{"type": "FeatureCollection", "features": [{"id": "10.1007/978-3-031-12176-0_11", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:14:04Z", "type": "Report", "created": "2022-11-28", "title": "Integrating X-ray CT Data into Models", "description": "Open AccessXP is a Mar\u00eda Zambrano Fellow at the Public University of Navarra (UPNA) and acknowledges funding from the European Union - NextGenerationEU through the Spanish program 'Ayuda para la Recualificaci\u00f3n del Sistema Universitario Espa\u00f1ol'. AE acknowledges funding from Swiss National Science Foundation: Grants P2EZP2 175128 and P400PB_186751. TR was funded by ERC Consolidator grant 646809 DIMR.", "keywords": ["2. Zero hunger", "570", "550", "X-Ray computed tomography", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation", "Soil properties", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "15. Life on land", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation", "6. Clean water"], "contacts": [{"organization": "Portell, Xavier, Pot, Valerie, Ebrahimi, Ali, Monga, Olivier, Roose, Tiina,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/978-3-031-12176-0_11"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/978-3-031-12176-0_11", "name": "item", "description": "10.1007/978-3-031-12176-0_11", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/978-3-031-12176-0_11"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10.1007/s11242-015-0572-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:14:55Z", "type": "Journal Article", "created": "2015-09-14", "title": "Visualization and Characterization of Heterogeneous Water Flow in Double-Porosity Media by Means of X-ray Computed Tomography", "description": "Three-dimensional visualization of dynamic water transport process in soil by 1 computed tomography (CT) technique is still limited by its low temporal resolution. In order 2 to monitor dynamically water transport in soil, a compromise has to be found between water 3 flow velocity and CT acquisition time. Furthermore, an efficient image analysis method is 1 4 necessary. In this work, we followed the water transport in three dimensions by CT imaging 5 across a double-porosity media constituted of two distinct materials, i.e. sand and porous 6 clay spheres. The CT acquisition parameters were adjusted to the water pore velocity so that 7 we succeeded to register the water front displacement per time range of 25 min. We also used 8 the image subtraction method to extract water distribution evolution with time with a space 9 resolution of 6 \u00d7 10 \u22123 cm. Both time and space resolution are relatively high compared with 10 other dynamic studies. The water content profiles showed that the clay spheres remained 11 in their dry state during water infiltration, while the water transport only occurred in the 12 sand matrix. These results are consistent with macroscopic experiments. The water front 13 visualized by CT showed a non-symmetrical shape which was related to water transfer in 14 non-equilibrium as shown by column displacement experiments.", "keywords": ["2. Zero hunger", "550", "[SDE.IE]Environmental Sciences/Environmental Engineering", "0208 environmental biotechnology", "Porous media", "0207 environmental engineering", "02 engineering and technology", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "6. Clean water", "620", "Image analysis", "3D visualization", "[SDU.STU.HY] Sciences of the Universe [physics]/Earth Sciences/Hydrology", "[SDE.IE] Environmental Sciences/Environmental Engineering", "[SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "Computed tomography", "Water transport"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11242-015-0572-z"}, {"href": "https://doi.org/10.1007/s11242-015-0572-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Transport%20in%20Porous%20Media", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11242-015-0572-z", "name": "item", "description": "10.1007/s11242-015-0572-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11242-015-0572-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-09-14T00:00:00Z"}}, {"id": "10.1016/j.geoderma.2025.117299", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:20Z", "type": "Journal Article", "created": "2025-04-19", "title": "Synchrotron-based 3D X-ray computed tomography reveals root system architecture: Plastic responses to phosphorus placement", "description": "We used synchrotron-based X-ray computed tomography (SRXCT) to visualize root distribution in soil cores. X-ray CT is emerging as a leading technique to study plant roots, but SRXCT offers potential advantages compared with conventional X-ray sources, including producing X-rays of higher intensity that are collimated, monochromatic and tuneable; delivering high-resolution data whilst avoiding issues such as beam-hardening and source divergence. We demonstrate the suitability of SRXCT for observing the root system of wheat plants growing in two soils (Calcisol and Ultisol) in response to placement of different phosphorus fertilisers. To optimize scanning quality, we tested the use of an inverse \u2018mask\u2019 in front of the soil cores to achieve a more uniform attenuation along the sample, thereby avoiding saturation of the detector along the thinnest parts of the soil cores. Secondly, we developed a deep learning approach for segmentation and quantification of root length and diameter. Our results demonstrate the use of SRXCT as a tool for studying root system architecture in soil at high spatial resolution. The SRXCT method marks a new stride towards advancing our understanding of root structures in unprecedented detail, opening further avenues for exploring plant-soil interactions.", "keywords": ["X-ray computed tomography", "Image segmentation", "Plant roots", "Root system architecture", "Soil phosphorus", "Science", "Q", "Root distribution", "Synchrotron"]}, "links": [{"href": "https://doi.org/10.1016/j.geoderma.2025.117299"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Geoderma", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.geoderma.2025.117299", "name": "item", "description": "10.1016/j.geoderma.2025.117299", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.geoderma.2025.117299"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-05-01T00:00:00Z"}}, {"id": "10.1016/j.jbiomech.2016.04.023", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-25T16:16:25Z", "type": "Journal Article", "created": "2016-04-30", "title": "Mapping soil deformation around plant roots using in vivo 4D X-ray Computed Tomography and Digital Volume Correlation", "description": "The mechanical impedance of soils inhibits the growth of plant roots, often being the most significant physical limitation to root system development. Non-invasive imaging techniques have recently been used to investigate the development of root system architecture over time, but the relationship with soil deformation is usually neglected. Correlative mapping approaches parameterised using 2D and 3D image data have recently gained prominence for quantifying physical deformation in composite materials including fibre-reinforced polymers and trabecular bone. Digital Image Correlation (DIC) and Digital Volume Correlation (DVC) are computational techniques which use the inherent material texture of surfaces and volumes, captured using imaging techniques, to map full-field deformation components in samples during physical loading. Here we develop an experimental assay and methodology for four-dimensional, in vivo X-ray Computed Tomography (XCT) and apply a Digital Volume