, we derive a three-dimensional description of rhizosphere soil structure suitable for use in multi-scale modelling frameworks. We describe an approach to mitigate sub-optimal root hair detection via structural root hair growth modelling. The growth model is explicitly parameterised with SRXCT data and simulates three-dimensional root hair ideotypes in silico, which are suitable for both ideotypic analysis and parameterisation of 3D geometry in mathematical models. The study considers different hypothetical conditions governing root hair interactions with soil matrices, with their respective effects on hair morphology being compared between idealised and image-derived soil/root geometries. The studies in idealised geometries suggest that packing arrangement of soil affects hair tortuosity more than the particle diameter. Results in field-derived soil suggest that hair access to poorly mobile nutrients is particularly sensitive to the physical interaction between the growing hairs and the phase of the soil in which soil water is present (i.e. the hydrated textural phase). The general trends in fluid-coincident hair length with distance from the root, and their dependence on hair/soil interaction mechanisms, are conserved across Cartesian and cylindrical geometries.", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Mathematical Concepts", "15. Life on land", "Models", " Biological", "Plant Roots", "Soil", "03 medical and health sciences", "Imaging", " Three-Dimensional", "Rhizosphere", "Original Article", "Computer Simulation", "Tomography", " X-Ray Computed", "Synchrotrons"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11538-017-0350-x.pdf"}, {"href": "https://doi.org/10.1007/s11538-017-0350-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bulletin%20of%20Mathematical%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11538-017-0350-x", "name": "item", "description": "10.1007/s11538-017-0350-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11538-017-0350-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-10-13T00:00:00Z"}}, {"id": "10.1093/jxb/erv544", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:18:21Z", "type": "Journal Article", "created": "2016-01-20", "title": "Image-based modelling of nutrient movement in and around the rhizosphere", "description": "In this study, we developed a spatially explicit model for nutrient uptake by root hairs based on X-ray computed tomography images of the rhizosphere soil structure. This work extends our previous work to larger domains and hence is valid for longer times. Unlike the model used previously, which considered only a small region of soil about the root, we considered an effectively infinite volume of bulk soil about the rhizosphere. We asked the question: At what distance away from root surfaces do the specific structural features of root-hair and soil aggregate morphology not matter because average properties start dominating the nutrient transport? The resulting model was used to capture bulk and rhizosphere soil properties by considering representative volumes of soil far from the root and adjacent to the root, respectively. By increasing the size of the volumes that we considered, the diffusive impedance of the bulk soil and root uptake were seen to converge. We did this for two different values of water content. We found that the size of region for which the nutrient uptake properties converged to a fixed value was dependent on the water saturation. In the fully saturated case, the region of soil we needed to consider was only of radius 1.1mm for poorly soil-mobile species such as phosphate. However, in the case of a partially saturated medium (relative saturation 0.3), we found that a radius of 1.4mm was necessary. This suggests that, in addition to the geometrical properties of the rhizosphere, there is an additional effect of soil moisture properties, which extends further from the root and may relate to other chemical changes in the rhizosphere. The latter were not explicitly included in our model.", "keywords": ["0301 basic medicine", "550", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "Models", " Biological", "Plant Roots", "630", "03 medical and health sciences", "Imaging", " Three-Dimensional", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Tomography", " X-Ray Computed", "Research Paper"]}, "links": [{"href": "https://doi.org/10.1093/jxb/erv544"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Experimental%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/jxb/erv544", "name": "item", "description": "10.1093/jxb/erv544", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/jxb/erv544"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-01-05T00:00:00Z"}}, {"id": "10.1111/nph.14705", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:18:59Z", "type": "Journal Article", "created": "2017-07-31", "title": "High\u2010resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation", "description": "Summary<p>   <p>In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root\uffe2\uff80\uff93soil interface during the early stage of crop establishment.