{"type": "FeatureCollection", "features": [{"id": "10.5281/zenodo.16310622", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-30T16:24:15Z", "type": "Dataset", "title": "Dataset for substrate stoichiometry drive the divergent accumulation of plant and microbial necromass carbon", "description": "To optimize the conversion of exogenous C into soil organic C, we manipulated the substrate stoichiometry (SS) match the requirements ranging from oligotrophs to copiotrophs. We assumed the stoichiometric ratios of fungi (C:N:P:S=10,000:1034:110:94) and bacteria (C:N:P:S=10,000:2004:494: 264) reflected substrate requirements of oligotrophs and copiotrophs. This study provided different SS levels by applying varying amounts of straw and N, P, and S. A total of five treatment groups were established: straw\u2011amended soil with no nutrient addition (NPS0), NPS0 with nutrient additions to meet the metabolic requirements from fungi (NPS1) to bacteria (NPS3), and a control soil (CK). The straw, cut into 2\u20135 mm pieces, was mixed with soil at a rate of 2 g per 100 g dry soil. The SS was regulated by adding or not adding the nutrient solutions (NS1, NS2 or NS3) containing ammonium nitrate, potassium dihydrogen phosphate, and ammonium sulfate (pH = 7). The concentrations of N, P, and S in NS1 were 6.42, 1.79, and 0.95 g L\u22121, in NS2 were 19.50, 3.52, and 1.90 g L\u22121, and in NS3 were 30.72, 9.98, and 4.23 g L\u22121, respectively. Topsoil (0\u201320 cm) and subsoil (20\u201340 cm) samples (8 kg each) were collected, sieved at 2 mm, and air-dry. The SS was regulated by adding 1 ml of NS1, NS2, or NS3 to 100 g of dry topsoil on a clean and smooth plastic sheet. The soil moisture was then adjusted to 60% field capacity with distilled water, followed by the addition and mixing of 2 g straw fragments. The mixture was then transferred to nylon mesh bags and sealed (aperture: 0.048 mm, length: 20 cm, and width: 15 cm). The subsoil was treated in the same manner. Nine replicates were maintained for each treatment for both topsoil or subsoil. Three soil pits (length: 1.5 m, width: 0.5 m, depth: 0.4 m) spaced at 0.6 m apart were dug in the field, and the topsoil and subsoil were stored separately. Three replicates of each treatment for subsoil were arranged in two rows (spaced approximately 20 cm) and vertically placed at 20\u201340 cm in each pit. Each pit was backfilled with the original subsoil. The same procedure was followed to fill the pits with the replicates of the five treatments for topsoil. All replicates from one pit were collected at 30, 90, and 150 days post-sowing, then brought back to the laboratory with dry ice and stored at \u201380\u2103. This study primarily investigated the following parameters: including (1) amino sugars, lignin phenols, soil water content, soil organic C (SOC), available N (AN), and available P (SAP); (2) C, N, and P cycling enzyme activities (cellobiohydrolase (CBH), \u03b2-glucosidase (BG), L-leucine aminopeptidase (LAP), \u00a0\u03b2-N-acetylglucosaminidase (NAG), and acid phosphatase (AP)); and (3) bacterial and fungal diversity and community composition at the phylum level. The main statistical analyses employed included one-way ANOVA, principal coordinates analysis (PCoA), and random forest models.", "keywords": ["agricultural residues", " microbial stoichiometry metabolism", " microbial necromass carbon"], "contacts": [{"organization": "Wu", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.16310622"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.16310622", "name": "item", "description": "10.5281/zenodo.16310622", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.16310622"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-07-22T00:00:00Z"}}, {"id": "10.1007/s00442-005-0249-3", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:15:00Z", "type": "Journal Article", "created": "2005-10-04", "title": "Fungal Community Composition And Metabolism Under Elevated Co2 And O-3", "description": "Atmospheric CO(2) and O(3) concentrations are increasing due to human activity and both trace gases have the potential to alter C cycling in forest ecosystems. Because soil microorganisms depend on plant litter as a source of energy for metabolism, changes in the amount or the biochemistry of plant litter produced under elevated CO(2) and O(3) could alter microbial community function and composition. Previously, we have observed that elevated CO(2) increased the microbial metabolism of cellulose and chitin, whereas elevated O(3) dampened this response. We hypothesized that this change in metabolism under CO(2) and O(3) enrichment would be accompanied by a concomitant change in fungal community composition. We tested our hypothesis at the free-air CO(2) and O(3) enrichment (FACE) experiment at Rhinelander, Wisconsin, in which Populus tremuloides, Betula papyrifera, and Acer saccharum were grown under factorial CO(2) and O(3) treatments. We employed extracellular enzyme analysis to assay microbial metabolism, phospholipid fatty acid (PLFA) analysis to determine changes in microbial community composition, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) to analyze the fungal community composition. The activities of 1,4-beta-glucosidase (+37%) and 1,4,-beta-N-acetylglucosaminidase (+84%) were significantly increased under elevated CO(2), whereas 1,4-beta-glucosidase activity (-25%) was significantly suppressed by elevated O(3). There was no significant main effect of elevated CO(2) or O(3) on fungal relative abundance, as measured by PLFA. We identified 39 fungal taxonomic units from soil using DGGE, and found that O(3) enrichment significantly altered fungal community composition. We conclude that fungal metabolism is altered under elevated CO(2) and O(3), and that there was a concomitant change in fungal community composition under elevated O(3). Thus, changes in plant inputs to soil under elevated CO(2) and O(3) can propagate through the microbial food web to alter the cycling of C in soil.", "keywords": ["0106 biological sciences", "Food Chain", "Extracellular Enzymes", "Science", "Ecology and Evolutionary Biology", "Polymerase Chain Reaction\u2013Denaturing Gradient Gel Electrophoresis", "Polymerase Chain Reaction", "01 natural sciences", "Soil Microbial Community", "Soil", "Ozone", "Health Sciences", "Acetylglucosaminidase", "Cellular and Developmental Biology", "Ecosystem", "Soil Microbiology", "beta-Glucosidase", "Fatty Acids", "Fungi", "Natural Resources and Environment", "Molecular", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "Fungal Metabolism", "Carbon", "Free-air CO 2 and O 3 Enrichment", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Extracellular Space"]}, "links": [{"href": "https://doi.org/10.1007/s00442-005-0249-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-005-0249-3", "name": "item", "description": "10.1007/s00442-005-0249-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-005-0249-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-10-05T00:00:00Z"}}, {"id": "10.1007/s00425-017-2647-2", "type": "Feature", "geometry": null, "properties": {"license": "Restricted", "updated": "2026-05-30T16:14:59Z", "type": "Journal Article", "created": "2017-01-04", "title": "The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis", "description": "Different nitrogen forms affect different metabolic pathways in lichens. In particular, the most relevant changes in protein expression were observed in the fungal partner, with NO 3- mostly affecting the energetic metabolism and NH 4+ affecting transport and regulation of proteins and the energetic metabolism much more than NO 3- did. Excess deposition of reactive nitrogen is a well-known agent of stress for lichens, but which symbiont is most affected and how, remains a mystery. Using proteomics can expand our understanding of stress effects on lichens. We investigated the effects of different doses and forms of reactive nitrogen, with and without supplementary phosphorus and potassium, on the proteome of the lichen Cladonia portentosa growing in a 'real-world' simulation of nitrogen deposition. Protein expression changed with the nitrogen treatments but mostly in the fungal partner, with NO3- mainly affecting the energetic metabolism and NH4+ also affecting the protein synthesis machinery. The photobiont mainly responded overexpressing proteins involved in energy production. This suggests that in response to nitrogen stress, the photobiont mainly supports the defensive mechanisms initiated by the mycobiont with an increased energy production. Such surplus energy is then used by the cell to maintain functionality in the presence of NO3-, while a futile cycle of protein production can be hypothesized to be induced by NH4+ excess. External supply of potassium and phosphorus influenced differently the responses of particular enzymes, likely reflecting the many processes in which potassium exerts a regulatory function.", "keywords": ["Chlorophyll", "Proteomics", "0301 basic medicine", "570", "mycobiont", "Lichens", "Nitrogen", "Cell Respiration", "Nitrate", "Mass Spectrometry", "Molecular mechanism", "03 medical and health sciences", "nitrate", "Ammonia", "Electrophoresis", " Gel", " Two-Dimensional", "Photosynthesis", "Ammonium", " Molecular mechanism", " Mycobiont", " Nitrate", " Photobiont", " Stress response", "Ammonium; Molecular mechanism; Mycobiont; Nitrate; Photobiont; Stress response; Genetics; Plant Science", "0303 health sciences", "Nitrates", "Stress response", "Chlorophyll A", "stress response", "Mycobiont", "ammonium", "Photobiont", "photobiont", "molecular mechanism", "Energy Metabolism", "Ammonium"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s00425-017-2647-2.pdf"}, {"href": "https://doi.org/10.1007/s00425-017-2647-2"}, {"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/s00425-017-2647-2", "name": "item", "description": "10.1007/s00425-017-2647-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00425-017-2647-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-04T00:00:00Z"}}, {"id": "10.1007/s00442-002-1005-6", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:14:59Z", "type": "Journal Article", "created": "2003-02-13", "title": "Effects Of Elevated Co2 On Foliar Chemistry Of Saplings Of Nine Species Of Tropical Tree", "description": "This study examined the effects of elevated CO2 on secondary metabolites for saplings of tropical trees. In the first experiment, nine species of trees were grown in the ground in open-top chambers in central Panama at ambient and elevated CO2 (about twice ambient). On average, leaf phenolic contents were 48% higher under elevated CO2. Biomass accumulation was not affected by CO2, but starch, total non-structural carbohydrates and C/N ratios all increased. In a second experiment with Ficus, an early successional species, and Virola, a late successional species, treatments were enriched for both CO2 and nutrients. For both species, nutrient fertilization increased plant growth and decreased leaf carbohydrates, C/N ratios and phenolic contents, as predicted by the carbon/nutrient balance hypothesis. Changes in leaf C/N levels were correlated with changes in phenolic contents for Virola (r=0.95, P<0.05), but not for Ficus. Thus, elevated CO2, particularly under conditions of low soil fertility, significantly increased phenolic content as well as the C/N ratio of leaves. The magnitude of the changes is sufficient to negatively affect herbivore growth, survival and fecundity, which should have impacts on plant/herbivore interactions.", "keywords": ["0106 biological sciences", "2. Zero hunger", "elevated CO2", "Ecology", "Panama", "No3 Availability", "Performance", "Insect Herbivore Interactions", "Secondary Metabolism", "phenolic compounds", "15. Life on land", "01 natural sciences", "fertilization", "Atmospheric Co2", "Leaf Quality", "Responses", "tropical trees", "Deciduous Trees", "Phenolic-compounds", "Carbon-nutrient Balance"]}, "links": [{"href": "https://doi.org/10.1007/s00442-002-1005-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-002-1005-6", "name": "item", "description": "10.1007/s00442-002-1005-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-002-1005-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2002-09-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2012.04.019", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:17:31Z", "type": "Journal Article", "created": "2012-05-03", "title": "Ammonia Volatilization Losses From Surface-Applied Urea With Urease And Nitrification Inhibitors", "description": "Abstract Urease inhibitor (UI) and nitrification inhibitor (NI) have the potential to improve N-use efficiency of applied urea and minimize N losses via gaseous emissions of ammonia (NH3) to the atmosphere and nitrate ( NO 3 \u2212 ) leaching into surface and ground water bodies. There is a growing interest in the formulations of coating chemical fertilizers with both UI and NI. However, limited information is available on the combined use of UI and NI applied with urea fertilizer. Therefore the aim of this study was to investigate the effects of treating urea with both UI and NI to minimize NH3 volatilization. Two experiments were set up in volatilization chambers under controlled conditions to examine this process. In the first experiment, UR was treated with the urease inhibitor NBPT [N-(n-butyl) thiophosphoric acid triamide] at a rate of 1060\u00a0mg\u00a0kg\u22121 urea and/or with the nitrification inhibitor DCD (dicyandiamide) at rates equivalent to 5 or 10% of the urea N. A randomized experimental design with five treatments and five replicates was used: 1) UR, 2) UR\u00a0+\u00a0NBPT, 3) UR\u00a0+\u00a0DCD 10%, 4) UR\u00a0+\u00a0NBPT\u00a0+\u00a0DCD 5%, and 5) UR\u00a0+\u00a0NBPT\u00a0+\u00a0DCD 10%. The fertilizer treatments were applied to the surface of an acidic Red Latosol soil moistened to 60% of the maximum water retention and placed inside volatilization chambers. Controls chambers were added to allow for NH3 volatilized from unfertilized soil or contained in the air that swept over the soil surface. The second experiment had an additional treatment with surface-applied DCD. The chambers were glass vessels (1.5\u00a0L) fit with air inlet and outlet tubings to allow air to pass over the soil. Ammonia volatilized was swept and carried to a flask containing a boric acid solution to trap the gas and then measured daily by titration with a standardized H2SO4 solution. Continuous measurements were recorded for 19 and 23 days for the first and second experiment, respectively. The soil samples were then analyzed for UR\u2013, NH 4 + \u2013 , and NO 3 \u2212 \u2013 N . Losses of NH3 by volatilization with unamended UR ranged from 28 to 37% of the applied N, with peak of losses observed the third day after fertilization. NBPT delayed the peak of NH3 losses due to urease inhibition and reduced NH3 volatilization between 54 and 78% when compared with untreated UR. Up to 10 days after the fertilizer application, NH3 losses had not been affected by DCD in the UR or the UR\u00a0+\u00a0NBPT treatments; thereafter, NH3 volatilization tended to decrease, but not when DCD was present. As a consequence, the addition of DCD caused a 5\u201316% increase in NH3 volatilization