{"type": "FeatureCollection", "features": [{"id": "10.1016/j.gca.2023.01.029", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:13Z", "type": "Journal Article", "created": "2023-02-06", "title": "Competitive incorporation of Mn and Mg in vivianite at varying salinity and effects on crystal structure and morphology", "description": "Open AccessVivianite, a ferrous phosphate mineral, can be an important phosphorus (P) sink in non-sulfidic, reducing coastal sediments. The Fe in the crystal structure of vivianite can be substituted by other divalent metal cations such as Mn2+ or Mg2+. Since Mg is much more abundant in coastal porewaters than Mn, the more frequent reports of Mn substitution in vivianites of coastal sediments has been suggested to indicate a preferential incorporation of Mn over Mg into the crystal structure of vivianite. However, although both Mn and Mg substitution in vivianite are environmentally relevant, it is yet unknown whether Mn or Mg is preferentially incorporated and how these isomorphic substitutions alter the crystal structure and morphology of vivianite, parameters which may influence vivianite reactivity. Here, we studied the incorporation of Mn and/or Mg in vivianites formed by co-precipitation at pH 7 in the presence of varying dissolved Mn and/or Mg concentrations and solution salinities resembling an estuarine gradient from 0 to 9 psu. In total, 19 different vivianites were synthesized, with up to 50% of Fe substituted by Mn and Mg. Thermodynamic equilibrium calculations showed that aqueous Mg speciation was altered with increasing salinity, while Mn speciation was less affected, likely explaining the preferential incorporation of Mn in the vivianite structure at higher salinities. 57Fe-M\u00f6ssbauer spectroscopy revealed that both Mn and Mg were preferentially incorporated in the double-octahedral Fe position, at which intervalence charge transfer is possible during the oxidation of vivianite. In contrast to Mg, which is redox inactive, incorporated Mn can participate in heteronuclear intervalence charge transfer with Fe. Thus, incorporation of either cation may impact the reactivity of vivianite under oxidizing conditions in element specific ways. Results of complementary analyses including X-ray diffraction, electron microscopy and Fe K-edge X-ray absorption spectroscopy further showed that incorporation of Mn and/or Mg led to smaller particle size, increased crystal roughness and thinner crystals, as well as systematic changes in unit cell parameters. These observed changes in crystal morphology might impact the reactivity of vivianite in natural environments and thus the effect of cation incorporation in vivianite should be considered when studying Fe and P cycling in coastal sediments.", "keywords": ["M\u00f6ssbauer Spectroscopy", "550", "Isomorphic substitution", "13. Climate action", "Ferrous phosphate minerals", "Electron microscopy", "Ferrous phosphate minerals; Phosphorus burial; Isomorphic substitution; M\u00f6ssbauer Spectroscopy; Electron microscopy", "Phosphorus burial", "01 natural sciences", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.gca.2023.01.029"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Geochimica%20et%20Cosmochimica%20Acta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.gca.2023.01.029", "name": "item", "description": "10.1016/j.gca.2023.01.029", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.gca.2023.01.029"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-01T00:00:00Z"}}, {"id": "10.1007/s11104-023-06151-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:14:54Z", "type": "Journal Article", "created": "2023-07-26", "title": "Smart soils track the formation of pH gradients across the rhizosphere", "description": "Abstract                 Aims                 <p>Our understanding of the rhizosphere is limited by the lack of techniques for in situ live microscopy. Current techniques are either destructive or unsuitable for observing chemical changes within the pore space. To address this limitation, we have developed artificial substrates, termed smart soils, that enable the acquisition and 3D reconstruction of chemical sensors attached to soil particles.</p>                                Methods                 <p>The transparency of smart soils was achieved using polymer particles with refractive index matching that of water. The surface of the particles was modified both to retain water and act as a local sensor to report on pore space pH via fluorescence emissions. Multispectral signals were acquired from the particles using a light sheet microscope, and machine learning algorithms predicted the changes and spatial distribution in pH at the surface of the smart soil particles.</p>                                Results                 <p>The technique was able to predict pH live and in situ within \uffc2\uffb1\uffe2\uff80\uff890.5 units of the true pH value. pH distribution could be reconstructed across a volume of several cubic centimetres around plant roots at 10\uffc2\uffa0\uffce\uffbcm resolution. Using smart soils of different composition, we revealed how root exudation and pore structure create variability in chemical properties.</p>                                Conclusion                 <p>Smart soils captured the pH gradients forming around a growing plant root. Future developments of the technology could include the fine tuning of soil physicochemical properties, the addition of chemical sensors and improved data processing. Hence, this technology could play a critical role in advancing our understanding of complex rhizosphere processes.