Correlation (DVC) approach to the data to quantify deformation. The method is validated for a field-derived soil under conditions of uniaxial compression, and a calibration study is used to quantify thresholds of displacement and strain measurement. The validated and calibrated approach is then demonstrated for an in vivo test case in which an extending maize root in field-derived soil was imaged hourly using XCT over a growth period of 19h. This allowed full-field soil deformation data and 3D root tip dynamics to be quantified in parallel for the first time. This fusion of methods paves the way for comparative studies of contrasting soils and plant genotypes, improving our understanding of the fundamental mechanical processes which influence root system development.", "keywords": ["0301 basic medicine", "Soil", "03 medical and health sciences", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "Four-Dimensional Computed Tomography", "15. Life on land", "Plant Roots", "Zea mays", "620", "Mechanical Phenomena"]}, "links": [{"href": "https://eprints.soton.ac.uk/394374/1/__filestore.soton.ac.uk_users_fh1d15_mydesktop_Keyes_et_al_Journal_of_Biomechaincs_Root_DVC_2016.pdf"}, {"href": "https://doi.org/10.1016/j.jbiomech.2016.04.023"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Biomechanics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jbiomech.2016.04.023", "name": "item", "description": "10.1016/j.jbiomech.2016.04.023", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jbiomech.2016.04.023"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "20.500.14243/420312", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:18Z", "type": "Journal Article", "created": "2022-11-11", "title": "The impact of xylem geometry on olive cultivar resistance to Xylella fastidiosa: An image\u2010based study", "description": "Abstract                   <p>                     Xylella fastidiosa                     is a xylem\uffe2\uff80\uff90limited plant pathogen infecting many crops globally and is the cause of the recent olive disease epidemic in Italy. One strategy proposed to mitigate losses is to replant susceptible crops with resistant varieties. Several genetic, biochemical and biophysical traits are associated to                     X                     .                     fastidiosa                     disease resistance. However, mechanisms underpinning resistance are poorly understood. We hypothesize that the susceptibility of olive cultivars to infection will correlate to xylem vessel diameters, with narrower vessels being resistant to air embolisms and having slower flow rates limiting pathogen spread. To test this, we scanned stems from four olive cultivars of varying susceptibility to                     X                     .                     fastidiosa                     using X\uffe2\uff80\uff90ray computed tomography. Scans were processed by a bespoke methodology that segmented vessels, facilitating diameter measurements. Though significant differences were not found comparing stem\uffe2\uff80\uff90average vessel section diameters among cultivars, they were found when comparing diameter distributions. Moreover, the measurements indicated that although vessel diameter distributions may play a role regarding the resistance of Leccino, it is unlikely they do for FS17. Considering Young\uffe2\uff80\uff93Laplace and Hagen\uffe2\uff80\uff93Poiseuille equations, we inferred differences in embolism susceptibility and hydraulic conductivity of the vasculature. Our results suggest susceptible cultivars, having a greater proportion of larger vessels, are more vulnerable to air embolisms. In addition, results suggest that under certain pressure conditions, functional vasculature in susceptible cultivars could be subject to greater stresses than in resistant cultivars. These results support investigation into xylem morphological screening to help inform olive replanting. Furthermore, our framework could test the relevance of xylem geometry to disease resistance in other crops.                   </p", "keywords": ["2. Zero hunger", "X-ray computed tomography", "0106 biological sciences", "15. Life on land", "Xylella", "01 natural sciences", "630", "olive dieback"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/420312/1/prod_473732-doc_193088.pdf"}, {"href": "https://eprints.soton.ac.uk/471748/9/Plant_Pathology_2022_Walker_The_Impact_of_Xylem_Geometry_on_Olive_Cultivar_Resistance_to_Xylella_fastidiosa_An.pdf"}, {"href": "https://doi.org/20.500.14243/420312"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Pathology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.14243/420312", "name": "item", "description": "20.500.14243/420312", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.14243/420312"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-19T00:00:00Z"}}, {"id": "10.1071/sr21268", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:59Z", "type": "Journal Article", "created": "2022-01-18", "title": "Lessons from a landmark 1991 article on soil structure: distinct precedence of non-destructive assessment and benefits of fresh perspectives in soil research", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>In 1991, at the launch of a national symposium devoted to soil structure, the Australian Society of Soil Science invited Professor John Letey to deliver a keynote address, which was later published in the society\u2019s journal. In his lecture, he shared the outcome of his reflexion about what the assessment of soil structure should amount to, in order to produce useful insight into the functioning of soils. His viewpoint was that the focus should be put on the openings present in the structure, rather than on the chunks of material resulting from its mechanical dismantlement. In the present article, we provide some historical background for Letey\u2019s analysis, and try to explain why it took a number of years for the paradigm shift that he advocated to begin to occur. Over the last decade, his perspective that soil structure needs to be characterised via non-destructive methods appears to have gained significant momentum, which is likely to increase further in the near future, as we take advantage of recent technological advances. Other valuable lessons that one can derive from Letey\u2019s pioneering article relate to the extreme value for everyone, even neophytes, to constantly ask questions about where research on given topics is heading, what its goals are, and whether the methods that are used at a certain time are optimal.