losses of the fertilizer N applied as UR from both the UR and the UR\u00a0+\u00a0NBPT treatments. Because the effectiveness of NBPT to inhibit soil urease activity was strong only in the first week, it could be concluded that DCD did not affect the action of NBPT but rather, enhanced volatilization losses by maintaining higher soil NH 4 + concentration and pH for a longer time. Depending on the combination of factors influencing NH3 volatilization, DCD could even offset the beneficial effect of NBPT in reducing NH3 volatilization losses.", "keywords": ["soil chemistry", "Urease inhibitors", "Surface treatment", "nutrient use efficiency", "Ammonia volatilization", "01 natural sciences", "630", "Ammonia", "Oxidation", "DCD", "Urea", "Urea fertilizers", "Fertilizers", "volatilization", "Groundwater", "0105 earth and related environmental sciences", "soil surface", "coating", "fertilizer application", "Urease inhibitor", "04 agricultural and veterinary sciences", "Nitrification inhibitor", "Nitrification", "Inorganic acids", "6. Clean water", "enzyme activity", "inhibitor", "pH effects", "Metabolism", "NBPT", "Denitrification", "Leaching", "Soils", "0401 agriculture", " forestry", " and fisheries", "Experiments", "Stabilized fertilizer"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2012.04.019"}, {"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.2012.04.019", "name": "item", "description": "10.1016/j.soilbio.2012.04.019", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2012.04.019"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-09-01T00:00:00Z"}}, {"id": "10.1007/s11356-014-3661-6", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:15:37Z", "type": "Journal Article", "created": "2014-10-13", "title": "Effects Of Ambient And Elevated Co2 On Growth, Chlorophyll Fluorescence, Photosynthetic Pigments, Antioxidants, And Secondary Metabolites Of Catharanthus Roseus (L.) G Don. Grown Under Three Different Soil N Levels", "description": "Catharanthus roseus L. plants were grown under ambient (375\u2009\u00b1\u200930 ppm) and elevated (560\u2009\u00b1\u200925 ppm) concentrations of atmospheric CO2 at different rates of N supply (without supplemental N, 0 kg N ha(-1); recommended N, 50 kg N ha(-1); and double recommended N, 100 kg N ha(-1)) in open top chambers under field condition. Elevated CO2 significantly increased photosynthetic pigments, photosynthetic efficiency, and organic carbon content in leaves at recommended (RN) and double recommended N (DRN), while significantly decreased total nitrogen content in without supplemental N (WSN). Activities of superoxide dismutase, catalase, and ascorbate peroxidase were declined, while glutathione reductase, peroxidase, and phenylalanine-ammonia lyase were stimulated under elevated CO2. However, the responses of the above enzymes were modified with different rates of N supply. Elevated CO2 significantly reduced superoxide production rate, hydrogen peroxide, and malondialdehyde contents in RN and DRN. Compared with ambient, total alkaloids content increased maximally at recommended level of N, while total phenolics in WSN under elevated CO2. Elevated CO2 stimulated growth of plants by increasing plant height and numbers of branches and leaves, and the magnitude of increment were maximum in DRN. The study suggests that elevated CO2 has positively affected plants by increasing growth and alkaloids production and reducing the level of oxidative stress. However, the positive effects of elevated CO2 were comparatively lesser in plants grown under limited N availability than in moderate and higher N availability. Furthermore, the excess N supply in DRN has stimulated the growth but not the alkaloids production under elevated CO2.", "keywords": ["Chlorophyll", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Catharanthus", "Nitrogen", "Secondary Metabolism", "Hydrogen Peroxide", "Carbon Dioxide", "Plants", "15. Life on land", "Antioxidants", "Fluorescence", "6. Clean water", "3. Good health", "Plant Leaves", "Oxidative Stress", "Soil", "03 medical and health sciences", "Superoxides", "Malondialdehyde", "Photosynthesis"], "contacts": [{"organization": "Madhoolika Agrawal, Aradhana Singh,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s11356-014-3661-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20and%20Pollution%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11356-014-3661-6", "name": "item", "description": "10.1007/s11356-014-3661-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11356-014-3661-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-10-12T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2006.12.071", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:16:21Z", "type": "Journal Article", "created": "2007-02-21", "title": "The Copper Tolerance Strategies And The Role Of Antioxidative Enzymes In Three Plant Species Grown On Copper Mine", "description": "This study was undertaken to identify the strategies and the status of antioxidant enzyme activities involved in three plant species tolerance against Cu-toxicity in copper mine. The following methods were used for evaluations in three wild type species; Datura stramonium, Malva sylvestris and Chenopodium ambrosioides. The level of chlorophyll and the activities of superoxide dismutase (SOD), glutathione peroxidase (GPX) and catalase (CAT) by spectrometry, malondialdehyde (MDA) and dityrosine by HPLC and the levels of Cu in tissues and soils by atomic absorption spectrometry (AAS). Analysis showed that total and available copper were at toxic levels for plants growing on contaminated soil (zone 1). However, there were not any visual and conspicuous symptoms of Cu toxicity in plant species. Among three species, excess copper was transferred only into the D. stramonium and C. ambrosioides tissues. The C. ambrosioides accumulated Cu in roots and then in leaves, in which the leaves chloroplasts stored Cu around two times of vacuoles. In D. stramonium most of Cu was accumulated in leaves in which the storage rate in vacuoles and chloroplasts were 42% and 8%, respectively. In zone 1, the chlorophyll levels increased significantly in leaves of C. ambrosioides with respect to the same plant growing on uncontaminated soil (zone 2). There was insignificant decrease in chlorophyll content of D. stramonium leaves, collected from zone 1 with respect to zone 2. The D. stramonium and C. ambrosioides in zone 1, both revealed significant increase in their tissues antioxidant enzyme activities in comparison with the same samples of zone 2. There was significant elevation in oxidative damage biomarkers; MDA and dityrosine, when the aerial parts of D. stramonium in zone 1 were compared with the same parts of zone 2. We concluded that there were different tolerance strategies in studied plant species that protected them against copper toxicity. In M. sylvestris, exclusion of Cu from the roots or its stabilization in the soil restricted Cu toxicity effects. On the other hand D. stramonium and C. ambrosioides, elevated their antioxidative enzyme activities in response to cu-toxicity. In addition, the species D. stramonium accumulated excess of Cu in leaves vacuoles.", "keywords": ["Chlorophyll", "0106 biological sciences", "0301 basic medicine", "Chloroplasts", "Malva", "Plants", "15. Life on land", "Lipid Metabolism", "Plant Roots", "01 natural sciences", "Antioxidants", "Mining", "6. Clean water", "Chenopodium", "Oxidative Stress", "Soil", "03 medical and health sciences", "Malondialdehyde", "Vacuoles", "Datura", "Tyrosine", "Biomass", "Copper", "Plant Proteins"], "contacts": [{"organization": "Massod Mashhadi Akbar Boojar, Faranak Goodarzi,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2006.12.071"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2006.12.071", "name": "item", "description": "10.1016/j.chemosphere.2006.12.071", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2006.12.071"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-05-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2008.07.056", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:16:21Z", "type": "Journal Article", "created": "2008-10-01", "title": "Integration Of Toxicological And Chemical Tools To Assess The Bioavailability Of Metals And Energetic Compounds In Contaminated Soils", "description": "Bioavailability is critical for understanding effects that might result from exposure of biota to contaminated soils. Soils from military range and training areas (RTAs) are contaminated principally by energetic materials (EM) and metals. Their chemical characteristics are relatively well known and toxicity assessment of soils from RTAs are in some cases available. However, bioavailability on these sites needs to be comprehensively characterized. A holistic approach to bioavailability, incorporating both chemical and earthworm toxicological indicators, was applied to soils from an anti-tank firing range at a Canadian Forces Base. Results showed that HMX and the metals Zn, Pb, Bi and Cd, though not consistently the prevailing toxicants, were the most accessible to earthworms. Some metals (notably Cu, Zn, Cr and Bi) were also accumulated in earthworm tissue but those were not necessarily expected given their bioaccessibility (i.e., the chemical availability of contaminants in the environment for the organisms) at the beginning of the exposure. The tested soils impaired earthworm reproduction and reduced adult growth. Measurement of selected sublethal parameters indicated that lysosomal integrity (determined as the neutral red retention time--NRRT) was decreased, while elevated superoxide dismutase (SOD) activity suggested that earthworms experienced oxidative stress. The correspondence between the NRRT and metal contamination pattern suggested that metals may be the main cause of lysosomal disruption in EM-contaminated soils. The approach to bioavailability appraisal adopted in this case appears to be a promising practice for site-specific assessment of contaminated land.", "keywords": ["zinc/metabolism/pharmacokinetics/toxicity", "assessment", "metals", "Biological Availability", "lead/metabolism/pharmacokinetics/toxicity", "01 natural sciences", "biological availability", "soil pollutants/metabolism/pharmacokinetics/toxicity", "Animals", "Soil Pollutants", "bismuth/metabolism/pharmacokinetics/toxicity", "Oligochaeta", "oligochaeta/rug effects/growth & development/metabolism", "soils", "0105 earth and related environmental sciences", "metals/metabolism/pharmacokinetics/ toxicity", "explosives", "04 agricultural and veterinary sciences", "bioaccessibility", "6. Clean water", "Zinc", "Lead", "Metals", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "cadmium/metabolism/pharmacokinetics/toxicity", "bioavailability", "Bismuth", "Cadmium"], "contacts": [{"organization": "\u00c9meline Valton, Bertin Trottier, Aurelie Auroy, Aurelie Auroy, Yann Berthelot, Pierre Yves Robidoux, Pierre Yves Robidoux,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2008.07.056"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2008.07.056", "name": "item", "description": "10.1016/j.chemosphere.2008.07.056", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2008.07.056"}, {"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.soilbio.2012.04.004", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:17:31Z", "type": "Journal Article", "created": "2012-04-23", "title": "Biochar But Not Earthworms Enhances Rice Growth Through Increased Protein Turnover", "description": "The aim of this work was to compare the effects of biochar and earthworms on rice growth and to investigate the possible interactions between both. In addition to classic macroscopic variables we also monitored some leaf-level cellular processes involved in protein turnover. Both biochar and earthworms significantly increased shoot biomass production. However, biochar had a higher effect on the number of leaves (\u00fe87%) and earthworms on leaf area (\u00fe89%). Biochar also significantly increased the leaf turnover. At the cellular level, biochar but not earthworms enhanced protein catabolism by an increase in leaf proteolytic activities. This could be related to the increased expression of three of the six genes tested related to protein catabolism, one serine protease gene OsSP2 (\u00fe24%), one aspartic acid protease gene, Oryzasin (\u00fe162%) and one cysteine protease gene OsCatB (\u00fe257%). Furthermore, biochar also enhanced the expression level of two genes linked to protein anabolism, coding for the small and large subunits of rubisco (\u00fe33% and \u00fe30%, for rbcS and rbcL, respectively), the most abundant protein in leaves. In conclusion, our data gives evidence that biochar increased rice biomass production through increased leaf protein turnover (both catabolism and anabolism) whereas earthworms also increased rice biomass production but not through changes in the rate of protein turnover. We hypothesize that earthworms increase nitrogen uptake at a low cost for the plant through a simultaneous increase in mineralization rate and root biomass, probably through the release in the soil of plant growth factors. This could allow plants to accumulate more biomass without an increase in nitrogen metabolism at the leaf level, and without having to support the consecutive energy cost that must bear plants in the biochar treatment. 2012 Elsevier Ltd. All rights reserved.", "keywords": ["0106 biological sciences", "0301 basic medicine", "earthworms", "FAUNE DU SOL", "7. Clean energy", "01 natural sciences", "03 medical and health sciences", "AZOTE", "PROTEINE", "CROISSANCE", "ETUDE COMPARATIVE", "lombriz de tierra", "2. Zero hunger", "BIOMASSE", "BIOCHAR", "biomass", "carbon", "microbiology", "MACROFAUNE", "CHARBON DE BOIS", "carbono", "RIZICULTURE", "biomasa", "oryza sativa", "METABOLISME", "FERTILISATION DU SOL", "carb\u00f3n vegetal", "LOMBRIC", "FEUILLE", "charcoal"], "contacts": [{"organization": "Kam-Rigne Laossi, Juan Andr\u00e9s Cardoso, Patrick Lavelle, Patrick Lavelle, Diana Cristina Noguera, Diana Cristina Noguera, Diana Cristina Noguera, M.H. Cruz de Carvalho, S\u00e9bastien Barot,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2012.04.004"}, {"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.2012.04.004", "name": "item", "description": "10.1016/j.soilbio.2012.04.004", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2012.04.004"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-09-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2023.109259", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:17:37Z", "type": "Journal Article", "created": "2023-12-01", "title": "A pulse of simulated root exudation alters the composition and temporal dynamics of microbial metabolites in its immediate vicinity", "description": "Root exudation increases the concentration of readily available carbon (C) compounds in its immediate environment. This creates \u2018hotspots\u2019 of microbial activity characterized by accelerated soil organic matter turnover with direct implications for nutrient availability for plants. However, our knowledge of the microbial metabolic processes occurring in the immediate vicinity of roots during and after a root exudation event is still limited.