</p>", "keywords": ["/dk/atira/pure/subjectarea/asjc/1100/1111", "light sheet microscopy", "0301 basic medicine", "570", "0303 health sciences", "name=Soil Science", "/dk/atira/pure/subjectarea/asjc/1100/1110", "Sensing soil", "live imaging", "15. Life on land", "root", "530", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "03 medical and health sciences", "Root", "13. Climate action", "Rhizosphere", "Light sheet microscopy", "name=Plant Science", "rhizosphere", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "Live imaging"]}, "links": [{"href": "https://doi.org/10.1007/s11104-023-06151-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-023-06151-y", "name": "item", "description": "10.1007/s11104-023-06151-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-023-06151-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-07-26T00:00:00Z"}}, {"id": "10.1016/j.biombioe.2018.10.004", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:15:35Z", "type": "Journal Article", "created": "2018-10-11", "title": "How and why does willow biochar increase a clay soil water retention capacity?", "description": "Abstract   Addition of biochar into a soil changes its water retention properties by modifying soil textural and structural properties. In addition, internal micrometer-scale porosity that is able to directly store readily plant available water affects soil water retention properties. This study shows how precise knowledge of the internal micrometer-scale pore size distribution of biochar can deepen the understanding of the biochar-water interactions in soils. The micrometer-scale porosity of willow biochar was quantitatively and qualitatively characterized using X-ray tomography, 3D image analysis and Helium ion microscopy. The effect of biochar application on clay soil water retention was studied by conventional water retention curve approach. The results indicate that the internal pores of biochar, with sizes of at 50 and 10\u202f\u03bcm (equivalent pore diameter), increased soil porosity and the amount of readily plant available water. After biochar addition, changes in soil porosity were detected at pore size regimes 5\u201310 and 25\u202f\u03bcm, i.e. biochar pore sizes multiplied by factor 0.5. The detected pore size distribution of biochar does not predict directly (1:1 compatibility) the changes observed in the soil moisture characteristics. It is likely that biochar chemistry and pore morphology affect biochar-water interactions via e.g. surface roughness and contact angle. In addition, biochar induced changes in soil structure and texture affected soil moisture characteristics. However, the approach presented is an attractive pathway to more generalized understanding on how and why biochar internal porosity affects soil moisture characteristics.", "keywords": ["570", "Fysiikka", "ta1171", "mikroskopia", "savi", "01 natural sciences", "630", "huokoisuus", "soil water retention", "tomografia", "219", "3D image analysis", "biochar", "3D-mallinnus", "ta216", "ta218", "219 Environmental biotechnology", "0105 earth and related environmental sciences", "x-ray tomography", "biohiili", "maaper\u00e4", "ta114", "Physics", "ta1182", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "mikrorakenteet", "plant available water", "helium ion microscopy", "0401 agriculture", " forestry", " and fisheries", "vesipitoisuus", "X-ray tomography"]}, "links": [{"href": "https://doi.org/10.1016/j.biombioe.2018.10.004"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biomass%20and%20Bioenergy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biombioe.2018.10.004", "name": "item", "description": "10.1016/j.biombioe.2018.10.004", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biombioe.2018.10.004"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-01T00:00:00Z"}}, {"id": "10.1016/j.foodchem.2019.03.027", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:02Z", "type": "Journal Article", "created": "2019-03-12", "title": "Optimization of ultrasound-microwave assisted acid extraction of pectin from potato pulp by response surface methodology and its characterization", "description": "The ultrasound-microwave assisted HCl extraction of pectin from potato pulp was optimized using the response surface methodology. Effects of extraction temperature, pH, and time on the yield were evaluated, and structural characteristics of pectin extracted under optimal conditions were determined. The yield was 22.86\u202f\u00b1\u202f1.29% under optimal conditions of temperature 93\u202f\u00b0C, pH 2.0, and time 50\u202fmin. The obtained pectin was rich in branched rhamnogalacturonan I (61.54\u202fmol%). Furthermore, the pectin was a low-methoxyl (degree of methylation, 32.58%) but highly acetylated (degree of acetylation, 17.84%) pectin and the molecular weight was 1.537\u202f\u00d7\u202f105\u202fg/mol. Fourier transform infrared spectroscopy and 1H nuclear magnetic resonance indicated that pectin had a linear region of \u03b1-1, 4-linked galacturonic acids which could be methyl and acetyl-esterified, and rhamnose linked with galacturonic acid to form rhamnogalacturonan which was branched with side chains. Scanning electron microscopy showed most of pectin had a lamellae structure.", "keywords": ["Plant Extracts", "Hexuronic Acids", "Temperature", "Acetylation", "04 agricultural and veterinary sciences", "Methylation", "Plant Tubers", "0404 agricultural biotechnology", "Spectroscopy", " Fourier Transform Infrared", "Microscopy", " Electron", " Scanning", "Pectins", "Ultrasonics", "Microwaves", "0405 other agricultural sciences", "Solanum tuberosum"], "contacts": [{"organization": "Yang, Jin-Shu, Mu, Tai-Hua, Ma, Meng-Mei,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.foodchem.2019.03.027"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Food%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foodchem.2019.03.027", "name": "item", "description": "10.1016/j.foodchem.2019.03.027", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foodchem.2019.03.027"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-01T00:00:00Z"}}, {"id": "10.1016/j.foodres.2018.01.020", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:03Z", "type": "Journal Article", "created": "2018-01-12", "title": "The impact of newly produced protein and dietary fiber rich fractions of yellow pea ( Pisum sativum L.) on the structure and mechanical properties of pasta-like sheets", "description": "Two fractions from pea (Pisum sativum L.), protein