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2019 - Modeling the Impact of Biopores on Root Growth and.pdf", "md5": "c8ca85d9de58b87d45e9d4f4ac65ed8a", "mtime": 1654767401094, "tags": [], "relations": {}, "dateAdded": "2022-06-09T09:36:41Z", "dateModified": "2022-06-09T09:36:41Z" } }, { "key": "CVK6KCRD", "version": 272, "library": { "type": "group", "id": 263264, "name": "R-SWMS", "links": { "alternate": { "href": "https://www.zotero.org/groups/r-swms", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/263264/items/CVK6KCRD", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/r-swms/items/CVK6KCRD", "type": "text/html" } }, "meta": { "createdByUser": { "id": 935445, "username": "mjavaux", "name": "Mathieu Javaux", "links": { "alternate": { "href": "https://www.zotero.org/mjavaux", "type": "text/html" } } }, "creatorSummary": "Landl et al.", "parsedDate": "2019", "numChildren": 2 }, "data": { "key": "CVK6KCRD", "version": 272, "itemType": "journalArticle", "title": "Modeling the Impact of Biopores on Root Growth and Root Water Uptake", "creators": [ { "creatorType": "author", "firstName": "Magdalena", "lastName": "Landl" }, { "creatorType": "author", "firstName": "Andrea", "lastName": "Schnepf" }, { "creatorType": "author", "firstName": "Daniel", "lastName": "Uteau" }, { "creatorType": "author", "firstName": "Stephan", "lastName": "Peth" }, { "creatorType": "author", "firstName": "Miriam", "lastName": "Athmann" }, { "creatorType": "author", "firstName": "Timo", "lastName": "Kautz" }, { "creatorType": "author", "firstName": "Ute", "lastName": "Perkons" }, { "creatorType": "author", "firstName": "Harry", "lastName": "Vereecken" }, { "creatorType": "author", "firstName": "Jan", "lastName": "Vanderborght" } ], "abstractNote": "Core Ideas A 3D soil–root model was used to investigate root–biopore interactions. Known effects of biopores on root growth, i.e., increased root length and depth were reproduced. Despite reducing root–soil contact, biopores led to increased water uptake in dry periods. Biopores had a larger impact on water uptake for more compact and less conductive soils. Roots are known to use biopores as preferential growth pathways to overcome hard soil layers and access subsoil water resources. This study evaluates root–biopore interactions at the root-system scale under different soil physical and environmental conditions using a mechanistic simulation model and extensive experimental field data. In a field experiment, spring wheat (Triticum aestivum L.) was grown on silt loam with a large biopore density. X-ray computed tomography scans of soil columns from the field site were used to provide a realistic biopore network as input for the three-dimensional numerical R-SWMS model, which was then applied to simulate root architecture as well as water flow in the root–biopore–soil continuum. The model was calibrated against observed root length densities in both the bulk soil and biopores by optimizing root growth model input parameters. By implementing known interactions between root growth and soil penetration resistance into our model, we could simulate root systems whose response to biopores in the soil corresponded well to experimental observations described in the literature, such as increased total root length and increased rooting depth. For all considered soil physical (soil texture and bulk density) and environmental conditions (years of varying dryness), we found biopores to substantially mitigate transpiration deficits in times of drought by allowing roots to take up water from wetter and deeper soil layers. This was even the case when assuming reduced root water uptake in biopores due to limited root–soil contact. The beneficial impact of biopores on root water uptake was larger for more compact and less conductive soils.", "publicationTitle": "Vadose Zone Journal", "publisher": "", "place": "", "date": "2019", "volume": "18", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "180196", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.2136/vzj2018.11.0196", "citationKey": "", "url": "https://onlinelibrary.wiley.com/doi/abs/10.2136/vzj2018.11.0196", "accessDate": "2022-06-09T09:36:39Z", "PMID": "", "PMCID": "", "ISSN": "1539-1663", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "Wiley Online Library", "callNumber": "", "rights": "", "extra": "_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2136/vzj2018.11.0196", "tags": [], "collections": [ "3J999N7V" ], "relations": {}, "dateAdded": "2022-06-09T09:36:39Z", "dateModified": "2022-06-09T09:36:39Z" } }, { "key": "C8TYS9ZH", "version": 270, "library": { "type": "group", "id": 