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

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

Our findings indicate that the punctual release of low-molecular-weight organic C compounds into intact soil significantly changes microbial metabolism and activity in its immediate surroundings, enhancing mineralization of native organic nitrogen. This highlights the versatility of microbial metabolic pathways in response to rapidly changing C availability and their effectiveness in increasing nutrient availability near plant roots.", "keywords": ["Oxygen depletion", "2. Zero hunger", "570", "106022 Mikrobiologie", "Root exudation", "short-chain fatty acids", "Reverse microdialysis", "reverse microdialysis", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "15. Life on land", "root exudation", "6. Clean water", "Short-chain fatty acids", "Sugar metabolism", "106026 \u00d6kosystemforschung", "thizosphere priming effect", "crabtree effect", "sugar metabolism", "106022 Microbiology", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "106026 Ecosystem research", "Rhizosphere priming effect"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2023.109259"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2023.109259", "name": "item", "description": "10.1016/j.soilbio.2023.109259", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2023.109259"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-01T00:00:00Z"}}, {"id": "10.1016/j.still.2006.07.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:40Z", "type": "Journal Article", "created": "2006-08-18", "title": "Tillage And Fertility Management Effects On Soil Organic Matter And Sorghum Yield In Semi-Arid West Africa", "description": "Whether it is traditional, modern or \u2018\u2018sustainable\u2019\u2019 agriculture, soil organic matter plays a key role in sustaining crop production and in preventing land degradation. A field experiment was conducted on a Ferric Lixisol at Gampela (Burkina Faso) in 2000 and 2001 to carried out the effects of tillage, fertilisation and their interaction on soil organic carbon (SOC) (0\u201310 cm), crop performance and microbial activities. Maize straw or sheep dung were applied separately or combined with urea in a till or no-till systems and compared with urea only and a control treatment. Sampling was done each year at 2 months after sowing and at harvest. SOC was increased in the tillage treatments in 2000 by 35% but only with 18% in 2001 suggesting reduced carbon accumulation in the absence of organic and mineral restitution. Ploughing in maize straw under conditions of N deficiency led to a drastic decrease in SOC due microbial priming effect that, was not observed when ploughing in sheep dung. In no-till system, losses, organic amendment N concentration and the soil N status determined the impact on SOC and crop productivity. The negative effect on SOC in the tillage treatment with maize straw (4.1 g kg \ufffd 1 ) was less when maize straw was combined with urea (6.2 g kg \ufffd 1 ). It is concluded that in semi-arid West Africa, without both organic resource and N inputs, soil organic matter \u2018\u2018pays\u2019\u2019 for crop N nutrition. Increasing SOC accumulation while improving crop yield may be conflicting under low-input agricultural systems in semi-arid West Africa. Therefore, optimum soil organic carbon and crop performance results from a judicious combination of organic resources and inorganic N mediated by microbial activity. # 2006 Elsevier B.V. All rights reserved.", "keywords": ["sustainable land-use", "Soil nutrients", "2. Zero hunger", "Soil management", "Soil organic matter", "microbial biomass", "Crop performance", "carbon", "dynamics", "04 agricultural and veterinary sciences", "15. Life on land", "Soil carbon", "Tillage", "Manure", "biocidal treatments", "13. Climate action", "Fertilization", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Field Scale", "metabolism", "Conservation tillage", "Organic amendments"]}, "links": [{"href": "https://doi.org/10.1016/j.still.2006.07.001"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20and%20Tillage%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.still.2006.07.001", "name": "item", "description": "10.1016/j.still.2006.07.001", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.still.2006.07.001"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-05-01T00:00:00Z"}}, {"id": "10.3168/jds.2010-4042", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:21:33Z", "type": "Journal Article", "created": "2011-05-25", "title": "Dietary Inclusion Of Diallyl Disulfide, Yucca Powder, Calcium Fumarate, An Extruded Linseed Product, Or Medium-Chain Fatty Acids Does Not Affect Methane Production In Lactating Dairy Cows", "description": "Two similar experiments were conducted to assess the effect of diallyl disulfide (DADS), yucca powder (YP), calcium fumarate (CAFU), an extruded linseed product (UNSAT), or a mixture of capric and caprylic acid (MCFA) on methane production, energy balance, and dairy cow performance. In experiment 1, a control diet (CON1) and diets supplemented with 56 mg of DADS/kg of dry matter (DM), 3g of YP/kg of DM, or 25 g of CAFU/kg of DM were evaluated. In experiment 2, an inert saturated fat source in the control diet (CON2) was exchanged isolipidically for an extruded linseed source (100g/kg of DM; UNSAT) or a mixture of C8:0 and C10:0 (MCFA; 20.3g/kg of DM). In experiment 2, a higher inclusion level of DADS (200mg/kg of DM) was also tested. Both experiments were conducted using 40 lactating Holstein-Friesian dairy cows. Cows were adapted to the diet for 12 d and were subsequently kept in respiration chambers for 5 d to evaluate methane production, diet digestibility, energy balance, and animal performance. Feed intake was restricted to avoid confounding effects of possible differences in ad libitum feed intake on methane production. Feed intake was, on average, 17.5 and 16.6 kg of DM/d in experiments 1 and 2, respectively. None of the additives reduced methane production in vivo. Methane production in experiment 1 was 450, 453, 446, and 423 g/d for CON1 and the diets supplemented with DADS, YP, and CAFU, respectively. In experiment 2, methane production was 371, 394, 388, and 386 g/d for CON2 and the diets supplemented with UNSAT, MCFA, and DADS, respectively. No effects of the additives on energy balance or neutral detergent fiber digestibility were observed. The addition of MCFA increased milk fat content (5.38% vs. 4.82% for control) and fat digestibility (78.5% vs. 59.8% for control), but did not affect milk yield or other milk components. The other products did not affect milk yield or composition. Results from these experiments emphasize the need to confirm methane reductions observed in vitro with in vivo data.", "keywords": ["production in-vitro", "ruminal fermentation", "0404 agricultural biotechnology", "linolenic acids", "rumen microbial fermentation", "Fumarates", "Flax", "Yucca", "Animals", "Lactation", "schidigera", "Disulfides", "essential oils", "beef-cattle", "2. Zero hunger", "garlic oil", "0402 animal and dairy science", "04 agricultural and veterinary sciences", "Diet", "Allyl Compounds", "Milk", "Dietary Supplements", "Animal Nutritional Physiological Phenomena", "Cattle", "Digestion", "Female", "Caprylates", "Energy Metabolism", "metabolism", "Decanoic Acids", "Methane", "metaanalysis"]}, "links": [{"href": "https://doi.org/10.3168/jds.2010-4042"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Dairy%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3168/jds.2010-4042", "name": "item", "description": "10.3168/jds.2010-4042", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3168/jds.2010-4042"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-01T00:00:00Z"}}, {"id": "10.3168/jds.2011-4236", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:21:33Z", "type": "Journal Article", "created": "2011-07-26", "title": "Persistency Of Methane Mitigation By Dietary Nitrate Supplementation In Dairy Cows", "description": "Feeding nitrate to dairy cows may lower ruminal methane production by competing for reducing equivalents with methanogenesis. Twenty lactating Holstein-Friesian dairy cows (33.2\u00b16.0 kg of milk/d; 104\u00b158 d in milk at the start of the experiment) were fed a total mixed ration (corn silage-based; forage to concentrate ratio 66:34), containing either a dietary urea or a dietary nitrate source [21 g of nitrate/kg of dry matter (DM)] during 4 successive 24-d periods, to assess the methane-mitigating potential of dietary nitrate and its persistency. The study was conducted as paired comparisons in a randomized design with repeated measurements. Cows were blocked by parity, lactation stage, and milk production at the start of the experiment. A 4-wk adaptation period allowed the rumen microbes to adapt to dietary urea and nitrate. Diets were isoenergetic and isonitrogenous. Methane production, energy balance, and diet digestibility were measured in open-circuit indirect calorimetry chambers. Cows were limit-fed during measurements. Nitrate persistently decreased methane production by 16%, whether expressed in grams per day, grams per kilogram of dry matter intake (DMI), or as percentage of gross energy intake, which was sustained for the full experimental period (mean 368 vs. 310\u00b112.5 g/d; 19.4 vs. 16.2\u00b10.47 g/kg of DMI; 5.9 vs.4.9\u00b10.15% of gross energy intake for urea vs. nitrate, respectively). This decrease was smaller than the stoichiometrical methane mitigation potential of nitrate (full potential=28% methane reduction). The decreased energy loss from methane resulted in an improved conversion of dietary energy intake into metabolizable energy (57.3 vs. 58.6\u00b10.70%, urea vs. nitrate, respectively). Despite this, milk energy output or energy retention was not affected by dietary nitrate. Nitrate did not affect milk yield or apparent digestibility of crude fat, neutral detergent fiber, and starch. Milk protein content (3.21 vs. 3.05\u00b10.058%, urea vs. nitrate respectively) but not protein yield was lower for dietary nitrate. Hydrogen production between morning and afternoon milking was measured during the last experimental period. Cows fed nitrate emitted more hydrogen. Cows fed nitrate displayed higher blood methemoglobin levels (0.5 vs. 4.0\u00b11.07% of hemoglobin, urea vs. nitrate respectively) and lower hemoglobin levels (7.1 vs. 6.3\u00b10.11 mmol/L, urea vs. nitrate respectively). Dietary nitrate persistently decreased methane production from lactating dairy cows fed restricted amounts of feed, but the reduction in energy losses did not improve milk production or energy balance.", "keywords": ["combination", "2. Zero hunger", "sheep", "Nitrates", "Rumen", "0402 animal and dairy science", "l-cysteine", "04 agricultural and veterinary sciences", "Animal Feed", "Diet", "0403 veterinary science", "rumen fermentation", "Milk", "cattle", "ruminants", "hydrogen", "manipulation", "Dietary Supplements", "Animals", "Lactation", "Cattle", "Female", "nitrite", "Energy Metabolism", "Methane"]}, "links": [{"href": "https://doi.org/10.3168/jds.2011-4236"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Dairy%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3168/jds.2011-4236", "name": "item", "description": "10.3168/jds.2011-4236", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3168/jds.2011-4236"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-08-01T00:00:00Z"}}, {"id": "10.1073/pnas.0600359103", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:18:42Z", "type": "Journal Article", "created": "2006-03-14", "title": "Reduced Nitrate Leaching And Enhanced Denitrifier Activity And Efficiency In Organically Fertilized Soils", "description": "