isolate (PPI) and dietary fiber (PF), were newly produced by extraction-fractionation method and characterized in terms of particle size distribution and structural morphology using SEM. The newly produced PPI and PF fractions were processed into pasta-like sheets with varying protein to fiber ratios (100/0, 90/10, 80/20, 70/30 and 50/50, respectively) using high temperature compression molding. We studied protein polymerization, molecular structure and protein-fiber interactions, as well as mechanical performance and cooking characteristics of processed PPI-PF blends. Bi-modal particle size distribution and chemical composition of the PPI and PF fractions influenced significantly the physicochemical properties of the pasta-like sheets. Polymerization was most pronounced for the 100 PPI, 90/10 and 80/20 PPI-PF samples as studied by SE-HPLC, and polymerization decreased with addition of the PF fraction. The mechanical properties, as strength and extensibility, were likewise the highest for the 100 PPI and 90/10 PPI-PF blends, while the E-modulus was similar for all the studied blends (around 38\u202fMPa). The extensibility decreased with the increasing amount of PF in the blend. The highest amounts of \u03b2-sheets were found in the pasta-like sheets with high amounts of PPI (100, 90 and 80%), by FT-IR. An increase in PF fraction in the blend, resulted into the high amounts of unordered structures as observed by FT-IR, as well as in an increase in the molecular scattering distances observed by SAXS. The water uptake increased and cooking loss decreased with increased proportions of the PF fraction, and the consistency of 10\u202fmin cooked pasta-like sheets were alike al dente texture. The new knowledge obtained in this study on the use of extraction-fractionation method to produce novel PPI and PF fractions for developing innovative high nutritious food can be of a great importance. The obtained knowledge on the pea protein and fiber processing behaviour could greatly contribute to a better control of functional properties of various temperature-processed products from yellow pea.", "keywords": ["Dietary Fiber", "2. Zero hunger", "Hot Temperature", "Food Handling", "Protein Conformation", "04 agricultural and veterinary sciences", "Plant Proteins", " Dietary", "Polymerization", "Structure-Activity Relationship", "0404 agricultural biotechnology", "Functional Food", "Elastic Modulus", "Scattering", " Small Angle", "Spectroscopy", " Fourier Transform Infrared", "Carbohydrate Conformation", "Chromatography", " Gel", "Dietary Carbohydrates", "Microscopy", " Electron", " Scanning", "Cooking", "Particle Size", "Nutritive Value", "Chromatography", " High Pressure Liquid", "Pisum sativum"]}, "links": [{"href": "https://doi.org/10.1016/j.foodres.2018.01.020"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Food%20Research%20International", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foodres.2018.01.020", "name": "item", "description": "10.1016/j.foodres.2018.01.020", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foodres.2018.01.020"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-01T00:00:00Z"}}, {"id": "10.1016/j.jflm.2018.03.016", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:29Z", "type": "Journal Article", "created": "2018-03-28", "title": "Poisoning histories in the Italian renaissance: The case of Pico Della Mirandola and Angelo Poliziano", "description": "Giovanni Pico della Mirandola and Angelo Poliziano were two of the most important humanists of the Italian Renaissance. They died suddenly in 1494 and their deaths have been for centuries a subject of debate. The exhumation of their remains offered the opportunity to study the cause of their death through a multidisciplinary research project. Anthropological analyses, together with documentary evidences, radiocarbon dating and ancient DNA analysis supported the identification of the remains attributed to Pico. Macroscopic examination did not reveal paleopathological lesions or signs related to syphilis. Heavy metals analysis, carried out on bones and mummified tissues, showed that in Pico's remains there were potentially lethal levels of arsenic, supporting the philosopher's poisoning theory reported by documentary sources. The arsenic concentrations obtained from analysis of Poliziano's remains, are probably more related to an As chronic exposure or diagenetic processes rather than poisoning.", "keywords": ["Male", "Microscopy", "Spectrum Analysis", "Environmental Exposure", "Mummies", "06 humanities and the arts", "Bone and Bones", "Arsenic", "Forensic Toxicology", "03 medical and health sciences", "0302 clinical medicine", "Italy", "Arsenic Poisoning", "Microscopy", " Electron", " Scanning", "Humans", "0601 history and archaeology", "Carbon Radioisotopes", "Ancient DNA; Angelo Poliziano; Arsenic poisoning; Girolamo benivieni; Pico della Mirandola; Radiocarbon dating", "DNA", " Ancient", "History", " 15th Century"]}, "links": [{"href": "https://doi.org/10.1016/j.jflm.2018.03.016"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Forensic%20and%20Legal%20Medicine", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jflm.2018.03.016", "name": "item", "description": "10.1016/j.jflm.2018.03.016", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jflm.2018.03.016"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-05-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2014.06.074", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:29Z", "type": "Journal Article", "created": "2014-07-14", "title": "Molecular Characterization Of Biochars And Their Influence On Microbiological Properties Of Soil", "description": "The tentative connection between the biochar surface chemical properties and their influence on microbially mediated mineralization of C, N, and S with the help of enzymes is not well established. This study was designed to investigate the effect of different biomass conversion processes (microwave pyrolysis, carbon optimized gasification, and fast pyrolysis using electricity) on the