263264, "name": "R-SWMS", "links": { "alternate": { "href": "https://www.zotero.org/groups/r-swms", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/263264/items/C8TYS9ZH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/r-swms/items/C8TYS9ZH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 935445, "username": "mjavaux", "name": "Mathieu Javaux", "links": { "alternate": { "href": "https://www.zotero.org/mjavaux", "type": "text/html" } } }, "creatorSummary": "Guerra", "parsedDate": "2022-05", "numChildren": 1 }, "data": { "key": "C8TYS9ZH", "version": 270, "itemType": "thesis", "title": "Upscaling salt accumulation and passive solute uptake from single root to root system scale", "creators": [ { "creatorType": "author", "firstName": "Helena JORDÀ", "lastName": "Guerra" } ], "abstractNote": "Producing enough food for an increasing world population is one of the major challenges of the 21st century. Improving management practices that optimize the usage of water, nutrients and other agricultural resources is vital to increase crop production and productivity while maintaining a healthy environment. The usage of computational models has been integrated in the decision making of agricultural management practices such as in irrigation scheduling or pesticide application. However, most models that are applied at the plant or field scale lack an appropriate representation of processes that occur at the scale of single roots. This thesis aimed at investigating differences between conditions at the soil-root interface and the bulk soil, and the impact on the transport of two substances: sodium and pesticides. On the one hand, Na+ is a major contributor to soil salinity, which is a significant abiotic stress limiting crop production, especially in arid and semiarid areas. On the other hand, the study of pesticide transport and uptake by plants is crucial to managing their usage and prevent leaching to groundwater bodies. For these purposes, we used the coupled 3D R-SWMS-ParTrace models, which link flow and transport in the soil profile and root zone with flow and transport processes towards single root segments and with flow and transport in the entire root system. First, Na+accumulation around single roots and its impact on root water uptake was modeled. We assumed a full exclusion scenario where the root prevents the transport of Na+ into the xylem and Na+ transported towards the root accumulate at the root surface. This accumulation leads to an increase in the osmotic potential at the soil-root interface, which, in turn, affects the water potential gradient between the root and the soil that may result in reduced transpiration. Simulation results from single root scenarios showed increasing the root water uptake per unit root length led to larger Na+ accumulation and earlier onset of osmotic stress. Macroscopic parameters obtained by fitting a macroscopic stress function to the simulated data were found to be dependent on the water uptake per unit root length, indicating that macroscopic parameters are not constant throughout a growing season as it is usually assumed. Finally, differences in bulk and soil-root interface osmotic potentials depended not only on transpiration rate, but also on the transpiration rate per unit of root length. Thus, models that translate bulk concentrations to concentrations at the soil-root interface need to incorporate root length density information. In a next step, salt accumulation around roots as a function of salinity and transpiration demand was studied in an experimental setup. Tomato plants were grown in 2D rhizoslides for two weeks. At the end of the experimental period, Na+ concentration was measured at three distances from the root surface. The R-SWMS-ParTrace models were parameterized according to the experimental setup and used further to investigate Na+ concentration gradients. Both experimental and simulated results showed larger Na+ concentration at the root surface than in the bulk soil. Under high transpiration, the model simulated larger Na+ concentrations at the root surface than the measurements. This could indicate that roots took up Na+ and thus questioned the model’s assumption of full exclusion. Moreover, the model predicted redistribution fluxes of low salinity water to areas with high salinity, resulting in a reduction in Na+ concentration around roots. This indicates that upscaled models need to account for heterogeneous distribution of Na+ and its impact on compensation processes. Finally, the transport and passive uptake of pesticides by roots was investigated.The R-SWMS-ParTrace models were further developed to account for diffusive transport of organic neutral compounds across root membranes driven by concentration gradients between the soil and the root, and a diffusive permeability dependent on root and solute properties. The