BACKGROUND: In spite of increasing knowledge of allelopathic rice as an efficient component involved in paddy weed management, relatively little is known about its reproduction in response to competing weeds. Reproduction allocation of individual allelopathic rice plants in relation to monoculture and mixed culture with competing barnyardgrass in a paddy field was studied, along with analyses of soil nutrients and microbial communities to understand the potential mechanism.
RESULTS: At a 1:1 barnyardgrass and rice mixture proportion identified from a replacement series study, biomass, grain yield and major parameters of individual allelopathic rice plants at the mature stage were increased by competing barnyardgrass. There was no difference in allelopathic rice root\uffe2\uff80\uff90zone soil ammonium N and Olsen P between monoculture and mixed culture. However, mixed culture altered soil microbial biomass C and communities. When mixed with barnyardgrass, allelopathic rice root zone had an 87% increase in soil microbial biomass C. Phospholipid fatty acid (PLFA) profiling indicated that the signature lipid biomarkers of bacteria, actinobacteria and fungi were affected by mixed culture. Principal component analysis clearly identified differences in the composition of PLFA in different soil samples.
CONCLUSION: Allelopathic rice specific changes in soil microbial communities may generate a positive feedback on its own growth and reproduction in the presence of competing barnyardgrass in a given paddy system. Copyright \uffc2\uffa9 2012 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "0106 biological sciences", "China", "Reproduction", "Population Dynamics", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "01 natural sciences", "Pheromones", "Soil", "Echinochloa", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Soil Microbiology"], "contacts": [{"organization": "Chui-Hua Kong, Peng Wang, Xiang-Rui Meng, Hanwen Ni, Ming-Li Wang,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1002/ps.3380"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Pest%20Management%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ps.3380", "name": "item", "description": "10.1002/ps.3380", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ps.3380"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-08-07T00:00:00Z"}}, {"id": "10.1007/s00374-006-0139-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:38Z", "type": "Journal Article", "created": "2006-10-10", "title": "Effect Of Intercropping On Crop Yield And Chemical And Microbiological Properties In Rhizosphere Of Wheat (Triticum Aestivum L.), Maize (Zea Mays L.), And Faba Bean (Vicia Faba L.)", "description": "In this study, we investigated crop yield and various chemical and microbiological properties in rhizosphere of wheat, maize, and faba bean grown in the field solely and intercropped (wheat/faba bean, wheat/maize, and maize/faba bean) in the second and third year after establishment of the cropping systems. In both years, intercropping increased crop yield, changed N and P availability, and affected the microbiological properties in rhizosphere of the three species compared to sole cropping. Generally, intercropping increased microbial biomass C, N, and P availability, whereas it reduced microbial biomass N in rhizosphere of wheat. The rhizosphere bacterial community composition was studied by denaturing gradient gel electrophoresis of 16S rRNA. In the third year of different cropping systems, intercropping significantly changed bacterial community composition in rhizosphere compared with sole cropping, and the effects were most pronounced in the wheat/faba bean intercropping system. The effects were less pronounced in the second year. The results show that intercropping has significant effects on microbiological and chemical properties in the rhizosphere, which may contribute to the yield enhancement by intercropping.", "keywords": ["PCR-DGGE", "2. Zero hunger", "Intercropping", "571", "Bacterial community composition", "Rhizosphere", "Microbial biomass", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences"]}, "links": [{"href": "https://doi.org/10.1007/s00374-006-0139-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-006-0139-9", "name": "item", "description": "10.1007/s00374-006-0139-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-006-0139-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-10-11T00:00:00Z"}}, {"id": "10.1007/s00374-014-0975-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:40Z", "type": "Journal Article", "created": "2014-10-23", "title": "Liming Of Anthropogenically Acidified Soil Promotes Phosphorus Acquisition In The Rhizosphere Of Wheat", "description": "We studied the effect of liming and P fertilization of extremely acid soil (accidently acidified by sulfidic mining waste) on P availability and the subsequent adaptive responses of wheat roots. The wheat plants were grown in rhizoboxes allowing precise sampling of rhizosphere and bulk soil for sequential extraction of P fractions and determination of exchangeable Al. Root exudates were collected by pieces of paper for electrophoresis and subjected to HPLC analysis. Expression of organic anions and Pi transporter genes was analyzed by a real-time quantitative PCR. The concomitant application of lime with P fertilization increased the concentrations of plant-available P fractions in both rhizosphere and bulk compartments. The applied soil amendments strongly affected plant growth, biomass partitioning and shoot P accumulation. Liming enhanced root exudation of citrate in P unfertilized plants, while the high malate efflux was maintained until both P deficiency and Al toxicity were eliminated by the amendments. We showed the importance of liming for recovering of P acquisition potential of wheat roots, which can be strongly impaired in acid soils. Our results clearly demonstrated that P-deficient roots not subjected to Al stress in the limed soil can maintain high efflux of malate and even increase efflux of citrate along with the enhanced expression of related anion transporters (TaMATE1 and TaALMT1).", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "03 medical and health sciences", "Wheat", "Rhizosphere", "Liming", "15. Life on land", "Root exudates", "Phosphorus deficiency", "Polluted acid soil"]}, "links": [{"href": "https://doi.org/10.1007/s00374-014-0975-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-014-0975-y", "name": "item", "description": "10.1007/s00374-014-0975-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-014-0975-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-10-24T00:00:00Z"}}, {"id": "10.1007/s00425-024-04556-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:42Z", "type": "Journal Article", "created": "2024-10-23", "title": "Root exudation patterns of contrasting rice (Oryza sativa L.) lines in response to P limitation", "description": "Abstract Main conclusionRice exudation patterns changed in response to P deficiency. Higher exudation rates were associated with lower biomass production. Total carboxylate exudation rates mostly decreased under P-limiting conditions.
AbstractWithin the rhizosphere, root exudates are believed to play an important role in plant phosphorus (P) acquisition. This could be particularly beneficial in upland rice production where P is often limited. However, knowledge gaps remain on how P deficiency shapes quality and quantity of root exudation in upland rice genotypes. We therefore investigated growth, plant P uptake, and root exudation patterns of two rice genotypes differing in P efficiency in semi-hydroponics at two P levels (low P\uffe2\uff80\uff89=\uffe2\uff80\uff891\uffc2\uffa0\uffc2\uffb5M, adequate P\uffe2\uff80\uff89=\uffe2\uff80\uff89100\uffc2\uffa0\uffc2\uffb5M). Root exudates were collected hydroponically 28 and 40\uffc2\uffa0days after germination to analyze total carbon (C), carbohydrates, amino acids, phenolic compounds spectrophotometrically and carboxylates using a targeted LC\uffe2\uff80\uff93MS approach. Despite their reported role in P solubilization, we observed that carboxylate exudation rates per unit root surface area were not increased under P deficiency. In contrast, exudation rates of total C, carbohydrates, amino acids and phenolics were mostly enhanced in response to low P supply. Overall, higher exudation rates were associated with lower biomass production in the P-inefficient genotype Nerica4, whereas the larger root system with lower C investment (per unit root surface area) in root exudates of the P-efficient DJ123 allowed for better plant growth under P deficiency. Our results reveal new insights into genotype-specific resource allocation in rice under P-limiting conditions that warrant follow-up research including more genotypes.