</p></article>", "keywords": ["570", "soil image analysis", "soil microorganisms", "[SDE.MCG]Environmental Sciences/Global Changes", "Soil measuring", "earthworms", "micromorphology", "Aggregate stability", "Soil functions", "01 natural sciences", "630", "Soil fauna", "soil organic matter", "Earthworms", "Micromorphology", "Computed tomography", "aggregate stability", "0105 earth and related environmental sciences", "soil measuring", "2. Zero hunger", "Soil organic matter", "computed tomography", "04 agricultural and veterinary sciences", "soil functions", "15. Life on land", "[SDE.MCG] Environmental Sciences/Global Changes", "Soil image analysis", "0401 agriculture", " forestry", " and fisheries", "soil fauna", "earthworms; micromorphology", "Soil microorganisms"]}, "links": [{"href": "https://doi.org/10.1071/sr21268"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1071/sr21268", "name": "item", "description": "10.1071/sr21268", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1071/sr21268"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-19T00:00:00Z"}}, {"id": "10.1071/sr18293", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:59Z", "type": "Journal Article", "created": "2019-02-21", "title": "Orchard management and preferential flow in Andosols \u2013 comparing two kiwifruit orchards in New Zealand", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Sustainable horticulture depends on the integrity of soil functions, which directly depend on soil architecture affecting aggregation, root growth, as well as liquid and gas permeability. We hypothesised that changes in soil architecture resulting from feedback mechanisms between management, soil organic carbon contents (SOC), biota and vegetation can be captured with X-ray computed tomography (CT), and that these affect the soil filtering function, which thus, can be manipulated through orchard management. We compared the transport of copper, a widely used fungicide, through intact soil cores from vine rows of kiwifruit orchards under organic and integrated management. We first derived 3D-macropore characteristics from CT-images, followed by leaching a pulse of copper and a tracer through the same cores. The organic orchard soil had a significantly higher SOC content than the integrated orchard soil, and this was positively correlated with total porosity. Macropores (&amp;gt;92 \u00b5m) were larger with a higher connectivity, but significantly fewer in the organic than the integrated orchard soil. This resulted in a lower macroporosity and a better copper filtering capacity of the organic than the integrated orchard soil. Copper distribution was reasonably predicted when combining SOC contents, pH and macropore characteristics. Significant relationships between soil parameters and indicators of the strength of preferential flow verified that CT-derived macropore characteristics can be used to predict functional solute transport parameters. The relevance of our results and relationships observed between macropore characteristics, functional indicators of preferential flow and the fate of copper needs verification with samples representing more soils and sites.</p></article>", "keywords": ["X-ray computed tomography", "[SDE] Environmental Sciences", "2. Zero hunger", "[SDE.MCG]Environmental Sciences/Global Changes", "carbon", "computed tomography", "04 agricultural and veterinary sciences", "15. Life on land", "630", "X-ray", "kiwifruit orchard", "soil architecture", "[SDE.MCG] Environmental Sciences/Global Changes", "[SDE]Environmental Sciences", "filtering function", "0401 agriculture", " forestry", " and fisheries"]}, "links": [{"href": "https://www.publish.csiro.au/SR/pdf/SR18293"}, {"href": "https://doi.org/10.1071/sr18293"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1071/sr18293", "name": "item", "description": "10.1071/sr18293", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1071/sr18293"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-22T00:00:00Z"}}, {"id": "10.1111/nph.17980", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:02Z", "type": "Journal Article", "created": "2022-01-19", "title": "Multimodal correlative imaging and modelling of phosphorus uptake from soil by hyphae of mycorrhizal fungi", "description": "Summary<p>   <p>Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore\uffe2\uff80\uff90space, and models of AMF\uffe2\uff80\uff90enhanced P\uffe2\uff80\uff90uptake are poorly validated.</p>  <p>We used synchrotron X\uffe2\uff80\uff90ray computed tomography to visualize mycorrhizas in soil and synchrotron X\uffe2\uff80\uff90ray fluorescence/X\uffe2\uff80\uff90ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling.</p>  <p>We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co\uffe2\uff80\uff90locate with areas of high P and low Al, and preferentially associate with organic\uffe2\uff80\uff90type P species over Al\uffe2\uff80\uff90rich inorganic P.</p>  <p>We discovered that AMF avoid Al\uffe2\uff80\uff90rich areas as a source of P. Sulphur\uffe2\uff80\uff90rich regions were found to be correlated with higher hyphal density and an increased organic\uffe2\uff80\uff90associated P\uffe2\uff80\uff90pool, whilst oxidized S\uffe2\uff80\uff90species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome\uffe2\uff80\uff90related. Our experimentally\uffe2\uff80\uff90validated model led to an estimate of P\uffe2\uff80\uff90uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated \uffe2\uff80\uff93 a result with significant implications for the modelling of plant\uffe2\uff80\uff93soil\uffe2\uff80\uff93AMF interactions.</p>  </p", "keywords": ["580", "X-ray computed tomography", "570", "Research", "X-ray fluorescence", "Fungi", "Hyphae", "500", "Phosphorus", "mycorrhizas", "04 agricultural and veterinary sciences", "15. Life on land", "plant phosphorus uptake", "Plant Roots", "Soil", "rhizosphere modelling", "Mycorrhizae", "synchrotron", "0401 agriculture", " forestry", " and fisheries", "Soil Microbiology"]}, "links": [{"href": "https://eprints.soton.ac.uk/454110/1/Keyes_et_al_Myco_Paper_TR_04_01_2022_unmarked.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/2/Figures_TR_22_12_2021.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/3/SI_1_TR_22_12_2021_no_markup.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/4/SI_2_TR_22_12_2021.pdf"}, {"href": "https://doi.org/10.1111/nph.17980"}, {"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.17980", "name": "item", "description": "10.1111/nph.17980", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.17980"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-15T00:00:00Z"}}, {"id": "10.1111/pce.13638", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:03Z", "type": "Journal Article", "created": "2019-08-05", "title": "Soil carbon dioxide venting through rice roots", "description": "Abstract<p>The growth of rice in submerged soils depends on its ability to form continuous gas channels\uffe2\uff80\uff94aerenchyma\uffe2\uff80\uff94through which oxygen (O2) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO2) in the opposite direction. Large, potentially toxic concentrations of dissolved CO2 develop in submerged rice soils. We show using X\uffe2\uff80\uff90ray computed tomography and image\uffe2\uff80\uff90based mathematical modelling that CO2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO2 and associated bicarbonate (HCO3\uffe2\uff88\uff92) in root cells would have been well above levels known to be toxic to roots. Removal of CO2 and hence carbonic acid (H2CO3) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions.</p", "keywords": ["580", "0106 biological sciences", "0301 basic medicine", "570", "Oryza", "Original Articles", "Carbon Dioxide", "15. Life on land", "Models", " Biological", "Plant Roots", "01 natural sciences", "6. Clean water", "biological transport", "X\u2010ray computed tomography", "Soil", "03 medical and health sciences", "13. Climate action", "biological models"]}, "links": [{"href": "https://eprints.soton.ac.uk/433011/1/_system_appendPDF_proof_hi_4.pdf"}, {"href": "https://eprints.soton.ac.uk/433011/2/Kirk_et_al_2019_Plant_Cell_Environment.