</p>  <p>This was achieved by use of high\uffe2\uff80\uff90resolution (c. 5\uffc2\uffa0\uffce\uffbcm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant\uffe2\uff80\uff93soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8\uffc2\uffa0d in microcosms packed with sandy loam soil at 1.2\uffc2\uffa0g\uffc2\uffa0cm\uffe2\uff88\uff923 dry bulk density. Root hairs were visualised within air\uffe2\uff80\uff90filled pore spaces, but not in the fine\uffe2\uff80\uff90textured soil regions.</p>  <p>We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (&gt;\uffc2\uffa05\uffc2\uffa0\uffce\uffbcm) in the rhizosphere, as compared with the no\uffe2\uff80\uff90hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1\uffc2\uffa0mm from the root surface. Interestingly the root\uffe2\uff80\uff90hair\uffe2\uff80\uff90bearing genotype had a significantly greater soil pore volume\uffe2\uff80\uff90fraction at the root\uffe2\uff80\uff93soil interface.</p>  <p>Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image\uffe2\uff80\uff90based modelling.</p>  </p", "keywords": ["construction", "EP/M020355/1", "QH301 Biology", "non-invasive imaging", "Plant Roots", "630", "root hairs", "noninvasive imaging", "QH301", "Soil", "Imaging", " Three-Dimensional", "646809DIMR", "synchrotron", "Computer Simulation", "BB/L025620/1", "BB/J00868/1", "NE/L00237/1", "Hordeum vulgare", "580", "2. Zero hunger", "Civil_env_eng", "Natural Environment Research Council (NERC)", "Research", "Hordeum", "04 agricultural and veterinary sciences", "15. Life on land", "image-based modelling", "Engineering and Physical Sciences Research Council (EPSRC)", "Rhizosphere", "Biotechnology and Biological Sciences Research Council (BBSRC)", "0401 agriculture", " forestry", " and fisheries", "rhizosphere", "soil structure", "synchroton", "Porosity", "BB/P004180/1", "Synchrotrons", "BB/L025825/1", "European Research Council"]}, "links": [{"href": "https://repository.uwl.ac.uk/id/eprint/4981/1/Koebernick_et_al-2017-New_Phytologist.pdf"}, {"href": "https://eprints.soton.ac.uk/412143/1/s1_ln2680534218582232741703867393Hwf_1771574461IdV_16951475526805342FIRST_LOOK_PDF0001.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.14705"}, {"href": "https://doi.org/10.1111/nph.14705"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.14705", "name": "item", "description": "10.1111/nph.14705", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.14705"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-31T00:00:00Z"}}, {"id": "10.1111/nph.15516", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:19:00Z", "type": "Journal Article", "created": "2018-10-06", "title": "Imaging microstructure of the barley rhizosphere: particle packing and root hair influences", "description": "Summary<p>   <p>Soil adjacent to roots has distinct structural and physical properties from bulk soil, affecting water and solute acquisition by plants. Detailed knowledge on how root activity and traits such as root hairs affect the three\uffe2\uff80\uff90dimensional pore structure at a fine scale is scarce and often contradictory.</p>  <p>Roots of hairless barley (Hordeum vulgare L. cv Optic) mutant (NRH) and its wildtype (WT) parent were grown in tubes of sieved (&lt;250\uffc2\uffa0\uffce\uffbcm) sandy loam soil under two different water regimes. The tubes were scanned by synchrotron\uffe2\uff80\uff90based X\uffe2\uff80\uff90ray computed tomography to visualise pore structure at the soil\uffe2\uff80\uff93root interface. Pore volume fraction and pore size distribution were analysed vs distance within 1\uffc2\uffa0mm of the root surface.</p>  <p>Less dense packing of particles at the root surface was hypothesised to cause the observed increased pore volume fraction immediately next to the epidermis. The pore size distribution was narrower due to a decreased fraction of larger pores. There were no statistically significant differences in pore structure between genotypes or moisture conditions.