", "keywords": ["Genotype", "Hydroponics", "carbohydrates ; phenolics ; amino acids ; carboxylates ; phosphorus", "Plant Exudates", "Rhizosphere", "Original Article", "Oryza", "Phosphorus", "Biomass", "Amino Acids", "Plant Roots", "Carbon"], "contacts": [{"organization": "Henning Schwalm, Christiana Staudinger, Mohammad-Reza Hajirezaei, Eva Mundschenk, Alireza Golestanifard, Maire Holz, Matthias Wissuwa, Eva Oburger,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s00425-024-04556-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Planta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00425-024-04556-2", "name": "item", "description": "10.1007/s00425-024-04556-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00425-024-04556-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-10-23T00:00:00Z"}}, {"id": "10.1007/s10021-004-0218-4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:47Z", "type": "Journal Article", "created": "2004-08-21", "title": "Climate Change Affects Carbon Allocation To The Soil In Shrublands", "description": "Climate change may affect ecosystem functioning through increased temperatures or changes in precipitation patterns. Temperature and water availability are important drivers for ecosystem processes such as photosynthesis, carbon translocation, and organic matter decomposition. These climate changes may affect the supply of carbon and energy to the soil microbial population and subsequently alter decomposition and mineralization, important ecosystem processes in carbon and nutrient cycling. In this study, carried out within the cross-European research project CLIMOOR, the effect of climate change, resulting from imposed manipulations, on carbon dynamics in shrubland ecosystems was examined. We performed a 14C-labeling experiment to probe changes in net carbon uptake and allocation to the roots and soil compartments as affected by a higher temperature during the year and a drought period in the growing season. Differences in climate, soil, and plant characteristics resulted in a gradient in the severity of the drought effects on net carbon uptake by plants with the impact being most severe in Spain, followed by Denmark, with the UK showing few negative effects at significance levels of p \u2264 0.10. Drought clearly reduced carbon flow from the roots to the soil compartments. The fraction of the 14C fixed by the plants and allocated into the soluble carbon fraction in the soil and to soil microbial biomass in Denmark and the UK decreased by more than 60%. The effects of warming were not significant, but, as with the drought treatment, a negative effect on carbon allocation to soil microbial biomass was found. The changes in carbon allocation to soil microbial biomass at the northern sites in this study indicate that soil microbial biomass is a sensitive, early indicator of drought- or temperature-initiated changes in these shrubland ecosystems. The reduced supply of substrate to the soil and the response of the soil microbial biomass may help to explain the observed acclimation of CO2 exchange in other ecosystems.", "keywords": ["2. Zero hunger", "0106 biological sciences", "decomposition", "photosynthesis", "temperature", "translocation", "plant", "04 agricultural and veterinary sciences", "15. Life on land", "01 natural sciences", "6. Clean water", "dioxide", "calluna-vulgaris", "13. Climate action", "lolium-perenne", "0401 agriculture", " forestry", " and fisheries", "rhizosphere", "respiration"]}, "links": [{"href": "https://doi.org/10.1007/s10021-004-0218-4"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecosystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10021-004-0218-4", "name": "item", "description": "10.1007/s10021-004-0218-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10021-004-0218-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2004-08-06T00:00:00Z"}}, {"id": "10.1007/s10533-015-0159-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:57Z", "type": "Journal Article", "created": "2015-12-17", "title": "Mediation Of Soil C Decomposition By Arbuscular Mycorrizhal Fungi In Grass Rhizospheres Under Elevated Co2", "description": "Arbuscular mycorrhizal (AMF) function has mostly been studied from the plant perspective, but there is a shortage of empirical assessments of their ecosystem level impacts on soil carbon (C). Our understanding of the role of AMF on C processing belowground has been restricted mostly to fresh plant residues, not stabilized soil organic matter. The mechanisms by which elevated CO2 (eCO2) alter soil C remain an open question but AMF likely play a role via C and nutrients, which could in turn, be plant species dependent. We assessed AMF as mediators of C processing in the rhizosphere of two grasses under eCO2. We exposed a C4 and a C3 grass to a combination of ambient and eCO2 with and without modification of the AMF communities and using stable isotopes quantified the respiration of native soil C (as rhizosphere priming), its contribution to dissolved and microbial C and the final remaining C pool. The AMF treatment impacted soil C respiration under the C3-plant and only under eCO2. eCO2 suppressed decomposition (negative priming) but this effect disappeared when the AMF community was reduced. In contrast to studies of fresh plant residues suggesting that AMF can enhance C loss, our observations indicate that AMF may promote C storage in the soil organic matter pool. Results support that AMF can mediate the effect of eCO2 on soil C in the rhizosphere of some plant species, a potential mechanism explaining variation in impacts of eCO2 on soil C storage and C balances across species and ecosystems.", "keywords": ["vesicular-arbuscular mycorrhizas", "580", "2. Zero hunger", "grasses", "13. Climate action", "XXXXXX - Unknown", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "rhizosphere", "biodegradation"]}, "links": [{"href": "https://doi.org/10.1007/s10533-015-0159-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biogeochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10533-015-0159-3", "name": "item", "description": "10.1007/s10533-015-0159-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10533-015-0159-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-12-17T00:00:00Z"}}, {"id": "10.1007/s10661-012-2795-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:59Z", "type": "Journal Article", "created": "2012-07-24", "title": "Temporal Changes Of Soil Respiration Under Different Tree Species", "description": "Soil respiration rates were measured monthly (from April 2007 to March 2008) under four adjacent coniferous plantation sites [Oriental spruce (Picea orientalis L.), Austrian pine (Pinus nigra Arnold), Turkish fir (Abies bornmulleriana L.), and Scots pine (Pinus sylvestris L.)] and adjacent natural Sessile oak forest (Quercus petraea L.) in Belgrad Forest-Istanbul/Turkey. Also, soil moisture, soil temperature, and fine root biomass were determined to identify the underlying environmental variables among sites which are most likely causing differences in soil respiration. Mean annual soil moisture was determined to be between 6.3\u00a0% and 8.1\u00a0%, and mean annual temperature ranged from 13.0\u00b0C to 14.2\u00b0C under all species. Mean annual fine root biomass changed between 368.09\u00a0g/m(2) and 883.71\u00a0g/m(2) indicating significant differences among species. Except May 2007, monthly soil respiration rates show significantly difference among species. However, focusing on tree species, differences of mean annual respiration rates did not differ significantly. Mean annual soil respiration ranged from 0.56 to 1.09\u00a0g\u2009C/m(2)/day. The highest rates of soil respiration reached on autumn months and the lowest rates were determined on summer season. Soil temperature, soil moisture, and fine root biomass explain mean annual soil respiration rates at the highest under Austrian pine (R (2)\u2009=\u20090.562) and the lowest (R (2)\u2009=\u20090.223) under Turkish fir.", "keywords": ["0106 biological sciences", "Turkey", "Temperature", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "01 natural sciences", "Carbon Cycle", "Trees", "Soil", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Soil Microbiology", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1007/s10661-012-2795-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Monitoring%20and%20Assessment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10661-012-2795-6", "name": "item", "description": "10.1007/s10661-012-2795-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10661-012-2795-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-07-26T00:00:00Z"}}, {"id": "10.1007/s11104-014-2214-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:12Z", "type": "Journal Article", "created": "2014-08-09", "title": "The Intercropping Cowpea-Maize Improves Soil Phosphorus Availability And Maize Yields In An Alkaline Soil", "description": "This study assessed whether growing cowpea can increase phosphorus (P) availability in the rhizosphere and improve the yield of legume-cereal systems. In alkaline Mediterranean soils with P deficiency, it is assumed that legumes increase inorganic P availability. A field experiment was conducted at the Staoueli experimental station, in Algiers province, Algeria, to compare the growth, grain yield, P availability, and P uptake by plants with sole-cropped cowpea (Vigna unguiculata L. cv. Moh Ouali) and maize (Zea mays L. cv. ILT), intercropped cowpea-maize, and fallow. P availability in the rhizosphere was increased in both sole cropping and intercropping systems compared with fallow. It was highest in intercropping. The increase in P availability was associated with (i) significant pH changes of the rhizosphere of cowpea in sole cropping and intercropping systems, with the rhizosphere acidification significantly higher in intercropping (\u22120.73\u00a0units) than in sole cropping (\u22120.42\u00a0units); (ii) significant increase in the rhizosphere pH of intercropped maize (+0.49\u00a0units) compared to fallow; (iii) increased soil respiration (C-CO2 from microbial and root activity) in intercropping compared with sole cropping and fallow; and (iv) higher efficiency in utilization of the rhizobial symbiosis in intercropping than in sole-cropped cowpea. With cowpea-maize intercropping, cowpea increased the P uptake, by increasing the P availability by rhizosphere pH changes in an alkaline soil. Overall, this study showed that intercropping cowpea improved the plant biomass and grain yield of maize in this soil.", "keywords": ["2. Zero hunger", "[SDV]Life Sciences [q-bio]", "P availability", "04 agricultural and veterinary sciences", "15. Life on land", "630", "6. Clean water", "[SDV] Life Sciences [q-bio]", "acidification", "Intercropping", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Biological N-2-fixation", "Biological N2-fixation", "Rhizosphere acidification"]}, "links": [{"href": "https://doi.org/10.1007/s11104-014-2214-6"}, {"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/s11104-014-2214-6", "name": "item", "description": "10.1007/s11104-014-2214-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-014-2214-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-08-10T00:00:00Z"}}, {"id": "10.1007/s11104-016-2949-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:13Z", "type": "Journal Article", "created": "2016-06-14", "title": "Phosphorus Availability And Microbial Community In The Rhizosphere Of Intercropped Cereal And Legume Along A P-Fertilizer Gradient", "description": "Positive below-ground interactions (facilitation) should be more pronounced when resources limit crop growth, according to the stress-gradient hypothesis. Our aim was to test this hypothesis for intercropped durum wheat and faba bean along a P-fertilizer gradient. A field experiment was conducted in a long-term P-fertilizer trial with three rates of P-fertilization (No, Low and High P). Microbial biomass was assessed by chloroform fumigation-extraction. Quantitative PCR was applied to evaluate the abundance of relevant microbial groups. Phosphorus availability and microbial biomass systematically increased in the rhizosphere compared to bulk soil. P-fertilization resulted in higher abundance of targeted bacterial phyla, whole bacterial and fungal communities, and depressed mycorrhizal colonization of durum wheat, but not faba bean. Microbial biomass carbon significantly increased in the rhizosphere only in P-fertilized treatments, pointing to P limitation of microbial communities. Intercropping yielded a significant effect on rhizosphere microbial properties only at High P. Microbial biomass P increased in the rhizosphere of intercropped faba bean only at No P level, and was thus the sole finding supporting the stress-gradient hypothesis. P-fertilization was the main driver of microbial