{"type": "FeatureCollection", "features": [{"id": "10.1016/j.scitotenv.2017.02.229", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:16:35Z", "type": "Journal Article", "created": "2017-03-03", "title": "The Influence Of Tree Species On Small Scale Spatial Heterogeneity Of Soil Respiration In A Temperate Mixed Forest", "description": "Soil respiration is the largest terrestrial carbon flux into the atmosphere, and different tree species could directly influence root derived respiration and indirectly regulate soil respiration rates by altering soil chemical and microbial properties. In this study, we assessed the small scale spatial heterogeneity of soil respiration and the microbial community below the canopy of three dominant tree species (Korean pine (Pinus koraiensis), Mongolian oak (Quercus mongolica), and Manchuria ash (Fraxinus mandshurica)) in a temperate mixed forest in Northeast China. Soil respiration differed significantly during several months and increased in the order of oak Terrestrial biosphere\uffe2\uff80\uff93atmosphere carbon dioxide (CO 2 ) exchange is dominated by tropical forests, where photosynthetic carbon (C) uptake is thought to be phosphorus (P)-limited. In P-poor tropical forests, P may also limit organic matter decomposition and soil C losses. We conducted a field-fertilization experiment to show that P fertilization stimulates soil respiration in a lowland tropical rain forest in Costa Rica. In the early wet season, when soluble organic matter inputs to soil are high, P fertilization drove large increases in soil respiration. Although the P-stimulated increase in soil respiration was largely confined to the dry-to-wet season transition, the seasonal increase was sufficient to drive an 18% annual increase in CO 2 efflux from the P-fertilized plots. Nitrogen (N) fertilization caused similar responses, and the net increases in soil respiration in response to the additions of N and P approached annual soil C fluxes in mid-latitude forests. Human activities are altering natural patterns of tropical soil N and P availability by land conversion and enhanced atmospheric deposition. Although our data suggest that the mechanisms driving the observed respiratory responses to increased N and P may be different, the large CO 2 losses stimulated by N and P fertilization suggest that knowledge of such patterns and their effects on soil CO 2 efflux is critical for understanding the role of tropical forests in a rapidly changing global C cycle.