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.13638"}, {"href": "https://doi.org/10.1111/pce.13638"}, {"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.13638", "name": "item", "description": "10.1111/pce.13638", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/pce.13638"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-19T00:00:00Z"}}, {"id": "10.1111/ppa.13674", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-25T16:19:03Z", "type": "Journal Article", "created": "2022-11-11", "title": "The impact of xylem geometry on olive cultivar resistance to Xylella fastidiosa: An image\u2010based study", "description": "Abstract<p>Xylella fastidiosa is a xylem\uffe2\uff80\uff90limited plant pathogen infecting many crops globally and is the cause of the recent olive disease epidemic in Italy. One strategy proposed to mitigate losses is to replant susceptible crops with resistant varieties. Several genetic, biochemical and biophysical traits are associated to X. fastidiosa disease resistance. However, mechanisms underpinning resistance are poorly understood. We hypothesize that the susceptibility of olive cultivars to infection will correlate to xylem vessel diameters, with narrower vessels being resistant to air embolisms and having slower flow rates limiting pathogen spread. To test this, we scanned stems from four olive cultivars of varying susceptibility to X. fastidiosa using X\uffe2\uff80\uff90ray computed tomography. Scans were processed by a bespoke methodology that segmented vessels, facilitating diameter measurements. Though significant differences were not found comparing stem\uffe2\uff80\uff90average vessel section diameters among cultivars, they were found when comparing diameter distributions. Moreover, the measurements indicated that although vessel diameter distributions may play a role regarding the resistance of Leccino, it is unlikely they do for FS17. Considering Young\uffe2\uff80\uff93Laplace and Hagen\uffe2\uff80\uff93Poiseuille equations, we inferred differences in embolism susceptibility and hydraulic conductivity of the vasculature. Our results suggest susceptible cultivars, having a greater proportion of larger vessels, are more vulnerable to air embolisms. In addition, results suggest that under certain pressure conditions, functional vasculature in susceptible cultivars could be subject to greater stresses than in resistant cultivars. These results support investigation into xylem morphological screening to help inform olive replanting. Furthermore, our framework could test the relevance of xylem geometry to disease resistance in other crops.</p", "keywords": ["2. Zero hunger", "X-ray computed tomography", "0106 biological sciences", "15. Life on land", "Xylella", "01 natural sciences", "630", "olive dieback"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/420312/1/prod_473732-doc_193088.pdf"}, {"href": "https://eprints.soton.ac.uk/471748/9/Plant_Pathology_2022_Walker_The_Impact_of_Xylem_Geometry_on_Olive_Cultivar_Resistance_to_Xylella_fastidiosa_An.pdf"}, {"href": "https://doi.org/10.1111/ppa.13674"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Pathology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/ppa.13674", "name": "item", "description": "10.1111/ppa.13674", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/ppa.13674"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-19T00:00:00Z"}}, {"id": "10.1111/ppa.13835", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-25T16:19:03Z", "type": "Journal Article", "created": "2023-11-28", "title": "A high\u2010throughput analysis of high\u2010resolution X\u2010ray CT images of stems of olive and citrus plants resistant and susceptible to Xylella fastidiosa", "description": "Abstract<p>The bacterial plant pathogen Xylella fastidiosa causes disease in several globally important crops. However, some cultivars harbour reduced bacterial loads and express few symptoms. Evidence considering plant species in isolation suggests xylem structure influences cultivar susceptibility to X. fastidiosa. We test this theory more broadly by analysing high\uffe2\uff80\uff90resolution synchrotron X\uffe2\uff80\uff90ray computed tomography of healthy and infected plant vasculature from two taxonomic groups containing susceptible and resistant varieties: two citrus cultivars (sweet orange cv. Pera, tangor cv. Murcott) and two olive cultivars (Koroneiki, Leccino). Results found the susceptible plants had more vessels than resistant ones, which could promote within\uffe2\uff80\uff90host pathogen spread. However, features associated with resistance were not shared by citrus and olive. While xylem vessels in resistant citrus stems had comparable diameters to those in susceptible plants, resistant olives had narrower vessels that could limit biofilm spread. And while differences among olive cultivars were not detected, results suggest greater vascular connectivity in resistant compared to susceptible citrus plants. We hypothesize that this provides alternate flow paths for sustaining hydraulic functionality under infection. In summary, this work elucidates different physiological resistance mechanisms between two taxonomic groups, while supporting the existence of an intertaxonomical metric that could speed up the identification of candidate\uffe2\uff80\uff90resistant plants.</p", "keywords": ["2. Zero hunger", "resistance", "X-ray computed tomography", "Xylella fastidiosa", "Olive quick decline syndrome", "citrus variegated chlorosis", "olive quick decline syndrome", "Resistance", "Citrus variegated chlorosis", "15. Life on land", "xylem", "630"]}, "links": [{"href": "https://doi.org/10.1111/ppa.13835"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Pathology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/ppa.13835", "name": "item", "description": "10.1111/ppa.13835", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/ppa.13835"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-11-27T00:00:00Z"}}, {"id": "10.3389/fpls.2021.698640", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:20:44Z", "type": "Journal Article", "created": "2021-08-06", "title": "High-Resolution X-Ray Computed Tomography: A New Workflow for the Analysis of Xylogenesis and Intra-Seasonal Wood Biomass Production", "description": "<p>Understanding tree growth and carbon sequestration are of crucial interest to forecast the feedback of forests to climate change. To have a global understanding of the wood formation, it is necessary to develop new methodologies for xylogenesis measurements, valid across diverse wood structures and applicable to both angiosperms and gymnosperms. In this study, the authors present a new workflow to study xylogenesis using high-resolution X-ray computed tomography (HRXCT), which is generic and offers high potential for automatization. The HXRCT-based approach was benchmarked with the current classical approach (microtomy) on three tree species with contrasted wood anatomy (Pinus nigra, Fagus sylvatica, and Quercus robur). HRXCT proved to estimate the relevant xylogenesis parameters (timing, duration, and growth rates) across species with high accuracy. HRXCT showed to be an efficient avenue to investigate tree xylogenesis for a wide range of wood anatomies, structures, and species. HRXCT also showed its potential to provide quantification of intra-annual dynamics of biomass production through high-resolution 3D mapping of wood biomass within the forming growth ring.