communities in this field trial, and P-fertilizer application modulated the species-specific effect in the intercrop. Plant performance did not validate the stress-gradient hypothesis as positive plant-plant interactions occurred regardless of the level of P-fertilization.", "keywords": ["[SDE] Environmental Sciences", "engrais phosphat\u00e9", "F08 - Syst\u00e8mes et modes de culture", "[SDV]Life Sciences [q-bio]", "F62 - Physiologie v\u00e9g\u00e9tale - Croissance et d\u00e9veloppement", "mycorhization", "Triticum turgidum", "630", "fertilisation", "[SHS]Humanities and Social Sciences", "http://aims.fao.org/aos/agrovoc/c_37554", "http://aims.fao.org/aos/agrovoc/c_5800", "http://aims.fao.org/aos/agrovoc/c_10795", "http://aims.fao.org/aos/agrovoc/c_24199", "2. Zero hunger", "Mycorrhizal colonization", "04 agricultural and veterinary sciences", "Vicia faba", "[SDV] Life Sciences [q-bio]", "fertilit\u00e9 du sol", "http://aims.fao.org/aos/agrovoc/c_6569", "Rhizosphere", "Long-term fertilization", "[SDE]Environmental Sciences", "[SHS] Humanities and Social Sciences", "Intercrop", "http://aims.fao.org/aos/agrovoc/c_8220", "rhizosph\u00e8re", "http://aims.fao.org/aos/agrovoc/c_4819", "http://aims.fao.org/aos/agrovoc/c_7170", "plante c\u00e9r\u00e9ali\u00e8re", "flore microbienne", "disponibilit\u00e9 nutriments (sol)", "http://aims.fao.org/aos/agrovoc/c_25512", "mod\u00e8le math\u00e9matique", "http://aims.fao.org/aos/agrovoc/c_36163", "Microbial community", "http://aims.fao.org/aos/agrovoc/c_3081", "phosphate", "P availability", "P34 - Biologie du sol", "15. Life on land", "http://aims.fao.org/aos/agrovoc/c_16367", "plante l\u00e9gumi\u00e8re", "http://aims.fao.org/aos/agrovoc/c_7958", "628", "http://aims.fao.org/aos/agrovoc/c_3910", "http://aims.fao.org/aos/agrovoc/c_35986", "0401 agriculture", " forestry", " and fisheries", "culture intercalaire", "http://aims.fao.org/aos/agrovoc/c_8165", "F04 - Fertilisation"]}, "links": [{"href": "https://doi.org/10.1007/s11104-016-2949-3"}, {"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/s11104-016-2949-3", "name": "item", "description": "10.1007/s11104-016-2949-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-016-2949-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-14T00:00:00Z"}}, {"id": "10.1007/s11104-016-2872-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:13Z", "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": "10.1007/s11104-019-03939-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:14Z", "type": "Journal Article", "created": "2019-02-01", "title": "Surface tension, rheology and hydrophobicity of rhizodeposits and seed mucilage influence soil water retention and hysteresis", "description": "Rhizodeposits collected from hydroponic solutions with roots of maize and barley, and seed mucilage washed from chia, were added to soil to measure their impact on water retention and hysteresis in a sandy loam soil at a range of concentrations. We test the hypothesis that the effect of plant exudates and mucilages on hydraulic properties of soils depends on their physicochemical characteristics and origin.Surface tension and viscosity of the exudate solutions were measured using the Du No\u00fcy ring method and a cone-plate rheometer, respectively. The contact angle of water on exudate treated soil was measured with the sessile drop method. Water retention and hysteresis were measured by equilibrating soil samples, treated with exudates and mucilages at 0.46 and 4.6\u00a0mg\u00a0g-1 concentration, on dialysis tubing filled with polyethylene glycol (PEG) solution of known osmotic potential.Surface tension decreased and viscosity increased with increasing concentration of the exudates and mucilage in solutions. Change in surface tension and viscosity was greatest for chia seed exudate and least for barley root exudate. Contact angle increased with increasing maize root and chia seed exudate concentration in soil, but not barley root. Chia seed mucilage and maize root rhizodeposits enhanced soil water retention and increased hysteresis index, whereas barley root rhizodeposits decreased soil water retention and the hysteresis effect. The impact of exudates and mucilages on soil water retention almost ceased when approaching wilting point at -1500\u00a0kPa matric potential.Barley rhizodeposits behaved as surfactants, drying the rhizosphere at smaller suctions. Chia seed mucilage and maize root rhizodeposits behaved as hydrogels that hold more water in the rhizosphere, but with slower rewetting and greater hysteresis.", "keywords": ["DYNAMICS", "/dk/atira/pure/subjectarea/asjc/1100/1111", "seed exudate", "FLOW", "QH301 Biology", "/dk/atira/pure/subjectarea/asjc/1100/1110", "root exudate", "630", "QH301", "soil water retention", "ROOT", "surface tension", "DIMR 646809", "Contact angle", "contact angle", "PHOSPHOLIPID SURFACTANTS", "2. Zero hunger", "STABILITY", "BB/J000868/1", "Surface tension", "Civil_env_eng", "Viscosity", "Hysteresis", "name=Soil Science", "Root exudate", "RHIZOSPHERE HYDRAULIC-PROPERTIES", "EXUDATION", "Regular Article", "04 agricultural and veterinary sciences", "15. Life on land", "540", "Soil water retention", "6. Clean water", "Seed exudate", "BB/J011460/1", "hysteresis", "BB/L026058/1", "viscosity", "Biotechnology and Biological Sciences Research Council (BBSRC)", "0401 agriculture", " forestry", " and fisheries", "name=Plant Science", "MAIZE", "BB/P004180/1", "European Research Council"]}, "links": [{"href": "https://repository.uwl.ac.uk/id/eprint/5787/1/Naveed2019_Article_SurfaceTensionRheologyAndHydro.pdf"}, {"href": "https://eprints.soton.ac.uk/428238/1/Naveed2019_Article_SurfaceTensionRheologyAndHydro.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1007/s11104-019-03939-9.pdf"}, {"href": "https://doi.org/10.1007/s11104-019-03939-9"}, {"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/s11104-019-03939-9", "name": "item", "description": "10.1007/s11104-019-03939-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-019-03939-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-02T00:00:00Z"}}, {"id": "10.1007/s11104-019-04308-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:14Z", "type": "Journal Article", "created": "2019-12-06", "title": "Significance of root hairs at the field scale \u2013 modelling root water and phosphorus uptake under different field conditions", "description": "Abstract Background and aimsRoot hairs play a significant role in phosphorus (P) extraction at the pore scale. However, their importance at the field scale remains poorly understood.
MethodsThis study uses a continuum model to explore the impact of root hairs on the large-scale uptake of P, comparing root hair influence under different agricultural scenarios. High vs low and constant vs decaying P concentrations down the soil profile are considered, along with early vs late precipitation scenarios.
ResultsSimulation results suggest root hairs accounted for 50% of total P uptake by plants. Furthermore, a delayed initiation time of precipitation potentially limits the P uptake rate by over 50% depending on the growth period. Despite the large differences in the uptake rate, changes in the soil P concentration in the domain due to root solute uptake remains marginal when considering a single growth season. However, over the duration of 6\uffc2\uffa0years, simulation results showed that noticeable differences arise over time.
ConclusionRoot hairs are critical to P capture, with uptake efficiency potentially enhanced by coordinating irrigation with P application during earlier growth stages of crops.
", "keywords": ["/dk/atira/pure/subjectarea/asjc/1100/1111", "0106 biological sciences", "330", "550", "EP/M020355/1", "ERC 646809 DIMR", "QH301 Biology", "/dk/atira/pure/subjectarea/asjc/1100/1110", "Soil Science", "A. B", "Field", "610", "Plant Science", "01 natural sciences", "NERC NE/L00237/1", "QH301", "Soil", "Plant roots", "Root hairs", "BBSRC SARIC BB/P004180/", "2. Zero hunger", "BBSRC SARISA BB/L025620/1. S. D.", "Mathematical modelling", "Natural Environment Research Council (NERC)", "name=Soil Science", "Water", "Phosphorus", "Regular Article", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Engineering and Physical Sciences Research Council (EPSRC)", "Rhizosphere", "Biotechnology and Biological Sciences Research Council (BBSRC)", "0401 agriculture", " forestry", " and fisheries", "name=Plant Science", "European Research Council"]}, "links": [{"href": "https://eprints.soton.ac.uk/434043/1/Manuscript_No_Tracked_Changes.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1007/s11104-019-04308-2.pdf"}, {"href": "https://doi.org/10.1007/s11104-019-04308-2"}, {"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/s11104-019-04308-2", "name": "item", "description": "10.1007/s11104-019-04308-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-019-04308-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-06T00:00:00Z"}}, {"id": "10.1007/s11104-021-04945-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:14Z", "type": "Journal Article", "created": "2021-04-15", "title": "Wheat-root associated prokaryotic community: interplay between plant selection and location", "description": "Background Root-associated microbiomes are important for plant nutrient uptake, disease suppression and plant growth. It is important to reveal wheat-root associated microbial community assembly and dominant drivers determining their variability. Methods Using 16S rRNA gene profiling, we investigated the effects of sample type, location, growth stage and variety on prokaryotic communities in the root endosphere and rhizosphere of wheat and bulk soil based on the field samples including 5 varieties from 4 locations along similar latitude with the distance about 157 to 800 km apart between any two locations. Results Prokaryotic communities were more diverse in the bulk soil and rhizosphere than in root endosphere. Wheat-root associated prokaryotic community assembly was shaped predominantly by sample type, while within each sample type, location had stronger effects on the variation in prokaryotic community than growth stage or variety. Wheat variety effects varied substantially among different locations and growth stages in root endosphere and rhizosphere samples, and the variety effects were location-specific and growth stage-specific. Root endosphere specially enriched Pseudomonas, relative to other two sample types, while rhizosphere mainly enriched Bacillus. Conclusions This study characterized prokaryotic communities of wheat-root endosphere and rhizosphere and their relationships, and demonstrated significant interactive effects between wheat variety, location and growth stage on prokaryotic community assembly in field condition.", "keywords": ["2. Zero hunger", "Triticum aestivum L", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Key drivers", "Prokaryotic community", "Rhizosphere", "Endosphere", "15. Life on land"]}, "links": [{"href": "https://doi.org/10.1007/s11104-021-04945-6"}, {"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/s11104-021-04945-6", "name": "item", "description": "10.1007/s11104-021-04945-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-021-04945-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-15T00:00:00Z"}}, {"id": "10.1007/s11104-022-05340-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:14Z", "type": "Journal Article", "created": "2022-03-22", "title": "The role of microbes in the increase of organic phosphorus availability in the rhizosheath of cover crops", "description": "AbstractBackground and aimsThe characterisation of plant-available phosphorus (P) pools and the assessment of the microbial community in the rhizosheath of cover crops can improve our understanding of plant\uffe2\uff80\uff93microbe interactions and P availability.
MethodsMustard (Sinapis alba), phacelia (Phacelia tanacetifolia) and buckwheat (Fagopyrum esculentum) were grown as cover crops before soybean (Glycine max) in an on-farm experiment on a soil low in available P in southwest Germany. The cycling of P through the cover crop biomass and the enzyme-availability of organic P (Porg) pools in the cover crop rhizosheath were characterised. The soil microbial community (PLFA), activity (acid and alkaline phosphomonoesterase, as well as phosphodiesterase), and microbial P were assessed. The abundance of 16S-rRNA andphoD, coding for alkaline phosphomonoesterase in bacteria, were quantified using real-time qPCR.
ResultsMustard contained the greatest amount of P in its large biomass. In the rhizosheath of all cover crops, the concentration of enzyme-labile Porgwas higher than that in the control bulk soil, along with substantial increases of microbial abundance and activity. There were little differences among cover crop species, few changes in the bulk soil and only a limited carryover effect to soybean, except for fungi.