", "keywords": ["2. Zero hunger", "Tropical Climate", "Atmosphere", "Temperature", "Humidity", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "Plant Roots", "Trees", "Soil", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Nutritional Physiological Phenomena", "Biomass", "Seasons", "Fertilizers"]}, "links": [{"href": "https://doi.org/10.1073/pnas.0600989103"}, {"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.0600989103", "name": "item", "description": "10.1073/pnas.0600989103", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.0600989103"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-07-05T00:00:00Z"}}, {"id": "10.1016/j.tplants.2018.08.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:16:57Z", "type": "Journal Article", "created": "2018-09-18", "title": "Growing Research Networks on Mycorrhizae for Mutual Benefits", "description": "Research on mycorrhizal interactions has traditionally developed into separate disciplines addressing different organizational levels. This separation has led to an incomplete understanding of mycorrhizal functioning. Integration of mycorrhiza research at different scales is needed to understand the mechanisms underlying the context dependency of mycorrhizal associations, and to use mycorrhizae for solving environmental issues. Here, we provide a road map for the integration of mycorrhiza research into a unique framework that spans genes to ecosystems. Using two key topics, we identify parallels in mycorrhiza research at different organizational levels. Based on two current projects, we show how scientific integration creates synergies, and discuss future directions. Only by overcoming disciplinary boundaries, we will achieve a more comprehensive understanding of the functioning of mycorrhizal associations.", "keywords": ["580", "0301 basic medicine", "570", "synergies", "0303 health sciences", "500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::579 Mikroorganismen", " Pilze", " Algen", "Integration", "mycorrhiza", "integration", "579", "Plant Roots", "Article", "Organizational level", "03 medical and health sciences", "Synergies", "500 Naturwissenschaften und Mathematik::580 Pflanzen (Botanik)::580 Pflanzen (Botanik)", "international", "Mycorrhizae", "Mycorrhiza", "Symbiosis", "organizational level"]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1677180/1/Ferlian%20et%20al_TIPS.pdf"}, {"href": "https://doi.org/10.1016/j.tplants.2018.08.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Trends%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.tplants.2018.08.008", "name": "item", "description": "10.1016/j.tplants.2018.08.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.tplants.2018.08.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-01T00:00:00Z"}}, {"id": "10.1021/acs.est.0c01051", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:02Z", "type": "Journal Article", "created": "2020-04-14", "title": "Effects of Microplastic Fibers and Drought on Plant Communities", "description": "Microplastics in soils can affect plant performance, as shown in studies using individual plants. However, we currently have no information about potential effects on plant community productivity and structure. In a plant community consisting of seven plant species that co-occur in temperate grassland ecosystems, we thus investigated the effect of microplastics (i.e., microfibers) and drought, a factor with which microfibers might interact, on plant productivity and community structure. Our results showed that at the community level, shoot and root mass decreased with drought but increased with microfibers, an effect likely linked to reduced soil bulk density, improved aeration, and better penetration of roots in the soil. Additionally, we observed that microfibers affected plant community structure. Species such as Calamagrostis, invasive in Europe, and the allelophatic Hieracium, became more dominant with microfibers, while species that potentially have the ability to facilitate the establishment of other plant species (e.g., Holcus), decreased in biomass. As microfibers affect plant species dominance, the examination of cascade effects on ecosystem functions should be a high priority for future research.", "keywords": ["2. Zero hunger", "Microplastics", "15. Life on land", "Grassland", "Plant Roots", "01 natural sciences", "6. Clean water", "Droughts", "Europe", "Soil", "Biomass", "Plastics", "Ecosystem", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.0c01051"}, {"href": "https://doi.org/10.1021/acs.est.0c01051"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.0c01051", "name": "item", "description": "10.1021/acs.est.0c01051", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.0c01051"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-14T00:00:00Z"}}, {"id": "10.1021/acs.est.7b06136", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:03Z", "type": "Journal Article", "created": "2018-02-21", "title": "A Model of Uranium Uptake by Plant Roots Allowing for Root-Induced Changes in the soil", "description": "We develop a model with which to study the poorly understood mechanisms of uranium (U) uptake by plants. The model is based on equations for transport and reaction of U and acids and bases in the rhizosphere around cylindrical plant roots. It allows for the speciation of U with hydroxyl, carbonate, and organic ligands in the soil solution; the nature and kinetics of sorption reactions with the soil solid; and the effects of root-induced changes in rhizosphere pH. A sensitivity analysis showed the importance of soil sorption and speciation parameters as influenced by pH and CO2 pressure; and of root geometry and root-induced acid-base changes linked to the form of nitrogen taken up by the root. The root absorbing coefficient for U, relating influx to the concentration of U species in solution at the root surface, was also important. Simplified empirical models of U uptake by different plant species and soil types need to account for these effects.", "keywords": ["580", "2. Zero hunger", "Soil", "550", "Rhizosphere", "Soil Pollutants", " Radioactive", "Uranium", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "Plant Roots", "01 natural sciences", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.7b06136"}, {"href": "https://doi.org/10.1021/acs.est.7b06136"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.7b06136", "name": "item", "description": "10.1021/acs.est.7b06136", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.7b06136"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-21T00:00:00Z"}}, {"id": "10.1021/acs.jafc.1c02821", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:03Z", "type": "Journal Article", "created": "2021-08-04", "title": "Determination of the Effect of Co-cultivation on the Production and Root Exudation of Flavonoids in Four Legume Species Using LC\u2013MS/MS Analysis", "description": "Flavonoids play a key role in the regulation of plant-plant and plant-microbe interactions, and factors determining their release have been investigated in most of the common forage legumes. However, little is known about the response of flavonoid production and release to co-cultivation with other crop species. This study investigated alterations in the concentration of flavonoids in plant tissues and root exudates in four legumes [alfalfa (Medicago sativa L.), black medic (Medicago polymorpha L.), crimson clover (Trifolium incarnatum L.), and subterranean clover (Trifolium subterraneum L.)] co-cultivated with durum wheat [Triticum turgidum subsp. durum (Desf.) Husn.]. For this purpose, we carried out two experiments in a greenhouse, one with glass beads as growth media for root exudate extraction and one with soil as growth media for flavonoid detection in shoot and root biomass, using LC-MS/MS analysis. This study revealed that interspecific competition with wheat negatively affected legume growth and led to a significant reduction in shoot and root biomass compared with the same legume species grown in monoculture. In contrast, the concentration of flavonoids significantly increased both in legume biomass and in root exudates. Changes in flavonoid concentration involved daidzein, genistein, medicarpin, and formononetin, which have been found to be involved in legume nodulation and regulation of plant-plant interaction. We hypothesize that legumes responded to the co-cultivation with wheat by promoting nodulation and increasing exudation of allelopathic compounds, respectively, to compensate for the lack of nutrients caused by the presence of wheat in the cultivation system and to reduce the competitiveness of neighboring plants. Future studies should elucidate the bioactivity of flavonoid compounds in cereal-legume co-cultivation systems and their specific role in the nodulation process and inter-specific plant interactions such as potential effects on weeds.", "keywords": ["Flavonoids", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "medicarpin", "living mulch", "root exudate", "Fabaceae", "15. Life on land", "plant interactions", "Plant Roots", "03 medical and health sciences", "Tandem Mass Spectrometry", "wheat", "allelopathy", "intercropping", "wheat", " intercropping", " living mulch", " root exudate", " plant interactions", " medicarpin", " allelopathy", "Chromatography", " Liquid"]}, "links": [{"href": "https://www.iris.sssup.it/bitstream/11382/540035/1/Leoni%20et%20al_2021_jafc_1c02821.pdf"}, {"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.jafc.1c02821"}, {"href": "https://doi.org/10.1021/acs.jafc.1c02821"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Agricultural%20and%20Food%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.jafc.1c02821", "name": "item", "description": "10.1021/acs.jafc.1c02821", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.jafc.1c02821"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-04T00:00:00Z"}}, {"id": "10.1021/jf040077x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:05Z", "type": "Journal Article", "created": "2004-08-18", "title": "Effects Of Selenium Treatments On Potato (Solanum Tuberosum L.) Growth And Concentrations Of Soluble Sugars And Starch", "description": "The effect of selenium (Se) treatments on potato growth and Se, soluble sugar, and starch accumulation was investigated. Potato plants were cultivated in quartz sand without or with sodium selenate (0, 0.075, 0.3 mg Se kg(-1) sand). In young potato plants, Se treatment resulted in higher starch concentrations in upper leaves. The tuber yield of Se-treated potato plants was higher and composed of relatively few but large tubers. At harvest, the starch concentration in tubers did not differ significantly between treatments. The higher Se addition (0.3 mg Se kg(-1)) may have delayed the aging of stolons and roots, which was observed as high concentrations of soluble sugar and starch. Together with the earlier results showing elevated starch concentration in Se-treated lettuce, the findings of this research justify the conclusion that Se has positive effects also on potato carbohydrate accumulation and possibly on yield formation.", "keywords": ["0106 biological sciences", "2. Zero hunger", "Dose-Response Relationship", " Drug", "Carbohydrates", "Starch", "04 agricultural and veterinary sciences", "Selenic Acid", "Plant Roots", "01 natural sciences", "Plant Leaves", "Plant Tubers", "Selenium", "0401 agriculture", " forestry", " and fisheries", "Selenium Compounds", "Solanum tuberosum"], "contacts": [{"organization": "Helin\u00e4 Hartikainen, Mervi Sepp\u00e4nen, Marja Turakainen,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1021/jf040077x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Agricultural%20and%20Food%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/jf040077x", "name": "item", "description": "10.1021/jf040077x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/jf040077x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2004-07-27T00:00:00Z"}}, {"id": "10.1021/jf3005788", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:05Z", "type": "Journal Article", "created": "2012-05-25", "title": "Selenate-Enriched Urea Granules Are A Highly Effective Fertilizer For Selenium Biofortification Of Paddy Rice Grain", "description": "This study examined the effects of applied selenium (Se) species, time of application, method of application, and soil water management regimen on the accumulation of Se in rice plants. Plants were grown to maturity in a temperature- and humidity-controlled growth chamber using three water management methods: field capacity (FC), submerged until harvest, and submerged and drained 2 weeks before harvest. Two Se species, selenate (SeO4(2-)) and selenite (SeO3(2-)), were applied at a rate equivalent to 30 g ha(-1). Four application methods were employed as follows: (i) Se applied at soil preparation, (ii) Se-enriched urea granules applied to floodwater at heading; (iii) foliar Se applied at heading; and (iv) fluid fertilizer Se applied to soil or floodwater at heading. Total Se concentrations in rice grains, husks, leaves, culms, and roots were measured, as well as Se speciation in grains from the Se-enriched urea granule treatment. Highest Se concentrations in the grain occurred with SeO4(2-) and with fertilizer applied at heading stage; SeO4(2-)-enriched urea granules applied at heading increased grain Se concentrations 5-6-fold (by 450-600 \u03bcg kg(-1)) compared to the control (no fertilizer Se applied) in all water treatments. Under paddy conditions other Se fertilization strategies were much less effective. Drainage before harvesting caused Se to accumulate in/on rice roots, possibly through adsorption onto iron plaque on roots. Rice grains contained Se mainly in the organic form as selenomethionine (SeM), which comprised >90% of the total grain Se in treatments fertilized with SeO4(2-)-enriched urea granules. The results of this study clearly show that of the fertilizer strategies tested biofortification of Se in rice grains can best be achieved in lowland rice by broadcast application of SeO4(2-)-enriched urea granules to floodwater at heading stage.", "keywords": ["0106 biological sciences", "selenate", "Selenic Acid", "Plant Roots", "01 natural sciences", "Selenate", "biofortification", "Selenium", "Soil", "Fertilizer", "Urea", "selenium", "Fertilizers", "Selenomethionine", "Se enriched urea", "580", "2. Zero hunger", "rice", "Water", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "fertilizer", "6. Clean water", "Plant Leaves", "Se-enriched urea", "Selenite", "0401 agriculture", " forestry", " and fisheries", "Rice", "selenite", "Biofortification"]}, "links": [{"href": "https://doi.org/10.1021/jf3005788"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Agricultural%20and%20Food%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/jf3005788", "name": "item", "description": "10.1021/jf3005788", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/jf3005788"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-06-05T00:00:00Z"}}, {"id": "10.1023/b:egah.0000039597.75201.57", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:10Z", "type": "Journal Article", "created": "2004-08-27", "title": "Effects Of The Interactions Between Selenium And Phosphorus On The Growth And Selenium Accumulation In Rice (Oryza Sativa)", "description": "The solution culture, paddy soil culture and the simulation experiments in the laboratory were conducted to clarify the interactions between selenium and phosphorus, and its effects on the growth and selenium accumulation in rice. Results revealed that a suitable supply of selenium could promote rice growth and excessive selenium could injure rice plant, causing lower biomass, especially in the roots. The supply of selenite could enhance the selenium contents of rice shoots and roots in solution culture and in soil culture. The selenium concentrations in roots were much higher than those in shoots supplied with the same rates of selenium and phosphorus. The interaction between selenium and phosphorus was evident. When the phosphorus supply increased to meet the needs of plant growth, phosphorus could promote absorption and accumulation of selenium in the shoots. If the phosphorus supply was excessive, phosphorus could inhibit the accumulation of selenium in the shoots at the lower selenite level (2 micromol l(-1)), but could not at the higher selenite level (10 micromol l(-1)). With the supply of phosphate increased, the selenium concentrations in the roots decreased significantly at both selenite levels. The presence of phosphate could decrease Se sorption on the soil surface and increase the selenium concentration in the soil solution. The concentrations of selenium in shoots and roots supplied with 0.08 g kg(-1) phosphorus were lower than those with no phosphorus supplied. With the increase of phosphorus added to 0.4 g kg(-1), the selenium concentration in shoots and roots increased. The effect of phosphorus on the concentration was statistically significant at all three selenium levels.", "keywords": ["0106 biological sciences", "2. Zero hunger", "Selenium", "0401 agriculture", " forestry", " and fisheries", "Oryza", "Phosphorus", "Biomass", "04 agricultural and veterinary sciences", "15. Life on land", "Plant Roots", "01 natural sciences", "6. Clean water", "Absorption"], "contacts": [{"organization": "Dan Wang, Xinru Jiang, Qinghe Liu, Zongwei Cao,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1023/b:egah.0000039597.75201.57"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Geochemistry%20and%20Health", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1023/b:egah.0000039597.75201.57", "name": "item", "description": "10.1023/b:egah.0000039597.75201.57", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1023/b:egah.0000039597.75201.57"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2004-06-01T00:00:00Z"}}, {"id": "10.1038/ismej.2007.89", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:14Z", "type": "Journal Article", "created": "2007-10-25", "title": "The Effect Of Experimental Warming On The Root-Associated Fungal Community Of Salix Arctica", "description": "Abstract