Conventional agriculture has improved in crop yield but at large costs to the environment, particularly off-site pollution from mineral N fertilizers. In response to environmental concerns, organic agriculture has become an increasingly popular option. One component of organic agriculture that remains in question is whether it can reduce agricultural N losses to groundwater and the atmosphere relative to conventional agriculture. Here we report reduced N pollution from organic and integrated farming systems compared with a conventional farming system. We evaluated differences in denitrification potential and a suite of other soil biological and chemical properties in soil samples taken from organic, integrated, and conventional treatments in an experimental apple orchard. Organically farmed soils exhibited higher potential denitrification rates, greater denitrification efficiency, higher organic matter, and greater microbial activity than conventionally farmed soils. The observed differences in denitrifier function were then assessed under field conditions after fertilization. N 2 O emissions were not significantly different among treatments; however, N 2 emissions were highest in organic plots. Annual nitrate leaching was 4.4\uffe2\uff80\uff935.6 times higher in conventional plots than in organic plots, with the integrated plots in between. This study demonstrates that organic and integrated fertilization practices support more active and efficient denitrifier communities, shift the balance of N 2 emissions and nitrate losses, and reduce environmentally damaging nitrate losses. Although this study specifically examines a perennial orchard system, the ecological and biogeochemical processes we evaluated are present in all agroecosystems, and the reductions in nitrate loss in this study could also be achievable in other cropping systems.

", "keywords": ["Nitrates - metabolism", "2. Zero hunger", "Nitrates", "Soil Pollutants - analysis", "Nitrates - analysis", "Agriculture", "Fertilizers - analysis", "04 agricultural and veterinary sciences", "15. Life on land", "Soil - analysis", "01 natural sciences", "630", "6. Clean water", "Soil", "13. Climate action", "Soil Pollutants - metabolism", "Soil Pollutants", "0401 agriculture", " forestry", " and fisheries", "Environmental Pollution", "Fertilizers", "Ecosystem", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Kramer, Sasha B, Reganold, John P, Glover, Jerry D, Bohannan, Brendan J M, Mooney, Harold A,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1073/pnas.0600359103"}, {"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.0600359103", "name": "item", "description": "10.1073/pnas.0600359103", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.0600359103"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-03-13T00:00:00Z"}}, {"id": "10.1038/s41396-021-01064-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:18:18Z", "type": "Journal Article", "created": "2021-07-27", "title": "Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities", "description": "Abstract

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that\uffe2\uff80\uff94like for AOB\uffe2\uff80\uff94ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.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": "2026-05-30T16:18:20Z", "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.Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia fabaL.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13\uffe2\uff80\uff89Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the\uffc2\uffa0improvement of sustainable protein production across the\uffc2\uffa0Mediterranean, subtropical and northern temperate agroecological zones.Globally, inland waters emit over 2 Pg of carbon per year as carbon dioxide, of which the majority originates from streams and rivers. Despite the global significance of fluvial carbon dioxide emissions, little is known about their diel dynamics. Here we present a large-scale assessment of day- and night-time carbon dioxide fluxes at the water-air interface across 34 European streams. We directly measured fluxes four times between October 2016 and July 2017 using drifting chambers. Median fluxes are 1.4 and 2.1\uffe2\uff80\uff89mmol\uffe2\uff80\uff89m\uffe2\uff88\uff922 h\uffe2\uff88\uff921 at midday and midnight, respectively, with night fluxes exceeding those during the day by 39%. We attribute diel carbon dioxide flux variability mainly to changes in the water partial pressure of carbon dioxide. However, no consistent drivers could be identified across sites. Our findings highlight widespread day-night changes in fluvial carbon dioxide fluxes and suggest that the time of day greatly influences measured carbon dioxide fluxes across European streams.As a primary limiting factor in arid and semiarid regions, precipitation strongly influences soil microbial properties. However, the patterns and mechanisms of soil microbial responses to precipitation have not been well documented. In this study, changes in soil microorganisms along an experimental precipitation gradient with seven levels of precipitation manipulation (i.e., ambient precipitation as a control and \uffc2\uffb120%, \uffc2\uffb140% and \uffc2\uffb160% of ambient precipitation) were explored in a semiarid temperate steppe in northern China. Soil microbial biomass carbon and respiration as well as the ratio of fungal to bacterial biomass varied along the experimental precipitation gradient and peaked under the +40% precipitation treatment. The shifts in microbial community composition could be largely attributable to the changes in soil water and nutrient availability. The metabolic quotient increased (indicating reduced carbon use efficiency) with increasing precipitation due to the leaching of dissolved organic carbon. The relative contributions of microbial respiration to soil and ecosystem respiration increased with increasing precipitation, suggesting that heterotrophic respiration will be more sensitive than autotrophic respiration if precipitation increases in the temperate steppe as predicted under future climate-change scenarios.

", "keywords": ["2. Zero hunger", "China", "Bacteria", "Rain", "Fungi", "04 agricultural and veterinary sciences", "15. Life on land", "Biota", "Grassland", "Article", "Carbon", "13. Climate action", "11. Sustainability", "0401 agriculture", " forestry", " and fisheries", "Desert Climate", "Energy Metabolism", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep24317"}, {"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/srep24317", "name": "item", "description": "10.1038/srep24317", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep24317"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-14T00:00:00Z"}}, {"id": "10.1093/jxb/erac437", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:19:01Z", "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.Carbon (C) assimilation can be severely impaired during periods of environmental stress, like drought or defoliation, making trees heavily dependent on the use of C reserve pools for survival; yet, the dynamics of reserve use during periods of reduced C supply are still poorly understood. We used stem girdling in mature poplar trees (Populus tremula L. hybrids), a lipid-storing species, to permanently interrupt the phloem C transport and induced C shortage in the isolated stem section below the girdle and monitored metabolic activity during three campaigns in the growing seasons of 2018, 2019 and 2021. We measured respiratory fluxes (CO2 and O2), non-structural carbon concentration, the respiratory substrate (based on isotopic analysis and CO2/O2 ratio) and the age of the respiratory substrate (based on radiocarbon analysis). Our study shows that poplar trees can survive long periods of reduced C supply from the canopy by switching in metabolism from recent carbohydrates to older storage pools with a potential mixture of respiratory substrates, including lipids. This mechanism of stress resilience can explain why tree decline may take many years before death occurs.Plant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organismArabidopsis thaliana. Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.Ammonia\uffe2\uff80\uff90oxidising archaea (AOA) are important microorganisms contributing towards the nitrogen flux in the environment. Unlike archaea from other major phyla, genetic tools are yet to be developed for the AOA, and identification of antibiotic resistance markers for selecting mutants is required for a genetic system. The aim of this study was to test the effects of selected antibiotics (hygromycin B, neomycin, apramycin, puromycin, novobiocin) on pure cultures of three well studied AOA strains, \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandianus C13\uffe2\uff80\uff99, Nitrososphaera viennensis EN76 and Nitrosopumilus maritimus SCM1. Puromycin, hygromycin B and neomycin inhibited some but not all tested archaeal strains. All strains were resistant to apramycin and inhibited by novobiocin to various degrees. As N. viennensis EN76 was relatively more resistant to the tested antibiotics, a wider range of concentrations and compounds (chloramphenicol, trimethoprim, statins) was tested against this strain. N. viennensis EN76 was inhibited by trimethoprim, but not by chloramphenicol, and growth recovered within days in the presence of simvastatin, suggesting either degradation of, or spontaneous resistance against, this compound. This study highlights the physiological differences between different genera of AOA and has identified new candidate antibiotics for selective enrichment and the development of selectable markers for genetic systems in AOA.Featured paper: See Editorial p553

", "keywords": ["0106 biological sciences", "Time Factors", "550", "plant community", "carbon fixation", "Carbon use efficiency", "Cell Respiration", "Amazon rain forest", "drought", "Gross primary productivity", "01 natural sciences", "experimental study", "metabolism Amazon rain forest", "Trees", "Soil", "cell respiration", "Keywords: carbon", "partitioning", "Ecosystem", "ecosystem", "Carbon cycling", "Drought", "Bacteria", "article", "carbon dioxide", "net primary production", "Carbon Dioxide", "15. Life on land", "bacterium", "Carbon", "6. Clean water", "Net primary productivity", "Droughts", "carbon flux", "Carbon dioxide", "rainforest", "respiration", "Partitioning", "Brazil"]}, "links": [{"href": "https://openresearch-repository.anu.edu.au/bitstream/1885/79387/5/f5625xPUB78382010.pdf.jpg"}, {"href": "https://openresearch-repository.anu.edu.au/bitstream/1885/79387/7/01_Metcalfe_Shifts_in_plant_respiration_2010.pdf.jpg"}, {"href": "https://doi.org/10.1111/j.1469-8137.2010.03319.x"}, {"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": "10.1111/j.1469-8137.2010.03319.x", "name": "item", "description": "10.1111/j.1469-8137.2010.03319.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1469-8137.2010.03319.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-07-19T00:00:00Z"}}, {"id": "10.1111/nph.16047", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:19:49Z", "type": "Journal Article", "created": "2019-07-08", "title": "Winter's bite: beech trees survive complete defoliation due to spring late\u2010frost damage by mobilizing old C reserves", "description": "Summary

Late frost can destroy the photosynthetic apparatus of trees. We hypothesized that this can alter the normal cyclic dynamics of C\uffe2\uff80\uff90reserves in the wood.

