{"type": "FeatureCollection", "features": [{"id": "10.1007/s11104-016-2872-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:13Z", "type": "Journal Article", "created": "2016-04-08", "title": "Challenges in imaging and predictive modeling of rhizosphere processes", "description": "Background: Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope: In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions: We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes.", "keywords": ["2. Zero hunger", "X-ray CT", "Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften", " Biologie", "Soil Science", "Plant Science", "Chemical mapping", "04 agricultural and veterinary sciences", "15. Life on land", "Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik)", "13. Climate action", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Mathematical modeling", "Correlative imaging"]}, "links": [{"href": "https://eprints.soton.ac.uk/390303/1/Roose%2520et%2520al%25202016%2520Plant%2520Soil%2520Marschner%2520Review%2520Accepted.pdf"}, {"href": "https://doi.org/10.1007/s11104-016-2872-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-016-2872-7", "name": "item", "description": "10.1007/s11104-016-2872-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-016-2872-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-08T00:00:00Z"}}, {"id": "10.1016/j.geoderma.2025.117290", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:43Z", "type": "Journal Article", "created": "2025-04-11", "title": "Soil structural indicators as predictors of biological activity under various soil management practices", "description": "Soil structure is a key feature in controlling the turnover of organic matter in soils. The spatial arrangement of solids and pores in agricultural topsoil can be actively influenced by management practices, such as tillage and cropping systems, which in turn can affect the resident microbial communities and their activities. However, carbon mineralisation and microbial activity are usually measured in sieved samples, which provides information on gross potentials under optimal conditions. Under these conditions, the spatial heterogeneities that are specific to different management practices are reduced or totally removed. In this study, we combined X-ray computer tomography (X-ray CT) and isothermal calorimetry to investigate the effect of soil structure on heat dissipation, as an indicator of biological activity. Samples were collected from the topsoil of a long-term field experiment (12\u00a0years) that included four different land uses: conventional vs. reduced tillage, each with either maize or winter wheat as the main crop in the rotation. We compared the response of undisturbed soil cores (3\u00a0cm in height, 2.7\u00a0cm in diameter) to the addition of water and glucose in specific pore sizes, ranging in radii of 15 to 75\u00a0\u00b5m or 3 to 75\u00a0\u00b5m. The pore structure and indicators of particulate organic material were quantified using X-ray CT with a voxel resolution of 15\u00a0\u00b5m. This allowed us to distinguish between the effects of crop rotation and tillage regime on biological activity, soil structure and the feedback between the two. Heat dissipation correlated significantly with X-ray CT derived porosity, pore surface density and soil matrix grey value, all of which were affected by both tillage regime and crop rotation. Heat dissipation in maize plots after glucose addition to the pore size range with radii of 3 to 75\u00a0\u00b5m was greater than in the winter wheat systems, but not when added to the pore size range with radii of 15 to 75\u00a0\u00b5m. The study showed that structural indicators can explain up to 81\u00a0% and 95\u00a0% of the variance in total heat dissipation after glucose and water addition, respectively, but only 60\u00a0% of the heat dynamics, here defined as the time taken for 50\u00a0% of total heat to be dissipated. The results emphasise the importance of soil structure in regulating microbial decomposition of soil organic matter and warrants further investigations.", "keywords": ["X-ray CT", "Crop rotation", "Biological activity", "Science", "Soil structure", "Q", "[SDU.STU] Sciences of the Universe [physics]/Earth Sciences", "Soil Science", "Tillage regime", "Micro-habitat", "Calorimetry"]}, "links": [{"href": "https://pub.epsilon.slu.se/37077/1/leuther-f-et-al-20250508.pdf"}, {"href": "https://doi.org/10.1016/j.geoderma.2025.117290"}, {"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.2025.117290", "name": "item", "description": "10.1016/j.geoderma.2025.117290", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.geoderma.2025.117290"}, {"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.still.2012.02.