The effect of experimental warming on the root-associated fungal community of arctic willow (Salix arctica) was studied in three distinct habitats at a tundra site in the Canadian High Arctic. Plots were passively warmed for 5\uffe2\uff80\uff937 years using open-top chambers and compared to control plots at ambient temperature. Fungal communities were assessed using terminal restriction fragment length polymorphisms. We found the following: (1) the root-associated fungal community in these high arctic tundra habitats is highly diverse; (2) site and soil characteristics are the most important drivers of community structure and (3) warming increased the density of different genotypes on individual root sections but has not (yet) affected the composition, richness or evenness of the community. The change in genotype density in the warmed plots was associated with an increase in PCR amplification efficiency, suggesting that increased C allocation belowground is increasing the overall biomass of the fungal community.

", "keywords": ["0106 biological sciences", "0301 basic medicine", "Canada", "Fungi", "Salix", "15. Life on land", "Plant Roots", "01 natural sciences", "Heating", "03 medical and health sciences", "Cluster Analysis", "DNA", " Fungal", "Ecosystem", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"], "contacts": [{"organization": "Gregory H. R. Henry, Keith N. Egger, Kei E. Fujimura,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1038/ismej.2007.89"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2007.89", "name": "item", "description": "10.1038/ismej.2007.89", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2007.89"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-10-25T00:00:00Z"}}, {"id": "10.1038/s41396-022-01193-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:16Z", "type": "Journal Article", "created": "2022-01-18", "title": "Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks", "description": "Abstract

Inter-kingdom belowground carbon (C) transfer is a significant, yet hidden, biological phenomenon, due to the complexity and highly dynamic nature of soil ecology. Among key biotic agents influencing C allocation belowground are ectomycorrhizal fungi (EMF). EMF symbiosis can extend beyond the single tree-fungus partnership to form common mycorrhizal networks (CMNs). Despite the high prevalence of CMNs in forests, little is known about the identity of the EMF transferring the C and how these in turn affect the dynamics of C transfer. Here, Pinus halepensis and Quercus calliprinos saplings growing in forest soil were labeled using a 13CO2 labeling system. Repeated samplings were applied during 36 days to trace how 13C was distributed along the tree-fungus-tree pathway. To identify the fungal species active in the transfer, mycorrhizal fine root tips were used for DNA-stable isotope probing (SIP) with 13CO2 followed by sequencing of labeled DNA. Assimilated 13CO2 reached tree roots within four days and was then transferred to various EMF species. C was transferred across all four tree species combinations. While Tomentella ellisii was the primary fungal mediator between pines and oaks, Terfezia pini, Pustularia spp., and Tuber oligospermum controlled C transfer among pines. We demonstrate at a high temporal, quantitative, and taxonomic resolution, that C from EMF host trees moved into EMF and that C was transferred further to neighboring trees of similar and distinct phylogenies.

", "keywords": ["0301 basic medicine", "Quercus", "Soil", "0303 health sciences", "03 medical and health sciences", "Mycorrhizae", "Carbon Dioxide", "15. Life on land", "Plant Roots", "Carbon", "Trees"]}, "links": [{"href": "https://www.nature.com/articles/s41396-022-01193-z.pdf"}, {"href": "https://doi.org/10.1038/s41396-022-01193-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41396-022-01193-z", "name": "item", "description": "10.1038/s41396-022-01193-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41396-022-01193-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-18T00:00:00Z"}}, {"id": "10.1038/s41467-019-11993-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:17Z", "type": "Journal Article", "created": "2019-09-04", "title": "Plant roots increase both decomposition and stable organic matter formation in boreal forest soil", "description": "Abstract

Boreal forests are ecosystems with low nitrogen (N) availability that store globally significant amounts of carbon (C), mainly in plant biomass and soil organic matter (SOM). Although crucial for future climate change predictions, the mechanisms controlling boreal C and N pools are not well understood. Here, using a three-year field experiment, we compare SOM decomposition and stabilization in the presence of roots, with exclusion of roots but presence of fungal hyphae and with exclusion of both roots and fungal hyphae. Roots accelerate SOM decomposition compared to the root exclusion treatments, but also promote a different soil N economy with higher concentrations of organic soil N compared to inorganic soil N accompanied with the build-up of stable SOM-N. In contrast, root exclusion leads to an inorganic soil N economy (i.e., high level of inorganic N) with reduced stable SOM-N build-up. Based on our findings, we provide a framework on how plant roots affect SOM decomposition and stabilization.

", "keywords": ["roots", "0106 biological sciences", "330", "Nitrogen", "Science", "ta1171", "Hyphae", "Models", " Biological", "Plant Roots", "01 natural sciences", "Article", "LITTER DECOMPOSITION", "Soil", "POLYPHENOLS", "CARBON SEQUESTRATION", "soil organic matter", "Taiga", "SDG 13 - Climate Action", "SUGAR MAPLE", "Biomass", "Organic Chemicals", "forest ecology", "106026 Ecosystem research", "Ecosystem", "Soil Microbiology", "TANNINS", "2. Zero hunger", "106022 Mikrobiologie", "ECTOMYCORRHIZAL FUNGI", "MYCORRHIZA", "Q", "ta1182", "Forestry", "04 agricultural and veterinary sciences", "Plants", "15. Life on land", "Carbon", "Environmental sciences", "NITROGEN", "Boreal forests", "106026 \u00d6kosystemforschung", "13. Climate action", "SDG 13 \u2013 Ma\u00dfnahmen zum Klimaschutz", "106022 Microbiology", "ta1181", "0401 agriculture", " forestry", " and fisheries", "COMMUNITIES", "STORAGE"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-11993-1.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-11993-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-11993-1", "name": "item", "description": "10.1038/s41467-019-11993-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-11993-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-09-04T00:00:00Z"}}, {"id": "10.1038/s41467-019-14197-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:17Z", "type": "Journal Article", "created": "2020-01-24", "title": "High-quality genome sequence of white lupin provides insight into soil exploration and seed quality", "description": "Abstract

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n\uffe2\uff80\uff89=\uffe2\uff80\uff8950, 451\uffe2\uff80\uff89Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.