We measured soluble sugar concentrations and radiocarbon signatures (\uffce\uff9414C) of soluble nonstructural carbon (NSC) in woody tissues sampled from a Mediterranean beech forest that was completely defoliated by an exceptional late frost in 2016. We used the bomb radiocarbon approach to estimate the time elapsed since fixation of mobilized soluble sugars.

During the leafless period after the frost event, soluble sugar concentrations declined sharply while \uffce\uff9414C of NSC increased. This can be explained by the lack of fresh assimilate supply and a mobilization of C from reserve pools. Soluble NSC became increasingly older during the leafless period, with a maximum average age of 5\uffc2\uffa0yr from samples collected 27\uffc2\uffa0d before canopy recovery. Following leaf re\uffe2\uff80\uff90growth, soluble sugar concentrations increased and \uffce\uff9414C of soluble NSC decreased, indicating the allocation of new assimilates to the stem soluble sugars pool.

These data highlight that beech trees rapidly mobilize reserve C to survive strong source\uffe2\uff80\uff93sink imbalances, for example due to late frost, and show that NSC is a key trait for tree resilience under global change.

Our ability to understand the effect of nutrient limitation on ecosystem productivity is key to the prediction of future terrestrial carbon storage. Significant progress has been made to include phosphorus (P) cycle processes in land surface models (LSMs), but these efforts are focused on the soil component of the P cycle. Incorporating the soil component is important to estimate plant\uffe2\uff80\uff90available P, but does not necessarily address the vegetation response to P limitation or plant\uffe2\uff80\uff93soil interactions. A more detailed representation of plant P processes is needed to link nutrient availability and ecosystem productivity. We review physiological and biochemical evidence for vegetation responses to P availability, and recommend ways to move towards a more physiological representation of vegetation P processes in LSMs.

", "keywords": ["2. Zero hunger", "0106 biological sciences", "plants", "Phosphorus", "growth (plants)", "15. Life on land", "Models", " Biological", "01 natural sciences", "Carbon", "13. Climate action", "XXXXXX - Unknown", "Biomass", "phosphorus content", "Photosynthesis", "metabolism", "soils", "Plant Physiological Phenomena", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15688"}, {"href": "https://doi.org/10.1111/nph.15688"}, {"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": "10.1111/nph.15688", "name": "item", "description": "10.1111/nph.15688", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.15688"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-19T00:00:00Z"}}, {"id": "10.1111/pce.14124", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:19:50Z", "type": "Journal Article", "created": "2021-06-07", "title": "The size and the age of the metabolically active carbon in tree roots.", "description": "Abstract

Little is known about the sources and age of C respired by tree roots. Previous research in stems identified two functional pools of non\uffe2\uff80\uff90structural carbohydrates (NSC): an \uffe2\uff80\uff9cactive\uffe2\uff80\uff9d pool supplied directly from canopy photo\uffe2\uff80\uff90assimilates supporting metabolism and a \uffe2\uff80\uff9cstored\uffe2\uff80\uff9d pool used when fresh C supplies are limited. We compared the C isotope composition of water\uffe2\uff80\uff90soluble NSC and respired CO2for aspen roots (Populus tremulahybrids) cut off from fresh C supply after stem\uffe2\uff80\uff90girdling or prolonged incubation of excised roots. We used bomb radiocarbon to estimate the time elapsed since C fixation for respired CO2, water\uffe2\uff80\uff90soluble NSC and structural \uffce\uffb1\uffe2\uff80\uff90cellulose. While freshly excised roots (mostly <2.9\uffe2\uff80\uff89mm in diameter) respired CO2fixed <1\uffc2\uffa0year previously, the age increased to 1.6\uffe2\uff80\uff932.9\uffc2\uffa0year within a week after root excision. Freshly excised roots from trees girdled ~3\uffc2\uffa0months ago had respiration rates and NSC stocks similar to un\uffe2\uff80\uff90girdled trees but respired older C (~1.2\uffc2\uffa0year). We estimate that over 3\uffc2\uffa0months NSC in girdled roots must be replaced 5\uffe2\uff80\uff937 times by reserves remobilized from root\uffe2\uff80\uff90external sources. Using a mixing model and observed correlations between \uffce\uff9414C of water\uffe2\uff80\uff90soluble C and \uffce\uffb1\uffe2\uff80\uff90cellulose, we estimate ~30% of C is \uffe2\uff80\uff9cactive\uffe2\uff80\uff9d (~5\uffc2\uffa0mg C g\uffe2\uff88\uff921).

", "keywords": ["0106 biological sciences", "Carbon Isotopes", "Carbon Dioxide", "Forests", "15. Life on land", "Plant Roots", "01 natural sciences", "Carbon", "Trees", "Populus", "Germany", "Carbohydrate Metabolism", "Carbon Radioisotopes", "Cellulose"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14124"}, {"href": "https://doi.org/10.1111/pce.14124"}, {"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/pce.14124", "name": "item", "description": "10.1111/pce.14124", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/pce.14124"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-09T00:00:00Z"}}, {"id": "10.3390/metabo15020097", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:21:53Z", "type": "Journal Article", "created": "2025-02-05", "title": "Metabolomic-Based Assessment of Earthworm (Eisenia fetida) Exposure to Different Petroleum Fractions in Soils", "description": "

Background/Objectives: Petroleum contamination in soil exerts toxic effects on earthworms (Eisenia fetida) through non-polar narcotic mechanisms. However, the specific toxicities of individual petroleum components remain insufficiently understood. Methods: This study investigates the effects of four petroleum components\u2014saturated hydrocarbons, aromatic hydrocarbons, resins, and asphaltenes\u2014on earthworms in artificially contaminated soil, utilizing a combination of biochemical biomarker analysis and metabolomics to uncover the underlying molecular mechanisms. Results: The results revealed that aromatic hydrocarbons are the most toxic fraction, with EC50 concentrations significantly lower than those of other petroleum fractions. All tested fractions triggered notable metabolic disturbances and immune responses in earthworms after 7 days of exposure, as evidenced by significant changes in metabolite abundance within critical pathways such as arginine synthesis, a-linolenic acid metabolism, and the pentose phosphate pathway. According to the KEGG pathway analysis, saturated hydrocarbon fractions induced marked changes in glycerophospholipid metabolism, and arginine and proline metabolism pathways, contributing to the stabilization of the protein structure and membrane integrity. Aromatic hydrocarbon fractions disrupted the arachidonic acid metabolic pathway, leading to increased myotube production and enhanced immune defense mechanisms. The TCA cycle and riboflavin metabolic pathway were significantly altered during exposure to the colloidal fraction, affecting energy production and cellular respiration. The asphaltene fraction significantly impacted glycolysis, accelerating energy cycling to meet stress-induced increases in energy demands. Conclusions: Aromatic hydrocarbons accounted for the highest level of toxicity among the four components in petroleum-contaminated soils. However, the contributions of other fractions to overall toxicity should not be ignored, as each fraction uniquely affects key metabolic pathways and biological functions. These findings emphasize the importance of monitoring metabolic perturbations caused by petroleum components in non-target organisms such as earthworms. They also reveal the specificity of the toxic metabolic effects of different petroleum components on earthworms.

", "keywords": ["hydrocarbon series of petroleum", "ecotoxicity", "assessment", "earthworms", "metabolism", "Microbiology", "QR1-502", "Article", "soil"], "contacts": [{"organization": "Meiyu Liu, Mutian Wang, Xiaowen Fu, Fanyong Song, Fangyuan Zhou, Tianyuan Li, Jianing Wang,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3390/metabo15020097"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Metabolites", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/metabo15020097", "name": "item", "description": "10.3390/metabo15020097", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/metabo15020097"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-02-05T00:00:00Z"}}, {"id": "10.1126/science.ade9204", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:19:55Z", "type": "Journal Article", "created": "2023-01-19", "title": "Nanobody-driven signaling reveals the core receptor complex in root nodule symbiosis", "description": "

Understanding the composition and activation of multicomponent receptor complexes is a challenge in biology. To address this, we developed a synthetic approach based on nanobodies to drive assembly and activation of cell surface receptors and apply the concept by manipulating receptors that govern plant symbiosis with nitrogen-fixing bacteria. We show that the Lotus japonicus Nod factor receptors NFR1 and NFR5 constitute the core receptor complex initiating the cortical root nodule organogenesis program as well as the epidermal program controlling infection. We find that organogenesis signaling is mediated by the intracellular kinase domains whereas infection requires functional ectodomains. Finally, we identify evolutionarily distant barley receptors that activate root nodule organogenesis, which could enable engineering of biological nitrogen-fixation into cereals. In order to compare the maximum potential environmental impact savings that may result from the implementation of innovative biorefinery alternatives at a regional scale, the Territorial Metabolism-Life Cycle Assessment (TM-LCA) framework is implemented. With the goal of examining environmental impacts arising from technology-to-region (territory) compatibility, the framework is applied to two biorefinery alternatives, treating a mixture of cow manure and grape marc. The biorefineries produce either biogas alone or biogas and polyhydroxyalkanoates (PHA), a naturally occurring polymer. The production of PHA substitutes either polyethylene terephthalate (PET) or biosourced polylactide (PLA) production. The assessment is performed for two regions, one in Southern France and the other in Oregon, USA. Changing energy systems are taken into account via multiple dynamic energy provision scenarios. Territorial scale impacts are quantified using both LCA midpoint impact categories and single score indicators derived through multi-criteria decision assessment (MCDA). It is determined that in all probable future scenarios, a biorefinery with PHA-biogas co-production is preferable to a biorefinery only producing biogas. The TM-LCA framework facilitates the capture of technology and regionally specific impacts, such as impacts caused by local energy provision and potential impacts due to limitations in the availability of the defined feedstock leading to additional transport.