</p>  <p>A model is proposed that describes the variation in porosity near roots taking into account soil compaction and the surface effect at the root surface.</p>  </p>", "keywords": ["name=Physiology", "STABILIZATION", "Physiology", "EP/M020355/1", "Supplementary Data", "QH301 Biology", "Plant Science", "Supplementary data available", "Plant Roots", "630", "noninvasive imaging", "Soil", "646809DIMR", "STRENGTH", "BB/J00868/1", "Hordeum vulgare", "2. Zero hunger", "04 agricultural and veterinary sciences", "Rhizosphere", "COMPRESSION", "soil structure", "Porosity", "European Research Council", "/dk/atira/pure/subjectarea/asjc/1300/1314", "/dk/atira/pure/subjectarea/asjc/1100/1110", "root hairs", "COMPACTION", "QH301", "Imaging", " Three-Dimensional", "synchrotron", "particle packing", "SOIL-STRUCTURE", "BB/L025620/1", "WATER-STRESS", "NE/L00237/1", "580", "ELONGATION", "Civil_env_eng", "Natural Environment Research Council (NERC)", "POROSITY", "Water", "Hordeum", "15. Life on land", "Engineering and Physical Sciences Research Council (EPSRC)", "Mutation", "Biotechnology and Biological Sciences Research Council (BBSRC)", "0401 agriculture", " forestry", " and fisheries", "PENETRATION", "name=Plant Science", "rhizosphere", "Tomography", " X-Ray Computed", "MAIZE", "BB/P004180/1", "Synchrotrons", "BB/L025825/1"]}, "links": [{"href": "https://repository.uwl.ac.uk/id/eprint/5489/1/AS6808504337817661539338801587_content_1.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15516"}, {"href": "https://doi.org/10.1111/nph.15516"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.15516", "name": "item", "description": "10.1111/nph.15516", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.15516"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-20T00:00:00Z"}}, {"id": "10.1111/pce.12983", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:19:01Z", "type": "Journal Article", "created": "2017-05-15", "title": "Quantification of root water uptake in soil using X\u2010ray computed tomography and image\u2010based modelling", "description": "Abstract<p>Spatially averaged models of root\uffe2\uff80\uff93soil interactions are often used to calculate plant water uptake. Using a combination of X\uffe2\uff80\uff90ray computed tomography (CT) and image\uffe2\uff80\uff90based modelling, we tested the accuracy of this spatial averaging by directly calculating plant water uptake for young wheat plants in two soil types. The root system was imaged using X\uffe2\uff80\uff90ray CT at 2, 4, 6, 8 and 12\uffc2\uffa0d after transplanting. The roots were segmented using semi\uffe2\uff80\uff90automated root tracking for speed and reproducibility. The segmented geometries were converted to a mesh suitable for the numerical solution of Richards' equation. Richards' equation was parameterized using existing pore scale studies of soil hydraulic properties in the rhizosphere of wheat plants. Image\uffe2\uff80\uff90based modelling allows the spatial distribution of water around the root to be visualized and the fluxes into the root to be calculated. By comparing the results obtained through image\uffe2\uff80\uff90based modelling to spatially averaged models, the impact of root architecture and geometry in water uptake was quantified. We observed that the spatially averaged models performed well in comparison to the image\uffe2\uff80\uff90based models with &lt;2% difference in uptake. However, the spatial averaging loses important information regarding the spatial distribution of water near the root system.</p", "keywords": ["0106 biological sciences", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "550", "Water", "15. Life on land", "01 natural sciences", "Models", " Biological", "Plant Roots", "6. Clean water", "Soil", "03 medical and health sciences", "Imaging", " Three-Dimensional", "Tomography", " X-Ray Computed", "Porosity"]}, "links": [{"href": "https://eprints.nottingham.ac.uk/42292/1/170405_WP2_Paper_update_final%20Mooney.