composition and surface chemistry of biochar materials produced from corn stover (Zea mays L.), switchgrass (Panicum virgatum L.), and Ponderosa pine wood residue (Pinus ponderosa Lawson and C. Lawson) and determine the effect of biochars on mineralization of C, N, and S and associated soil enzymatic activities including esterase (fluorescein diacetate hydrolase, FDA), dehydrogenase (DHA), \u03b2-glucosidase (GLU), protease (PROT), and aryl sulfatase (ARSUL) in two different soils collected from footslope (Brookings) and crest (Maddock) positions of a landscape. Chemical properties of biochar materials produced from different batches of gasification process were fairly consistent. Biochar materials were found to be highly hydrophobic (low H/C values) with high aromaticity, irrespective of biomass feedstock and pyrolytic process. The short term incubation study showed that biochar had negative effects on microbial activity (FDA and DHA) and some enzymes including \u03b2-glucosidase and protease.", "keywords": ["2. Zero hunger", "Nitrogen", "04 agricultural and veterinary sciences", "15. Life on land", "Panicum", "Pinus", "Zea mays", "01 natural sciences", "Carbon", "6. Clean water", "Enzymes", "13. Climate action", "Charcoal", "Microscopy", " Electron", " Scanning", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Soil Microbiology", "Sulfur", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2014.06.074"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2014.06.074", "name": "item", "description": "10.1016/j.jhazmat.2014.06.074", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2014.06.074"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-08-01T00:00:00Z"}}, {"id": "10.1016/j.jplph.2012.02.014", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:31Z", "type": "Journal Article", "created": "2012-04-24", "title": "Drought Stress Has Contrasting Effects On Antioxidant Enzymes Activity And Phenylpropanoid Biosynthesis In Fraxinus Ornus Leaves: An Excess Light Stress Affair?", "description": "The experiment was conducted using Fraxinus ornus plants grown outside under full sunlight irradiance, and supplied with 100% (well-watered, WW), 40% (mild drought, MD), or 20% (severe drought, SD) of the daily evapotranspiration demand, with the main objective of exploring the effect of excess light stress on the activity of antioxidant enzymes and phenylpropanoid biosynthesis. Net CO\u2082 assimilation rate at saturating light and daily assimilated CO\u2082 were significantly smaller in SD than in WW and MD plants. Xanthophyll-cycle pigments supported nonphotochemical quenching to a significantly greater extent in SD than in MD and WW leaves. As a consequence, the actual efficiency of PSII (\u03a6(PSII)) was smaller, while the excess excitation-energy in the photosynthetic apparatus was greater in SD than in WW or MD plants. The concentrations of violaxanthin-cycle pigments relative to total chlorophyll (Chl(tot)) exceeded 200 mmol mol\u207b\u00b9 Chl(tot) in SD leaves at the end of the experiment. This leads to hypothesize for zeaxanthin a role not only as nonphotochemical quencher, but also as chloroplast antioxidant. Reductions in ascorbate peroxidase and catalase activities, as drought-stress progressed, were paralleled by greater accumulations of esculetin and quercetin 3-O-glycosides, both phenylpropanoids having effective capacity to scavenge H\u2082O\u2082. The drought-induced accumulation of esculetin and quercetin 3-O-glycosides in the vacuoles of mesophyll cells is consistent with their putative functions as reducing agents for H\u2082O\u2082 in excess light-stressed leaves. Nonetheless, the concentration of H\u2082O\u2082 and the lipid peroxidation were significantly greater in SD than in MD and WW leaves. It is speculated that vacuolar phenylpropanoids may constitute a secondary antioxidant system, even on a temporal basis, activated upon the depletion of primary antioxidant defences, and aimed at keeping whole-cell H\u2082O\u2082 within a sub-lethal concentration range.", "keywords": ["0301 basic medicine", "Analysis of Variance", "Principal Component Analysis", "0303 health sciences", "Time Factors", "Light", "Propanols", "Antioxidant enzymes Drought stress Phenylpropanoids Water relations Violaxanthin-cycle pigments", "Hydrogen Peroxide", "Pigments", " Biological", "Carbon Dioxide", "15. Life on land", "Antioxidants", "6. Clean water", "Antioxidant enzymes; Drought stress; Phenylpropanoids; Violaxanthin-cycle pigments; Water relations; Analysis of Variance; Antioxidants; Carbon Dioxide; Fraxinus; Hydrogen Peroxide; Malondialdehyde; Mesophyll Cells; Microscopy", " Fluorescence; Photosynthesis; Pigments", " Biological; Plant Leaves; Principal Component Analysis; Propanols; Stress", " Physiological; Time Factors; Droughts; Light; Plant Science; Physiology; Agronomy and Crop Science", "Droughts", "Plant Leaves", "03 medical and health sciences", "Fraxinus", "Microscopy", " Fluorescence", "Stress", " Physiological", "Antioxidant enzymes; drought stress; flavonoids", "Malondialdehyde", "Photosynthesis", "Mesophyll Cells"]}, "links": [{"href": "https://doi.org/10.1016/j.jplph.2012.02.014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Plant%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jplph.2012.02.014", "name": "item", "description": "10.1016/j.jplph.2012.02.014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jplph.2012.02.014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-07-01T00:00:00Z"}}, {"id": "10.1016/j.tcsw.2021.100059", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:11Z", "type": "Journal Article", "created": "2021-07-16", "title": "High-resolution 3D mapping of rhizosphere glycan patterning using molecular probes in a transparent soil system", "description": "Rhizospheres are microecological zones at the interface of roots and soils. Interactions between bacteria and roots are critical for maintaining plant and soil health but are difficult to study because of constraints inherent in working with underground systems. We have developed an in-situ rhizosphere imaging system based on transparent soils and molecular probes that can be imaged using confocal microscopy. We observed spatial patterning of polysaccharides along roots and on cells deposited into the rhizosphere and also co-localised fluorescently tagged soil bacteria. These studies provide insight into the complex glycan landscape of rhizospheres and suggest a means by which root / rhizobacteria interactions can be non-disruptively studied.