", "keywords": ["Biogas", "02 engineering and technology", "/dk/atira/pure/sustainabledevelopmentgoals/responsible_consumption_and_production; name=SDG 12 - Responsible Consumption and Production", "7. Clean energy", "territorial metabolism", "12. Responsible consumption", "Life cycle assessment", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "life cycle assessment", "biogas", "agricultural residues", "0202 electrical engineering", " electronic engineering", " information engineering", "Agricultural residues", "Multi-criteria decision assessment", "biorefinery", "2. Zero hunger", "Territorial metabolism", "Polyhydroxyalkanoates", "polyhydroxyalkanoates", "Biorefinery", "Bioplastic", "multi-criteria decision assessment", "13. Climate action", "8. Economic growth", "bioplastic"]}, "links": [{"href": "http://www.mdpi.com/2071-1050/11/14/3836/pdf"}, {"href": "https://www.mdpi.com/2071-1050/11/14/3836/pdf"}, {"href": "https://doi.org/10.3390/su11143836"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sustainability", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/su11143836", "name": "item", "description": "10.3390/su11143836", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/su11143836"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-07-13T00:00:00Z"}}, {"id": "10.2307/2640985", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:21:23Z", "type": "Journal Article", "created": "2006-04-17", "description": "Elevated atmospheric CO2 has the potential to increase the production and alter the chemistry of organic substrates entering soil from plant production, the magnitude of which is constrained by soil-N availability. Because microbial growth in soil is limited by substrate inputs from plant production, we reasoned that changes in the amount and chemistry of these organic substrates could affect the composition of soil microbial com- munities and the cycling of N in soil. We studied microbial community composition and soil-N transformations beneath Populus tremuloides Michx. growing under experimental atmospheric CO2 (35.7 and 70.7 Pa) and soil-N-availability (low N 5 61 ng N\u00b7g 21 \u00b7d 21 and high N 5 319 ng N\u00b7g 21 \u00b7d 21 ) treatments. Atmospheric CO2 concentration was modified in large, open-top chambers, and we altered soil-N availability in open-bottom root boxes by mixing different proportions of A and C horizon material. We used phospholipid fatty-acid analysis to gain insight into microbial community composition and coupled this analysis to measurements of soil-N transformations using 15 N-pool dilution techniques. The infor- mation presented here is part of an integrated experiment designed to elucidate the phys- iological mechanisms controlling the flow of C and N in the plant-soil system. Our ob- jectives were (1) to determine whether changes in plant growth and tissue chemistry alter microbial community composition and soil-N cycling in response to increasing atmospheric CO2 and soil-N availability and (2) to integrate the results of our experiment into a synthesis of elevated atmospheric CO2 and the cycling of C and N in terrestrial ecosystems. After 2.5 growing seasons, microbial biomass, gross N mineralization, microbial im- mobilization, and nitrification (gross and net) were equivalent at ambient and elevated CO2, suggesting that increases in fine-root production and declines in fine-root N concentration were insufficient to alter the influence of native soil organic matter on microbial physiology; this was the case in both low- and high-N soil. Similarly, elevated CO2 did not alter the proportion of bacterial, actinomycetal, or fungal phospholipid fatty acids in low-N or high-N soil, indicating that changes in substrate input from greater plant growth under elevated CO2 did not alter microbial community composition. Our results differ from a substantial number of studies reporting increases and decreases in soil-N cycling under elevated CO 2. From our analysis, it appears that soil-N cycling responds to elevated atmospheric CO 2 in experimental situations where plant roots have fully colonized the soil and root-associated C inputs are sufficient to modify the influence of native soil organic matter on microbial physiology. In young developing ecosystems where plant roots have not fully exploited the soil, microbial metabolism appears to be regulated by relatively large pools of soil organic matter, rather than by the additional input of organic substrates under elevated CO 2.", "keywords": ["measurement-", "soil microorganisms", "Ecology and Evolutionary Biology", "nitrogen-: cycling-", "feedback", "microbial community composition", "techniques-", "Environmental-Sciences)", "01 natural sciences", "litter-plant", "biomass-", "gross and net", "124-38-9: CARBON DIOXIDE", "Spermatophytes-", "cycling-", "soil-organic-matter", "mineralization", "Spermatophyta-", "responses-", "phospholipid-fatty-acids", "2. Zero hunger", "Climatology- (Environmental-Sciences)", "Angiosperms-", "Angiospermae-", "Plants-", "global climate change", "microbial immobilization", "nutrient-", "Soil-Science", "6. Clean water", "metabolism-", "soil-N transformations", "transformation-", "substrates-", "7727-37-9: NITROGEN", "atmosphere-", "elevated atmospheric", "570", "nitrification-", "nitrogen immobilization", "Science", "Vascular-Plants", "poplars-", "phospholipid fatty acids (PFLAs)", "carbon-dioxide", "growth-", "soil-microbial-community-composition", "Salicaceae-: Dicotyledones-", "microbial-flora", "Populus tremuloides", "Plantae-", "organic-matter", "consortia-", "0105 earth and related environmental sciences", "communities-", "ecosystem", "analysis-", "atmospheric CO2 and soil-N availability", "soil-availability", "mineralization-", "carbon dioxide", "fatty-acids", "15. Life on land", "substrate-input", "Populus-tremuloides (Salicaceae-)", "13. Climate action", "roots-", "Terrestrial-Ecology (Ecology-", "composition-", "Dicots-", "immobilization-", "seasons-", "ecosystems-"], "contacts": [{"organization": "Zak, Donald R., Pregitzer, Kurt S., Curtis, Peter S., Holmes, William E.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.2307/2640985"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecological%20Applications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2307/2640985", "name": "item", "description": "10.2307/2640985", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2307/2640985"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2000-02-01T00:00:00Z"}}, {"id": "10.2307/2656979", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:21:23Z", "type": "Journal Article", "created": "2006-04-21", "title": "Genotypic Variation For Condensed Tannin Production In Trembling Aspen (Populs Tremuloides, Salicaceae) Under Elevated Co2 And In High- And Low-Fertility Soil", "description": "

The carbon/nutrient balance hypothesis suggests that leaf carbon to nitrogen ratios influence the synthesis of secondary compounds such as condensed tannins. We studied the effects of rising atmospheric carbon dioxide on carbon to nitrogen ratios and tannin production. Six genotypes of Populus tremuloides were grown under elevated and ambient CO2 partial pressure and high\uffe2\uff80\uff90 and low\uffe2\uff80\uff90fertility soil in field open\uffe2\uff80\uff90top chambers in northern lower Michigan, USA. During the second year of exposure, leaves were harvested three times (June, August, and September) and analyzed for condensed tannin concentration. The carbon/nutrient balance hypothesis was supported overall, with significantly greater leaf tannin concentration at high CO2 and low soil fertility compared to ambient CO2 and high soil fertility. However, some genotypes increased tannin concentration at elevated compared to ambient CO2, while others showed no CO2 response. Performance of lepidopteran leaf miner (Phyllonorycter tremuloidiella) larvae feeding on these plants varied across genotypes, CO2, and fertility treatments. These results suggest that with rising atmospheric CO2, plant secondary compound production may vary within species. This could have consequences for plant\uffe2\uff80\uff93herbivore and plant\uffe2\uff80\uff93microbe interactions and for the evolutionary response of this species to global climate change.