", "keywords": ["Repetitive Sequences", " Nucleic Acid/genetics", "0301 basic medicine", "[SDV]Life Sciences [q-bio]", "Plant Roots/genetics", "Gene Dosage", "Plant Science", "Crop", "Alkaloids/chemistry", "Plant Roots", "Gene", "Repetitive Sequences", "630", "Agricultural and Biological Sciences", "Domestication", "Soil", "Models", "Symbiotic Nitrogen Fixation in Legumes", "Gene Duplication", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_3224", "Plant Proteins/metabolism", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Genome", "Q", "http://aims.fao.org/aos/agrovoc/c_27583", "Life Sciences", "Transcriptome/genetics", "http://aims.fao.org/aos/agrovoc/c_92382", "Polymorphism", " Single Nucleotide/genetics", "Lupinus", "[SDV] Life Sciences [q-bio]", "Protein Crop", "Seeds", "http://aims.fao.org/aos/agrovoc/c_5956", "White (mutation)", "Single Nucleotide/genetics", "Sequence Analysis", "Genome", " Plant", "expression des g\u00e8nes", "http://aims.fao.org/aos/agrovoc/c_4464", "Synteny/genetics", "Evolution", "Lupin Seeds", "Science", "Centromere", "Lupinus/genetics", "Polymorphism", " Single Nucleotide", "Article", "g\u00e9nomique", "Evolution", " Molecular", "Evolution and Nutritional Properties of Lupin Seeds", "physiologie v\u00e9g\u00e9tale", "03 medical and health sciences", "Alkaloids", "Genetic", "Nucleic Acid/genetics", "Seeds/physiology", "Centromere/genetics", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Polymorphism", "Biology", "Ecology", " Evolution", " Behavior and Systematics", "Repetitive Sequences", " Nucleic Acid", "Sequence assembly", "http://aims.fao.org/aos/agrovoc/c_25189", "Ecotype", "Models", " Genetic", "g\u00e9nome", "Botany", "Molecular", "Genetic Variation", "Molecular Sequence Annotation", "Plant", "DNA", "Sequence Analysis", " DNA", "s\u00e9quence nucl\u00e9otidique", "15. Life on land", "http://aims.fao.org/aos/agrovoc/c_27527", "Agronomy", "Plant Leaves", "Evolution and Ecology of Endophyte-Grass Symbiosis", "Lupinus albus", "FOS: Biological sciences", "Genomic Structural Variation", "Plant Leaves/metabolism", "Gene expression", "Transcriptome", "am\u00e9lioration des plantes"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-14197-9.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-14197-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-14197-9", "name": "item", "description": "10.1038/s41467-019-14197-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-14197-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-24T00:00:00Z"}}, {"id": "10.1038/s41467-023-42911-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:17Z", "type": "Journal Article", "created": "2023-11-07", "title": "Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus", "description": "Abstract

Legume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we name SYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.Forest ecosystems release large amounts of carbon to the atmosphere from fine\uffe2\uff80\uff90root respiration (Rr), but the control of this flux and its temperature sensitivity (Q10) are poorly understood. We attempted to: (1) identify the factors limiting this flux using additions of glucose and an electron transport uncoupler (carbonyl cyanide m\uffe2\uff80\uff90chlorophenylhydrazone); and (2) improve yearly estimates of Rr by directly measuring its Q10in situ using temperature\uffe2\uff80\uff90controlled cuvettes buried around intact, attached roots. The proximal limits of Rr of loblolly pine (Pinus taeda L.) trees exposed to free\uffe2\uff80\uff90air CO2 enrichment (FACE) and N fertilization were seasonally variable; enzyme capacity limited Rr in the winter, and a combination of substrate supply and adenylate availability limited Rr in summer months. The limiting factors of Rr were not affected by elevated CO2 or N fertilization. Elevated CO2 increased annual stand\uffe2\uff80\uff90level Rr by 34% whereas the combination of elevated CO2 and N fertilization reduced Rr by 40%. Measurements of in situ Rr with high temporal resolution detected diel patterns that were correlated with canopy photosynthesis with a lag of 1\uffe2\uff80\uff83d or less as measured by eddy covariance, indicating a dynamic link between canopy photosynthesis and root respiration. These results suggest that Rr is coupled to daily canopy photosynthesis and increases with carbon allocation below ground.

", "keywords": ["580", "0106 biological sciences", "Analysis of Variance", "Nitrates", "Atmosphere", "Nitrogen", "Cell Respiration", "Temperature", "Pinus taeda", "Carbon Dioxide", "15. Life on land", "Plant Roots", "01 natural sciences", "Carbon", "Trees", "Glucose", "Oxygen Consumption", "050101 - Ecological Impacts of Climate Change", "13. Climate action", "North Carolina", "Seasons", "Least-Squares Analysis", "Photosynthesis", "Fertilizers", "Ecosystem"]}, "links": [{"href": "https://doi.org/10.1111/j.1365-3040.2008.01869.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%2C%20Cell%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1365-3040.2008.01869.x", "name": "item", "description": "10.1111/j.1365-3040.2008.01869.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-3040.2008.01869.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-10-06T00:00:00Z"}}, {"id": "10.1038/s41598-018-36294-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:20Z", "type": "Journal Article", "created": "2018-12-11", "title": "Decomposer diversity increases biomass production and shifts aboveground-belowground biomass allocation of common wheat", "description": "Abstract

Biodiversity is well known to enhance many ecosystem functions, but empirical evidence for the role of soil biodiversity for plant biomass production and allocation is scarce. Here we studied the effects of animal decomposer diversity (1, 2, and 4 species as well as a control without any decomposers) on the biomass production and aboveground-belowground biomass allocation of common wheat using two earthworm and two Collembola species using an additive design in two soil management types (organic and mineral fertilizer treatments) in a microcosm experiment. Shoot (+11%), spike (+7%), and root biomass (+56%), increased significantly with increasing decomposer diversity, and these effects were consistent across the two soil management types. Notably, decomposer diversity effects were stronger on root than on shoot biomass, significantly decreasing the shoot-to-root ratio (\uffe2\uff88\uff9227%). Increased plant biomass production was positively correlated with a decomposer richness-induced increase in soil water nitrate concentrations five weeks after the start of the experiment. However, elevated soil nitrate concentrations did not cause significantly higher plant tissue nitrogen concentrations and nitrogen amounts, suggesting that additional mechanisms might be at play. Consistent decomposer diversity effects across soil management types indicate that maintaining soil biodiversity is a robust and sustainable strategy to enhance crop yield.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "Nitrogen", "Water", "Biodiversity", "15. Life on land", "Plant Roots", "7. Clean energy", "Article", "Resource Allocation", "Soil", "03 medical and health sciences", "Animals", "Biomass", "Oligochaeta", "Ecosystem", "Plant Shoots", "Triticum"]}, "links": [{"href": "https://www.nature.com/articles/s41598-018-36294-3.pdf"}, {"href": "https://doi.org/10.1038/s41598-018-36294-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-018-36294-3", "name": "item", "description": "10.1038/s41598-018-36294-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-018-36294-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-17T00:00:00Z"}}, {"id": "10.1038/s42003-022-04178-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:21Z", "type": "Journal Article", "created": "2022-11-17", "title": "Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities", "description": "Abstract

Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.Stable Ca isotopes are fractionated between bones, urine and blood of animals and between soils, roots and leaves of plants by >1000\uffe2\uff80\uff89ppm for the 44Ca/40Ca ratio. These isotopic variations have important implications to understand Ca transport and fluxes in living organisms; however, the mechanisms of isotopic fractionation are unclear. Here we present ab initio calculations for the isotopic fractionation between various aqueous species of Ca and show that this fractionation can be up to 3000\uffe2\uff80\uff89ppm. We show that the Ca isotopic fractionation between soil solutions and plant roots can be explained by the difference of isotopic fractionation between the different first shell hydration degree of Ca2+ and that the isotopic fractionation between roots and leaves is controlled by the precipitation of Ca-oxalates. The isotopic fractionation between blood and urine is due to the complexation of heavy Ca with citrate and oxalates in urine. Calculations are presented for additional Ca species that may be useful to interpret future Ca isotopic measurements.

", "keywords": ["Calcium Isotopes", "Chemical Fractionation", "[SDU.ASTR] Sciences of the Universe [physics]/Astrophysics [astro-ph]", "FE", "Plant Roots", "01 natural sciences", "Article", "Bone and Bones", "[SDU] Sciences of the Universe [physics]", "Soil", "PHOSPHATE", "Animals", "Humans", "ION", "MONITOR", "0105 earth and related environmental sciences", "ENVIRONMENT", "CA", "PLASMA", "Temperature", "Plants", "6. Clean water", "3. Good health", "Plant Leaves", "MAGNESIUM", "13. Climate action", "OXALATE", "[SDU.STU] Sciences of the Universe [physics]/Earth Sciences", "BONE"], "contacts": [{"organization": "Moynier, Fr\u00e9d\u00e9ric, Fujii, Toshiyuki,", "roles": ["creator"]}]}, "links": [{"href": "https://www.nature.com/articles/srep44255.pdf"}, {"href": "https://doi.org/10.1038/srep44255"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep44255", "name": "item", "description": "10.1038/srep44255", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep44255"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-09T00:00:00Z"}}, {"id": "10.1071/fp22294", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:30Z", "type": "Journal Article", "created": "2023-05-10", "title": "A meta-analysis of plant tissue O2 dynamics", "description": "

Adequate tissue O2 supply is crucial for plant function. We aimed to identify the environmental conditions and plant characteristics that affect plant tissue O2 status. We extracted data and performed meta-analysis on >1500 published tissue O2 measurements from 112 species. Tissue O2 status ranged from anoxic conditions in roots to >53\u00a0kPa in submerged, photosynthesising shoots. Using information-theoretic model selection, we identified \u2018submergence\u2019, \u2018light\u2019, \u2018tissue type\u2019 as well as \u2018light\u00a0\u00d7\u00a0submergence\u2019 interaction as significant drivers of tissue O2 status. Median O2 status were especially low (<50% of atmospheric equilibrium) in belowground rhizomes, potato (Solanum tuberosum) tubers and root nodules. Mean shoot and root O2 were ~25% higher in light than in dark when shoots had atmospheric contact. However, light showed a significant interaction with submergence on plant O2, with a submergence-induced 44% increase in light, compared with a 42% decline in dark, relative to plants with atmospheric contact. During submergence, ambient water column O2 and shoot tissue O2 correlated stronger in darkness than in light conditions. Although use of miniaturised Clark-type O2 electrodes has enhanced understanding of plant O2 dynamics, application of non-invasive methods in plants is still lacking behind its widespread use in mammalian tissues.

", "keywords": ["Oxygen", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Water", "15. Life on land", "Photosynthesis", "Darkness", "Plant Roots"]}, "links": [{"href": "https://air.uniud.it/bitstream/11390/1246924/1/FP22294.pdf"}, {"href": "https://doi.org/10.1071/fp22294"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Functional%20Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1071/fp22294", "name": "item", "description": "10.1071/fp22294", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1071/fp22294"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-05-10T00:00:00Z"}}, {"id": "10.1073/pnas.2201072119", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:34Z", "type": "Journal Article", "created": "2022-07-18", "title": "Ethylene inhibits rice root elongation in compacted soil via ABA- and auxin-mediated mechanisms", "description": "

Soil compaction represents a major agronomic challenge, inhibiting root elongation and impacting crop yields. Roots use ethylene to sense soil compaction as the restricted air space causes this gaseous signal to accumulate around root tips. Ethylene inhibits root elongation and promotes radial expansion in compacted soil, but its mechanistic basis remains unclear. Here, we report that ethylene promotes abscisic acid (ABA) biosynthesis and cortical cell radial expansion. Rice mutants of ABA biosynthetic genes had attenuated cortical cell radial expansion in compacted soil, leading to better penetration. Soil compaction-induced ethylene also up-regulates the auxin biosynthesis gene OsYUC8 . Mutants lacking OsYUC8 are better able to penetrate compacted soil. The auxin influx transporter OsAUX1 is also required to mobilize auxin from the root tip to the elongation zone during a root compaction response. Moreover, osaux1 mutants penetrate compacted soil better than the wild-type roots and do not exhibit cortical cell radial expansion. We conclude that ethylene uses auxin and ABA as downstream signals to modify rice root cell elongation and radial expansion, causing root tips to swell and reducing their ability to penetrate compacted soil. Soil warming has the potential to alter both soil and plant processes that affect carbon storage in forest ecosystems. We have quantified these effects in a large, long-term (7-y) soil-warming study in a deciduous forest in New England. Soil warming has resulted in carbon losses from the soil and stimulated carbon gains in the woody tissue of trees. The warming-enhanced decay of soil organic matter also released enough additional inorganic nitrogen into the soil solution to support the observed increases in plant carbon storage. Although soil warming has resulted in a cumulative net loss of carbon from a New England forest relative to a control area over the 7-y study, the annual net losses generally decreased over time as plant carbon storage increased. In the seventh year, warming-induced soil carbon losses were almost totally compensated for by plant carbon gains in response to warming. We attribute the plant gains primarily to warming-induced increases in nitrogen availability. This study underscores the importance of incorporating carbon\uffe2\uff80\uff93nitrogen interactions in atmosphere\uffe2\uff80\uff93ocean\uffe2\uff80\uff93land earth system models to accurately simulate land feedbacks to the climate system.