ConclusionsTurnover of microbial biomass, especially saprotrophic fungi, increased by rhizodeposition of cover crop roots; this was likely responsible for the observed increases in enzyme-available Porg. Microbial function was correlated linearly with microbial biomass, and the data of enzyme activity andphoDdid not suggest a difference of their specific activity between bulk and rhizosheath soil.Our understanding of the rhizosphere is limited by the lack of techniques for in situ live microscopy. Current techniques are either destructive or unsuitable for observing chemical changes within the pore space. To address this limitation, we have developed artificial substrates, termed smart soils, that enable the acquisition and 3D reconstruction of chemical sensors attached to soil particles.
MethodsThe transparency of smart soils was achieved using polymer particles with refractive index matching that of water. The surface of the particles was modified both to retain water and act as a local sensor to report on pore space pH via fluorescence emissions. Multispectral signals were acquired from the particles using a light sheet microscope, and machine learning algorithms predicted the changes and spatial distribution in pH at the surface of the smart soil particles.
ResultsThe technique was able to predict pH live and in situ within \uffc2\uffb1\uffe2\uff80\uff890.5 units of the true pH value. pH distribution could be reconstructed across a volume of several cubic centimetres around plant roots at 10\uffc2\uffa0\uffce\uffbcm resolution. Using smart soils of different composition, we revealed how root exudation and pore structure create variability in chemical properties.
ConclusionSmart soils captured the pH gradients forming around a growing plant root. Future developments of the technology could include the fine tuning of soil physicochemical properties, the addition of chemical sensors and improved data processing. Hence, this technology could play a critical role in advancing our understanding of complex rhizosphere processes.
", "keywords": ["/dk/atira/pure/subjectarea/asjc/1100/1111", "light sheet microscopy", "0301 basic medicine", "570", "0303 health sciences", "name=Soil Science", "/dk/atira/pure/subjectarea/asjc/1100/1110", "Sensing soil", "live imaging", "15. Life on land", "root", "530", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "03 medical and health sciences", "Root", "13. Climate action", "Rhizosphere", "Light sheet microscopy", "name=Plant Science", "rhizosphere", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "Live imaging"]}, "links": [{"href": "https://doi.org/10.1007/s11104-023-06151-y"}, {"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/s11104-023-06151-y", "name": "item", "description": "10.1007/s11104-023-06151-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-023-06151-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-07-26T00:00:00Z"}}, {"id": "10.1007/s11104-023-06301-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:15Z", "type": "Journal Article", "created": "2023-10-04", "title": "Root phenotypes for improved nitrogen capture", "description": "Abstract BackgroundSuboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer.
ScopeIntraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes.
ConclusionsSubstantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.
", "keywords": ["2. Zero hunger", "0106 biological sciences", "0301 basic medicine", "Plasticity", "Marschner Review", "Nitrogen", "Physiology", "Nitrogen; Root; Anatomy; Architecture; Soil; Crop breeding; Root phenotyping; Modeling; Rhizosphere; Plasticity; Physiology", "Modeling", "Root phenotyping", "15. Life on land", "01 natural sciences", "Soil", "03 medical and health sciences", "Root", "FOS: Biological sciences", "Architecture", "Rhizosphere", "Crop breeding", "Anatomy", "FOS: Civil engineering"]}, "links": [{"href": "https://doi.org/10.1007/s11104-023-06301-2"}, {"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/s11104-023-06301-2", "name": "item", "description": "10.1007/s11104-023-06301-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-023-06301-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-04T00:00:00Z"}}, {"id": "10.1007/s11104-024-06691-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:15Z", "type": "Journal Article", "created": "2024-05-02", "title": "Changes in soil microbiota alter root exudation and rhizosphere pH of the gypsum endemic Ononis tridentata L.", "description": "Closed AccessThis work was supported by the Spanish Government [MICINN, CGL2015-71360-P and PID2019-111159GB-C31], and by European Union\u2019s Horizon 2020 [H2020-MSCA-RISE-777803 GYPWORLD]. LP was funded by fellowship FSE-Arag\u00f3n 2014-2020 by Gobierno de Arag\u00f3n, Spain; J.M.I. was supported by Project \u201cCLU-2019-05 \u2013 IRNASA/CSIC Unit of Excellence\u201d, funded by the Junta de Castilla y Le\u00f3n and co-financed by the European Union (ERDF \u201cEurope drives our growth\u201d), JPF and SP were supported by Reference Groups S74_23R and E03_23R, respectively (Gobierno de Arag\u00f3n, Spain).", "keywords": ["2. Zero hunger", "13. Climate action", "Gypsum soils", "Ononis tridentata", "15. Life on land", "Soil microbiota", "Rhizobox", "6. Clean water", "Rhizosphere acidification", "Seedling root"]}, "links": [{"href": "https://doi.org/10.1007/s11104-024-06691-x"}, {"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/s11104-024-06691-x", "name": "item", "description": "10.1007/s11104-024-06691-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-024-06691-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-05-02T00:00:00Z"}}, {"id": "10.1007/s11538-017-0350-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:21Z", "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": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Mathematical Concepts", "15. Life on land", "Models", " Biological", "Plant Roots", "Soil", "03 medical and health sciences", "Imaging", " Three-Dimensional", "Rhizosphere", "Original Article", "Computer Simulation", "Tomography", " X-Ray Computed", "Synchrotrons"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s11538-017-0350-x.pdf"}, {"href": "https://doi.org/10.1007/s11538-017-0350-x"}, {"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": "10.1007/s11538-017-0350-x", "name": "item", "description": "10.1007/s11538-017-0350-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11538-017-0350-x"}, {"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": "10.1016/j.apsoil.2022.104678", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:50Z", "type": "Journal Article", "created": "2022-10-07", "title": "Trichoderma enriched compost, BCAs and potassium phosphite control Fusarium wilt of lettuce without affecting soil microbiome at genus level", "description": "Fusarium oxysporum f. sp. lactucae (Fol) is the causal agent of Fusarium wilt of lettuce, one of the most troublesome diseases affecting lettuce worldwide. Chemical control strategies are inadequate due to limited fungicide availability and consumer interest in organic vegetable production. Alternative control strategies, such as biological control agents (BCAs), suppressive compost, and resistance inducers, have been intensively studied to test their ability to reduce pathogen attacks. Research has been recently focused on the influence of BCAs on the rhizosphere microbiota, which plays a critical role in soil suppressiveness. In this work, three strategies of integrated pest management (IPM) were tested against Fol attacks in two fields for two consecutive years: (i) a compost enriched with Trichoderma, (ii) a combination of T. gamsii + T. asperellum, Bacillus amyloliquefaciens and potassium posphite and (iii) a combination of T. polysporum + T. atroviride. The rhizosphere microbiota was characterized by high-throughput sequencing of bacterial and eukaryotic rRNA gene markers. Obtained results indicated IPM strategies statistically reduced disease severity, in both fields and years, from 50 % to 70 % compared to untreated controls. An increased crop yield compared to untreated controls was also observed. Predominant phyla were Proteobacteria, Firmicutes and Actinobacteria for bacteria, and Ascomycota for fungi. However, microbiota populations were not affected by any of the treatments, nor were significant differences observed when the soil microbial community was compared to that of untreated controls. Conversely, large differences were observed when comparing the two fields and years, indicating an important microbial buffering effect triggered by the soil.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Microbiota; Rhizosphere; Biocontrol agents; Resistance inducers; Seed born pathogen; Fusarium oxysporum f; sp; lactucae"], "contacts": [{"organization": "Bellini, A, Gilardi, G, Idbella, M, Zotti, M, Pugliese, M, Bonanomi, G, Gullino, ML,", "roles": ["creator"]}]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1891861/2/Bellini%20IRIS%20aperto.pdf"}, {"href": "https://iris.unito.it/bitstream/2318/1891861/8/Bellini%20post%20print_Pugliese.pdf"}, {"href": "https://doi.org/10.1016/j.apsoil.2022.104678"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2022.104678", "name": "item", "description": "10.1016/j.apsoil.2022.104678", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2022.104678"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-01T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2016.08.016", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:49Z", "type": "Journal Article", "created": "2016-09-07", "title": "Associative Interplay Of Plant Growth Promoting Rhizobacteria (Pseudomonas Aeruginosa Qs40) With Nitrogen Fertilizers Improves Sunflower (Helianthus Annuus L.) Productivity And Fertility Of Aridisol", "description": "Abstract The environmental and economic impacts of chemical fertilizer have encouraged farmers to integrate them with organic materials, an important nutrient management strategy for sustainable agriculture production. In the present study, we conducted field experiments to study the effects of nitrogen enriched compost (NEC) and mineral nitrogen (MN) fertilizer with a selected plant growth promoting rhizobacterial (PGPR) strain, Pseudomonas aeruginosa QS40, on productivity of sunflower and soil fertility. The results demonstrated that integrated application of PGPR with organic-inorganic N significantly increased shoot and root length, leaf area, total chlorophyll, head diameter, fresh biomass, straw-achene yield and N uptake in sunflower compared to unamended control and PGPR alone. The results also showed that integrated N biofertilizer regime enhanced soil microbial biomass, enzymatic activities and soil nitrogen contents. We also observed significant changes in rhizosphere soil pH, abundance of cultivable bacteria and arbuscular mycorrhizae fungi (AMF) root colonization. Treatment and year interaction was significant for dissolved organic carbon (DOC) and microbial biomass carbon (MBC) only. These results suggest that the efficiency of PGPR could be improved with increased availability of labile C substrate resource in NEC amended aridisol. We conclude that the application of NEC fertilizer with efficient PGPR biofertilizer may improve sunflower productivity and soil chemical and biological fertility