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "QH573-671", "15. Life on land", "630", "Article", "Transparent Soil", "03 medical and health sciences", "Fluorescence Microscopy", "Rhizosphere", "Rhizobacteria", "Polysaccharide", "Cytology"]}, "links": [{"href": "https://eprints.ncl.ac.uk/fulltext.aspx?url=279778/5D67D23B-DAA5-4CF5-A60A-16112D9E3664.pdf&pub_id=279778"}, {"href": "https://doi.org/10.1016/j.tcsw.2021.100059"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Cell%20Surface", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.tcsw.2021.100059", "name": "item", "description": "10.1016/j.tcsw.2021.100059", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.tcsw.2021.100059"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-01T00:00:00Z"}}, {"id": "10.1016/j.trac.2022.116819", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:11Z", "type": "Journal Article", "created": "2022-11-11", "title": "Microplastics and nanoplastics in food, water, and beverages, part II. Methods", "description": "Since microplastics (MPs) and nanoplastics (NPs) have started emerging as ubiquitous contaminants in the environment, a variety of analytical techniques has been developed and tested for the detection and characterization of polymer particles at a micro- and nano-scale. Yet, no unique method stands out for its ability to yield all the relevant information required to properly address MP and NP contamination in the environment, and even less so in food material. In this review, several approaches to sample preparation and isolation of MPs from food matrices are reported, well-established and promising emerging analytical techniques for the detection and characterization of MPs and NPs are described and discussed. The information reported in this review shows that even the most widely used methods are still under development and MP/NP analysis is still far away from method validation and standardization. The establishment of rigorous best practices to yield reliable data and build a comprehensive knowledge of MP and NP occurrence in food is essential for the implementation of strategies and policies to address MP/NP pollution. Therefore, an outlook of the field towards harmonization and quality improvement of MP/NP analysis is included in this review.", "keywords": ["Vibrational spectroscopy", "Microscopy", "Mass spectrometry", "Sample preparation", "0211 other engineering and technologies", "02 engineering and technology", "01 natural sciences", "6. Clean water", "12. Responsible consumption", "FTIR", "13. Climate action", "Validation", "AFM-IR", "Raman", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.trac.2022.116819"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/TrAC%20Trends%20in%20Analytical%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.trac.2022.116819", "name": "item", "description": "10.1016/j.trac.2022.116819", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.trac.2022.116819"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-01T00:00:00Z"}}, {"id": "10.1016/j.ultsonch.2019.104826", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:12Z", "type": "Journal Article", "created": "2019-10-19", "title": "Liposome destruction by hydrodynamic cavitation in comparison to chemical, physical and mechanical treatments", "description": "Liposomes are widely applied in research, diagnostics, medicine and in industry. In this study we show for the first time the effect of hydrodynamic cavitation on liposome stability and compare it to the effect of well described chemical, physical and mechanical treatments. Fluorescein loaded giant 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid vesicles were treated with hydrodynamic cavitation as promising method in inactivation of biological samples. Hydrodynamic treatment was compared to various chemical, physical and mechanical stressors such as ionic strength and osmolarity agents (glucose, Na+, Ca2+, and Fe3+), free radicals, shear stresses (pipetting, vortex mixing, rotational shear stress), high pressure, electroporation, centrifugation, surface active agents (Triton X-100, ethanol), microwave irradiation, heating, freezing-thawing, ultrasound (ultrasonic bath, sonotrode). The fluorescence intensity of individual fluorescein loaded lipid vesicles was measured with confocal laser microscopy. The distribution of lipid vesicle size, vesicle fluorescence intensity, and the number of fluorescein loaded vesicles was determined before and after treatment with different stressors. The different environmental stressors were ranked in order of their relative effect on liposome fluorescein release. Of all tested chemical, physical and mechanical treatments for stability of lipid vesicles, the most detrimental effect on vesicles stability had hydrodynamic cavitation, vortex mixing with glass beads and ultrasound. Here we showed, for the first time that hydrodynamic cavitation was among the most effective physico-chemical treatments in destroying lipid vesicles. This work provides a benchmark for lipid vesicle robustness to a variety of different physico-chemical and mechanical parameters important in lipid vesicle preparation and application.", "keywords": ["fluorescein", "kemijski postopki", "mehanski postopki", "confocal laser microscopy", "04 agricultural and veterinary sciences", "stability", "modelne membrane", "Lipids", "lipidni vezikli", "Surface-Active Agents", "0404 agricultural biotechnology", "Microscopy", " Fluorescence", "DOPC", "fluorescen\u010dna mikroskopija", "hydrodynamic cavitation", "Liposomes", "Hydrodynamics", "fluorescein