", "keywords": ["Atmosphere", "Nitrogen", "Temperature", "Plant Development", "04 agricultural and veterinary sciences", "Plants", "15. Life on land", "Models", " Biological", "Plant Roots", "01 natural sciences", "Carbon", "Trees", "Soil", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Ecosystem", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1073/pnas.1018189108"}, {"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.1018189108", "name": "item", "description": "10.1073/pnas.1018189108", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.1018189108"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-05-23T00:00:00Z"}}, {"id": "10.1073/pnas.0403491101", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:33Z", "type": "Journal Article", "created": "2004-06-22", "title": "Fine-Root Production Dominates Response Of A Deciduous Forest To Atmospheric Co2 Enrichment", "description": "

Fine-root production and turnover are important regulators of the biogeochemical cycles of ecosystems and key components of their response to global change. We present a nearly continuous 6-year record of fine-root production and mortality from minirhizotron analysis of a closed-canopy, deciduous sweetgum forest in a free-air CO 2 enrichment experiment. Annual production of fine roots was more than doubled in plots with 550 ppm CO 2 compared with plots in ambient air. This response was the primary component of the sustained 22% increase in net primary productivity. Annual fine-root mortality matched annual production, and the mean residence time of roots was not altered by elevated CO 2 , but peak fine-root standing crop in midsummer was significantly higher in CO 2 -enriched plots, especially deeper in the soil profile. The preferential allocation of additional carbon to fine roots, which have a fast turnover rate in this species, rather than to stemwood reduces the possibility of long-term enhancement by elevated CO 2 of carbon sequestration in biomass. However, sequestration of some of the fine-root carbon in soil pools is not precluded, and there may be other benefits to the tree from a seasonally larger and deeper fine-root system. Root-system dynamics can explain differences among ecosystems in their response to elevated atmospheric CO 2 ; hence, accurate assessments of carbon flux and storage in forests in a globally changing atmosphere must account for this unseen and difficult-to-measure component.

", "keywords": ["0106 biological sciences", "Time Factors", "Atmosphere", "Nitrogen", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "Plant Roots", "Tennessee", "01 natural sciences", "Trees", "Soil", "Liquidambar", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Seasons", "Ecosystem"]}, "links": [{"href": "https://doi.org/10.1073/pnas.0403491101"}, {"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.0403491101", "name": "item", "description": "10.1073/pnas.0403491101", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.0403491101"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2004-06-21T00:00:00Z"}}, {"id": "10.1073/pnas.2109176118", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:33Z", "type": "Journal Article", "created": "2021-02-13", "title": "Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere", "description": "Abstract

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": "10.1073/pnas.2406373122", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:34Z", "type": "Journal Article", "created": "2025-02-05", "title": "Abscisic acid signaling gates salt-induced responses of plant roots", "description": "

Soil salinity presents a dual challenge for plants, involving both osmotic and ionic stress. In response, plants deploy distinct yet interconnected mechanisms to cope with these facets of salinity stress. In this investigation, we observed a substantial overlap in the salt (NaCl)-induced transcriptional responses of Arabidopsis roots with those triggered by osmotic stress or the plant stress hormone abscisic acid (ABA), as anticipated. Notably, a specific cluster of genes responded uniquely to sodium (Na + ) ions and are not regulated by the known monovalent cation sensing mechanism MOCA1 . Surprisingly, expression of sodium-induced genes exhibited a negative correlation with the ABA response and preceded the activation of genes induced by the osmotic stress component of salt. Elevated exogenous ABA levels resulted in the complete abolition of sodium-induced responses. Consistently, the ABA insensitive snrk2.2/2.3 double mutant displayed prolonged sodium-induced gene expression, coupled with increased root cell damage and root swelling under high salinity conditions. Moreover, ABA biosynthesis and signaling mutants were unable to redirect root growth to avoid high sodium concentrations and had increased sodium accumulation in the shoot. In summary, our findings unveil an unexpected and pivotal role for ABA signaling in mitigating cellular damage induced by salinity stress and modulating sodium-induced responses in plant roots. Previous laboratory studies have suggested selection for root hair traits in future crop breeding to improve resource use efficiency and stress tolerance. However, data on the interplay between root hairs and open-field systems, under contrasting soils and climate conditions, are limited. As such, this study aims to experimentally elucidate some of the impacts that root hairs have on plant performance on a field scale.

Methods

A field experiment was set up in Scotland for two consecutive years, under contrasting climate conditions and different soil textures (i.e. clay loam vs. sandy loam). Five barley (Hordeum vulgare) genotypes exhibiting variation in root hair length and density were used in the study. Root hair length, density and rhizosheath weight were measured at several growth stages, as well as shoot biomass, plant water status, shoot phosphorus (P) accumulation and grain yield.

Key Results

Measurements of root hair density, length and its correlation with rhizosheath weight highlighted trait robustness in the field under variable environmental conditions, although significant variations were found between soil textures as the growing season progressed. Root hairs did not confer a notable advantage to barley under optimal conditions, but under soil water deficit root hairs enhanced plant water status and stress tolerance resulting in a less negative leaf water potential and lower leaf abscisic acid concentration, while promoting shoot P accumulation. Furthermore, the presence of root hairs did not decrease yield under optimal conditions, while root hairs enhanced yield stability under drought.

Conclusions

Selecting for beneficial root hair traits can enhance yield stability without diminishing yield potential, overcoming the breeder\uffe2\uff80\uff99s dilemma of trying to simultaneously enhance both productivity and resilience. Therefore, the maintenance or enhancement of root hairs can represent a key trait for breeding the next generation of crops for improved drought tolerance in relation to climate change.Gypsum drylands are widespread worldwide. In these arid ecosystems, the ability of different species to access different water sources during drought is a key determining factor of the composition of plant communities. Gypsum crystallization water could be a relevant source of water for shallow-rooted plants, but the segregation in the use of this source of water among plants remains unexplored. We analysed the principal water sources used by 20 species living in a gypsum hilltop, the effect of rooting depth and gypsum affinity, and the interaction of the plants with the soil beneath them.

Methods

We characterized the water stable isotope composition, \uffce\uffb4\uffe2\uff80\uff8a2H and \uffce\uffb4\uffe2\uff80\uff8a18O, of plant xylem water and related it to the free and gypsum crystallization water extracted from different depths throughout the soil profile and the groundwater, in both spring and summer. Bayesian isotope mixing models were used to estimate the contribution of water sources to plant xylem sap.

Key Results

In spring, all species used free water from the top soil as the main source. In summer, there was segregation in water sources used by different species depending on their rooting depth, but not on their gypsum affinity. Gypsum crystallization water was the main source for most shallow-rooted species, whereas free water from 50 to 100 cm depth was the main source for deep-rooted species. We detected plant\uffe2\uff80\uff93soil interactions in spring, and indirect evidence of possible hydraulic lift by deep-rooted species in summer.

Conclusions

Plants coexisting in gypsum communities segregate their hydrological niches according to their rooting depth. Crystallization water of gypsum represents an unaccounted for, vital source for most of the shallow-rooted species growing on gypsum drylands. Thus, crystallization water helps shallow-rooted species to endure arid conditions, which eventually accounts for the maintenance of high biodiversity in these specialized ecosystems.Soil salinity, in both natural and managed environments, is highly heterogeneous, and understanding how plants respond to this spatiotemporal heterogeneity is increasingly important for sustainable agriculture in the era of global climate change. While the vast majority of research on crop response to salinity utilizes homogeneous saline conditions, a much smaller, but important, effort has been made in the past decade to understand plant molecular and physiological responses to heterogeneous salinity mainly by using split-root studies. These studies have begun to unravel how plants compensate for water/nutrient deprivation and limit salt stress by optimizing root-foraging in the most favourable parts of the soil.

Scope

This paper provides an overview of the patterns of salinity heterogeneity in rain-fed and irrigated systems. We then discuss results from split-root studies and the recent progress in understanding the physiological and molecular mechanisms regulating plant responses to heterogeneous root-zone salinity and nutrient conditions. We focus on mechanisms by which plants (salt/nutrient sensing, root-shoot signalling and water uptake) could optimize the use of less-saline patches within the root-zone, thereby enhancing growth under heterogeneous soil salinity conditions. Finally, we place these findings in the context of defining future research priorities, possible irrigation management and crop breeding opportunities to improve productivity from salt-affected lands.