</p>", "keywords": ["0106 biological sciences", "[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", "XYLEM", "tree growth", "secondary growth phenology", "Plant Science", "01 natural sciences", "7. Clean energy", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics", "SB1-1110", "Tree growth", "Secondary growth phenology", "microtomy", "PHENOLOGY", "[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "FAGUS-SYLVATICA", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "Biology", "TREE", "Xylogenesis", "580", "xylogenesis", "high-resolution X-ray computed tomography", "Biology and Life Sciences", "Plant culture", "Phylogenetics and taxonomy", "Microtomy", "[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics", "15. Life on land", "BEECH", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "13. Climate action", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "PLANT STRUCTURE", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "environment/Ecosystems", "Engineering sciences. Technology"]}, "links": [{"href": "https://doi.org/10.3389/fpls.2021.698640"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fpls.2021.698640", "name": "item", "description": "10.3389/fpls.2021.698640", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2021.698640"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-06T00:00:00Z"}}, {"id": "10.17863/cam.81466", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:49Z", "type": "Journal Article", "created": "2022-01-19", "title": "Multimodal correlative imaging and modelling of phosphorus uptake from soil by hyphae of mycorrhizal fungi", "description": "Summary<p>   <p>Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore\uffe2\uff80\uff90space, and models of AMF\uffe2\uff80\uff90enhanced P\uffe2\uff80\uff90uptake are poorly validated.</p>  <p>We used synchrotron X\uffe2\uff80\uff90ray computed tomography to visualize mycorrhizas in soil and synchrotron X\uffe2\uff80\uff90ray fluorescence/X\uffe2\uff80\uff90ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling.</p>  <p>We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co\uffe2\uff80\uff90locate with areas of high P and low Al, and preferentially associate with organic\uffe2\uff80\uff90type P species over Al\uffe2\uff80\uff90rich inorganic P.</p>  <p>We discovered that AMF avoid Al\uffe2\uff80\uff90rich areas as a source of P. Sulphur\uffe2\uff80\uff90rich regions were found to be correlated with higher hyphal density and an increased organic\uffe2\uff80\uff90associated P\uffe2\uff80\uff90pool, whilst oxidized S\uffe2\uff80\uff90species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome\uffe2\uff80\uff90related. Our experimentally\uffe2\uff80\uff90validated model led to an estimate of P\uffe2\uff80\uff90uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated \uffe2\uff80\uff93 a result with significant implications for the modelling of plant\uffe2\uff80\uff93soil\uffe2\uff80\uff93AMF interactions.</p>  </p>", "keywords": ["580", "X-ray computed tomography", "570", "Research", "X-ray fluorescence", "Fungi", "Hyphae", "500", "Phosphorus", "mycorrhizas", "04 agricultural and veterinary sciences", "15. Life on land", "plant phosphorus uptake", "Plant Roots", "Soil", "rhizosphere modelling", "Mycorrhizae", "synchrotron", "0401 agriculture", " forestry", " and fisheries", "Soil Microbiology"]}, "links": [{"href": "https://eprints.soton.ac.uk/454110/1/Keyes_et_al_Myco_Paper_TR_04_01_2022_unmarked.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/2/Figures_TR_22_12_2021.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/3/SI_1_TR_22_12_2021_no_markup.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/4/SI_2_TR_22_12_2021.pdf"}, {"href": "https://doi.org/10.17863/cam.81466"}, {"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": "10.17863/cam.81466", "name": "item", "description": "10.17863/cam.81466", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.17863/cam.81466"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-15T00:00:00Z"}}, {"id": "2916609369", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:42Z", "type": "Journal Article", "created": "2019-02-22", "title": "Orchard management and preferential flow in Andosols \u2013 comparing two kiwifruit orchards in New Zealand", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Sustainable horticulture depends on the integrity of soil functions, which directly depend on soil architecture affecting aggregation, root growth, as well as liquid and gas permeability. We hypothesised that changes in soil architecture resulting from feedback mechanisms between management, soil organic carbon contents (SOC), biota and vegetation can be captured with X-ray computed tomography (CT), and that these affect the soil filtering function, which thus, can be manipulated through orchard management. We compared the transport of copper, a widely used fungicide, through intact soil cores from vine rows of kiwifruit orchards under organic and integrated management. We first derived 3D-macropore characteristics from CT-images, followed by leaching a pulse of copper and a tracer through the same cores. The organic orchard soil had a significantly higher SOC content than the integrated orchard soil, and this was positively correlated with total porosity. Macropores (&amp;gt;92\u00b5m) were larger with a higher connectivity, but significantly fewer in the organic than the integrated orchard soil. This resulted in a lower macroporosity and a better copper filtering capacity of the organic than the integrated orchard soil. Copper distribution was reasonably predicted when combining SOC contents, pH and macropore characteristics. Significant relationships between soil parameters and indicators of the strength of preferential flow verified that CT-derived macropore characteristics can be used to predict functional solute transport parameters. The relevance of our results and relationships observed between macropore characteristics, functional indicators of preferential flow and the fate of copper needs verification with samples representing more soils and sites.</p></article>", "keywords": ["X-ray computed tomography", "[SDE] Environmental Sciences", "2. Zero hunger", "[SDE.MCG]Environmental Sciences/Global Changes", "carbon", "computed tomography", "04 agricultural and veterinary sciences", "15. Life on land", "630", "X-ray", "kiwifruit orchard", "soil architecture", "[SDE.MCG] Environmental Sciences/Global Changes", "[SDE]Environmental Sciences", "filtering function", "0401 agriculture", " forestry", " and fisheries"]}, "links": [{"href": "https://www.publish.csiro.au/SR/pdf/SR18293"}, {"href": "https://doi.org/2916609369"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2916609369", "name": "item", "description": "2916609369", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2916609369"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-01T00:00:00Z"}}, {"id": "10.5061/dryad.x69p8czjv", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:21:33Z", "type": "Dataset", "title": "Dataset of nanoplastic transport in soil via bioturbation by Lumbricus terrestris", "description": "Open AccessPlease read ReadMe file before usage and contact authors for  further information or questions.", "keywords": ["2. Zero hunger", "X-ray computed tomography", "transport processes", "bioturbation", "environmental fate", "FOS: Earth and related environmental sciences", "Nanoplastics"], "contacts": [{"organization": "Heinze, Wiebke Mareile, Mitrano, Denise M., Lahive, Elma, Koestel, John, Cornelis, Geert,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.x69p8czjv"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.x69p8czjv", "name": "item", "description": "10.5061/dryad.x69p8czjv", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.x69p8czjv"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-23T00:00:00Z"}}, {"id": "2343258291", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:30Z", "type": "Journal Article", "created": "2016-04-30", "title": "Mapping soil deformation around plant roots using in vivo 4D X-ray Computed Tomography and Digital Volume Correlation", "description": "The mechanical impedance of soils inhibits the growth of plant roots, often