{"type": "FeatureCollection", "features": [{"id": "10.1007/s11104-022-05508-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:16:26Z", "type": "Journal Article", "created": "2022-06-22", "title": "Harnessing belowground processes for sustainable intensification of agricultural systems", "description": "Abstract

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.\u00a0Zn >\u00a0Cu deficiency. We observed a stronger expression of PS pathway genes and greater PS exudation in the barley line with large micronutrient grain yield suggesting that a highly expressed PS pathway might be an important trait involved in high micronutrient accumulation. In addition to several metal specific transporters, we also found that the expression of IRO2 and bHLH156 transcription factors was not only induced under Fe but also under Zn and Cu deficiency. Our study delivers important insights into the role of the PS pathway in the acquisition of different micronutrients.", "keywords": ["2. Zero hunger", "Phytosiderophore", "/dk/atira/pure/subjectarea/asjc/1300/1311", "/dk/atira/pure/subjectarea/asjc/1100/1102", "Root exudation", "name=Genetics", "Iron", "/dk/atira/pure/subjectarea/asjc/1100/1110", "Hordeum", "Copper deficiency", "Plant Roots", "630", "Mugineic acid", "name=Agronomy and Crop Science", "Zinc", "Barley", "Humans", "Micronutrients", "name=Plant Science", "Biofortification", "Copper"]}, "links": [{"href": "https://doi.org/10.1016/j.plantsci.2023.111919"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.plantsci.2023.111919", "name": "item", "description": "10.1016/j.plantsci.2023.111919", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.plantsci.2023.111919"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2023.109259", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:19:15Z", "type": "Journal Article", "created": "2023-12-01", "title": "A pulse of simulated root exudation alters the composition and temporal dynamics of microbial metabolites in its immediate vicinity", "description": "Root exudation increases the concentration of readily available carbon (C) compounds in its immediate environment. This creates \u2018hotspots\u2019 of microbial activity characterized by accelerated soil organic matter turnover with direct implications for nutrient availability for plants. However, our knowledge of the microbial metabolic processes occurring in the immediate vicinity of roots during and after a root exudation event is still limited.

Using reverse microdialysis, we simulated root exudation by releasing a13C-labelled mix of low-molecular-weight organic C compounds at mm-sized locations in undisturbed soil. Combined with stable isotope tracing, we investigated the fine-scale temporal and spatial response of microbial metabolism, soil chemistry, and traced microbial respiration and uptake of exuded compounds.

Our results show that a 9-h simulated root exudation pulse leads to i) a large local respiration event and ii) alteration of the temporal dynamics of soil metabolites over the following 12\u202fday\u202fat the exudation spot. Notably, we observed a threefold increase in ammonium concentrations at 12\u202fh and increased nitrate concentrations five days after the pulse. Moreover, various short-chain fatty acids (acetate, propionate, formate) increased over the following days, indicating altered microbial metabolic pathways and activity. Phospholipid and neutral lipid fatty acids (PLFAs, NLFAs) of all major microbial groups were significantly 13C-enriched within a 5\u202fmm radius around the microdialysis probes, but not beyond. The highest relative 13C enrichment was observed in fungal NLFAs, indicating that a significant proportion of the exuded compounds had been incorporated into fungal storage compounds.

Our findings indicate that the punctual release of low-molecular-weight organic C compounds into intact soil significantly changes microbial metabolism and activity in its immediate surroundings, enhancing mineralization of native organic nitrogen. This highlights the versatility of microbial metabolic pathways in response to rapidly changing C availability and their effectiveness in increasing nutrient availability near plant roots.", "keywords": ["Oxygen depletion", "2. Zero hunger", "570", "106022 Mikrobiologie", "Root exudation", "short-chain fatty acids", "Reverse microdialysis", "reverse microdialysis", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "15. Life on land", "root exudation", "6. Clean water", "Short-chain fatty acids", "Sugar metabolism", "106026 \u00d6kosystemforschung", "thizosphere priming effect", "crabtree effect", "sugar metabolism", "106022 Microbiology", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "106026 Ecosystem research", "Rhizosphere priming effect"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2023.109259"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2023.109259", "name": "item", "description": "10.1016/j.soilbio.2023.109259", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2023.109259"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-01T00:00:00Z"}}, {"id": "10.1101/2025.03.30.646173", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:21:26Z", "type": "Journal Article", "created": "2025-08-19", "title": "Deciphering spatiotemporal patterns of rhizodeposition with a functional-structural root model: RhizoDep", "description": "Abstract Background and Aims

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.

Methods

We 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.

Results

Our 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.