", "keywords": ["Nutrient heterogeneity", "Water uptake", "Root-to-shoot signalling", "Salinity", "550", "Plant Biology & Botany", "Plant Biology", "Irrigation; nutrient heterogeneity; phytohormones; root foraging; root-to-shoot signalling; salt sensing; stomatal conductance; water uptake", "Stomatal conductance", "Salt sensing", "Plant Roots", "630", "12. Responsible consumption", "root foraging", "Soil", "Irrigation", "salt sensing", "Root foraging", "580", "2. Zero hunger", "Ecology", "Forestry Sciences", "Research", "nutrient heterogeneity", "Water", "15. Life on land", "6. Clean water", "root-to-shoot signalling", "phytohormones", "Phytohormones", "stomatal conductance", "13. Climate action", "Zero Hunger", "water uptake"]}, "links": [{"href": "https://eprints.lancs.ac.uk/id/eprint/166913/1/21783_2_merged_1643798007.pdf"}, {"href": "https://academic.oup.com/aob/article-pdf/129/5/499/43374309/mcac022.pdf"}, {"href": "https://escholarship.org/content/qt7t32v7cc/qt7t32v7cc.pdf"}, {"href": "https://doi.org/10.1093/aob/mcac022"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Annals%20of%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/aob/mcac022", "name": "item", "description": "10.1093/aob/mcac022", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/aob/mcac022"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-16T00:00:00Z"}}, {"id": "10.1093/femsec/fiw024", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:45Z", "type": "Journal Article", "created": "2016-02-06", "title": "Mycorrhizal Fungal Communities Respond To Experimental Elevation Of Soil Ph And P Availability In Temperate Hardwood Forests", "description": "Many forests are affected by chronic acid deposition, which can lower soil pH and limit the availability of nutrients such as phosphorus (P), but the response of mycorrhizal fungi to changes in soil pH and P availability and how this affects tree acquisition of nutrients is not well understood. Here, we describe an ecosystem-level manipulation in 72 plots, which increased pH and/or P availability across six forests in Ohio, USA. Two years after treatment initiation, mycorrhizal fungi on roots were examined with molecular techniques, including 454-pyrosequencing. Elevating pH significantly increased arbuscular mycorrhizal (AM) fungal colonization and total fungal biomass, and affected community structure of AM and ectomycorrhizal (EcM) fungi, suggesting that raising soil pH altered both mycorrhizal fungal communities and fungal growth. AM fungal taxa were generally negatively correlated with recalcitrant P pools and soil enzyme activity, whereas EcM fungal taxa displayed variable responses, suggesting that these groups respond differently to P availability. Additionally, the production of extracellular phosphatase enzymes in soil decreased under elevated pH, suggesting a shift in functional activity of soil microbes with pH alteration. Thus, our findings suggest that elevating pH increased soil P availability, which may partly underlie the mycorrhizal fungal responses we observed.", "keywords": ["Fungi", "Phosphorus", "04 agricultural and veterinary sciences", "Forests", "Hydrogen-Ion Concentration", "15. Life on land", "Plant Roots", "Trees", "Soil", "Mycorrhizae", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1093/femsec/fiw024"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiw024", "name": "item", "description": "10.1093/femsec/fiw024", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiw024"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-02-04T00:00:00Z"}}, {"id": "10.1093/femsec/fiz133", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:45Z", "type": "Journal Article", "created": "2019-08-22", "title": "Restriction of plant roots in boreal forest organic soils affects the microbial community but does not change the dominance from ectomycorrhizal to saprotrophic fungi", "description": "ABSTRACT

Boreal forest soils store significant amounts of carbon and are cohabited by saprotrophic and ectomycorrhizal fungi (ECM). The \uffe2\uff80\uff98Gadgil effect\uffe2\uff80\uff99 implies antagonistic interactions between saprotrophic fungi and ECM. Plant photosynthates support the competitive fitness of the ECM, and may also shape the soil bacterial communities. Many \uffe2\uff80\uff98Gadgil effect\uffe2\uff80\uff99 experiments have focused on litter layer (OL) or have litter and root-fragments present, and thus possibly favor the saprotrophs. We compared how the restriction of plant roots and exudates affect soil microbial community structures in organic soil (mixed OF and OH). For this, we established a 3-yr field experiment with 3 different mesh treatments affecting the penetration of plant roots and external fungal hyphae. Exclusion of plant photosynthates induced modest changes in both fungal and bacterial community structures, but not to potential functionality of the microbial community. The microbial community was resilient towards rather short-term disturbances. Contrary to the \uffe2\uff80\uff98Gadgil effect\uffe2\uff80\uff99, mesh treatments restricting the entrance of plant roots and external fungal hyphae did not favor saprotrophs that originally inhabited the soil. Thus, we propose that different substrate preferences (fresh litter vs. fermented or humified soil), rather than antagonism, maintain the spatial separation of saprotrophs and mycorrhizal fungi in boreal forest soils.

", "keywords": ["0301 basic medicine", "570", "Hyphae", "577", "Plant Roots", "ectomycorrhiza", "Trees", "Soil", "03 medical and health sciences", "boreal forest soil", "Mycorrhizae", "Taiga", "saprotrophs", "Soil Microbiology", "2. Zero hunger", "0303 health sciences", "Microbiota", "Fungi", "Plants", "15. Life on land", "Gadgil effect", "Carbon", "functional gene profile", "13. Climate action", "ta1181", "microbial community"]}, "links": [{"href": "http://academic.oup.com/femsec/article-pdf/95/9/fiz133/29808832/fiz133.pdf"}, {"href": "https://doi.org/10.1093/femsec/fiz133"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiz133", "name": "item", "description": "10.1093/femsec/fiz133", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiz133"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-23T00:00:00Z"}}, {"id": "10.1093/jxb/erac437", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:46Z", "type": "Journal Article", "created": "2022-11-02", "title": "In situcontrol of root\u2013bacteria interactions using optical trapping in transparent soil", "description": "Abstract