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:35Z", "type": "Journal Article", "created": "2012-04-04", "title": "Long-Term Rotation And Tillage Effects On Soil Structure And Crop Yield", "description": "Tillage and rotation are fundamental factors influencing soil quality and thus the sustainability of cropping systems. Many studies have focused on the effects of either tillage or rotation, but few have quantified the long term integrated effects of both. We studied the issue using a 30-year old long-term rotation and tillage treatment experiment on a Canadian silt loam soil. Topsoil measurements were carried out for three different rotations: R1, (C\u2013C\u2013C\u2013C) continuous corn (Zea mays L.), R6, (C\u2013C\u2013O(RC), B(RC)) corn, corn, oats (Avena fatua L.) and spring barley (Hordeum vulgare L.) and R8, (C\u2013C\u2013S\u2013S) corn, corn, soybean (Glycine max L.), soybean. A red clover (Trifolium pretense L.) cover crop was under seeded in oats and spring barley in R6. In 2010, first year corn was grown in R6 and R8. The tillage treatments included no tillage, NT and mouldboard ploughing, MP. Topsoil structural quality was visually evaluated in early June and mid October. Minimal disturbed soil cores collected in early June were used for X-ray CT scanning and to quantify water content and porosity. Soil friability was determined on the soil samples using a drop shatter test. Crop yield was determined and correlated to the soil quality estimates. We found significant effect of both rotation and tillage on visual soil structure at both times of assessment. Poor soil structure was found for NT except when combined with a diverse crop rotation (R6). The soil core pore characteristics data also displayed a significant effect of tillage but only a weak insignificant effect of rotation. The drop shatter results were in accordance with the visual assessment data. Crop yield correlated significantly with the visual soil structure scores. We conclude that a diverse crop rotation was needed for an optimal performance of NT for the studied soil.", "keywords": ["2. Zero hunger", "X-ray CT", "tillage", "0401 agriculture", " forestry", " and fisheries", "soil quality", "04 agricultural and veterinary sciences", "15. Life on land", "yield", "rotation", "visual soil structure evaluation"]}, "links": [{"href": "https://doi.org/10.1016/j.still.2012.02.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20and%20Tillage%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.still.2012.02.007", "name": "item", "description": "10.1016/j.still.2012.02.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.still.2012.02.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-03-01T00:00:00Z"}}, {"id": "10.15488/17031", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:20:31Z", "type": "Journal Article", "created": "2016-04-08", "title": "Challenges in imaging and predictive modeling of rhizosphere processes", "description": "Background: Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope: In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions: We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes.", "keywords": ["2. Zero hunger", "X-ray CT", "Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften", " Biologie", "Soil Science", "Plant Science", "Chemical mapping", "04 agricultural and veterinary sciences", "15. Life on land", "Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik)", "13. Climate action", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Mathematical modeling", "Correlative imaging"]}, "links": [{"href": "https://eprints.soton.ac.uk/390303/1/Roose%2520et%2520al%25202016%2520Plant%2520Soil%2520Marschner%2520Review%2520Accepted.pdf"}, {"href": "https://doi.org/10.15488/17031"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.15488/17031", "name": "item", "description": "10.15488/17031", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.15488/17031"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-08T00:00:00Z"}}, {"id": "10.3389/fenvs.2018.00032", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:21:39Z", "type": "Journal Article", "created": "2018-05-25", "title": "Correlative Visualization of Root Mucilage Degradation Using X-ray CT and MRI", "description": "Root exudates are a crucial component of the rhizosphere. Often, they take a form of a gel exuded by the plant roots and are thought to influence the soil aggregation, root penetration into soil, soil nutrient availability, immobilization of toxic cations, and microbial activity amongst other things. In addition, the capacity of exudates to store water makes the plants potentially less susceptive to drought. Major components of root exudates are high molecular weight organic compounds consisting of predominantly polysaccharides and proteins, which makes it challenging to visualize using current rhizosphere visualization techniques, such as X-ray computed tomography (CT). In this contribution, we use correlative X-ray CT (resolution ~20 \u03bcm) in combination with Magnetic Resonance Imaging (MRI, resolution ~120 \u03bcm) to set up groundwork to enable in situ visualization of mucilage in soil. This multimodal approach is necessary because mucilage density closely matches that of water. We use chia seeds as mucilage analog, because it has been found to have a similar consistency to root mucilage. Moreover, to understand mucilage development in time, a series of samples made by chia seeds placed in different porous media were prepared. Structurally and chemically, mucilage breaks down toward a water-like substance over a course of 2 weeks. Depending on its relative concentration, these changes were found to be less dominant when seeds were mixed in porous media. Having set up the groundwork for correlative imaging of chia seeds in water and an artificial soil (Nafion and sand/beads) this enables us to expand this imaging to deal with plant root exudates under natural conditions.", "keywords": ["2. Zero hunger", "570", "X-ray