Conclusion

RhizoDep 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": "10.13130/rd_unimi/zretnd", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-25T16:22:50Z", "type": "Dataset", "title": "SENSE_WP1_D1.2 List of compounds exudated by Arabidopsis roots under PCBs stress v.03.ods", "description": "This is the dataset of the metabolomic analysis for the identification of root exudates released by Arabidopsis under pCB-18 stress", "keywords": ["Agricultural Sciences", "root exudates", "metabolomics", "root exudation"], "contacts": [{"organization": "Rolli, Eleonora", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.13130/rd_unimi/zretnd"}, {"rel": "self", "type": "application/geo+json", "title": "10.13130/rd_unimi/zretnd", "name": "item", "description": "10.13130/rd_unimi/zretnd", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.13130/rd_unimi/zretnd"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "10.5061/dryad.41ns1rnjs", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:25:54Z", "type": "Dataset", "title": "Plant growth strategy determines the magnitude and direction of drought-induced changes in root exudates in subtropical forests", "description": "Root exudates are an important pathway for plant-microbial interactions and are highly sensitive to climate change. However, how extreme drought affects root exudates and the main components, as well as species-specific differences in response magnitude and direction, are poorly understood. In this study, root exudation rates of total carbon (C) and its components (e.g., sugar, organic acid, and amino acid) were measured under the control and extreme drought treatments (i.e., 70% throughfall reduction) by in situ collection of four tree species with different growth rates in a subtropical forest. We also quantified soil properties, root morphological traits, and mycorrhizal infection rates to examine the driving factors underlying variations in root exudation. Our results showed that extreme drought significantly decreased root exudation rates of total C, sugar, and amino acid by 17.8%, 30.8%, and 35.0%, respectively, but increased root exudation rate of organic acid by 38.6%, which were largely associated with drought-induced changes in tree growth rates, root morphological traits, and mycorrhizal infection rates. Specifically, trees with relatively high growth rates were more responsive to drought for root exudation rates compared to those with relatively low growth rates, which were closely related to root morphological traits and mycorrhizal infection rates. These findings highlight the importance of plant growth strategy in mediating drought-induced changes in root exudation rates. The co-ordinations among root exudation rates, root morphological traits, and mycorrhizal symbioses in response to drought could be incorporated into land surface models to improve the prediction of climate change impacts on rhizosphere C dynamics in forest ecosystems.", "keywords": ["2. Zero hunger", "root morphological traits", "Drought", "subtropical forsts", "13. Climate action", "Root exudation", "tree growth", "FOS: Earth and related environmental sciences", "15. Life on land", "Organic acid", "6. Clean water", "amino acid", "mycorrhizal infection"], "contacts": [{"organization": "Jiang, Zheng, Fu, Yuling, Zhou, Lingyan, He, Yanghui, Zhou, Guiyao, Dietrich, Peter, Long, Jilan, Wang, Xinxin, Jia, Shuxian, Ji, Yuhuang, Jia, Zhen, Song, Bingqian, Liu, Ruiqiang, Zhou, Xuhui,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.41ns1rnjs"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.41ns1rnjs", "name": "item", "description": "10.5061/dryad.41ns1rnjs", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.41ns1rnjs"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-20T00:00:00Z"}}, {"id": "37992897", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-25T16:34:11Z", "type": "Journal Article", "created": "2023-11-20", "title": "Phytosiderophore pathway response in barley exposed to iron, zinc or copper starvation", "description": "Efficient micronutrient acquisition is a critical factor in selecting micronutrient dense crops for human consumption. Enhanced exudation and re-uptake of metal chelators, so-called phytosiderophores, by roots of graminaceous plants has been implicated in efficient micronutrient acquisition. We compared PS biosynthesis and exudation as a response mechanism to either Fe, Zn or Cu starvation. Two barley (Hordeum vulgare L.) lines with contrasting micronutrient grain yields were grown hydroponically and PS exudation (LC-MS) and root gene expression (RNAseq) were determined after either Fe, Zn, or Cu starvation. The response strength of the PS pathway was micronutrient dependent and decreased in the order Fe >\u00a0Zn >\u00a0Cu deficiency. We observed a stronger expression of PS pathway genes and greater PS exudation in the barley line with large micronutrient grain yield suggesting that a highly expressed PS pathway might be an important trait involved in high micronutrient accumulation. In addition to several metal specific transporters, we also found that the expression of IRO2 and bHLH156 transcription factors was not only induced under Fe but also under Zn and Cu deficiency. Our study delivers important insights into the role of the PS pathway in the acquisition of different micronutrients.", "keywords": ["2. Zero hunger", "Phytosiderophore", "/dk/atira/pure/subjectarea/asjc/1300/1311", "/dk/atira/pure/subjectarea/asjc/1100/1102", "Root exudation", "name=Genetics", "Iron", "/dk/atira/pure/subjectarea/asjc/1100/1110", "Hordeum", "Copper deficiency", "Plant Roots", "630", "Mugineic acid", "name=Agronomy and Crop Science", "Zinc", "Barley", "Humans", "Micronutrients", "name=Plant Science", "Biofortification", "Copper"]}, "links": [{"href": "https://doi.org/37992897"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "37992897", "name": "item", "description": "37992897", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/37992897"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-01T00:00:00Z"}}, {"id": "PMC9579094", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-25T16:37:26Z", "type": "Journal Article", "created": "2022-06-22", "title": "Harnessing belowground processes for sustainable intensification of agricultural systems", "description": "Abstract

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.