model was parameterized according to a FOCUS scenario used in the registration of pesticides in the EU for a pesticide application at the soil surface and compared to results from the 1D reference PEARL model. Simulation results with a single root and advective uptake, whose hydraulic properties were adjusted to match root water uptake distributions estimated by PEARL, led to similar pesticide uptake as PEARL, which validated our model implementation. Simulations with diffusive uptake predicted 3 times larger uptake of pesticide than the advective scenario as a result of diluting effects caused by vertical concentration gradients of pesticide in the soil. Finally, when simulating uptake with a 3D maize root system architecture, differences in root water uptake distribution, resulting from the root system architecture and root hydraulic properties, led to 1.25 times larger pesticide uptake as compared to the single root scenario. This study illustrated the impact of accounting for heterogeneous solute distribution as well as mechanistic descriptions of solute uptake on the fate of pesticides in soils", "thesisType": "", "university": "KULeuven", "place": "Leuven, Belgium", "date": "May, 2022", "series": "", "seriesNumber": "", "numPages": "160", "DOI": "", "ISBN": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "Zotero", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "QECDGXGT" ], "relations": {}, "dateAdded": "2022-06-09T09:27:08Z", "dateModified": "2022-06-09T09:30:41Z" } }, { "key": "WCVXU8X3", "version": 267, "library": { "type": "group", "id": 263264, "name": "R-SWMS", "links": { "alternate": { "href": "https://www.zotero.org/groups/r-swms", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/263264/items/WCVXU8X3", "type": 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"libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3J999N7V" ], "relations": {}, "dateAdded": "2022-06-09T09:23:31Z", "dateModified": "2022-06-09T09:23:31Z" } }, { "key": "SBX94GEY", "version": 241, "library": { "type": "group", "id": 263264, "name": "R-SWMS", "links": { "alternate": { "href": "https://www.zotero.org/groups/r-swms", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/263264/items/SBX94GEY", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/r-swms/items/SBX94GEY", "type": "text/html" } }, "meta": { "createdByUser": { "id": 935445, "username": "mjavaux", "name": "Mathieu Javaux", "links": { "alternate": { "href": "https://www.zotero.org/mjavaux", "type": "text/html" } } }, "creatorSummary": "Meunier et al.", "parsedDate": "2022", "numChildren": 0 }, "data": { "key": "SBX94GEY", "version": 241, "itemType": "bookSection", "title": "Investigating Soil–Root Interactions with the Numerical Model R-SWMS", "creators": [ { "creatorType": "author", "firstName": "Félicien", "lastName": "Meunier" }, { "creatorType": "author", "firstName": "Valentin", "lastName": "Couvreur" }, { "creatorType": "author", "firstName": "Xavier", "lastName": "Draye" }, { "creatorType": "author", "firstName": "Guillaume", "lastName": "Lobet" }, { "creatorType": "author", "firstName": "Katrin", "lastName": "Huber" }, { "creatorType": "author", "firstName": "Nathalie", "lastName": "Schroeder" }, { "creatorType": "author", "firstName": "Helena", "lastName": "Jorda" }, { "creatorType": "author", "firstName": "Axelle", "lastName": "Koch" }, { "creatorType": "author", "firstName": "Magdalena", "lastName": "Landl" }, { "creatorType": "author", "firstName": "Andrea", "lastName": "Schnepf" } ], "abstractNote": "", "bookTitle": "Plant Systems Biology", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2022", "publisher": "Springer", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "259–283", "ISBN": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3J999N7V" ], "relations": {}, "dateAdded": "2022-06-09T09:22:49Z", "dateModified": "2022-06-09T09:22:49Z" } }, { "key": "WFXF7ZH8", "version": 254, "library": { "type": "group", "id": 263264, "name": "R-SWMS", "links": { "alternate": { "href": "https://www.zotero.org/groups/r-swms", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/263264/items/WFXF7ZH8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/r-swms/items/WFXF7ZH8", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/263264/items/7MKWCX4R", "type": "application/json" } }, "meta": { "createdByUser": { "id": 935445, "username": "mjavaux", "name": "Mathieu Javaux", "links": { "alternate": { "href": "https://www.zotero.org/mjavaux", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "WFXF7ZH8", "version": 254, "parentItem": "7MKWCX4R", "itemType": "attachment", "linkMode": "imported_file", "title": "Rao et al. - 2020 - Imaging plant responses to water deficit using ele.