being the most significant physical limitation to root system development. Non-invasive imaging techniques have recently been used to investigate the development of root system architecture over time, but the relationship with soil deformation is usually neglected. Correlative mapping approaches parameterised using 2D and 3D image data have recently gained prominence for quantifying physical deformation in composite materials including fibre-reinforced polymers and trabecular bone. Digital Image Correlation (DIC) and Digital Volume Correlation (DVC) are computational techniques which use the inherent material texture of surfaces and volumes, captured using imaging techniques, to map full-field deformation components in samples during physical loading. Here we develop an experimental assay and methodology for four-dimensional, in vivo X-ray Computed Tomography (XCT) and apply a Digital Volume Correlation (DVC) approach to the data to quantify deformation. The method is validated for a field-derived soil under conditions of uniaxial compression, and a calibration study is used to quantify thresholds of displacement and strain measurement. The validated and calibrated approach is then demonstrated for an in vivo test case in which an extending maize root in field-derived soil was imaged hourly using XCT over a growth period of 19h. This allowed full-field soil deformation data and 3D root tip dynamics to be quantified in parallel for the first time. This fusion of methods paves the way for comparative studies of contrasting soils and plant genotypes, improving our understanding of the fundamental mechanical processes which influence root system development.", "keywords": ["0301 basic medicine", "Soil", "03 medical and health sciences", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "Four-Dimensional Computed Tomography", "15. Life on land", "Plant Roots", "Zea mays", "620", "Mechanical Phenomena"]}, "links": [{"href": "https://eprints.soton.ac.uk/394374/1/__filestore.soton.ac.uk_users_fh1d15_mydesktop_Keyes_et_al_Journal_of_Biomechaincs_Root_DVC_2016.pdf"}, {"href": "https://doi.org/2343258291"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Biomechanics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2343258291", "name": "item", "description": "2343258291", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2343258291"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "10.5281/zenodo.10454335", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:21:55Z", "type": "Journal Article", "created": "2023-01-31", "title": "Long-term contrasting tillage in Cambisol: effect on water-stable aggregates, macropore network and soil chemical properties", "description": "The aggregate stability of the soil is subject to theinfluence of anthropogenic factors and is of great interest all overthe world. The research aimed to quantify the correlations betweensoil organic carbon, total nitrogen, total phosphorus, and totalpotassium, soil macropore parameters and water-stable aggregatesunder no-tillage and conventional tillage in Cambisol. The contentof water-stable aggregates and macroporosity tended to increasein the following order: conventional tillage (returned residues)< conventional tillage (removed residues) < no-tillage (removedresidues) < no-tillage (returned residues) in both fertilizations.The relationships between total nitrogen and various soil factorswere investigated: soil organic carbon (r = 0.65, p < 0.05), totalphosphorus (r = 0.65, p < 0.05), were statistically significant. Soilorganic carbon and total nitrogen were positively correlated withwater-stable aggregates (r = 0.81, p < 0.01 and r = 0.68, p < 0.05,respectively), whereas the relationship between total potassiumand water-stable aggregates was negative. The relationshipbetween total phosphorus and water-stable aggregates (r = 0.62,p < 0.05) was positive. The soil chemical properties, macroporesand water-stable aggregates that were averaged across theresidues and fertilizations were higher in no-tillage than in conventionaltillage. Soil organic carbon, total nitrogen and totalphosphorus all had a positive direct influence on the formation ofwater-stable aggregates under different tillage conditions. Sinceour results are largely based on correlations, the mechanismsof interaction between the soil chemical properties, water-stableaggregates and the formation of pores in the soil need to beexplored further in future investigations.", "keywords": ["soil organic carbon", "2. Zero hunger", "Cambisoil", "13. Climate action", "conventional tillage", "no-tillage", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "X-ray computed tomography", ""]}, "links": [{"href": "https://doi.org/10.5281/zenodo.10454335"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Agrophysics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.10454335", "name": "item", "description": "10.5281/zenodo.10454335", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.10454335"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-31T00:00:00Z"}}, {"id": "10261/259704", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:30Z", "type": "Journal Article", "created": "2022-01-18", "title": "Lessons from a landmark 1991 article on soil structure: distinct precedence of non-destructive assessment and benefits of fresh perspectives in soil research", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>In 1991, at the launch of a national symposium devoted to soil structure, the Australian Society of Soil Science invited Professor John Letey to deliver a keynote address, which was later published in the society\u2019s journal. In his lecture, he shared the outcome of his reflexion about what the assessment of soil structure should amount to, in order to produce useful insight into the functioning of soils. His viewpoint was that the focus should be put on the openings present in the structure, rather than on the chunks of material resulting from its mechanical dismantlement. In the present article, we provide some historical background for Letey\u2019s analysis, and try to explain why it took a number of years for the paradigm shift that he advocated to begin to occur. Over the last decade, his perspective that soil structure needs to be characterised via non-destructive methods appears to have gained significant momentum, which is likely to increase further in the near future, as we take advantage of recent technological advances. Other valuable lessons that one can derive from Letey\u2019s pioneering article relate to the extreme value for everyone, even neophytes, to constantly ask questions about where research on given topics is heading, what its goals are, and whether the methods that are used at a certain time are optimal.