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.12983"}, {"href": "https://doi.org/10.1111/pce.12983"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%2C%20Cell%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/pce.12983", "name": "item", "description": "10.1111/pce.12983", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/pce.12983"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-05T00:00:00Z"}}, {"id": "10.1371%2fjournal.pone.0191403", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:19:20Z", "type": "Journal Article", "created": "2018-01-23", "title": "Effects Of Short-Term Warming And Nitrogen Addition On The Quantity And Quality Of Dissolved Organic Matter In A Subtropical Cunninghamia Lanceolata Plantation", "description": "Increasing temperature and nitrogen (N) deposition are two large-scale changes projected to occur over the coming decades. The effects of these changes on dissolved organic matter (DOM) are largely unknown. This study aimed to assess the effects of warming and N addition on the quantity and quality of DOM from a subtropical Cunninghamia lanceolata plantation. Between 2014 and 2016, soil solutions were collected from 0-15, 15-30, and 30-60 cm depths by using a negative pressure sampling method. The quantity and quality of DOM were measured under six different treatments. The spectra showed that the DOM of the forest soil solution mainly consisted of aromatic protein-like components, microbial degradation products, and negligible amounts of humic-like substances. Warming, N addition, and warming + N addition significantly inhibited the concentration of dissolved organic carbon (DOC) in the surface (0-15 cm) soil solution. Our results suggested that warming reduced the amount of DOM originating from microbes. The decrease in protein and carboxylic acid contents was mostly attributed to the reduction of DOC following N addition. The warming + N addition treatment showed an interactive effect rather than an additive effect. Thus, short-term warming and warming + N addition decreased the quantity of DOM and facilitated the migration of nutrients to deeper soils. Further, N addition increased the complexity of the DOM structure. Hence, the loss of soil nutrients and the rational application of N need to be considered in order to prevent the accumulation of N compounds in soil.", "keywords": ["China", "Nitrogen", "Science", "Global Warming", "Models", " Biological", "Carbon Cycle", "Soil", "Imaging", " Three-Dimensional", "Organic Chemicals", "Ecosystem", "2. Zero hunger", "Tropical Climate", "Cunninghamia", "Q", "R", "Temperature", "04 agricultural and veterinary sciences", "Nitrogen Cycle", "15. Life on land", "6. Clean water", "Spectrometry", " Fluorescence", "Solubility", "13. Climate action", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371%2fjournal.pone.0191403"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371%2fjournal.pone.0191403", "name": "item", "description": "10.1371%2fjournal.pone.0191403", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371%2fjournal.pone.0191403"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-01-23T00:00:00Z"}}, {"id": "20.500.11820/03f81a44-477a-4a8c-b34d-85892c85bd6f", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:24:26Z", "type": "Journal Article", "created": "2017-10-13", "title": "An Explicit Structural Model of Root Hair and Soil Interactions Parameterised by Synchrotron X-ray Computed Tomography", "description": "The rhizosphere is a zone of fundamental importance for understanding the dynamics of nutrient acquisition by plant roots. The canonical difficulty of experimentally investigating the rhizosphere led long ago to the adoption of mathematical models, the most sophisticated of which now incorporate explicit representations of root hairs and rhizosphere soil. Mathematical upscaling regimes, such as homogenisation, offer the possibility of incorporating into larger-scale models the important mechanistic processes occurring at the rhizosphere scale. However, we lack concrete descriptions of all the features required to fully parameterise models at the rhizosphere scale. By combining synchrotron X-ray computed tomography (SRXCT) and a novel root growth assay, we derive a three-dimensional description of rhizosphere soil structure suitable for use in multi-scale modelling frameworks. We describe an approach to mitigate sub-optimal root hair detection via structural root hair growth modelling. The growth model is explicitly parameterised with SRXCT data and simulates three-dimensional root hair ideotypes in silico, which are suitable for both ideotypic analysis and parameterisation of 3D geometry in mathematical models. The study considers different hypothetical conditions governing root hair interactions with soil matrices, with their respective effects on hair morphology being compared between idealised and image-derived soil/root geometries. The studies in idealised geometries suggest that packing arrangement of soil affects hair tortuosity more than the particle diameter. Results in field-derived soil suggest that hair access to poorly mobile nutrients is particularly sensitive to the physical interaction between the growing hairs and the phase of the soil in