in nutrient-poor agroecosystems of arid and semi-arid regions.", "keywords": ["[SDE] Environmental Sciences", "2. Zero hunger", "N Enriched compost", " Biofertilizer", " Arid soil", " Oil seed crops", " Rhizosphere", "[SDE]Environmental Sciences", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land"]}, "links": [{"href": "https://doi.org/10.1016/j.apsoil.2016.08.016"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2016.08.016", "name": "item", "description": "10.1016/j.apsoil.2016.08.016", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2016.08.016"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-12-01T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2022.104649", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:50Z", "type": "Journal Article", "created": "2022-08-30", "title": "Effects of microplastics on common bean rhizosphere bacterial communities", "description": "Microplastic pollution in terrestrial ecosystems is a growing concern due to its potential influences on soil properties and crop growth. Little is known about the effects of microplastics on the microbiome in the rhizosphere. Here, we studied the effects of two types of microplastics (MPs), low density polyethylene (LDPE-MPs) and biodegradable microplastic (Bio-MPs) of poly-butylene-adipate-co-terephthalate (PBAT) mixed with polylactic acid (PLA), on rhizosphere bacterial communities of Phaseolus vulgaris at doses of 0.5 %, 1.0 % and 2.5 % (w/w, dry weight ratio between MPs and soil). Bio-MPs and LDPE-MPs showed significant higher \u03b1-diversity (Chao 1, ACE, Shannon and Simpson) than control. For each type of microplastic material, 2.5 % of LDPE-MPs and Bio-MPs showed lowest \u03b1-diversity as compared to doses of 0.5 % and 1.0 %, indicating 2.5 % dose of MPs might pose selective effect on rhizosphere bacterial communities. \u03b2-Diversity of 1.0 % and 2.5 % Bio-MPs were distinctive from the control and other treatments. Microplastics also affected the relative abundance at family level, i.e. as compared to control, Comamonadaceae was higher in all the MPs treatments, Rhizobiaceae was highest in 2.5 % LDPE-MPs and lowest in 2.5 % Bio-MPs. LefSe results showed, as compared to control, Bio-MPs induced more indictive taxa than LDPE-MPs. Our findings evidenced that LDPE-MPs and Bio-MPs exerted profound effects on rhizosphere bacterial communities, and these effects might have far-reaching effects on soil nutrient cycling and plant health in agroecosystems.", "keywords": ["2. Zero hunger", "0301 basic medicine", "03 medical and health sciences", "Low density polyethylene plastic", "13. Climate action", "Microplastics", "16S rRNA", "15. Life on land", "Biodegradable plastic", "Rhizosphere bacterial community", "01 natural sciences", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.apsoil.2022.104649"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2022.104649", "name": "item", "description": "10.1016/j.apsoil.2022.104649", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2022.104649"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-01T00:00:00Z"}}, {"id": "10.3390/microorganisms8101506", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:25Z", "type": "Journal Article", "created": "2020-08-24", "title": "Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant Health", "description": "The targeted application of plant growth promoting rhizobacteria (PGPR) provides the key for a future sustainable agriculture with reduced pesticide application. PGPR interaction with the indigenous microbiota is poorly understood but essential to develop reliable applications. Therefore, Stenotrophomonas rhizophila SPA-P69 was applied as seed coating and in combination with a fungicide based on the active ingredients fludioxonil, metalaxyl-M, captan and ziram. Plant performance and rhizosphere composition of treated and non-treated maize plants of two field trials were analyzed. Plant health was significantly increased by treatment; however overall corn yield was not changed. By applying high-throughput amplicon sequencing of the 16S rRNA and the ITS genes, the bacterial and fungal changes in the rhizosphere due to different treatments were determined. Despite treatments had a significant impact on the rhizosphere microbiota (9- 12%), the field site was identified as main driver (27- 37%). Soil microbiota composition from each site was significantly different, which explains the site-specific effects. In this study we were able to show first indications how PGPR treatments increase plant health via microbiome shifts in a site-specific manner. This way first steps towards a detailed understanding of PGPRs and developments of consistently efficient applications in diverse environments are set.
", "keywords": ["Zea mays", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "plant growth promoting rhizobacteria", "QH301-705.5", "15. Life on land", "maize", "Zea mays", "Article", "12. Responsible consumption", "corn", "03 medical and health sciences", "agricultural_sciences_agronomy", "fungicide", "16S rRNA gene", "ITS", "Biology (General)", "rhizosphere"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/10/1506/pdf"}, {"href": "https://doi.org/10.3390/microorganisms8101506"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms8101506", "name": "item", "description": "10.3390/microorganisms8101506", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms8101506"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-21T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2022.156952", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:59Z", "type": "Journal Article", "created": "2022-06-22", "title": "Integrated organic and inorganic fertilization and reduced irrigation altered prokaryotic microbial community and diversity in different compartments of wheat root zone contributing to improved nitrogen uptake and wheat yield", "description": "Open AccessThe effect of long-term water and integrated fertilization on prokaryotic microorganisms and their regulation for crop nutrient uptake remains unknown. Therefore, the impact of soil water and integrated fertilization after eight years on prokaryotic microbial communities in different compartments of root zone and their association with wheat nitrogen (N) absorption and yield were investigated. The results showed that compared with fertilization treatments (F), water regimes (W) more drastically modulated the prokaryotic microbial community structure and diversity in bulk soil, rhizosphere and endosphere. The increase of irrigation improved the prokaryotic diversity in the rhizosphere and endosphere while decreased the diversity in the bulk soil. Application of organic fertilizers significantly improved soil organic matter (SOM) and nutrient contents, increased rhizosphere and endophytic prokaryotic microbial diversity, and elevated the relative abundance of aerobic ammonia oxidation and nitrification-related functional microorganisms in rhizosphere and endosphere. Increasing irrigation elevated the relative abundance of functional microorganisms related to aerobic ammonia oxidation and nitrification in the rhizosphere and endosphere. Soil water content (SWC) and NH4+-N as well as NO3\u2212-N were key predictors of prokaryotic microbial community composition under W and F treatments, respectively. Appropriate application of irrigation and organic fertilizers increased the relative abundance of some beneficial bacteria such as Flavobacterium. Water and fertilization treatments regulated the prokaryotic microbial communities of bulk soil, rhizosphere and endosphere by altering SWC and SOM, and provided evidence for the modulation of prokaryotic microorganisms to promote nitrogen uptake and wheat yield under long-term irrigation and fertilization. Conclusively, the addition of organic manure (50 %) with inorganic fertilizers (50 %) and reduced amount of irrigation (pre-sowing and jointing-period irrigation) decreased the application amount of chemical fertilizers and water, while increased SOM and nutrient content, improved prokaryotic diversity, and changed prokaryotic microbial community structure in the wheat root zone, resulting in enhanced nutrient uptake and wheat yield.", "keywords": ["0106 biological sciences", "Yield", "Microorganism", "Microbial population biology", "Nitrogen", "Soil Science", "Organic chemistry", "Plant Science", "01 natural sciences", "Environmental science", "Agricultural and Biological Sciences", "Soil", "Symbiotic Nitrogen Fixation in Legumes", "Soil water", "Genetics", "Fertilizers", "Biology", "Irrigation", "Soil Microbiology", "Triticum", "2. Zero hunger", "Soil organic matter", "Soil Fertility", "Physicochemical factors", "Ecology", "Bacteria", "Microbiota", "Marine Microbial Diversity and Biogeography", "Water", "Life Sciences", "04 agricultural and veterinary sciences", "15. Life on land", "Nitrification", "Agronomy", "6. Clean water", "Chemistry", "Human fertilization", "13. Climate action", "Fertilization", "FOS: Biological sciences", "Environmental Science", "Physical Sciences", "Rhizosphere", "Bulk soil", "0401 agriculture", " forestry", " and fisheries", "Prokaryotic microorganisms", "Endosphere", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Nutrient"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2022.156952"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2022.156952", "name": "item", "description": "10.1016/j.scitotenv.2022.156952", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2022.156952"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-10-01T00:00:00Z"}}, {"id": "10.1016/j.eja.2015.09.015", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:08Z", "type": "Journal Article", "created": "2015-10-22", "title": "The Intercropping Common Bean With Maize Improves The Rhizobial Efficiency, Resource Use And Grain Yield Under Low Phosphorus Availability", "description": "In order to better understand how mixed crop cultures mitigate stressful conditions, this study aims to highlight the beneficial effect of the intercropping legume-cereal in enhancing soil phosphorus (P) availability for plant growth and productivity in a P-deficient soil of a northern Algerian agroecosystem. To address this question, common bean (Phaseolus vulgaris L. cv. El Djadida) and maize (Zea mays L. cv. Filou), were grown as sole- and inter-crops in two experimental sites; S1 (P-deficient) and S2 (P-sufficient) during two growing seasons (2011 and 2012). Growth, nodulation and grain yield were assessed and correlated with the rhizosphere soil P availability. Results showed that P availability significantly increased in the rhizosphere of both species, especially in intercropping under the P-deficient soil conditions. This increase was associated with high efficiency in use of the rhizobial symbiosis (high correlation between plant biomass and nodulation), plant growth and resource (nitrogen (N) and P) use efficiency as indicated by higher land equivalent ratio (LER > 1) and N nutrition index (for maize) in intercropping over sole cropping treatments. Moreover, the rhizosphere P availability and nodule biomass were positively correlated (r2 = 0.71, p < 0.01 and r2 = 0.62, p < 0.01) in the intercropped common bean grown in the P-deficient soil during 2011 and 2012. The increased P availability presumably