CT", "chia", "polysaccharides", "04 agricultural and veterinary sciences", "15. Life on land", "630", "6. Clean water", "root-exudate", "Environmental sciences", "1H-MRI", "0401 agriculture", " forestry", " and fisheries", "GE1-350", "mucilage"]}, "links": [{"href": "https://eprints.soton.ac.uk/421014/1/NMRI_imaging_chia_review_final_2_TR_01_05_2018.pdf"}, {"href": "https://eprints.soton.ac.uk/421014/2/fenvs_06_00032.pdf"}, {"href": "https://doi.org/10.3389/fenvs.2018.00032"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Environmental%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fenvs.2018.00032", "name": "item", "description": "10.3389/fenvs.2018.00032", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fenvs.2018.00032"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-05-25T00:00:00Z"}}, {"id": "20.500.11820/03f81a44-477a-4a8c-b34d-85892c85bd6f", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:26:46Z", "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": "2319912902", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:27:07Z", "type": "Journal Article", "created": "2016-04-08", "title": "Challenges in imaging and predictive modeling of rhizosphere processes", "description": "Background: Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope: In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions: We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes.", "keywords": ["2. Zero hunger", "X-ray CT", "Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften", " Biologie", "Soil Science", "Plant Science", "Chemical mapping", "04 agricultural and veterinary sciences", "15. Life on land", "Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik)", "13. Climate action", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Mathematical modeling", "Correlative imaging"]}, "links": [{"href": "https://eprints.soton.ac.uk/390303/1/Roose%2520et%2520al%25202016%2520Plant%2520Soil%2520Marschner%2520Review%2520Accepted.pdf"}, {"href": "https://doi.org/2319912902"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2319912902", "name": "item", "description": "2319912902", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2319912902"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-08T00:00:00Z"}}, {"id": "2801205749", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:27:17Z", "type": "Journal Article", "created": "2018-05-25", "title": "Correlative Visualization of Root Mucilage Degradation Using X-ray CT and MRI", "description": "Root exudates are a crucial component of the rhizosphere. Often, they take a form of a gel exuded by the plant roots and are thought to influence the soil aggregation, root penetration into soil, soil nutrient availability, immobilization of toxic cations, and microbial activity amongst other things. In addition, the capacity of exudates to store water makes the plants potentially less susceptive to drought. Major components of root exudates are high molecular weight organic compounds consisting of predominantly polysaccharides and proteins, which makes it challenging to visualize using current rhizosphere visualization techniques, such as X-ray computed tomography (CT). In this contribution, we use correlative X-ray CT (resolution ~20 \u03bcm) in combination with Magnetic Resonance Imaging (MRI, resolution ~120 \u03bcm) to set up groundwork to enable in situ visualization of mucilage in soil. This multimodal approach is necessary because mucilage density closely matches that of water. We use chia seeds as mucilage analog, because it has been found to have a similar consistency to root mucilage. Moreover, to understand mucilage development in time, a series of samples made by chia seeds placed in different porous media were prepared. Structurally and chemically, mucilage breaks down toward a water-like substance over a course of 2 weeks. Depending on its relative concentration, these changes were found to be less dominant when seeds were mixed in porous media. Having set up the groundwork for correlative imaging of chia seeds in water and an artificial soil (Nafion and sand/beads) this enables us to expand this imaging to deal with plant root exudates under natural conditions.", "keywords": ["2. Zero hunger", "570", "X-ray CT", "chia", "polysaccharides", "04 agricultural and veterinary sciences", "15. Life on land", "630", "6. Clean water", "root-exudate", "Environmental sciences", "1H-MRI", "0401 agriculture", " forestry", " and fisheries", "GE1-350", "mucilage"]}, "links": [{"href": "https://eprints.soton.ac.uk/421014/1/NMRI_imaging_chia_review_final_2_TR_01_05_2018.pdf"}, {"href": "https://eprints.soton.ac.uk/421014/2/fenvs_06_00032.pdf"}, {"href": "https://doi.org/2801205749"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Environmental%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2801205749", "name": "item", "description": "2801205749", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2801205749"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-05-25T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=X-ray+CT&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=X-ray+CT&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=X-ray+CT&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=X-ray+CT&offset=8", "hreflang": "en-US"}], "numberMatched": 8, "numberReturned": 8, "distributedFeatures": [], "timeStamp": "2026-04-15T20:49:58.007438Z"}