", "keywords": ["0106 biological sciences", "Salicaceae", "genotype", "plant\u2013herbivore interaction", "Phyllonorycter-tremuloidiella", "Quaking aspen", "01 natural sciences", "plant-composition", "tannin", "nitrogen-", "carbon-dioxide: elevation-", "124-38-9: CARBON DIOXIDE", "Spermatophytes-", "Spermatophyta-", "genotypic-variation", "Population-Genetics (Population-Studies)", "2. Zero hunger", "carbon-", "Climatology- (Environmental-Sciences)", "Angiosperms-", "Angiospermae-", "Plants-", "GLOBAL-ECOLOGY", "Populus-tremuloides", "plant-pests", "climate-change", "genetic-variation", "forest-trees", "condensed tannins", "Nitrogen", "Science", "Vascular-Plants", "carbon-dioxide-enrichment", "Nutrition-", "genotypes-", "Phyllonorycter tremuloidiella", "Populus-tremuloides [trembling-aspen] (Salicaceae-)", "soil-fertility", "Populus tremuloides", "Salicaceae-: Dicotyledones-", "Biology", "Plantae-", "global change", "tannins-", "condensed-tannin: production-", "foliage-", "forest-pests", "Tannic acid", "Metabolism-", "Botany", "carbon dioxide", "forest-soils", "15. Life on land", "Carbon", "climate-", "Carbon dioxide", "13. Climate action", "Dicots-", "insect-pests"], "contacts": [{"organization": "Donald R. Zak, Jennifer L Mansfield, Kurt S. Pregitzer, Kurt S. Pregitzer, Peter S. Curtis, Peter S. Curtis,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.2307/2656979"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/American%20Journal%20of%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2307/2656979", "name": "item", "description": "10.2307/2656979", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2307/2656979"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1999-08-01T00:00:00Z"}}, {"id": "10.2527/2001.7971892x", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-30T16:21:27Z", "type": "Journal Article", "created": "2016-08-09", "description": "A balance trial was conducted to titrate the effects of tallow on the energy metabolism of wethers fed barley finishing diets. Six dietary levels of tallow (0, 2, 4, 6, 8, or 10%) in a barley finishing diet were fed to six crossbred wethers (35+/-1.1 kg) in a randomized complete block design. Diets were 73% barley, 10% tallow and(or) bentonite, 10% alfalfa pellets, and 7% supplement. There was no effect of tallow level on OM intake (1,103.1+/-51 g/d), OM digestibility (84+/-0.9%), GE digestibility (83+/-1.1%), or cell solubles digestibility (84.2+/-1.2%). The level of tallow quadratically decreased ADF digestibility (P < 0.05), methane emissions, and methane energy as a percentage of GE P < 0.01). There were linear increases in dietary GE (megacalories per kilogram of OM [P < 0.01]), dietary DE (megacalories per kilogram of OM [P < 0.05]), and dietary ME (megacalories per kilogram of OM [P < 0.01]), as dietary tallow increased. Numbers of ruminal protozoa (Entodinium spp. and Polyplastron sp.) decreased linearly (P < 0.05) with increased level of tallow. The energy value of tallow (calculated by difference) was low. The total-tract fatty acid digestibility of tallow was calculated by linear regression, without intercept, after accounting for the fatty acids digested from the base diet (0% tallow fed to a wether in a period). Fatty acids of the same carbon length were pooled for the regression analysis. All linear regressions were significant (P < 0.10) indicating no effect of tallow level on fatty acid digestibility. Lauric acid had low digestibility. The high digestibility of all C16 (89%) and C18 (104%) fatty acids suggests an effect of tallow on endogenous and microbial fatty acid excretion. Fatty acid digestibility was probably a minor contributor to the low energy content of tallow, calculated by difference, in these diets.", "keywords": ["Fats", "Male", "2. Zero hunger", "Sheep", "Fermentation", "Microscopy", " Electron", " Scanning", "0402 animal and dairy science", "Animals", "Hordeum", "04 agricultural and veterinary sciences", "Energy Metabolism", "Animal Feed"], "contacts": [{"organization": "H H Westberg, Mark L. Nelson, Steven M. Parish,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.2527/2001.7971892x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Animal%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2527/2001.7971892x", "name": "item", "description": "10.2527/2001.7971892x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2527/2001.7971892x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2001-01-01T00:00:00Z"}}, {"id": "10.2527/jas1986.6362044x", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-30T16:21:28Z", "type": "Journal Article", "created": "2016-08-09", "description": "Eight steers (327 kg average) were fed diets containing either nontreated or anhydrous NH3-treated wheat straw in a two-period crossover design. Intake and digestibilities of dry matter, gross energy, neutral detergent fiber, acid detergent fiber and crude protein were measured by total collection. Energy losses in urine and methane were determined. Heat production was determined by indirect respiration calorimetry on steers fed both diets and after they were fasted. Ammoniation of the straw raised its N content from .49 to 1.59% (P less than .001). Dry matter (DM) intake was increased (P less than .01) by the process from 1.0 to 1.3% of body weight. Digestibility coefficients of dry matter and energy, as well as those for fiber, were increased (P less than .001) by four percentage units or more. Crude protein digestibility, however, was depressed (P less than .001) from 67.8% to 53.5% by ammoniation. Urinary energy as a percentage of gross energy intake (GEI) was reduced (P less than .05) by NH3 treatment from 4.10 to 3.74%. Methane energy was not different (P greater than .10). Metabolizable energy was improved (P less than .001) by ammoniation, increasing from 45.2 to 50.0% of GEI. Daily heat production was higher (P less than .01) for steers consuming the ammoniated straw diet, increasing from 113.7 to 125.3 kcal/wt.75), and was due to higher metabolizable energy intake (MEI) since partial efficiency of MEI used for maintenance did not differ (P greater than .10) between diets. The higher net energy value of the ammoniated wheat straw diet (1.45 vs 1.26 kcal/g DM) was due mainly to decreased fecal loss and a slight decline in urinary loss.", "keywords": ["Male", "2. Zero hunger", "Ammonia", "0402 animal and dairy science", "Animals", "Cattle", "04 agricultural and veterinary sciences", "Energy Metabolism", "Animal Feed", "Nutritive Value", "6. Clean water"], "contacts": [{"organization": "C. P. Birkelo, D. E. Johnson, Gerald M. Ward,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.2527/jas1986.6362044x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Animal%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2527/jas1986.6362044x", "name": "item", "description": "10.2527/jas1986.6362044x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2527/jas1986.6362044x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1986-12-01T00:00:00Z"}}, {"id": "10.3168/jds.2010-3635", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:21:33Z", "type": "Journal Article", "created": "2011-02-20", "title": "Effects Of A Combination Of Feed Additives On Methane Production, Diet Digestibility, And Animal Performance In Lactating Dairy Cows", "description": "Two experiments were conducted to assess the effects of a mixture of dietary additives on enteric methane production, rumen fermentation, diet digestibility, energy balance, and animal performance in lactating dairy cows. Identical diets were fed in both experiments. The mixture of feed additives investigated contained lauric acid, myristic acid, linseed oil, and calcium fumarate. These additives were included at 0.4, 1.2, 1.5, and 0.7% of dietary dry matter, respectively (treatment ADD). Experimental fat sources were exchanged for a rumen inert source of fat in the control diet (treatment CON) to maintain isolipidic rations. Cows (experiment 1, n=20; experiment 2, n=12) were fed restricted amounts of feed to avoid confounding effects of dry matter intake on methane production. In experiment 1, methane production and energy balance were studied using open-circuit indirect calorimetry. In experiment 2, 10 rumen-fistulated animals were used to measure rumen fermentation characteristics. In both experiments animal performance was monitored. The inclusion of dietary additives decreased methane emissions (g/d) by 10%. Milk yield and milk fat content tended to be lower for ADD in experiment 1. In experiment 2, milk production was not affected by ADD, but milk fat content was lower. Fat- and protein-corrected milk was lower for ADD in both experiments. Milk urea nitrogen content was lowered by ADD in experiment 1 and tended to be lower in experiment 2. Apparent total tract digestibility of fat, but not that of starch or neutral detergent fiber, was higher for ADD. Energy retention did not differ between treatments. The decrease in methane production (g/d) was not evident when methane emission was expressed per kilogram of milk produced. Feeding ADD resulted in increases of C12:0 and C14:0 and the intermediates of linseed oil biohydrogenation in milk in both experiments. In experiment 2, ADD-fed cows tended to have a decreased number of protozoa in rumen fluid when compared with that in control cows. Total volatile fatty acid concentrations were lower for ADD, whereas molar proportions of propionate increased at the expense of acetate and butyrate.", "keywords": ["chain fatty-acids", "Linseed Oil", "Rumen", "extruded linseed", "Myristic Acid", "0403 veterinary science", "crude linseed", "Fumarates", "fumaric-acid", "ruminal methanogenesis", "Animals", "Lactation", "myristic acid", "beef-cattle", "coconut oil", "2. Zero hunger", "0402 animal and dairy science", "Lauric Acids", "04 agricultural and veterinary sciences", "linseed oil", "Animal Feed", "Diet", "Fermentation", "Cattle", "Digestion", "Female", "Food Additives", "detergent fiber", "Energy Metabolism", "Methane"]}, "links": [{"href": "https://doi.org/10.3168/jds.2010-3635"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Dairy%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3168/jds.2010-3635", "name": "item", "description": "10.3168/jds.2010-3635", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3168/jds.2010-3635"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-03-01T00:00:00Z"}}, {"id": "10.3390/su12093676", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:22:02Z", "type": "Journal Article", "created": "2020-05-05", "title": "Assessing New Biotechnologies by Combining TEA and TM-LCA for an Efficient Use of Biomass Resources", "description": "

An efficient use of biomass resources is a key element of the bioeconomy. Ideally, options leading to the highest environmental and economic gains can be singled out for any given region. In this study, to achieve this goal of singling out an ideal technology for a given region, biotechnologies are assessed by a combination of techno-economic assessment (TEA) and territorial metabolism life cycle assessment (TM-LCA). Three technology variations for anaerobic digestion (AD) were assessed at two different scales (200 kW and 1 MW) and for two different regions. First, sustainable feedstock availability for two European regions was quantified. Then, the environmental impact and economic potential of each technology when scaled up to the regional level, considering all of the region\uffe2\uff80\uff99s unique sustainably available feedstock, was investigated. Multiple criteria decision analysis and internalized damage monetization were used to generate single scores for the assessments. Preference for the technology scenario producing the most energy was shown for all regions and scales, while producing bioplastic was less preferable since the value of the produced bioplastic plastic was not great enough to offset the resultant reduction in energy production. Assessing alternatives in a regional context provided valuable information about the influence of different types of feedstock on environmental performance.

", "keywords": ["Techno-economic assessment", "anaerobic digestion", "Regional assessment", "0211 other engineering and technologies", "Biogas", "techno-economic assessment", "02 engineering and technology", "/dk/atira/pure/sustainabledevelopmentgoals/responsible_consumption_and_production; name=SDG 12 - Responsible Consumption and Production", "biomass valorization", "7. Clean energy", "territorial metabolism", "12. Responsible consumption", "regional assessment", "Life cycle assessment", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "life cycle assessment", "Anaerobic digestion", "11. Sustainability", "biogas", "0202 electrical engineering", " electronic engineering", " information engineering", "Territorial metabolism", "Polyhydroxyalkanoates", "polyhydroxyalkanoates", "Wet oxidation", "Biomass valorization", "wet oxidation", "13. Climate action", "8. Economic growth"]}, "links": [{"href": "http://www.mdpi.com/2071-1050/12/9/3676/pdf"}, {"href": "https://www.mdpi.com/2071-1050/12/9/3676/pdf"}, {"href": "https://doi.org/10.3390/su12093676"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sustainability", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/su12093676", "name": "item", "description": "10.3390/su12093676", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/su12093676"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-02T00:00:00Z"}}, {"id": "10.5061/dryad.22jr6", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-30T16:22:21Z", "type": "Dataset", "title": "Data from: Thermodynamic constraints on the utility of ecological stoichiometry for explaining global biogeochemical patterns", "description": "unspecifiedCarbon and nitrogen cycles are coupled through both stoichiometric requirements for microbial biomass and dissimilatory metabolic processes in which microbes catalyse reduction-oxidation reactions. Here, we integrate stoichiometric theory and thermodynamic principles to explain the commonly observed trade-off between high nitrate and high organic carbon concentrations, and the even stronger trade-off between high nitrate and high ammonium concentrations, across a wide range of aquatic ecosystems. Our results suggest these relationships are the emergent properties of both microbial biomass stoichiometry and the availability of terminal electron acceptors. Because elements with multiple oxidation states (i.e. nitrogen, manganese, iron and sulphur) serve as both nutrients and sources of chemical energy in reduced environments, both assimilative demand and dissimilatory uses determine their concentrations across broad spatial gradients. Conceptual and quantitative models that integrate rather than independently examine thermodynamic, stoichiometric and evolutionary controls on biogeochemical cycling are essential for understanding local to global biogeochemical patterns.", "keywords": ["13. Climate action", "nitrate", "dissimilatory microbial metabolism", "15. Life on land", "reduction-oxidation reactions", "organismal stoichiometry", "6. Clean water", "Carbon"], "contacts": [{"organization": "Helton, Ashley M., Ardon, Marcelo, Bernhardt, Emily S.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.22jr6"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.22jr6", "name": "item", "description": "10.5061/dryad.22jr6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.22jr6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-09-18T00:00:00Z"}}, {"id": "10.5061/dryad.qz612jmp3", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-30T16:22:30Z", "type": "Dataset", "created": "2023-12-05", "title": "Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism", "description": "unspecified| README.txt file\u00a0 | | | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------- | | | | | GENERAL INFORMATION | | | | | | 1. Title of Dataset: Data from: Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism | | | | | | 2. Author Information: | | | First author 1 | | | Name: Ye Li | | | Institution: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China | | | | | | Corresponding author 2 | | | Name: Zengming Chen | | | Institution: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China | | | Email: zmchen @issas.ac.cn | | | | | | Co-author 3 | | | Name: Cameron Wagg | | | Institution: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada | | | | | | Co-author 4 | | | Name: Michael J. Castellano | | | Institution: Department of Agronomy, Iowa State University, Ames, Iowa, USA | | | | | | Co-author 5 | | | Name: Nan Zhang | | | Institution: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, China | | | | | | Co-author 6 | | | Name: Weixin Ding | | | Institution: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China | | | | | | 3. Date of data collection: 2019-2023 | | | | | | 4. Geographic location of data collection: Baoqing county, in the east of Heilongjiang Province, northeast China (46\u00b020\u2019N, 132\u00b012\u2019E, elevation 70-75 m). | | | | | | 5. Funding sources that supported the collection of the data: National Key Research and Development Program of China (2022YFD1500303), Strategic Priority Research Program of Chinese Academy of Sciences (XDA28010302), Natural Science Foundation of Jiangsu Province (BK20211610), Natural Science Foundation of China (42077029, U1906220), Frontier Project from the Institute of Soil Science, Chinese Academy of Sciences (ISSASIP2212), and Youth Innovation Promotion Association of Chinese Academy of Sciences (2022313). | | | | | | 6. Recommended citation for this dataset: Li et al. (2024), Data from: Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism, Dryad, Dataset. | | | | | | | | | DATA FILES | | | | | | File: Belowground metabolism and SOC decomposition | | | Details: total enzyme activities, C and N/P limitations and SOC decomposition | | | | | | File: Biodiversity | | | Details: the richess, Shannon and Simpson indices | | | | | | File: Edaphic condition | | | Details: soil physicochemical factors | | | | | | File: Topological features | | | Details: Topological features of multitrophic networks | | | | | | VARIABLE LIST AND ABBREVIATION | | | | | | SOC | content of soil organic carbon | | C limitation | limitation of carbon in belowground metabolic activities calculated from vector length in enzymatic stochiometry | | P/N limitation | limitation of phosphorus or nitrogen\u00a0 in belowground metabolic activities calculated from vector angle in enzymatic stochiometry | | TN | content of total nitrogen | | TP | content oftotal phosphorus | | Zi | the sum of Z-score of enzyme activities | | C/N | ratio of soil organic matter to total nitrogen | | C/P | ratio of soil organic matter to total phosphorus | | AP | content of available phosphorus | | NH4+ | content of ammonium | | NO3- | content of nitrate | | nodes _num | the number of ASVs included in networks | | edge _number | the number of connections among all nodes | | neg _pos | the ratio of negative to positive connections | | average _degree | mean connections of all nodes with another unique node | | average _path _length | mean network distance between all paired nodes | | clustering _coefficient | the degree of nodes clumping | | betweenness _centralization | the times of a specific node acting as a bridge along the shortest path between another paired nodes | | closeness _centralization | inverse of the average distance of a specific node to any other nodes | | degree _centralization | evenness of connections among nodes in a network | | HC | samples with SOC content above 23 g C kg-1 | | LC | samples with SOC content below 23 g C kg-1 |", "keywords": ["soil organic carbon", "Mollisols", "agroecosystem", "FOS: Agricultural sciences", "multitrophic network", "Biodiversity", "carbon loss", "belowground metabolisms"], "contacts": [{"organization": "Chen, Zengming", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.qz612jmp3"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.qz612jmp3", "name": "item", "description": "10.5061/dryad.qz612jmp3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.qz612jmp3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-20T00:00:00Z"}}, {"id": "10.5061/dryad.rn8pk0ph1", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-30T16:22:31Z", "type": "Dataset", "title": "Long-term nitrogen deposition inhibits soil priming effects by enhancing phosphorus limitation in a subtropical forest", "description": "unspecifiedThis dataset was collected by sampling soils exposed to 9 years of manipulative N inputs in situ in a subtropical forest and then incubating them in a 30-day incubation experiment. The CO2 flux and PE were measured by NaOH trapping. Soil variables were measured at the end of incubation.", "keywords": ["2. Zero hunger", "SOM decomposition", "13. Climate action", "P limitation", "15. Life on land", "priming effects", "Microbial metabolism", "FOS: Natural sciences", "N deposition"], "contacts": [{"organization": "Wang, Xiaohong, Li, Shiyining, Zhu, Biao, Homyak, Peter M., Chen, Guangshui, Yao, Xiaodong, Wu, Dongmei, Yang, Zhijie, Lyu, Maokui, Yang, Yusheng,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.rn8pk0ph1"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.rn8pk0ph1", "name": "item", "description": "10.5061/dryad.rn8pk0ph1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.rn8pk0ph1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-19T00:00:00Z"}}, {"id": "10138/356895", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:25:44Z", "type": "Journal Article", "created": "2023-03-08", "title": "The giant diploid faba genome unlocks variation in a global protein crop", "description": "Abstract