which soil water is present (i.e. the hydrated textural phase). The general trends in fluid-coincident hair length with distance from the root, and their dependence on hair/soil interaction mechanisms, are conserved across Cartesian and cylindrical geometries.", "keywords": ["Plant biology", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "X-ray CT", "Biomedical imaging and signal processing", "Mathematical Concepts", "15. Life on land", "Models", " Biological", "Plant Roots", "root hairs", "Soil", "03 medical and health sciences", "Imaging", " Three-Dimensional", "in silico", "structural modelling", "synchrotron", "Rhizosphere", "Original Article", "Computer Simulation", "rhizosphere", "Tomography", " X-Ray Computed", "Synchrotrons"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11538-017-0350-x.pdf"}, {"href": "https://doi.org/20.500.11820/03f81a44-477a-4a8c-b34d-85892c85bd6f"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bulletin%20of%20Mathematical%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.11820/03f81a44-477a-4a8c-b34d-85892c85bd6f", "name": "item", "description": "20.500.11820/03f81a44-477a-4a8c-b34d-85892c85bd6f", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.11820/03f81a44-477a-4a8c-b34d-85892c85bd6f"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-10-13T00:00:00Z"}}, {"id": "2614033554", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-28T16:24:46Z", "type": "Journal Article", "created": "2017-05-15", "title": "Quantification of root water uptake in soil using X\u2010ray computed tomography and image\u2010based modelling", "description": "Abstract<p>Spatially averaged models of root\uffe2\uff80\uff93soil interactions are often used to calculate plant water uptake. Using a combination of X\uffe2\uff80\uff90ray computed tomography (CT) and image\uffe2\uff80\uff90based modelling, we tested the accuracy of this spatial averaging by directly calculating plant water uptake for young wheat plants in two soil types. The root system was imaged using X\uffe2\uff80\uff90ray CT at 2, 4, 6, 8 and 12\uffc2\uffa0d after transplanting. The roots were segmented using semi\uffe2\uff80\uff90automated root tracking for speed and reproducibility. The segmented geometries were converted to a mesh suitable for the numerical solution of Richards' equation. Richards' equation was parameterized using existing pore scale studies of soil hydraulic properties in the rhizosphere of wheat plants. Image\uffe2\uff80\uff90based modelling allows the spatial distribution of water around the root to be visualized and the fluxes into the root to be calculated. By comparing the results obtained through image\uffe2\uff80\uff90based modelling to spatially averaged models, the impact of root architecture and geometry in water uptake was quantified. We observed that the spatially averaged models performed well in comparison to the image\uffe2\uff80\uff90based models with &lt;2% difference in uptake. However, the spatial averaging loses important information regarding the spatial distribution of water near the root system.</p", "keywords": ["0106 biological sciences", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "550", "Water", "15. Life on land", "01 natural sciences", "Models", " Biological", "Plant Roots", "6. Clean water", "Soil", "03 medical and health sciences", "Imaging", " Three-Dimensional", "Tomography", " X-Ray Computed", "Porosity"]}, "links": [{"href": "https://eprints.nottingham.ac.uk/42292/1/170405_WP2_Paper_update_final%20Mooney.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.12983"}, {"href": "https://doi.org/2614033554"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%2C%20Cell%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2614033554", "name": "item", "description": "2614033554", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2614033554"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-05T00:00:00Z"}}, {"id": "2164/11950", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-28T16:24:38Z", "type": "Journal Article", "created": "2018-10-06", "title": "Imaging microstructure of the barley rhizosphere: particle packing and root hair influences", "description": "Summary<p>   <p>Soil adjacent to roots has distinct structural and physical properties from bulk soil, affecting water and solute acquisition by plants. Detailed knowledge on how root activity and traits such as root hairs affect the three\uffe2\uff80\uff90dimensional pore structure at a fine scale is scarce and often contradictory.