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Rao et al. - 2020 - Imaging plant responses to water deficit using ele.pdf", "md5": "1bb7046325477ffc83f5cb88626f5881", "mtime": 1599655730397, "tags": [], "relations": {}, "dateAdded": "2022-06-09T09:20:42Z", "dateModified": "2022-06-09T09:20:42Z" } }, { "key": "7MKWCX4R", "version": 240, "library": { "type": "group", "id": 263264, "name": "R-SWMS", "links": { "alternate": { "href": "https://www.zotero.org/groups/r-swms", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/263264/items/7MKWCX4R", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/r-swms/items/7MKWCX4R", "type": "text/html" } }, "meta": { "createdByUser": { "id": 935445, "username": "mjavaux", "name": "Mathieu Javaux", "links": { "alternate": { "href": "https://www.zotero.org/mjavaux", "type": "text/html" } } }, "creatorSummary": "Rao et al.", "parsedDate": "2020-08-01", "numChildren": 1 }, "data": { "key": "7MKWCX4R", "version": 240, "itemType": "journalArticle", "title": "Imaging plant responses to water deficit using electrical resistivity tomography", "creators": [ { "creatorType": "author", "firstName": "Sathyanarayan", "lastName": "Rao" }, { "creatorType": "author", "firstName": "Nolwenn", "lastName": "Lesparre" }, { "creatorType": "author", "firstName": "Adrián Flores", "lastName": "Orozco" }, { "creatorType": "author", "firstName": "Florian", "lastName": "Wagner" }, { "creatorType": "author", "firstName": "Mathieu", "lastName": "Javaux" } ], "abstractNote": "Background and aims Monitoring root water uptake dynamics under water deficit (WD) conditions in fields are crucial to assess plant drought tolerance. In this study, we investigate the ability of Electrical Resistivity Tomography (ERT) to capture specific soil water depletion induced by root water uptake.", "publicationTitle": "Plant and Soil", "publisher": "", "place": "", "date": "2020-8-1", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Plant Soil", "DOI": "10.1007/s11104-020-04653-7", "citationKey": "", "url": "http://link.springer.com/10.1007/s11104-020-04653-7", "accessDate": "2020-09-09T12:48:49Z", "PMID": "", "PMCID": "", "ISSN": "0032-079X, 1573-5036", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3J999N7V" ], "relations": {}, "dateAdded": "2022-06-09T09:20:42Z", "dateModified": "2022-06-09T09:20:42Z" } }, { "key": "PCD9LBL3", "version": 222, "library": { "type": "group", "id": 263264, "name": "R-SWMS", "links": { "alternate": { "href": "https://www.zotero.org/groups/r-swms", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/263264/items/PCD9LBL3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/r-swms/items/PCD9LBL3", "type": "text/html" } }, "meta": { "createdByUser": { "id": 935445, "username": "mjavaux", "name": "Mathieu Javaux", "links": { "alternate": { "href": "https://www.zotero.org/mjavaux", "type": "text/html" } } }, "creatorSummary": "Rao", "parsedDate": "2020", "numChildren": 0 }, "data": { "key": "PCD9LBL3", "version": 222, "itemType": "thesis", "title": "Investigating plant root signatures using geo-electrical methods", "creators": [ { "creatorType": "author", "firstName": "Sathyanarayan", "lastName": "Rao" } ], "abstractNote": "Thorough knowledge of root system architecture and functioning is essential for a better understanding of the impact of plants on climate change, for plant phenotyping or for designing more sustainable agro-ecosystems. Recently, electrical imaging of root zone soil has been gaining wide attention among agronomists and soil scientists (Zhao et al. 2019) because of its sensitivity to soil moisture. However, a quantitative understanding of electrical signatures of roots in electrical imaging is still somewhat missing in the scientific literature. For example, it is unclear how roots impact petrophysical relation and if electrical measurements contain geometrical information of root architectures. It is also unclear if the ERT method is sensitive enough to differentiate depletion zones of similar plant types but belonging to different species for phenotyping applications.\nThe general objective of this Ph.D. thesis is to quantify the direct and indirect impact of plant roots in soil electrical signature. Root affects the soil-plant system directly through its architecture but also indirectly via soil water depletion by uptake.\nThe first part of the thesis (Chapters 3 and 4) deals with understanding the direct impact of roots in small scale rhizotron and pot via process-based numerical models. We quantify the direct impact of roots while incorporating both direct (root explicit electrical properties) and indirect (root water uptake patterns) in the forward numerical model. To date this is the closest to reality, a numerical model can achieve in understanding electrical signatures of root systems in soils. We also prove that electrical response if measured in magnitude and phase components, magnitude part represents mainly indirect impact (root water uptake)\nxi\nwhile the phase part represents mainly direct impact (root architecture) and both magnitude and phase part contain root geometrical information.