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity 1 . However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value 2 . Faba bean ( Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13\uffe2\uff80\uff89Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the\uffc2\uffa0improvement of sustainable protein production across the\uffc2\uffa0Mediterranean, subtropical and northern temperate agroecological zones. \u201cNon-metabolizable\u201d glucose analogue shines new light on priming mechanisms: Triggering of microbial metabolism Soil Biology and Biochemistry 107, 68-76 https://doi.org/10.1016/j.soilbio.2016.12.015 * corresponding author: kmasonj@gwdg.de", "keywords": ["2. Zero hunger", "Soil organic matter", "Microbial activation", "Chemosensory triggering", "Carbon cycle", "Apparent priming", "Microbial metabolism"], "contacts": [{"organization": "Mason-Jones, Kyle, Kuzyakov, Yakov,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.1146786"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.1146786", "name": "item", "description": "10.5281/zenodo.1146786", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.1146786"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-05T00:00:00Z"}}, {"id": "10.5281/zenodo.17710964", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-30T16:24:20Z", "type": "Dataset", "title": "Dataset for: Metagenomic Insights Into Microbial Controls of Carbon Cycling in Alpine Soils", "description": "Dataset for: Metagenomic Insights Into Microbial Controls of Carbon Cycling in Alpine Soils. Manuscript and Supporting Information published as preprint on biorxiv: https://doi.org/10.1101/2025.09.22.677713", "keywords": ["soil redox dynamics", "microbial metabolism", "Soil organic carbon", "Alpine riparian soils", "microbial community composition", "shotgun metagenomics"], "contacts": [{"organization": "Bright, Kristina, Dienes, Bence, van Dongen, Bart, Strashnov, Ilya, Han, Xingguo, Aeppli, Meret,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.17710964"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.17710964", "name": "item", "description": "10.5281/zenodo.17710964", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.17710964"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-11-25T00:00:00Z"}}, {"id": "PMC11897584", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:29:48Z", "type": "Journal Article", "created": "2025-03-12", "title": "Distinct Patterns of Antibiotic Sensitivities in Ammonia\u2010Oxidising Archaea", "description": "ABSTRACT

Ammonia\uffe2\uff80\uff90oxidising archaea (AOA) are important microorganisms contributing towards the nitrogen flux in the environment. Unlike archaea from other major phyla, genetic tools are yet to be developed for the AOA, and identification of antibiotic resistance markers for selecting mutants is required for a genetic system. The aim of this study was to test the effects of selected antibiotics (hygromycin B, neomycin, apramycin, puromycin, novobiocin) on pure cultures of three well studied AOA strains, \uffe2\uff80\uff98 Candidatus Nitrosocosmicus franklandianus C13\uffe2\uff80\uff99, Nitrososphaera viennensis EN76 and Nitrosopumilus maritimus SCM1. Puromycin, hygromycin B and neomycin inhibited some but not all tested archaeal strains. All strains were resistant to apramycin and inhibited by novobiocin to various degrees. As N. viennensis EN76 was relatively more resistant to the tested antibiotics, a wider range of concentrations and compounds (chloramphenicol, trimethoprim, statins) was tested against this strain. N. viennensis EN76 was inhibited by trimethoprim, but not by chloramphenicol, and growth recovered within days in the presence of simvastatin, suggesting either degradation of, or spontaneous resistance against, this compound. This study highlights the physiological differences between different genera of AOA and has identified new candidate antibiotics for selective enrichment and the development of selectable markers for genetic systems in AOA.

Intercellular signalling is an indispensable part of multicellular life. Understanding the commonalities and differences in how signalling molecules function in two remote branches of the tree of life may shed light on the reasons these molecules were originally recruited for intercellular signalling. Here we review the plant function of three highly studied animal intercellular signalling molecules, namely glutamate, \u03b3-aminobutyric acid (GABA), and melatonin. By considering both their signalling function in plants and their broader physiological function, we suggest that molecules with an original function as key metabolites or active participants in reactive ion species scavenging have a high chance of becoming intercellular signalling molecules. Naturally, the evolution of machinery to transduce a message across the plasma membrane is necessary. This fact is demonstrated by three other well-studied animal intercellular signalling molecules, namely serotonin, dopamine, and acetylcholine, for which there is currently no evidence that they act as intercellular signalling molecules in plants.

", "keywords": ["0301 basic medicine", "0303 health sciences", "signalling molecules", "plant physiology", "QH301-705.5", "Science", "Q", "R", "Plant Biology", "Glutamic Acid", "Plants", "03 medical and health sciences", "Journal Article", "reactive ion species", "Medicine", "Animals", "comparative biology", "Biology (General)", "metabolism", "gamma-Aminobutyric Acid", "Melatonin", "Signal Transduction"]}, "links": [{"href": "https://doi.org/10.7554/elife.83361"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/eLife", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.7554/elife.83361", "name": "item", "description": "10.7554/elife.83361", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.7554/elife.83361"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-20T00:00:00Z"}}, {"id": "3133761231", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:27:29Z", "type": "Journal Article", "created": "2021-07-27", "title": "Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities", "description": "Abstract

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that\uffe2\uff80\uff94like for AOB\uffe2\uff80\uff94ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.Abstract

Natural based solutions, notably constructed/artificial wetland treatment systems, rely heavily on identification and use of macrophytes with the ability to tolerate multiple contaminants and grow for an extended period to reduce contamination. The potential to tolerate and remediate metal(loid) contaminated groundwater from an industrial site located in Flanders (Belgium) was assessed for 10 wetland macrophytes (including Carex riparia, Cyperus longus, Cyperus rotundus, Iris pseudacorus, Juncus effusus, Lythrum salicaria, Menta aquatica, Phragmites australis, Scirpus holoschoenus, and Typha angustifolia). The experiment was conducted under static conditions, where plants were exposed to polluted acidic (pH~4)water, having high level of metal(loid)s for 15 days. Plant biomass, morphology, and metal uptake by roots and shoots were analysed every 5 days for all species. T. angustifolia and S. holoschoenus produced ~3 and ~1.1 times more dried biomass than the controls, respectively. For S. holoschoenus, P. australis, and T. angustifolia, no apparent morphological stress symptoms were observed, and plant heights were similar between control and plants exposed to polluted groundwater. Higher concentrations of all metal(loid)s were detected in the roots indicating a potential for phytostabilization of metal(loid)s below the water column. For J. effusus and T. angustifolia, Cd, Ni, and Zn accumulation was observed higher in the shoots. S. holoschoenus, P. australis, and T. angustifolia are proposed for restoration and phytostabilization strategies in natural and/or constructed wetland and aquatic ecosystems affected by metal(loid) inputs.

", "keywords": ["580", "570", "Constructed wetlands ; Metals/metabolism [MeSH] ; Groundwater ; Phytostabilization ; Wetlands [MeSH] ; Metals", " Heavy/metabolism [MeSH] ; Heavy metals ; Macrophytes ; Water Pollutants", " Chemical/metabolism [MeSH] ; Research Article ; Biodegradation", " Environmental [MeSH] ; Belgium [MeSH]", "Constructed wetlands", "15. Life on land", "Biorremediaci\u00f3n", "6. Clean water", "Macrophytes", "Agua-Contaminaci\u00f3n", "Biodegradation", " Environmental", "Heavy metals", "Water-Pollution", "Belgium", "Metals", "13. Climate action", "Wetlands", "Metals", " Heavy", "Phytostabilization", "Groundwater", "Bioremediation", "Water Pollutants", " Chemical", "Research Article"]}, "links": [{"href": "https://doi.org/10259/9749"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20and%20Pollution%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10259/9749", "name": "item", "description": "10259/9749", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10259/9749"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-12T00:00:00Z"}}, {"id": "10261/395709", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:25:54Z", "type": "Journal Article", "created": "2022-10-24", "title": "Regulation and Function of a Polarly Localized Lignin Barrier in the Exodermis", "description": "ABSTRACT

Multicellular organisms control interactions with their environment through the development of specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS). The CS is made of polymerized lignin and forms a ring-like structure that seals the apoplastic space between the endodermal cells. Most angiosperms also have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation, as well as function, is limited as this cell type is absent from the model speciesArabidopsis thaliana. Using tomato (Solanum lycopersicum) as a model system we demonstrate that in this species, the exodermis does not form a CS. Instead, it forms a polar lignin cap with an equivalent barrier function to the endodermal CS. We demonstrate that although endodermal regulators are conserved between Arabidopsis and tomato, exodermal differentiation occurs by a distinct regulatory pathway involving theSlSCZandSlEXO1transcription factors. Although the exodermis and endodermis both produce barriers that restrict mineral ion uptake, they have unique and overlapping roles in their selectivity. Whether conservation and similarities between the endodermis and exodermis exist in other species remains to be determined. Nonetheless, in tomato, these distinct lignin structures have a convergent function with different genetic regulations.Plant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organismArabidopsis thaliana. Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.