</p>  <p>Roots of hairless barley (Hordeum vulgare L. cv Optic) mutant (NRH) and its wildtype (WT) parent were grown in tubes of sieved (&lt;250\uffc2\uffa0\uffce\uffbcm) sandy loam soil under two different water regimes. The tubes were scanned by synchrotron\uffe2\uff80\uff90based X\uffe2\uff80\uff90ray computed tomography to visualise pore structure at the soil\uffe2\uff80\uff93root interface. Pore volume fraction and pore size distribution were analysed vs distance within 1\uffc2\uffa0mm of the root surface.</p>  <p>Less dense packing of particles at the root surface was hypothesised to cause the observed increased pore volume fraction immediately next to the epidermis. The pore size distribution was narrower due to a decreased fraction of larger pores. There were no statistically significant differences in pore structure between genotypes or moisture conditions.</p>  <p>A model is proposed that describes the variation in porosity near roots taking into account soil compaction and the surface effect at the root surface.</p>  </p", "keywords": ["name=Physiology", "STABILIZATION", "Physiology", "EP/M020355/1", "Supplementary Data", "QH301 Biology", "Plant Science", "Supplementary data available", "Plant Roots", "630", "noninvasive imaging", "Soil", "646809DIMR", "STRENGTH", "BB/J00868/1", "Hordeum vulgare", "2. Zero hunger", "04 agricultural and veterinary sciences", "Rhizosphere", "COMPRESSION", "soil structure", "Porosity", "European Research Council", "/dk/atira/pure/subjectarea/asjc/1300/1314", "/dk/atira/pure/subjectarea/asjc/1100/1110", "root hairs", "COMPACTION", "QH301", "Imaging", " Three-Dimensional", "synchrotron", "particle packing", "SOIL-STRUCTURE", "BB/L025620/1", "WATER-STRESS", "NE/L00237/1", "580", "ELONGATION", "Civil_env_eng", "Natural Environment Research Council (NERC)", "POROSITY", "Water", "Hordeum", "15. Life on land", "Engineering and Physical Sciences Research Council (EPSRC)", "Mutation", "Biotechnology and Biological Sciences Research Council (BBSRC)", "0401 agriculture", " forestry", " and fisheries", "PENETRATION", "name=Plant Science", "rhizosphere", "Tomography", " X-Ray Computed", "MAIZE", "BB/P004180/1", "Synchrotrons", "BB/L025825/1"]}, "links": [{"href": "https://repository.uwl.ac.uk/id/eprint/5489/1/AS6808504337817661539338801587_content_1.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15516"}, {"href": "https://doi.org/2164/11950"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2164/11950", "name": "item", "description": "2164/11950", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2164/11950"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-20T00:00:00Z"}}, {"id": "2164/9249", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-28T16:24:39Z", "type": "Journal Article", "created": "2017-07-31", "title": "High\u2010resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation", "description": "Summary<p>   <p>In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root\uffe2\uff80\uff93soil interface during the early stage of crop establishment.</p>  <p>This was achieved by use of high\uffe2\uff80\uff90resolution (c. 5\uffc2\uffa0\uffce\uffbcm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant\uffe2\uff80\uff93soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8\uffc2\uffa0d in microcosms packed with sandy loam soil at 1.2\uffc2\uffa0g\uffc2\uffa0cm\uffe2\uff88\uff923 dry bulk density. Root hairs were visualised within air\uffe2\uff80\uff90filled pore spaces, but not in the fine\uffe2\uff80\uff90textured soil regions.</p>  <p>We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (&gt;\uffc2\uffa05\uffc2\uffa0\uffce\uffbcm) in the rhizosphere, as compared with the no\uffe2\uff80\uff90hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1\uffc2\uffa0mm from the root surface. Interestingly the root\uffe2\uff80\uff90hair\uffe2\uff80\uff90bearing genotype had a significantly greater soil pore volume\uffe2\uff80\uff90fraction at the root\uffe2\uff80\uff93soil interface.</p>  <p>Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image\uffe2\uff80\uff90based modelling.</p>  </p", "keywords": ["construction", "EP/M020355/1", "QH301 Biology", "non-invasive imaging", "Plant Roots", "630", "root hairs", "noninvasive imaging", "QH301", "Soil", "Imaging", " Three-Dimensional", "646809DIMR", "synchrotron", "Computer Simulation", "BB/L025620/1", "BB/J00868/1", "NE/L00237/1", "Hordeum vulgare", "580", "2. Zero hunger", "Civil_env_eng", "Natural Environment Research Council (NERC)", "Research", "Hordeum", "04 agricultural and veterinary sciences", "15. Life on land", "image-based modelling", "Engineering and Physical Sciences Research Council (EPSRC)", "Rhizosphere", "Biotechnology and Biological Sciences Research Council (BBSRC)", "0401 agriculture", " forestry", " and fisheries", "rhizosphere", "soil structure", "synchroton", "Porosity", "BB/P004180/1", "Synchrotrons", "BB/L025825/1", "European Research Council"]}, "links": [{"href": "https://repository.uwl.ac.uk/id/eprint/4981/1/Koebernick_et_al-2017-New_Phytologist.pdf"}, {"href": "https://eprints.soton.ac.uk/412143/1/s1_ln2680534218582232741703867393Hwf_1771574461IdV_16951475526805342FIRST_LOOK_PDF0001.