</p></article>", "keywords": ["570", "soil image analysis", "soil microorganisms", "[SDE.MCG]Environmental Sciences/Global Changes", "Soil measuring", "earthworms", "micromorphology", "Aggregate stability", "Soil functions", "01 natural sciences", "630", "Soil fauna", "soil organic matter", "Earthworms", "Micromorphology", "Computed tomography", "aggregate stability", "0105 earth and related environmental sciences", "soil measuring", "2. Zero hunger", "Soil organic matter", "computed tomography", "04 agricultural and veterinary sciences", "soil functions", "15. Life on land", "[SDE.MCG] Environmental Sciences/Global Changes", "Soil image analysis", "0401 agriculture", " forestry", " and fisheries", "soil fauna", "earthworms; micromorphology", "Soil microorganisms"]}, "links": [{"href": "https://doi.org/10261/259704"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10261/259704", "name": "item", "description": "10261/259704", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10261/259704"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-19T00:00:00Z"}}, {"id": "10261/355209", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-25T16:24:33Z", "type": "Journal Article", "created": "2023-11-27", "title": "A high\u2010throughput analysis of high\u2010resolution X\u2010ray CT images of stems of olive and citrus plants resistant and susceptible to Xylella fastidiosa", "description": "Abstract                   <p>                     The bacterial plant pathogen                     Xylella fastidiosa                     causes disease in several globally important crops. However, some cultivars harbour reduced bacterial loads and express few symptoms. Evidence considering plant species in isolation suggests xylem structure influences cultivar susceptibility to                     X                     .                     fastidiosa                     . We test this theory more broadly by analysing high\uffe2\uff80\uff90resolution synchrotron X\uffe2\uff80\uff90ray computed tomography of healthy and infected plant vasculature from two taxonomic groups containing susceptible and resistant varieties: two citrus cultivars (sweet orange cv. Pera, tangor cv. Murcott) and two olive cultivars (Koroneiki, Leccino). Results found the susceptible plants had more vessels than resistant ones, which could promote within\uffe2\uff80\uff90host pathogen spread. However, features associated with resistance were not shared by citrus and olive. While xylem vessels in resistant citrus stems had comparable diameters to those in susceptible plants, resistant olives had narrower vessels that could limit biofilm spread. And while differences among olive cultivars were not detected, results suggest greater vascular connectivity in resistant compared to susceptible citrus plants. We hypothesize that this provides alternate flow paths for sustaining hydraulic functionality under infection. In summary, this work elucidates different physiological resistance mechanisms between two taxonomic groups, while supporting the existence of an intertaxonomical metric that could speed up the identification of candidate\uffe2\uff80\uff90resistant plants.                   </p", "keywords": ["2. Zero hunger", "resistance", "X-ray computed tomography", "Xylella fastidiosa", "Olive quick decline syndrome", "citrus variegated chlorosis", "olive quick decline syndrome", "Resistance", "Citrus variegated chlorosis", "15. Life on land", "xylem", "630"]}, "links": [{"href": "https://doi.org/10261/355209"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Pathology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10261/355209", "name": "item", "description": "10261/355209", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10261/355209"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-11-27T00:00:00Z"}}, {"id": "1886144451", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-25T16:25:04Z", "type": "Journal Article", "created": "2015-09-14", "title": "Visualization and Characterization of Heterogeneous Water Flow in Double-Porosity Media by Means of X-ray Computed Tomography", "description": "Three-dimensional visualization of dynamic water transport process in soil by 1 computed tomography (CT) technique is still limited by its low temporal resolution. In order 2 to monitor dynamically water transport in soil, a compromise has to be found between water 3 flow velocity and CT acquisition time. Furthermore, an efficient image analysis method is 1 4 necessary. In this work, we followed the water transport in three dimensions by CT imaging 5 across a double-porosity media constituted of two distinct materials, i.e. sand and porous 6 clay spheres. The CT acquisition parameters were adjusted to the water pore velocity so that 7 we succeeded to register the water front displacement per time range of 25 min. We also used 8 the image subtraction method to extract water distribution evolution with time with a space 9 resolution of 6 \u00d7 10 \u22123 cm. Both time and space resolution are relatively high compared with 10 other dynamic studies. The water content profiles showed that the clay spheres remained 11 in their dry state during water infiltration, while the water transport only occurred in the 12 sand matrix. These results are consistent with macroscopic experiments. The water front 13 visualized by CT showed a non-symmetrical shape which was related to water transfer in 14 non-equilibrium as shown by column displacement experiments.", "keywords": ["2. Zero hunger", "550", "[SDE.IE]Environmental Sciences/Environmental Engineering", "0208 environmental biotechnology", "Porous media", "0207 environmental engineering", "02 engineering and technology", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "6. Clean water", "620", "Image analysis", "3D visualization", "[SDU.STU.HY] Sciences of the Universe [physics]/Earth Sciences/Hydrology", "[SDE.IE] Environmental Sciences/Environmental Engineering", "[SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "Computed tomography", "Water transport"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11242-015-0572-z"}, {"href": "https://doi.org/1886144451"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Transport%20in%20Porous%20Media", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1886144451", "name": "item", "description": "1886144451", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1886144451"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-09-14T00:00:00Z"}}, {"id": "27155747", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-25T16:25:35Z", "type": "Journal Article", "created": "2016-04-30", "title": "Mapping soil deformation around plant roots using in vivo 4D X-ray Computed Tomography and Digital Volume Correlation", "description": "The mechanical impedance of soils inhibits the growth of plant roots, often being the most significant physical limitation to root system development. Non-invasive imaging techniques have recently been used to investigate the development of root system architecture over time, but the relationship with soil deformation is usually neglected. Correlative mapping approaches parameterised using 2D and 3D image data have recently gained prominence for quantifying physical deformation in composite materials including fibre-reinforced polymers and trabecular bone. Digital Image Correlation (DIC) and Digital Volume Correlation (DVC) are computational techniques which use the inherent material texture of surfaces and volumes, captured using imaging techniques, to map full-field deformation components in samples during physical loading. Here we develop an experimental assay and methodology for four-dimensional, in vivo X-ray Computed Tomography (XCT) and apply a Digital Volume Correlation (DVC) approach to the data to quantify deformation. The method is validated for a field-derived soil under conditions of uniaxial compression, and a calibration study is used to quantify thresholds of displacement and strain measurement. The validated and calibrated approach is then demonstrated for an in vivo test case in which an extending maize root in field-derived soil was imaged hourly using XCT over a growth period of 19h. This allowed full-field soil deformation data and 3D root tip dynamics to be quantified in parallel for the first time. This fusion of methods paves the way for comparative studies of contrasting soils and plant genotypes, improving our understanding