Rhizodeposition, i.e. the release of organic matters by roots, constitutes a significant fraction of the plant carbon (C) budget and plays a key role in plant-soil interactions. However, its spatial and temporal dynamics remain poorly understood.
MethodsWe developed RhizoDep, a new functional-structural root model that simulates 3D root growth, respiration, and rhizodeposition based on C balance and root morphology at the individual root segment level.
ResultsOur model successfully reproduced the dynamics of belowground C flows observed in a previous pulse-labelling field experiment on spring wheat. Our simulations revealed that root C exudation largely dominated over mucilage secretion and cap cells sloughing in terms of C release. The spatial distribution of exudation rate along the roots was driven by the preferential unloading of sugars to support root elongation and emergence, and was modulated by the formation of apoplastic barriers. Furthermore, our results demonstrated that, for a given C allocation flow to roots, variations in root hairs or lateral root number had minimal effects on rhizodeposition, whereas changes in root tissue density had a significant impact.
ConclusionRhizoDep offers a new opportunity to explore the dynamics of C exchange at the plant-soil interface and to identify traits and environmental conditions that favor rhizodeposition.
", "keywords": ["cycle du carbone", "http://aims.fao.org/aos/agrovoc/c_24242", "Mucilage", "mod\u00e8le de simulation", "http://aims.fao.org/aos/agrovoc/c_16034", "enracinement", "bl\u00e9 de printemps", "hexose", "Root hairs", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_11547", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "mucilage", "http://aims.fao.org/aos/agrovoc/c_6651", "http://aims.fao.org/aos/agrovoc/c_32027", "FSPM", "syst\u00e8me racinaire", "ArchiSimple", "Root exudation", "croissance", "Root architecture", "racine", "http://aims.fao.org/aos/agrovoc/c_3394", "http://aims.fao.org/aos/agrovoc/c_7337", "http://aims.fao.org/aos/agrovoc/c_6569", "http://aims.fao.org/aos/agrovoc/c_6649", "http://aims.fao.org/aos/agrovoc/c_17299", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation", "rhizosph\u00e8re", "Cells sloughing"]}, "links": [{"href": "https://doi.org/10.1101/2025.03.30.646173"}, {"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": "10.1101/2025.03.30.646173", "name": "item", "description": "10.1101/2025.03.30.646173", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2025.03.30.646173"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-04-03T00:00:00Z"}}, {"id": "10.3389/fmicb.2018.02141", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:20:33Z", "type": "Journal Article", "created": "2018-09-12", "title": "Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model", "description": "Xylella fastidiosa is a notorious plant pathogenic bacterium that represents a threat to crops worldwide. Its subspecies, Xylella fastidiosa subsp. fastidiosa is the causal agent of Pierce's disease of grapevines. Pierce's disease has presented a serious challenge for the grapevine industry in the United States and turned into an epidemic in Southern California due to the invasion of the insect vector Homalodisca vitripennis. In an attempt to minimize the effects of Xylella fastidiosa subsp. fastidiosa in vineyards, various studies have been developing and testing strategies to prevent the occurrence of Pierce's disease, i.e., prophylactic strategies. Research has also been undertaken to investigate therapeutic strategies to cure vines infected by Xylella fastidiosa subsp. fastidiosa. This report explicitly reviews all the strategies published to date and specifies their current status. Furthermore, an epidemiological model of Xylella fastidiosa subsp. fastidiosa is proposed and key parameters for the spread of Pierce's disease deciphered in a sensitivity analysis of all model parameters. Based on these results, it is concluded that future studies should prioritize therapeutic strategies, while investments should only be made in prophylactic strategies that have demonstrated promising results in vineyards.", "keywords": ["VECTOR TRANSMISSION", "0301 basic medicine", "VITRIPENNIS HEMIPTERA CICADELLIDAE", "GLASSY-WINGED SHARPSHOOTER", "PARATRANSGENIC CONTROL", "epidemiological model", "control strategies", "BACTERIUM XYLELLA-FASTIDIOSA", "Microbiology", "03 medical and health sciences", "HOT-WATER TREATMENT", "GONATOCERUS-ASHMEADI", "MOLECULAR CHARACTERIZATION", "Pierce's disease", "Xylella fastidiosa", "2. Zero hunger", "HOMALODISCA-COAGULATA HEMIPTERA", "0303 health sciences", "VITIS-VINIFERA L.", "15. Life on land", "QR1-502", "grapevine", "3. Good health", "[SDV] Life Sciences [q-bio]", "therapeutic", "prophylactic", "Homalodisca