release", "fizikalni postopki", "info:eu-repo/classification/udc/577.11:576.3:547.915:620.193.16", "giant lipid vesicles", "hidrodinamska kavitacija", "0405 other agricultural sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.ultsonch.2019.104826"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ultrasonics%20Sonochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ultsonch.2019.104826", "name": "item", "description": "10.1016/j.ultsonch.2019.104826", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ultsonch.2019.104826"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}, {"id": "10.1021/acs.est.3c08734", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:19Z", "type": "Journal Article", "created": "2024-04-10", "title": "Plastic Fruit Stickers in Industrial Composting\u2500Surface and Structural Alterations Revealed by Electron Microscopy and Computed Tomography", "description": "Often large quantities of plastics are found in compost, with price look-up stickers being a major but little-explored component in the contamination path. Stickers glued to fruit or vegetable peels usually remain attached to the organic material despite sorting processes in the composting plant. Here, we investigated the effects of industrial composting on the structural alterations of these stickers. Commercial polypropylene (PP) stickers on banana peels were added to a typical organic material mixture for processing in an industrial composting plant and successfully resampled after a prerotting (11 days) and main rotting step (25 days). Afterward, both composted and original stickers were analyzed for surface and structural changes via scanning electron microscopy, Fourier-transform infrared spectroscopy, and micro- and nano-X-ray computed tomography (CT) combined with deep learning approaches. The composting resulted in substantial surface changes and degradation in the form of microbial colonization, deformation, and occurrence of cracks in all stickers. Their pore volumes increased from 16.7% in the original sticker to 26.3% at the end of the compost process. In a similar way, the carbonyl index of the stickers increased. Micro-CT images additionally revealed structural changes in the form of large adhesions that penetrated the surface of the sticker. These changes were accompanied by delamination after 25 days of composting, thus overall hinting at the degradation of the stickers and the subsequent formation of smaller microplastic pieces.", "keywords": ["Technology", "ddc:600", "ddc:550", "Composting", "600", "02 engineering and technology", "540", "Polypropylenes", "01 natural sciences", "620", "Soil", "Fruit", "Microscopy", " Electron", " Scanning", "info:eu-repo/classification/ddc/600", "Tomography", " X-Ray Computed", "0210 nano-technology", "Plastics", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.3c08734"}, {"href": "https://doi.org/10.1021/acs.est.3c08734"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.3c08734", "name": "item", "description": "10.1021/acs.est.3c08734", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.3c08734"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-10T00:00:00Z"}}, {"id": "10.1039/c8an01387j", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:46Z", "type": "Journal Article", "created": "2018-10-19", "title": "The in vivo effects of silver nanoparticles on terrestrial isopods, Porcellio scaber , depend on a dynamic interplay between shape, size and nanoparticle dissolution properties", "description": "<p>The effects of exposure to low concentrations of AgNPs in model tissue, are the result of the interplay between size, shape and dissolution of ions from NPs.</p>", "keywords": ["[PHYS]Physics [physics]", "Male", "0301 basic medicine", "570", "Microscopy", "Principal Component Analysis", "Silver", "Metal Nanoparticles", "540", "01 natural sciences", "03 medical and health sciences", "Solubility", "Spectroscopy", " Fourier Transform Infrared", "Animals", "Female", "Intestinal Mucosa", "Particle Size", "Isopoda", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://pubs.rsc.org/en/content/articlepdf/2019/AN/C8AN01387J"}, {"href": "https://doi.org/10.1039/c8an01387j"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Analyst", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1039/c8an01387j", "name": "item", "description": "10.1039/c8an01387j", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1039/c8an01387j"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-01T00:00:00Z"}}, {"id": "10.1038/s41396-022-01277-w", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:37Z", "type": "Journal Article", "created": "2022-07-07", "title": "Novel form of collective movement by soil bacteria", "description": "Abstract                <p>Although migrations are essential for soil microorganisms to exploit scarce and heterogeneously distributed resources, bacterial mobility in soil remains poorly studied due to experimental limitations. In this study, time-lapse images collected using live microscopy techniques captured collective and coordinated groups of B. subtilis cells exhibiting \uffe2\uff80\uff9ccrowd movement\uffe2\uff80\uff9d. Groups of B. subtilis cells moved through transparent soil (nafion polymer with particle size resembling sand) toward plant roots and re-arranged dynamically around root tips in the form of elongating and retracting \uffe2\uff80\uff9cflocks\uffe2\uff80\uff9d resembling collective behaviour usually associated with higher organisms (e.g., bird flocks or fish schools). Genetic analysis reveals B. subtilis flocks are likely driven by the diffusion of extracellular signalling molecules (e.g., chemotaxis, quorum sensing) and may be impacted by the physical obstacles and hydrodynamics encountered in the soil like environment. Our findings advance understanding of bacterial migration through soil matrices and expand known behaviours for coordinated bacterial movement.