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.14705"}, {"href": "https://doi.org/2164/9249"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2164/9249", "name": "item", "description": "2164/9249", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2164/9249"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-31T00:00:00Z"}}, {"id": "2229699546", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-28T16:24:40Z", "type": "Journal Article", "created": "2016-01-20", "title": "Image-based modelling of nutrient movement in and around the rhizosphere", "description": "In this study, we developed a spatially explicit model for nutrient uptake by root hairs based on X-ray computed tomography images of the rhizosphere soil structure. This work extends our previous work to larger domains and hence is valid for longer times. Unlike the model used previously, which considered only a small region of soil about the root, we considered an effectively infinite volume of bulk soil about the rhizosphere. We asked the question: At what distance away from root surfaces do the specific structural features of root-hair and soil aggregate morphology not matter because average properties start dominating the nutrient transport? The resulting model was used to capture bulk and rhizosphere soil properties by considering representative volumes of soil far from the root and adjacent to the root, respectively. By increasing the size of the volumes that we considered, the diffusive impedance of the bulk soil and root uptake were seen to converge. We did this for two different values of water content. We found that the size of region for which the nutrient uptake properties converged to a fixed value was dependent on the water saturation. In the fully saturated case, the region of soil we needed to consider was only of radius 1.1mm for poorly soil-mobile species such as phosphate. However, in the case of a partially saturated medium (relative saturation 0.3), we found that a radius of 1.4mm was necessary. This suggests that, in addition to the geometrical properties of the rhizosphere, there is an additional effect of soil moisture properties, which extends further from the root and may relate to other chemical changes in the rhizosphere. The latter were not explicitly included in our model.", "keywords": ["0301 basic medicine", "550", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "Models", " Biological", "Plant Roots", "630", "03 medical and health sciences", "Imaging", " Three-Dimensional", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Tomography", " X-Ray Computed", "Research Paper"]}, "links": [{"href": "https://doi.org/2229699546"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Experimental%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2229699546", "name": "item", "description": "2229699546", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2229699546"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-01-05T00:00:00Z"}}, {"id": "28503782", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-28T16:24:50Z", "type": "Journal Article", "created": "2017-05-15", "title": "Quantification of root water uptake in soil using X\u2010ray computed tomography and image\u2010based modelling", "description": "Abstract<p>Spatially averaged models of root\uffe2\uff80\uff93soil interactions are often used to calculate plant water uptake. Using a combination of X\uffe2\uff80\uff90ray computed tomography (CT) and image\uffe2\uff80\uff90based modelling, we tested the accuracy of this spatial averaging by directly calculating plant water uptake for young wheat plants in two soil types. The root system was imaged using X\uffe2\uff80\uff90ray CT at 2, 4, 6, 8 and 12\uffc2\uffa0d after transplanting. The roots were segmented using semi\uffe2\uff80\uff90automated root tracking for speed and reproducibility. The segmented geometries were converted to a mesh suitable for the numerical solution of Richards' equation. Richards' equation was parameterized using existing pore scale studies of soil hydraulic properties in the rhizosphere of wheat plants. Image\uffe2\uff80\uff90based modelling allows the spatial distribution of water around the root to be visualized and the fluxes into the root to be calculated. By comparing the results obtained through image\uffe2\uff80\uff90based modelling to spatially averaged models, the impact of root architecture and geometry in water uptake was quantified. We observed that the spatially averaged models performed well in comparison to the image\uffe2\uff80\uff90based models with &lt;2% difference in uptake. However, the spatial averaging loses important information regarding the spatial distribution of water near the root system.