improved biomass and grain yield in intercropping, though it mainly enhanced grain yield in intercropped maize. Our findings suggest that modification in the intercropped common bean rhizosphere-induced parameters facilitated P uptake, plant biomass and grain yield for the intercropped maize under P-deficiency conditions.", "keywords": ["[SDV.SA]Life Sciences [q-bio]/Agricultural sciences", "580", "2. Zero hunger", "[SDV.SA] Life Sciences [q-bio]/Agricultural sciences", "Phosphorus", "04 agricultural and veterinary sciences", "Nodulation", "15. Life on land", "Legumes", "Intercropping", "Algeria", "Rhizosphere", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "0401 agriculture", " forestry", " and fisheries", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Symbiosis"]}, "links": [{"href": "https://doi.org/10.1016/j.eja.2015.09.015"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/European%20Journal%20of%20Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.eja.2015.09.015", "name": "item", "description": "10.1016/j.eja.2015.09.015", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.eja.2015.09.015"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-01-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2008.05.029", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:13Z", "type": "Journal Article", "created": "2008-07-22", "title": "Feasibility Of Phytoextraction To Remediate Cadmium And Zinc Contaminated Soils", "description": "A Cd and Zn contaminated soil was mixed and equilibrated with an uncontaminated, but otherwise similar soil to establish a gradient in soil contamination levels. Growth of Thlaspi caerulescens (Ganges ecotype) significantly decreased the metal concentrations in soil solution. Plant uptake of Cd and Zn exceeded the decrease of the soluble metal concentrations by several orders of magnitude. Hence, desorption of metals must have occurred to maintain the soil solution concentrations. A coupled regression model was developed to describe the transfer of metals from soil to solution and plant shoots. This model was applied to estimate the phytoextraction duration required to decrease the soil Cd concentration from 10 to 0.5 mg kg(-1). A biomass production of 1 and 5 t dm ha(-1) yr(-1) yields a duration of 42 and 11 yr, respectively. Successful phytoextraction operations based on T. caerulescens require an increased biomass production.", "keywords": ["Time Factors", "Industrial Waste", "phytoremediation", "01 natural sciences", "metal-accumulating plants", "Soil", "hyperaccumulator thlaspi-caerulescens", "heavy-metals", "sandy soil", "Life Science", "Soil Pollutants", "Biomass", "0105 earth and related environmental sciences", "polluted soils", "04 agricultural and veterinary sciences", "field", "6. Clean water", "cd", "Thlaspi", "Zinc", "Biodegradation", " Environmental", "zn", "Feasibility Studies", "0401 agriculture", " forestry", " and fisheries", "rhizosphere", "Plant Shoots", "Cadmium"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2008.05.029"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envpol.2008.05.029", "name": "item", "description": "10.1016/j.envpol.2008.05.029", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2008.05.029"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-12-01T00:00:00Z"}}, {"id": "10.1016/j.envres.2019.108608", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:15Z", "type": "Journal Article", "created": "2019-07-26", "title": "Antibiotic resistance gene distribution in agricultural fields and crops. A soil-to-food analysis", "description": "Despite the social concern about the generalization of antibiotic resistance hotspots worldwide, very little is known about the contribution of different potential sources to the global risk. Here we present a quantitative analysis of the distribution of Antibiotic Resistance Genes (ARGs) in soil, rhizospheric soil, roots, leaves and beans in tomato, lettuce and broad beans crops (165 samples in total), grown in nine commercial plots distributed in four geographical zones in the vicinity of Barcelona (North East Spain). We also analyzed five soil samples from a nearby forest, with no record of agricultural activities. DNA samples were analyzed for their content in the ARGs sul1, tetM, qnrS1, blaCTX-M-32, blaOXA-58, mecA, and blaTEM, plus the integron intI1, using qPCR methods. In addition, soil microbiomes from the different plots were analyzed by amplicon-targeted 16S rRNA gene sequencing. Our data show a decreasing gradient of ARG loads from soil to fruits and beans, the latter showing only from 0.1 to 0.01% of the abundance values in soil. The type of crop was the main determinant for both ARG distribution and microbiome composition among the different plots, with minor contributions of geographic location and irrigation water source. We propose that soil amendment and/or fertilization, more than irrigation water, are the main drivers of ARG loads on the edible parts of the crop, and that they should therefore be specifically controlled.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Microbiomes", "Agriculture", "Drug Resistance", " Microbial", "Irrigation water", "15. Life on land", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "qPCR", "Soil", "03 medical and health sciences", "Antibiotic resistance genes", "Genes", " Bacterial", "Spain", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Endophytes", "Food Analysis", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envres.2019.108608"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envres.2019.108608", "name": "item", "description": "10.1016/j.envres.2019.108608", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envres.2019.108608"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-01T00:00:00Z"}}, {"id": "10.1016/j.gde.2018.03.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:29Z", "type": "Journal Article", "created": "2018-04-16", "title": "Micromechanics of root development in soil", "description": "Our understanding of how roots develop in soil may be at the eve of significant transformations. The formidable expansion of imaging technologies enables live observations of the rhizosphere micro-pore architecture at unprecedented resolution. Granular matter physics provides ways to understand the microscopic fluctuations of forces in soils, and the increasing knowledge of plant mechanobiology may shed new lights on how roots perceive soil heterogeneity. This opinion paper exposes how recent scientific achievements may contribute to refresh our views on root growth in heterogeneous environments.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "/dk/atira/pure/subjectarea/asjc/1300/1311", "name=Genetics", "15. Life on land", "Plant Roots", "name=Developmental Biology", "Genetic Heterogeneity", "Soil", "03 medical and health sciences", "13. Climate action", "Rhizosphere", "/dk/atira/pure/subjectarea/asjc/1300/1309", "Mechanical Phenomena"]}, "links": [{"href": "https://doi.org/10.1016/j.gde.2018.03.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Opinion%20in%20Genetics%20%26amp%3B%20Development", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.gde.2018.03.007", "name": "item", "description": "10.1016/j.gde.2018.03.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.gde.2018.03.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-08-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2019.121711", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:45Z", "type": "Journal Article", "created": "2019-11-17", "title": "Effects of plastic mulch film residues on wheat rhizosphere and soil properties", "description": "Plastic residues could accumulate in soils as a consequence of using plastic mulching, which results in a serious environmental concern for agroecosystems. As an alternative, biodegradable plastic films stand as promising products to minimize plastic debris accumulation and reduce soil pollution. However, the effects of residues from traditional and biodegradable plastic films on the soil-plant system are not well studied. In this study, we used a controlled pot experiment to investigate the effects of macro- and micro- sized residues of low-density polyethylene and biodegradable plastic mulch films on the rhizosphere bacterial communities, rhizosphere volatile profiles and soil chemical properties. Interestingly, we identified significant effects of biodegradable plastic residues on the rhizosphere bacterial communities and on the blend of volatiles emitted in the rhizosphere. For example, in treatments with biodegradable plastics, bacteria genera like Bacillus and Variovorax were present in higher relative abundances and volatile compounds like dodecanal were exclusively produced in treatment with biodegradable microplastics. Furthermore, significant differences in soil pH, electrical conductivity and C:N ratio were observed across treatments. Our study provides evidence for both biotic and abiotic impacts of plastic residues on the soil-plant system, suggesting the urgent need for more research examining their environmental impacts on agroecosystems.", "keywords": ["2. Zero hunger", "Volatile Organic Compounds", "Bacteria", "Microplastics", "national", "Plan_S-Compliant_NO", "Biodegradable Plastics", "Biodegradable plastics", "01 natural sciences", "Rhizosphere microbiome", "Soil", "Polyethylene", "13. Climate action", "Rhizosphere", "Soil Pollutants", "Soil properties", "Volatile organic compounds", "Biomass", "Triticum", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2019.121711"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2019.121711", "name": "item", "description": "10.1016/j.jhazmat.2019.121711", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2019.121711"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2013.05.035", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:55Z", "type": "Journal Article", "created": "2013-06-10", "title": "Impact Of Elevated Co2 And Temperature On Soil C And N Dynamics In Relation To Ch4 And N2o Emissions From Tropical Flooded Rice (Oryza Sativa L.)", "description": "A field experiment was carried out to investigate the impact of elevated carbon dioxide (CO2) (CEC, 550 \u03bcmol mol(-1)) and elevated CO2+elevated air temperature (CECT, 550 \u03bcmol mol(-1) and 2\u00b0C more than control chamber (CC)) on soil labile carbon (C) and nitrogen (N) pools, microbial populations and enzymatic activities in relation to emissions of methane (CH4) and nitrous oxide (N2O) in a flooded alluvial soil planted with rice cv. Naveen in open top chambers (OTCs). The labile soil C pools, namely microbial biomass C, readily mineralizable C, water soluble carbohydrate C and potassium permanganate oxidizable C were increased by 27, 23, 38 and 37% respectively under CEC than CC (ambient CO2, 394 \u03bcmol mol(-1)). The total organic carbon (TOC) in root exudates was 28.9% higher under CEC than CC. The labile N fractions were also increased significantly (29%) in CEC than CC. Methanogens and denitrifier populations in rhizosphere were higher under CEC and CECT. As a result, CH4 and N2O-N emissions were enhanced by 26 and 24.6% respectively, under CEC in comparison to open field (UC, ambient CO2, 394 \u03bcmol mol(-1)) on seasonal basis. The global warming potential (GWP) was increased by 25% under CEC than