vitripennis", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2018.02141"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2018.02141", "name": "item", "description": "10.3389/fmicb.2018.02141", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2018.02141"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-09-12T00:00:00Z"}}, {"id": "2809041101", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:25:49Z", "type": "Journal Article", "created": "2018-06-18", "title": "Estimating the water budget components of irrigated crops: Combining the FAO-56 dual crop coefficient with surface temperature and vegetation index data", "description": "Abstract The FAO-56 dual crop coefficient (FAO-2Kc) model has been extensively used at the field scale to estimate the crop water requirements by means of the simulated evapotranspiration (ET) and its two components evaporation (E) and transpiration (T). Given that the main limitation of FAO-2Kc for operational irrigation management over large areas is the unavailability (over most irrigated areas) of irrigation data, this study investigates the feasibility 1) to constrain the FAO-2Kc ET from LST and VI data, 2) to retrieve irrigation amounts and dates from LST and VI data and 3) to estimate the root-zone soil moisture (RZSM) at the daily scale. In practice, the vegetation and soil temperatures retrieved from LST/VI data are used to estimate the FAO-2Kc vegetation stress coefficient (Ks) and soil evaporation reduction coefficient (Kr), respectively. The modeling and remote sensing combined approach is tested over a wheat crop field in central Morocco, and results are evaluated in terms of ET, irrigation and RZSM estimates. ET is estimated with a RMSE of 0.68\u202fmm day-1 compared to 0.84\u202fmm day-1 for the standard (without using LST data) FAO-2Kc based on tabulated values for the parameters. The total irrigation depth (67\u202fmm) is correctly estimated and is very close to the actual effective irrigation (69.8\u202fmm) applied by the farmer. Daily RZSM is estimated with an R2 value of 0.68 (0.42) and a RMSE value of 0.034 (0.061) m3 m-3 by forcing FAO-2Kc using the retrieved irrigation (from LST-derived estimates and precipitation only). Since spaceborne LST data are currently not available at both high-spatial and high-temporal resolution, a sensitivity analysis is finally undertaken to assess the potential and applicability of the proposed methodology to temporally-sparse thermal data.", "keywords": ["FAO-56", "0106 biological sciences", "2. Zero hunger", "550", "Evapotranspiration", "[SDE.IE]Environmental Sciences/Environmental Engineering", "Root-zone soil moisture", "[SDV.SA.STA] Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture", "Root-Zone Soil Moisture", "Surface Temperature", "[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation", "01 natural sciences", "6. Clean water", "Surface temperature", "[SDV.SA.STA]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation", "[SDE.IE] Environmental Sciences/Environmental Engineering", "Irrigation", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/2809041101"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agricultural%20Water%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2809041101", "name": "item", "description": "2809041101", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2809041101"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-09-01T00:00:00Z"}}, {"id": "10.24072/pcjournal.11", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:20:21Z", "type": "Journal Article", "created": "2020-11-10", "title": "Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production", "description": "AbstractBackgroundThe red macroalgae Asparagopsis taxiformis is a potent natural supplement for reducing methane production from cattle. A. taxiformis contains several anti-methanogenic compounds including bromoform that inhibits directly methanogenesis. The positive and adverse effects of A. taxiformis on the rumen microbiota are dose-dependent and operate in a dynamic fashion. It is therefore key to characterize the dynamic response of the rumen microbial fermentation for identifying optimal conditions on the use of A. taxiformis as a dietary supplement for methane mitigation. Accordingly, the objective of this work was to model the effect of A. taxiformis supplementation on the rumen microbial fermentation under in vitro conditions. We adapted a published mathematical model of rumen microbial fermentation to account for A. taxiformis supplementation. We modelled the impact of A. taxiformis on the fermentation and methane production by two mechanisms, namely (i) direct inhibition of the growth rate of methanogens by bromoform and (ii) hydrogen control on sugars utilization and on the flux allocation towards volatile fatty acids production. We calibrated our model using a multi-experiment estimation approach that integrated experimental data with six macroalgae supplementation levels from a published in vitro study assessing the dose-response impact of A. taxiformis on rumen fermentation.