of the fundamental mechanical processes which influence root system development.", "keywords": ["0301 basic medicine", "Soil", "03 medical and health sciences", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "Four-Dimensional Computed Tomography", "15. Life on land", "Plant Roots", "Zea mays", "620", "Mechanical Phenomena"]}, "links": [{"href": "https://eprints.soton.ac.uk/394374/1/__filestore.soton.ac.uk_users_fh1d15_mydesktop_Keyes_et_al_Journal_of_Biomechaincs_Root_DVC_2016.pdf"}, {"href": "https://doi.org/27155747"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Biomechanics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "27155747", "name": "item", "description": "27155747", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/27155747"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "2966605969", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:44Z", "type": "Journal Article", "created": "2019-08-05", "title": "Soil carbon dioxide venting through rice roots", "description": "Abstract<p>The growth of rice in submerged soils depends on its ability to form continuous gas channels\uffe2\uff80\uff94aerenchyma\uffe2\uff80\uff94through which oxygen (O2) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO2) in the opposite direction. Large, potentially toxic concentrations of dissolved CO2 develop in submerged rice soils. We show using X\uffe2\uff80\uff90ray computed tomography and image\uffe2\uff80\uff90based mathematical modelling that CO2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO2 and associated bicarbonate (HCO3\uffe2\uff88\uff92) in root cells would have been well above levels known to be toxic to roots. Removal of CO2 and hence carbonic acid (H2CO3) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions.</p", "keywords": ["580", "0106 biological sciences", "0301 basic medicine", "570", "Oryza", "Original Articles", "Carbon Dioxide", "15. Life on land", "Models", " Biological", "Plant Roots", "01 natural sciences", "6. Clean water", "biological transport", "X\u2010ray computed tomography", "Soil", "03 medical and health sciences", "13. Climate action", "biological models"]}, "links": [{"href": "https://eprints.soton.ac.uk/433011/1/_system_appendPDF_proof_hi_4.pdf"}, {"href": "https://eprints.soton.ac.uk/433011/2/Kirk_et_al_2019_Plant_Cell_Environment.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.13638"}, {"href": "https://doi.org/2966605969"}, {"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": "2966605969", "name": "item", "description": "2966605969", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2966605969"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-19T00:00:00Z"}}, {"id": "PMC6972674", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-25T16:28:04Z", "type": "Journal Article", "created": "2019-08-05", "title": "Soil carbon dioxide venting through rice roots", "description": "Abstract<p>The growth of rice in submerged soils depends on its ability to form continuous gas channels\uffe2\uff80\uff94aerenchyma\uffe2\uff80\uff94through which oxygen (O2) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO2) in the opposite direction. Large, potentially toxic concentrations of dissolved CO2 develop in submerged rice soils. We show using X\uffe2\uff80\uff90ray computed tomography and image\uffe2\uff80\uff90based mathematical modelling that CO2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO2 and associated bicarbonate (HCO3\uffe2\uff88\uff92) in root cells would have been well above levels known to be toxic to roots. Removal of CO2 and hence carbonic acid (H2CO3) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions.</p", "keywords": ["580", "0106 biological sciences", "0301 basic medicine", "570", "Oryza", "Original Articles", "Carbon Dioxide", "15. Life on land", "Models", " Biological", "Plant Roots", "01 natural sciences", "6. Clean water", "biological transport", "X\u2010ray computed tomography", "Soil", "03 medical and health sciences", "13. Climate action", "biological models"]}, "links": [{"href": "https://eprints.soton.ac.uk/433011/1/_system_appendPDF_proof_hi_4.pdf"}, {"href": "https://eprints.soton.ac.uk/433011/2/Kirk_et_al_2019_Plant_Cell_Environment.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.13638"}, {"href": "https://doi.org/PMC6972674"}, {"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": "PMC6972674", "name": "item", "description": "PMC6972674", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC6972674"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-19T00:00:00Z"}}, {"id": "PMC9307049", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:07Z", "type": "Journal Article", "created": "2022-01-19", "title": "Multimodal correlative imaging and modelling of phosphorus uptake from soil by hyphae of mycorrhizal fungi", "description": "Summary<p>   <p>Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore\uffe2\uff80\uff90space, and models of AMF\uffe2\uff80\uff90enhanced P\uffe2\uff80\uff90uptake are poorly validated.</p>  <p>We used synchrotron X\uffe2\uff80\uff90ray computed tomography to visualize mycorrhizas in soil and synchrotron X\uffe2\uff80\uff90ray fluorescence/X\uffe2\uff80\uff90ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling.</p>  <p>We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co\uffe2\uff80\uff90locate with areas of high P and low Al, and preferentially associate with organic\uffe2\uff80\uff90type P species over Al\uffe2\uff80\uff90rich inorganic P.</p>  <p>We discovered that AMF avoid Al\uffe2\uff80\uff90rich areas as a source of P. Sulphur\uffe2\uff80\uff90rich regions were found to be correlated with higher hyphal density and an increased organic\uffe2\uff80\uff90associated P\uffe2\uff80\uff90pool, whilst oxidized S\uffe2\uff80\uff90species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome\uffe2\uff80\uff90related. Our experimentally\uffe2\uff80\uff90validated model led to an estimate of P\uffe2\uff80\uff90uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated \uffe2\uff80\uff93 a result with significant implications for the modelling of plant\uffe2\uff80\uff93soil\uffe2\uff80\uff93AMF interactions.</p>  </p", "keywords": ["580", "X-ray computed tomography", "570", "Research", "X-ray fluorescence", "Fungi", "Hyphae", "500", "Phosphorus", "mycorrhizas", "04 agricultural and veterinary sciences", "15. Life on land", "plant phosphorus uptake", "Plant Roots", "Soil", "rhizosphere modelling", "Mycorrhizae", "synchrotron", "0401 agriculture", " forestry", " and fisheries", "Soil Microbiology"]}, "links": [{"href": "https://eprints.soton.ac.uk/454110/1/Keyes_et_al_Myco_Paper_TR_04_01_2022_unmarked.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/2/Figures_TR_22_12_2021.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/3/SI_1_TR_22_12_2021_no_markup.pdf"}, {"href": "https://eprints.soton.ac.uk/454110/4/SI_2_TR_22_12_2021.pdf"}, {"href": "https://doi.org/PMC9307049"}, {"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": "PMC9307049", "name": "item", "description": "PMC9307049", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC9307049"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-15T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=computed+tomography&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=computed+tomography&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=computed+tomography&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=computed+tomography&offset=24", "hreflang": "en-US"}], "numberMatched": 24, "numberReturned": 24, "distributedFeatures": [], "timeStamp": "2026-05-25T19:13:40.416479Z"}