CC. However, emissions per unit of grain yield under elevated CO2 and temperature were similar to those observed at ambient CO2. The stimulatory effect on CH4 and N2O emissions under CEC was linked with the increased amount of soil labile C, C rich root exudates, lowered Eh, higher Fe(+2) concentration and increased activities of methanogens and extracellular enzymes.", "keywords": ["2. Zero hunger", "Tropical Climate", "Chromatography", " Gas", "Nitrogen", "Iron", "Nitrous Oxide", "Temperature", "India", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "Global Warming", "Plant Roots", "Carbon", "6. Clean water", "Soil", "13. Climate action", "Rhizosphere", "Regression Analysis", "0401 agriculture", " forestry", " and fisheries", "Methane", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2013.05.035"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2013.05.035", "name": "item", "description": "10.1016/j.scitotenv.2013.05.035", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2013.05.035"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-09-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2019.01.095", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:58Z", "type": "Journal Article", "created": "2019-01-10", "title": "The Cover Crop Determines The Amf Community Composition In Soil And In Roots Of Maize After A Ten-Year Continuous Crop Rotation", "description": "Intensive agricultural practices are responsible for soil biological degradation. By stimulating indigenous arbuscular mycorrhizal fungi (AMF), cover cropping enhances soil health and promotes agroecosystem sustainability. Still, the legacy effects of cover crops (CCs) and the major factors driving the AM fungal community are not well known; neither is the influence of the specific CC. This work describes a field experiment established in Central Spain to test the effect of replacing winter fallow by barley (Hordeum vulgare L.) or vetch (Vicia sativa L.) during the intercropping of maize (Zea mays L.). We examined the community composition of the AMF in the roots and rhizosphere soil associated with the subsequent cash crop after 10\u202fyears of cover cropping, using Illumina technology. The multivariate analysis showed that the AMF communities under the barley treatment differed significantly from those under fallow, whereas no legacy effect of the vetch CC was detected. Soil organic carbon, electrical conductivity, pH, Ca and microbial biomass carbon were identified as major factors shaping soil AMF communities. Specific AMF taxa were found to play a role in plant uptake of P, Fe, Zn, Mn, and Cd, which may shed light on the functionality of these taxa. In our conditions, the use of barley as a winter CC appears to be an appropriate choice with respect to promotion of AMF populations and biological activity in agricultural soils with intercropping systems. However, more research on CC species and their legacy effect on the microbial community composition and functionality are needed to guide decisions in knowledge-based agriculture.", "keywords": ["Crops", " Agricultural", "2. Zero hunger", "Diversity", "Cover cropping", "Grass", "Arbuscular mycorrhizal fungi", "Agriculture", "Hordeum", "04 agricultural and veterinary sciences", "15. Life on land", "Plant Roots", "Zea mays", "Crop Production", "Legume", "Spain", "Long-term experiment", "Mycorrhizae", "Long-term experiments", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Illumina technology", "Mediterranean climate", "Soil Microbiology", "Mycobiome"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2019.01.095"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2019.01.095", "name": "item", "description": "10.1016/j.scitotenv.2019.01.095", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2019.01.095"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2005.06.023", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:03Z", "type": "Journal Article", "created": "2005-07-28", "title": "Effects Of Elevated Co2 Concentration On Rhizodeposition From Lolium Perenne Grown On Soil Exposed To 9 Years Of Co2 Enrichment", "description": "Abstract The effects of enriched CO 2 atmosphere on partitioning of recently assimilated carbon were investigated in a plant-soil-microorganism system in which Lolium perenne seedlings were planted into cores inserted into the resident soil within a sward that had been treated with elevated CO 2 for 9 consecutive years, under two N fertilisation levels (Swiss FACE experiment). The planted cores were excavated from the ambient (35\u00a0Pa pCO 2 ) and enriched (60\u00a0Pa pCO 2 ) rings at two dates, in spring and autumn, during the growing season. The cores were brought back to the laboratory for 14 C labelling of shoots in order to trace the transfer of recently assimilated C both within the plant and to the soil and microbial biomass. At the spring sampling, high N supply stimulated shoot and total dry matter production. Consistently, high N enhanced the allocation of recently fixed C to shoots, and reduced it to belowground compartments. Elevated CO 2 had no consequences for DM or the pattern of C allocation. At the autumn sampling, at high N plot, yield of L. perenne was stimulated by elevated CO 2 . Consistently, 14 C was preferentially allocated aboveground and, consequently belowground recent C allocation was depressed and rhizodeposition reduced. At both experimental periods, total soil C content was similar in all treatments, providing no evidence for soil carbon sequestration in the Swiss Free Air CO 2 Enrichment experiment (FACE) after 9 years of enrichment. Recently assimilated C and soil C were mineralised faster in soils from enriched rings, suggesting a CO 2 -induced shift in the microbial biomass characteristics (structure, diversity, activity) and/or in the quality of the root-released organic compounds.", "keywords": ["580", "RHIZODEPOSITION", "0106 biological sciences", "2. Zero hunger", "RAY GRASS ANGLAIS", "MINERALISATION", "RHIZOSPHERE RESPIRATION", "04 agricultural and veterinary sciences", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "15. Life on land", "01 natural sciences", "MICROBIAL BIOMASSE", "CARBON SEQUESTRATION", "0401 agriculture", " forestry", " and fisheries", "ELEVATED CO2", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "NITROGEN FERTILISATION"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2005.06.023"}, {"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.2005.06.023", "name": "item", "description": "10.1016/j.soilbio.2005.06.023", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2005.06.023"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-04-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2012.10.013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:10Z", "type": "Journal Article", "created": "2012-11-02", "title": "Inorganic And Organic Carbon Dynamics In A Limed Acid Soil Are Mediated By Plants", "description": "Abstract Lime is commonly used to overcome soil acidification in agricultural production systems; however, its impact on inorganic and organic soil carbon dynamics remains largely unknown. In a column experiment, we monitored rhizosphere effects on lime dissolution, CO2 effluxes, and the concentrations of dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) in leachate from an acidic Kandosol. The experiment consisted of four treatments viz: soil only (control), soil\u00a0+\u00a0lime, soil\u00a0+\u00a0wheat, and soil\u00a0+\u00a0lime\u00a0+\u00a0wheat. We measured CO2-C effluxes at 7, 43 and 98 days after planting (DAP) and leachate was collected at 56 and 101 DAP. The soil CO2-C efflux rate increased significantly with lime addition at 7 and 43 DAP compared to control. At 43 DAP, the largest increase in CO2-C effluxes was observed in the lime\u00a0+\u00a0wheat treatment. However, at 98 DAP similar CO2-C effluxes were observed from wheat and lime\u00a0+\u00a0wheat treatments, suggesting that most of the lime was dissolved in the lime\u00a0+\u00a0wheat treatment. Both DOC and DIC concentrations in the leachate increased significantly with lime and wheat only treatments (cf. control). In contrast to DOC, there was an increase in the DIC concentration in the soil leachate from lime\u00a0+\u00a0wheat treatment columns at 101 DAP (significant wheat\u00a0\u00d7\u00a0lime interaction), thus, accentuating the pronounced role of wheat roots. We conclude that plant mediated dissolution of lime increased the concentration of DIC in the soil leachate, while both liming and presence of plants enhanced DOC leaching.", "keywords": ["2. Zero hunger", "Dissolved inorganic carbon", "Carbon effluxes", "Rhizosphere", "2404 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Liming", "04 agricultural and veterinary sciences", "15. Life on land", "1111 Soil Science", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2012.10.013"}, {"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.2012.10.013", "name": "item", "description": "10.1016/j.soilbio.2012.10.013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2012.10.013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-02-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2023.109259", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:15Z", "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.Ecology Letters (2011) 14: 187\uffe2\uff80\uff93194
AbstractThe degree to which rising atmospheric CO2 will be offset by carbon (C) sequestration in forests depends in part on the capacity of trees and soil microbes to make physiological adjustments that can alleviate resource limitation. Here, we show for the first time that mature trees exposed to CO2 enrichment increase the release of soluble C from roots to soil, and that such increases are coupled to the accelerated turnover of nitrogen (N) pools in the rhizosphere. Over the course of 3\uffe2\uff80\uff83years, we measured in situ rates of root exudation from 420 intact loblolly pine (Pinus taeda L.) roots. Trees fumigated with elevated CO2 (200 p.p.m.v. over background) increased exudation rates (\uffce\uffbcg\uffe2\uff80\uff83C\uffe2\uff80\uff83cm\uffe2\uff88\uff921\uffe2\uff80\uff83root\uffe2\uff80\uff83h\uffe2\uff88\uff921) by 55% during the primary growing season, leading to a 50% annual increase in dissolved organic inputs to fumigated forest soils. These increases in root\uffe2\uff80\uff90derived C were positively correlated with microbial release of extracellular enzymes involved in breakdown of organic N (R2\uffe2\uff80\uff83=\uffe2\uff80\uff830.66; P\uffe2\uff80\uff83=\uffe2\uff80\uff830.006) in the rhizosphere, indicating that exudation stimulated microbial activity and accelerated the rate of soil organic matter (SOM) turnover. In support of this conclusion, trees exposed to both elevated CO2 and N fertilization did not increase exudation rates and had reduced enzyme activities in the rhizosphere. Collectively, our results provide field\uffe2\uff80\uff90based empirical support suggesting that sustained growth responses of forests to elevated CO2 in low fertility soils are maintained by enhanced rates of microbial activity and N cycling fuelled by inputs of root\uffe2\uff80\uff90derived C. To the extent that increases in exudation also stimulate SOM decomposition, such changes may prevent soil C accumulation in forest ecosystems.