</p", "keywords": ["0106 biological sciences", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "550", "Water", "15. Life on land", "01 natural sciences", "Models", " Biological", "Plant Roots", "6. Clean water", "Soil", "03 medical and health sciences", "Imaging", " Three-Dimensional", "Tomography", " X-Ray Computed", "Porosity"]}, "links": [{"href": "https://eprints.nottingham.ac.uk/42292/1/170405_WP2_Paper_update_final%20Mooney.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.12983"}, {"href": "https://doi.org/28503782"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%2C%20Cell%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "28503782", "name": "item", "description": "28503782", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/28503782"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-05T00:00:00Z"}}, {"id": "PMC4753851", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-28T16:27:14Z", "type": "Journal Article", "created": "2016-01-20", "title": "Image-based modelling of nutrient movement in and around the rhizosphere", "description": "In this study, we developed a spatially explicit model for nutrient uptake by root hairs based on X-ray computed tomography images of the rhizosphere soil structure. This work extends our previous work to larger domains and hence is valid for longer times. Unlike the model used previously, which considered only a small region of soil about the root, we considered an effectively infinite volume of bulk soil about the rhizosphere. We asked the question: At what distance away from root surfaces do the specific structural features of root-hair and soil aggregate morphology not matter because average properties start dominating the nutrient transport? The resulting model was used to capture bulk and rhizosphere soil properties by considering representative volumes of soil far from the root and adjacent to the root, respectively. By increasing the size of the volumes that we considered, the diffusive impedance of the bulk soil and root uptake were seen to converge. We did this for two different values of water content. We found that the size of region for which the nutrient uptake properties converged to a fixed value was dependent on the water saturation. In the fully saturated case, the region of soil we needed to consider was only of radius 1.1mm for poorly soil-mobile species such as phosphate. However, in the case of a partially saturated medium (relative saturation 0.3), we found that a radius of 1.4mm was necessary. This suggests that, in addition to the geometrical properties of the rhizosphere, there is an additional effect of soil moisture properties, which extends further from the root and may relate to other chemical changes in the rhizosphere. The latter were not explicitly included in our model.", "keywords": ["0301 basic medicine", "550", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "Models", " Biological", "Plant Roots", "630", "03 medical and health sciences", "Imaging", " Three-Dimensional", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Tomography", " X-Ray Computed", "Research Paper"]}, "links": [{"href": "https://doi.org/PMC4753851"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Experimental%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC4753851", "name": "item", "description": "PMC4753851", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC4753851"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-01-05T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Three-Dimensional&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Three-Dimensional&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Three-Dimensional&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Three-Dimensional&offset=14", "hreflang": "en-US"}], "numberMatched": 14, "numberReturned": 14, "distributedFeatures": [], "timeStamp": "2026-07-28T21:09:30.361777Z"}