Resultsour model captured satisfactorily the effect of A. taxiformis on the dynamic profile of rumen microbial fermentation for the six supplementation levels of A. taxiformis with an average determination coefficient of 0.88 and an average coefficient of variation of the root mean squared error of 15.2% for acetate, butyrate, propionate, ammonia and methane.
Conclusionsour results indicated the potential of our model as prediction tool for assessing the impact of additives such as seaweeds on the rumen microbial fermentation and methane production in vitro. Additional dynamic data on hydrogen and bromoform are required to validate our model structure and look for model structure improvements. We expect this model development can be useful to help the design of sustainable nutritional strategies promoting healthy rumen function and low environmental footprint.
", "keywords": ["570", "Asparagopsis taxiformis", "[SDV.BIO]Life Sciences [q-bio]/Biotechnology", "methane inhibitors", "Science", "rumen model", "630", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "[INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering", "rumen microbiota", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "greenhouse gas mitigation", " hydrogen control", " methane inhibitors", " methane mitigation", " red seaweed", " rumen fermentation", " rumen microbiota", " rumen model.", "[SDV.SA.SPA] Life Sciences [q-bio]/Agricultural sciences/Animal production studies", "2. Zero hunger", "methane mitigation", "Q", "greenhouse gas mitigation", "0402 animal and dairy science", "04 agricultural and veterinary sciences", "15. Life on land", "[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation", "[SDV.BIO] Life Sciences [q-bio]/Biotechnology", "rumen fermentation", "Archaeology", "hydrogen control", "13. Climate action", "[SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "red seaweed", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation", "environment/Ecosystems", "[INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering", "CC1-960"]}, "links": [{"href": "https://peercommunityjournal.org/item/10.24072/pcjournal.11.pdf"}, {"href": "https://doi.org/10.24072/pcjournal.11"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Peer%20Community%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.24072/pcjournal.11", "name": "item", "description": "10.24072/pcjournal.11", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.24072/pcjournal.11"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-09T00:00:00Z"}}, {"id": "10.3389/fams.2019.00018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:20:30Z", "type": "Journal Article", "created": "2019-04-12", "title": "Metabolic Games", "description": "Metabolic networks have been used to successfully predict phenotypes based on optimization principles. However, a general framework that would extend to situations not governed by simple optimization, such as multispecies communities, is still lacking. Concepts from evolutionary game theory have been proposed to amend the situation. Alternative metabolic states can be seen as strategies in a \u201cmetabolic game,\u201d and phenotypes can be predicted based on the equilibria of this game. In this survey, we review the literature on applying game theory to the study of metabolism, present the general idea of a metabolic game, and discuss open questions and future challenges.", "keywords": ["T57-57.97", "[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Applied mathematics. Quantitative methods", "flux balance analysis", "microbial interactions", "01 natural sciences", "QA273-280", "metabolic modeling", "0103 physical sciences", "metabolic networks", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation", "evolutionary game theory", "Probabilities. Mathematical statistics", "[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"]}, "links": [{"href": "https://doi.org/10.3389/fams.2019.00018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Applied%20Mathematics%20and%20Statistics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fams.2019.00018", "name": "item", "description": "10.3389/fams.2019.00018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fams.2019.00018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-12T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=%5BINFO.INFO-MO%5D+Computer+Science+%5Bcs%5D%2FModeling+and+Simulation&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=%5BINFO.INFO-MO%5D+Computer+Science+%5Bcs%5D%2FModeling+and+Simulation&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=%5BINFO.INFO-MO%5D+Computer+Science+%5Bcs%5D%2FModeling+and+Simulation&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=%5BINFO.INFO-MO%5D+Computer+Science+%5Bcs%5D%2FModeling+and+Simulation&offset=8", "hreflang": "en-US"}], "numberMatched": 8, "numberReturned": 8, "distributedFeatures": [], "timeStamp": "2026-07-27T16:04:45.041382Z"}