</p", "keywords": ["light sheet microscopy", "0301 basic medicine", "570", "0303 health sciences", "Bacteria", "transparent soil", "Evolution", "/dk/atira/pure/subjectarea/asjc/2400/2404", "Polymers", "Quorum Sensing", "15. Life on land", "Soil", "03 medical and health sciences", "Behavior and Systematics", "root colonisation", "Sand", "collective movement", "name=Ecology", "name=Microbiology", "B. subtilis", "co-ordination", "bacterial flocculation", "/dk/atira/pure/subjectarea/asjc/1100/1105"]}, "links": [{"href": "https://www.nature.com/articles/s41396-022-01277-w.pdf"}, {"href": "https://doi.org/10.1038/s41396-022-01277-w"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41396-022-01277-w", "name": "item", "description": "10.1038/s41396-022-01277-w", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41396-022-01277-w"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-07T00:00:00Z"}}, {"id": "10.1038/s41598-019-56868-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:42Z", "type": "Journal Article", "created": "2020-01-09", "title": "Modelling photovoltaic soiling losses through optical characterization", "description": "Abstract<p>The accumulation of soiling on photovoltaic (PV) modules affects PV systems worldwide. Soiling consists of mineral dust, soot particles, aerosols, pollen, fungi and/or other contaminants that deposit on the surface of PV modules. Soiling absorbs, scatters, and reflects a fraction of the incoming sunlight, reducing the intensity that reaches the active part of the solar cell. Here, we report on the comparison of naturally accumulated soiling on coupons of PV glass soiled at seven locations worldwide. The spectral hemispherical transmittance was measured. It was found that natural soiling disproportionately impacts the blue and ultraviolet (UV) portions of the spectrum compared to the visible and infrared (IR). Also, the general shape of the transmittance spectra was similar at all the studied sites and could adequately be described by a modified form of the \uffc3\uff85ngstr\uffc3\uffb6m turbidity equation. In addition, the distribution of particles sizes was found to follow the IEST-STD-CC 1246E cleanliness standard. The fractional coverage of the glass surface by particles could be determined directly or indirectly and, as expected, has a linear correlation with the transmittance. It thus becomes feasible to estimate the optical consequences of the soiling of PV modules from the particle size distribution and the cleanliness value.</p>", "keywords": ["Photovoltaic Arrays", "Cleanliness", "Particle", "PV", "02 engineering and technology", "Oceanography", "7. Clean energy", "soiling; experimental; transmittance; spectrum", "Turbidity", "Size", "Materials Science and Engineering", "\u00c5ngstr\u00f6m turbidity equation", "Transmittance", "0202 electrical engineering", " electronic engineering", " information engineering", "Photovoltaic system", "Ultraviolet", "Microscopy", "Soiling", "Energy", "Ecology", "Physics", "Q", "R", "Imaging and sensing", "Geology", "Particle size", "6. Clean water", "Photovoltaic Efficiency", "Chemistry", "Physical chemistry", "Particle (ecology)", "Physical Sciences", "Sunlight", "Medicine", "Infrared", "570", "Particle-size distribution", "PV System", "Energy science and technology", "Science", "Optical spectroscopy", "Partial Shading", "530", "Modelling", "Article", "Environmental science", "Techniques and instrumentation", "Optical physics", "Meteorology", "Artificial Intelligence", "Machine Learning Methods for Solar Radiation Forecasting", "Optical techniques", "Optoelectronics", "Aerosol", "Biology", "Renewable Energy", " Sustainability and the Environment", "Electronics", " photonics and device physics", "Building Integrated Photovoltaics", "Optics", "Photovoltaic Maximum Power Point Tracking Techniques", "FOS: Earth and related environmental sciences", "Materials science", "Photovoltaics", "Optics and photonics", "13. Climate action", "FOS: Biological sciences", "Computer Science", "Solar Thermal Energy Technologies"]}, "links": [{"href": "https://iris.uniroma1.it/bitstream/11573/1625670/2/Smestad_Modelling_2020.pdf"}, {"href": "https://www.nature.com/articles/s41598-019-56868-z.pdf"}, {"href": "https://doi.org/10.1038/s41598-019-56868-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-019-56868-z", "name": "item", "description": "10.1038/s41598-019-56868-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-019-56868-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-09T00:00:00Z"}}, {"id": "10.1073/pnas.2109176118", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:01Z", "type": "Journal Article", "created": "2021-02-13", "title": "Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere", "description": "Abstract<p>Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.</p>", "keywords": ["0301 basic medicine", "570", "Microscopy", "Silicon", "0303 health sciences", "Temperature", "root-microbe interactions", "Equipment Design", "Biological Sciences", "Environment", "15. Life on land", "Plant Roots", "630", "Fluorescence", "Soil", "03 medical and health sciences", "Seedlings", "Calibration", "Rhizosphere", "Image Processing", " Computer-Assisted", "environmental imaging", "rhizosphere", "Soil Microbiology", "Bacillus subtilis", "Lactuca"]}, "links": [{"href": "https://eprints.whiterose.ac.uk/178939/18/e2109176118.full.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.2109176118"}, {"href": "https://doi.org/10.1073/pnas.2109176118"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.2109176118", "name": "item", "description": "10.1073/pnas.2109176118", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.2109176118"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-13T00:00:00Z"}}, {"id": "10.1101/2021.02.13.430456", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:24Z", "type": "Journal Article", "created": "2021-02-13", "title": "Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere", "description": "Abstract<p>Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.