", "keywords": ["0106 biological sciences", "Nitrogen", "Plant Exudates", "Pinus taeda", "04 agricultural and veterinary sciences", "15. Life on land", "Carbon Dioxide", "01 natural sciences", "Plant Roots", "Carbon", "Trees", "Soil", "13. Climate action", "Rhizosphere", "North Carolina", "0401 agriculture", " forestry", " and fisheries", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/j.1461-0248.2010.01570.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology%20Letters", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1461-0248.2010.01570.x", "name": "item", "description": "10.1111/j.1461-0248.2010.01570.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1461-0248.2010.01570.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-12-22T00:00:00Z"}}, {"id": "10.1038/s41598-025-00173-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:02Z", "type": "Journal Article", "created": "2025-05-08", "title": "Enhanced understanding of nitrogen fixing bacteria through DNA extraction with polyvinylidene fluoride membrane", "description": "AbstractThe rhizobiota, particularly nitrogen-fixing bacteria, play a crucial role in plant functioning by providing essential nutrients and defense against pathogens. This study investigated the diversity of nitrogen-fixing bacteria in a relatively understudied habitat: technosoils developed from industrial soda production. To analyze the bacterial diversity in the rhizosphere soils of wheat (Triticum aestivum L.) and aster (Tripolium pannonicum Jacq.), regions of the nifH gene were amplified and sequenced from the resident bacterial communities. A polyvinylidene fluoride (PVDF) membrane was employed for metagenomic DNA extraction, enhancing the detection of nitrogen-fixing bacteria. Prior to standard DNA extraction, an enrichment step was conducted in nitrogen-free JMV medium at 26\uffc2\uffa0\uffc2\uffb0C for 24\uffc2\uffa0h, with a modification that replaced soil with the PVDF membrane. This approach enabled a more comprehensive analysis of the rhizosphere bacterial community, revealing that unique amplicon sequence variants (ASVs) in aster and wheat membrane samples accounted for a notable proportion of all ASVs in the dataset (8.5% and 23%, respectively) that were not captured using the standard method. Additionally, our findings demonstrated higher alpha diversity of nitrogen-fixing bacteria in the wheat rhizosphere compared to the aster rhizosphere. In wheat, the dominant genus was Insolitispirillum (38.80%), followed by unclassified genera within Gammaproteobacteria (9.76%) and Rhodospirillaceae (4.74%). In contrast, the aster rhizosphere was predominantly occupied by Azotobacter (95.69%).Soil microbial communities are crucial for plant growth and are already depleted by anthropogenic activities. The application of microbial transplants provides a strategy to restore beneficial soil traits, but less is known about the microbiota of traditional inoculants used in biodynamic agriculture. In this study, we used amplicon sequencing and quantitative PCR to decipher microbial communities of composts, biodynamic manures, and plant preparations from Austria and France. In addition, we investigated the effect of extracts derived from biodynamic manure and compost on the rhizosphere microbiome of apple trees. Microbiota abundance, composition, and diversity of biodynamic manures, plant preparations, and composts were distinct. Microbial abundances ranged between 1010-1011(bacterial 16S rRNA genes) and 109-1011(fungal ITS genes). The bacterial diversity was significantly higher in biodynamic manures compared to compost without discernible differences in abundance. Fungal diversity was not significantly different while abundance was increased in biodynamic manures. The microbial communities of biodynamic manures and plant preparations were specific for each production site, but all contain potentially plant-beneficial bacterial genera. When applied in apple orchards, biodynamic preparations (extracts) had the non-significant effect of reducing bacterial and fungal abundance in apple rhizosphere (4 months post-application), while increasing fungal and lowering bacterial Shannon diversity. One to four months after inoculation, individual taxa indicated differential abundance. We observed the reduction of the pathogenic fungusAlternaria, and the enrichment of potentially beneficial bacterial genera such asPseudomonas.Our study paves way for the science-based adaptation of empirically developed biodynamic formulations under different farming practices to restore the vitality of agricultural soils.Projections of global\uffc2\uffa0rice yields\uffc2\uffa0account for climate change. They do not, however, consider the coupled stresses of impending climate change and arsenic in paddy soils. Here, we show in a greenhouse study that future conditions cause a greater proportion of pore-water arsenite, the more toxic form of arsenic, in the rhizosphere of Californian Oryza sativa L. variety M206, grown on Californian paddy soil. As a result, grain yields decrease by 39% compared to yields at today\uffe2\uff80\uff99s arsenic soil concentrations. In addition, future climatic conditions cause a nearly twofold increase of grain inorganic arsenic concentrations. Our findings indicate that climate-induced changes in soil arsenic behaviour and plant response will lead to currently unforeseen losses in rice grain productivity and quality. Pursuing rice varieties and crop management practices that alleviate the coupled stresses of soil arsenic and change in climatic factors are needed to overcome the currently impending food crisis.Citrate (Cit) and Deferoxamine B (DFOB) are two important organic ligands coexisting in soils with distinct different affinities for metal ions. It has been theorized that siderophores and weak organic ligands play a synergistic role during the transport of micronutrients in the rhizosphere, but the geochemical controls of this process remain unknown. Here we test the hypothesis that gradients in pH and ion strength regulate and enable the cooperation. To this end, first we use potentiometric titrations to identify the dominant Zn(II)\uffe2\uff80\uff93Cit and Zn(II)\uffe2\uff80\uff93DFOB complexes and to determine their ionic strength dependent stability constants between 0 and 1\uffc2\uffa0mol\uffc2\uffa0dm\uffe2\uff88\uff923. We parametrise the Extended Debye-H\uffc3\uffbcckel (EDH) equation and determine accurate intrinsic association constants (log\uffce\uffb20) for the formation of the complexes present. The speciation model developed confirms the presence of [Zn(Cit)]\uffe2\uff88\uff92, [Zn(HCit)], [Zn2(Cit)2(OH)2]4\uffe2\uff88\uff92, and [Zn(Cit)2]4\uffe2\uff88\uff92, with [Zn(Cit)]\uffe2\uff88\uff92 and [Zn2(Cit)2(OH)2]4\uffe2\uff88\uff92 the dominant species in the pH range relevant to rhizosphere. We propose the existence of a\uffc2\uffa0new [Zn(Cit)(OH)3]4\uffe2\uff88\uff92 complex above pH 10. We also verify the existence of two hexadentate Zn(II)\uffe2\uff80\uff93DFOB species, i.e., [Zn(DFOB)]\uffe2\uff88\uff92 and [Zn(HDFOB)], and of one tetradentate species [Zn(H2DFOB)]+. Second, we identify the pH and ionic strength dependent ligand exchange points (LEP) of Zn with citrate and DFOB and the stability windows for Zn(II)\uffe2\uff80\uff93Cit and Zn(II)\uffe2\uff80\uff93DFOB complexes in NaCl and rice soil solutions. We find that the LEPs fall within the pH and ionic strength gradients expected in rhizospheres and that the stability windows for Zn(II)\uffe2\uff80\uff93citrate and Zn(II)\uffe2\uff80\uff93DFOB, i.e., low and high affinity ligands, can be distinctly set off. This suggests that pH and ion strength gradients allow for Zn(II) complexes with citrate and DFOB to dominate in different parts of the rhizosphere and this explains why mixtures of low and high affinity ligands increase leaching of micronutrients in soils. Speciation models of soil solutions using newly determined association constants demonstrate that the presence of dissolved organic matter and inorganic ligands (i.e., bicarbonate, phosphate, sulphate, or chlorides) do neither affect the position of the LEP nor the width of the stability windows significantly. In conclusion, we demonstrate that cooperative and synergistic ligand interaction between low and high affinity ligands is a valid mechanism for\uffc2\uffa0controlling zinc transport in the rhizosphere and possibly in other environmental reservoirs such as in the phycosphere. Multiple production of weak and strong ligands is therefore a valid strategy of plants and other soil organisms to improve access to micronutrients.Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
", "keywords": ["0301 basic medicine", "570", "Microscopy", "Silicon", "0303 health sciences", "Temperature", "root-microbe interactions", "Equipment Design", "Biological Sciences", "Environment", "15. Life on land", "Plant Roots", "630", "Fluorescence", "Soil", "03 medical and health sciences", "Seedlings", "Calibration", "Rhizosphere", "Image Processing", " Computer-Assisted", "environmental imaging", "rhizosphere", "Soil Microbiology", "Bacillus subtilis", "Lactuca"]}, "links": [{"href": "https://eprints.whiterose.ac.uk/178939/18/e2109176118.full.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.2109176118"}, {"href": "https://doi.org/10.1073/pnas.2109176118"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.2109176118", "name": "item", "description": "10.1073/pnas.2109176118", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.2109176118"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-13T00:00:00Z"}}, {"id": "10.17863/cam.81466", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:20:15Z", "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
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.
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.
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.
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.
", "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": "10.1093/jxb/erac437", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:40Z", "type": "Journal Article", "created": "2022-11-02", "title": "In situcontrol of root\u2013bacteria interactions using optical trapping in transparent soil", "description": "AbstractBacterial attachment on root surfaces is an important step preceding the colonization or internalization and subsequent infection of plants by pathogens. Unfortunately, bacterial attachment is not well understood because the phenomenon is difficult to observe. Here we assessed whether this limitation could be overcome using optical trapping approaches. We have developed a system based on counter-propagating beams and studied its ability to guide Pectobacterium atrosepticum (Pba) cells to different root cell types within the interstices of transparent soils. Bacterial cells were successfully trapped and guided to root hair cells, epidermal cells, border cells, and tissues damaged by laser ablation. Finally, we used the system to quantify the bacterial cell detachment rate of Pba cells on root surfaces following reversible attachment. Optical trapping techniques could greatly enhance our ability to deterministically characterize mechanisms linked to attachment and formation of biofilms in the rhizosphere.Root architectural phenotypes are promising targets for crop breeding, but root architectural effects on microbial associations in agricultural fields are not well understood. Architecture determines the location of microbial associations within root systems, which, when integrated with soil vertical gradients, determines the functions and the metabolic capability of rhizosphere microbial communities. We argue that variation in root architecture in crops has important implications for root exudation, microbial recruitment and function, and the decomposition and fate of root tissues and exudates. Recent research has shown that the root microbiome changes along root axes and among root classes, that root tips have a unique microbiome, and that root exudates change within the root system depending on soil physicochemical conditions. Although fresh exudates are produced in larger amounts in root tips, the rhizosphere of mature root segments also plays a role in influencing soil vertical gradients. We argue that more research is needed to understand specific root phenotypes that structure microbial associations and discuss candidate root phenotypes that may determine the location of microbial hotspots within root systems with relevance to agricultural systems.Chemical exchange often serves as the first step in plant\uffe2\uff80\uff93microbe interactions and exchanges of various signals, nutrients, and metabolites continue throughout the interaction. Here, we highlight the role of metabolite exchanges and metabolic crosstalk in the microbiome\uffe2\uff80\uff93root\uffe2\uff80\uff93shoot\uffe2\uff80\uff93environment nexus. Roots secret a diverse set of metabolites; this assortment of root exudates, including secondary metabolites such as benzoxazinoids, coumarins, flavonoids, indolic compounds, and terpenes, shapes the rhizosphere microbiome. In turn, the rhizosphere microbiome affects plant growth and defense. These inter-kingdom chemical interactions are based on a metabolic circular economy, a seemingly wasteless system in which rhizosphere members exchange (i.e. consume, reuse, and redesign) metabolites. This review also describes the recently discovered phenomenon \uffe2\uff80\uff9cSystemically Induced Root Exudation of Metabolites\uffe2\uff80\uff9d in which the rhizosphere microbiome governs plant metabolism by inducing systemic responses that shift the metabolic profiles of root exudates. Metabolic exchange in the rhizosphere is based on chemical gradients that form specific microhabitats for microbial colonization and we describe recently developed high-resolution methods to study chemical interactions in the rhizosphere. Finally, we propose an action plan to advance the metabolic circular economy in the rhizosphere for sustainable solutions to the cumulative degradation of soil health in agricultural lands.Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12\uffe2\uff80\uff9324\uffe2\uff80\uff89h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700\uffe2\uff80\uff931000\uffe2\uff80\uff89\uffc2\uffb5m from the tip. Bacteria accumulated predominantly in confined pore spaces within 200\uffe2\uff80\uff89\uffc2\uffb5m from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.