\nThe second part of the thesis deals with quantifying the indirect impact of water, i.e., soil water depletion in field-scale ERT experiments. We propose a new methodology where we use a numerical model to interpret field data. The model informed us if the changes we observe in the ERT experiment was due to plants or an artifact. This allowed us to quantify even the slightest changes in water depletion from different plants. Finally, we show that it is possible to phenotype similar plants belonging to", "thesisType": "", "university": "Universite catholique de Louvain (UCL)", "place": "", "date": "2020", "series": "", "seriesNumber": "", "numPages": "277", "DOI": "", "ISBN": "", "citationKey": "", "url": "https://dial.uclouvain.be/pr/boreal/object/boreal:239364", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "QECDGXGT" ], "relations": {}, "dateAdded": "2021-02-07T09:28:08Z", "dateModified": "2021-02-07T09:32:19Z" } }, { "key": "EKMTE73X", "version": 313, "library": { "type": "group", "id": 263264, "name": "R-SWMS", "links": { "alternate": { "href": "https://www.zotero.org/groups/r-swms", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/263264/items/EKMTE73X", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/r-swms/items/EKMTE73X", "type": "text/html" } }, "meta": { "createdByUser": { "id": 935445, "username": "mjavaux", "name": "Mathieu Javaux", "links": { "alternate": { "href": "https://www.zotero.org/mjavaux", "type": "text/html" } } }, "lastModifiedByUser": { "id": 1431186, "username": "dadelforge", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dadelforge", "type": "text/html" } } }, "creatorSummary": "Jin et al.", "parsedDate": "2020-09-28", "numChildren": 2 }, "data": { "key": "EKMTE73X", "version": 313, "itemType": "journalArticle", "title": "Modeling root system growth around obstacles", "creators": [ { "creatorType": "author", "firstName": "Wencheng", "lastName": "Jin" }, { "creatorType": "author", "firstName": "Jayde", "lastName": "Aufrecht" }, { "creatorType": "author", "firstName": "Fernando", "lastName": "Patino-Ramirez" }, { "creatorType": "author", "firstName": "Heidy", "lastName": "Cabral" }, { "creatorType": "author", "firstName": "Chloé", "lastName": "Arson" }, { "creatorType": "author", "firstName": "Scott T.", "lastName": "Retterer" } ], "abstractNote": "State-of-the-Art models of Root System Architecture (RSA) do not allow simulating root growth around rigid obstacles. Yet, the presence of obstacles can be highly disruptive to the root system. We grew wheat seedlings in sealed petri dishes without obstacle and in custom 3D-printed rhizoboxes containing obstacles. Time-lapse photography was used to reconstruct the wheat root morphology network. We used the reconstructed wheat root network without obstacle to calibrate an RSA model implemented in the R-SWMS software. The root network with obstacles allowed calibrating the parameters of a new function that models the influence of rigid obstacles on wheat root growth. Experimental results show that the presence of a rigid obstacle does not affect the growth rate of the wheat root axes, but that it does influence the root trajectory after the main axis has passed the obstacle. The growth recovery time, i.e. the time for the main root axis to recover its geotropism-driven growth, is proportional to the time during which the main axis grows along the obstacle. Qualitative and quantitative comparisons between experimental and numerical results show that the proposed model successfully simulates wheat RSA growth around obstacles. Our results suggest that wheat roots follow patterns that could inspire the design of adaptive engineering flow networks.", "publicationTitle": "Scientific Reports", "publisher": "Nature Publishing Group", "place": "", "date": "2020-09-28", "volume": "10", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "15868", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1038/s41598-020-72557-8", "citationKey": "", "url": "https://www.nature.com/articles/s41598-020-72557-8", "accessDate": "2020-11-24T21:02:27Z", "PMID": "", "PMCID": "", "ISSN": "2045-2322", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.nature.com", "callNumber": "", "rights": "2020 The Author(s)", "extra": "Number: 1", "tags": [], "collections": [ "3J999N7V" ], "relations": {}, "dateAdded": "2020-11-24T21:02:27Z", "dateModified": "2020-11-24T21:02:45Z" } } ]