Bacterial 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.Excess water can induce flooding stress resulting in yield loss, even in wetland crops such as rice (Oryza). However, traits from species of wild Oryza have already been used to improve tolerance to abiotic stress in cultivated rice. This study aimed to establish root responses to sudden soil flooding among eight wild relatives of rice with different habitat preferences benchmarked against three genotypes of O. sativa. Plants were raised hydroponically, mimicking drained or flooded soils, to assess the plasticity of adventitious roots. Traits included were apparent permeance (PA) to O2 of the outer part of the roots, radial water loss, tissue porosity, apoplastic barriers in the exodermis, and root anatomical traits. These were analysed using a plasticity index and hierarchical clustering based on principal component analysis. For example, O. brachyantha, a wetland species, possessed very low tissue porosity compared with other wetland species, whereas dryland species O. latifolia and O. granulata exhibited significantly lower plasticity compared with wetland species and clustered in their own group. Most species clustered according to growing conditions based on PA, radial water loss, root porosity, and key anatomical traits, indicating strong anatomical and physiological responses to sudden soil flooding.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.Salinity stress constrains lateral root (LR) growth and severely affects plant growth. Auxin signaling regulates LR formation, but the molecular mechanism by which salinity affects root auxin signaling and whether salt induces other pathways that regulate LR development remains unknown. In Arabidopsis thaliana, the auxin-regulated transcription factor LATERAL ORGAN BOUNDARY DOMAIN 16 (LBD16) is an essential player in LR development under control conditions. Here, we show that under high-salt conditions, an alternative pathway regulates LBD16 expression. Salt represses auxin signaling but, in parallel, activates ZINC FINGER OF ARABIDOPSIS THALIANA 6 (ZAT6), a transcriptional activator of LBD16. ZAT6 activates LBD16 expression, thus contributing to downstream cell wall remodeling and promoting LR development under high-salt conditions. Our study thus shows that the integration of auxin-dependent repressive and salt-activated auxin-independent pathways converging on LBD16 modulates root branching under high-salt conditions.Soil salinity is a major contributor to crop yield losses. To improve our understanding of root responses to salinity, we developed and exploited a real-time salt-induced tilting assay. This assay follows root growth upon both gravitropic and salt challenges, revealing that root bending upon tilting is modulated by Na+ ions, but not by osmotic stress. Next, we measured this salt-specific response in 345 natural Arabidopsis (Arabidopsis thaliana) accessions and discovered a genetic locus, encoding the cell wall-modifying enzyme EXTENSIN ARABINOSE DEFICIENT TRANSFERASE (ExAD) that is associated with root bending in the presence of NaCl (hereafter salt). Extensins are a class of structural cell wall glycoproteins known as hydroxyproline (Hyp)-rich glycoproteins, which are posttranslationally modified by O-glycosylation, mostly involving Hyp-arabinosylation. We show that salt-induced ExAD-dependent Hyp-arabinosylation influences root bending responses and cell wall thickness. Roots of exad1 mutant seedlings, which lack Hyp-arabinosylation of extensin, displayed increased thickness of root epidermal cell walls and greater cell wall porosity. They also showed altered gravitropic root bending in salt conditions and a reduced salt-avoidance response. Our results suggest that extensin modification via Hyp-arabinosylation is a unique salt-specific cellular process required for the directional response of roots exposed to salinity.During nutrient scarcity, plants can adapt their developmental strategy to maximize their chance of survival. Such plasticity in development is underpinned by hormonal regulation, which mediates the relationship between environmental cues and developmental outputs. In legumes, endosymbiosis with nitrogen-fixing bacteria (rhizobia) is a key adaptation for supplying the plant with nitrogen in the form of ammonium. Rhizobia are housed in lateral root-derived organs termed nodules that maintain an environment conducive to Nitrogenase in these bacteria. Several phytohormones are important for regulating the formation of nodules, with both positive and negative roles proposed for gibberellin (GA). In this study, we determine the cellular location and function of bioactive GA during nodule organogenesis using a genetically encoded second-generation GA biosensor, GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula. We find endogenous bioactive GA accumulates locally at the site of nodule primordia, increasing dramatically in the cortical cell layers, persisting through cell divisions, and maintaining accumulation in the mature nodule meristem. We show, through misexpression of GA-catabolic enzymes that suppress GA accumulation, that GA acts as a positive regulator of nodule growth and development. Furthermore, increasing or decreasing GA through perturbation of biosynthesis gene expression can increase or decrease the size of nodules, respectively. This is unique from lateral root formation, a developmental program that shares common organogenesis regulators. We link GA to a wider gene regulatory program by showing that nodule-identity genes induce and sustain GA accumulation necessary for proper nodule formation.Rhizobial infection of legume roots during development of nitrogen fixing root nodules occurs either intracellularly though plant derived infection threads traversing the epidermal and cortical cell layers to deliver the bacteria or intercellularly via bacterial entry between epidermal plant cells. Although, around 25% of all legume genera are postulated to be intercellularly infected, the pathways and mechanisms supporting this process has remained virtually unexplored due to lack of genetically amenable legumes that have this infection mode. In this study, we report that the model legume Lotus japonicus is infected intercellularly by Rhizobium sp. IRBG74 and demonstrate that the resources available in Lotus enable insight into the genetic requirements and the fine-tuning of the pathway governing intercellular infection. Inoculation of Lotus mutants shows that Ern1 and RinRK1 are dispensable for intercellular infection in contrast to intracellular infection. Other symbiotic genes, including Nfr5, SymRK, CCaMK, Epr3, Cyclops, Nin, Nsp1, Nsp2, Cbs and Vpy1 are equally important for both entry modes. Comparative RNAseq analysis of roots inoculated with IRBG74 revealed a distinctive transcriptome response compared to intracellular colonization. In particular, a number of cytokinin-related genes were differentially regulated. Corroborating this observation cyp735A and ipt4 cytokinin biosynthesis mutants were significantly affected in their nodulation with IRBG74 while lhk1 cytokinin receptor mutants did not form any nodules. These results indicate that a differential requirement for cytokinin signalling conditions intercellular rhizobial entry and highlight the distinct modalities of the inter- and intra-cellular infection mechanisms.

", "keywords": ["name=Physiology", "580", "0301 basic medicine", "/dk/atira/pure/subjectarea/asjc/1300/1314", "0303 health sciences", "/dk/atira/pure/subjectarea/asjc/1300/1311", "571", "Regular Issue", "name=Genetics", "/dk/atira/pure/subjectarea/asjc/1100/1110", "Plant Roots", "03 medical and health sciences", "Gene Expression Regulation", " Plant", "Calcium-Calmodulin-Dependent Protein Kinases", "Lotus", "name=Plant Science", "Root Nodules", " Plant", "Plant Proteins", "Rhizobium", "Signal Transduction"]}, "links": [{"href": "http://academic.oup.com/plphys/article-pdf/185/3/1131/37166752/kiaa049.pdf"}, {"href": "https://doi.org/10.1093/plphys/kiaa049"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/plphys/kiaa049", "name": "item", "description": "10.1093/plphys/kiaa049", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/plphys/kiaa049"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-31T00:00:00Z"}}, {"id": "10.1093/plphys/kiae458", "type": "Feature", "geometry": null, "properties": {"updated": "2026-10-06T16:17:47Z", "type": "Journal Article", "created": "2024-08-28", "title": "Leaf Gas Film 1 promotes glycerol ester accumulation and formation of a tight root barrier to radial O2 loss in rice", "description": "Abstract

Rice (Oryza sativa L.) and many other wetland plants form an apoplastic barrier in the outer parts of the roots to restrict radial O2 loss to the rhizosphere during soil flooding. This barrier facilitates longitudinal internal O2 diffusion via gas-filled tissues from shoot to root apices, enabling root growth in anoxic soils. We tested the hypothesis that Leaf Gas Film 1 (LGF1), which influences leaf hydrophobicity in rice, plays a crucial role in tight outer apoplastic barrier formation in rice roots. We examined the roots of a rice mutant (dripping wet leaf 7, drp7) lacking functional LGF1, its wild type, and an LGF1 overexpression line for their capacity to develop outer apoplastic barriers that restrict radial O2 loss. We quantified the chemical composition of the outer part of the root and measured radial O2 diffusion from intact roots. The drp7 mutant exhibited a weak barrier to radial O2 loss compared to the wild type. However, introducing functional LGF1 into the mutant fully restored tight barrier function. The formation of a tight barrier to radial O2 loss was associated with increased glycerol ester levels in exodermal cells, rather than differences in total root suberization or lignification. These results demonstrate that, in addition to its role in leaf hydrophobicity regulation, LGF1 plays an important role in controlling the function of the outer apoplastic barriers in roots. Our study suggests that increased deposition of glycerol esters in the suberized root exodermis establishes a tight barrier to radial O2 loss in rice roots.