</p", "keywords": ["0301 basic medicine", "570", "Microscopy", "Silicon", "0303 health sciences", "Temperature", "root-microbe interactions", "Equipment Design", "Biological Sciences", "Environment", "15. Life on land", "Plant Roots", "630", "Fluorescence", "Soil", "03 medical and health sciences", "Seedlings", "Calibration", "Rhizosphere", "Image Processing", " Computer-Assisted", "environmental imaging", "rhizosphere", "Soil Microbiology", "Bacillus subtilis", "Lactuca"]}, "links": [{"href": "https://eprints.whiterose.ac.uk/178939/18/e2109176118.full.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.2109176118"}, {"href": "https://doi.org/10.1101/2021.02.13.430456"}, {"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": "10.1101/2021.02.13.430456", "name": "item", "description": "10.1101/2021.02.13.430456", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2021.02.13.430456"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-13T00:00:00Z"}}, {"id": "10.1101/2023.06.28.546105", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:25Z", "type": "Journal Article", "created": "2023-06-29", "title": "Construction and Characterisation of a Structured, Tuneable, and Transparent 3D Culture Platform for Soil Bacteria", "description": "2.Abstract<p>We have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the metabolic profile of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms,Bacillus subtilisandStreptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of other difficult-to-culture bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as interaction, competition, and warfare.</p>3.Graphical Abstract<p>A step-by-step method for creating a tailored 3D culture medium for study of soil microbes.</p><p>The complete workflow can be split into three parts: Growth and observation, metabolic profiling to provide a stable refractive index matching solution, and production of the 3D soil environment. The 3D culture scaffold was created by cryomilling Nafion\uffe2\uff84\uffa2 resin pellets and size filtration. Chemical processing altered the surface chemistry of Nafion\uffe2\uff84\uffa2 particles and facilitated nutrient binding by titration of a defined liquid culture medium. Metabolic profiling determined non-metabolisable sugars and provided an inert refractive index matching substrate, which was added to the final nutrient titration. Inoculation and growth of the test strain allowed for downstream assessment of colonisation behaviours and community dynamicsin situby, for example, optical microscopy.</p", "keywords": ["2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "Plant Microbiology and Soil Health (formerly Environmental Biology)", "15. Life on land", "Microbiology", "Carbon", "620", "Soil", "03 medical and health sciences", "Microscopy", " Fluorescence", "Microbial Interactions", "Bacillus subtilis"]}, "links": [{"href": "https://strathprints.strath.ac.uk/87995/7/Rooney-etal-Microbiology-2024-Construction-and-characterisation-of-a-structured-tuneable-and-transparent-3D-culture-platform.pdf"}, {"href": "https://doi.org/10.1101/2023.06.28.546105"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2023.06.28.546105", "name": "item", "description": "10.1101/2023.06.28.546105", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2023.06.28.546105"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-28T00:00:00Z"}}, {"id": "10.1101/728261", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:26Z", "type": "Journal Article", "created": "2020-05-29", "title": "\"Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, \\\"\"Silenusvirus\\\"\".\"", "description": "Abstract<p>Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database, but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus \uffe2\uff80\uff9cSilenusvirus\uffe2\uff80\uff9d.</p>", "keywords": ["0301 basic medicine", "0303 health sciences", "FRAMESHIFT", "Denmark", "BACTERIOPHAGES", "PROTEIN", "Wine", "Genome", " Viral", "Viral Plaque Assay", "SEQUENCE", "CLASSIFICATION", "Article", "12. Responsible consumption", "Microscopy", " Electron", "Waste Disposal Facilities", "03 medical and health sciences", "Bacteriolysis", "Species Specificity", "DNA", " Viral", "Bacteriophages", "Adsorption", "Phylogeny", "Lactobacillus plantarum"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/728261v1.full.pdf"}, {"href": "https://doi.org/10.1101/728261"}, {"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": "10.1101/728261", "name": "item", "description": "10.1101/728261", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/728261"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-07T00:00:00Z"}}, {"id": "10.1111/nph.16242", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:01Z", "type": "Journal Article", "created": "2019-10-08", "title": "Root\u2010induced soil deformation influences Fe, S and P: rhizosphere chemistry investigated using synchrotron XRF and XANES", "description": "Summary<p>   <p>Rhizosphere soil has distinct physical and chemical properties from bulk soil. However, besides root\uffe2\uff80\uff90induced physical changes, chemical changes have not been extensively measured in situ on the pore scale.</p>  <p>In this study, we couple structural information, previously obtained using synchrotron X\uffe2\uff80\uff90ray computed tomography (XCT), with synchrotron X\uffe2\uff80\uff90ray fluorescence microscopy (XRF) and X\uffe2\uff80\uff90ray absorption near\uffe2\uff80\uff90edge structure (XANES) to unravel chemical changes induced by plant roots.</p>  <p>Our results suggest that iron (Fe) and sulfur (S) increase notably in the direct vicinity of the root via solubilization and microbial activity. XANES further shows that Fe is slightly reduced, S is increasingly transformed into sulfate (SO42\uffe2\uff88\uff92) and phosphorus (P) is increasingly adsorbed to humic substances in this enrichment zone. In addition, the ferrihydrite fraction decreases drastically, suggesting the preferential dissolution and the formation of more stable Fe oxides. Additionally, the increased transformation of organic S to sulfate indicates that the microbial activity in this zone is increased. These changes in soil chemistry correspond to the soil compaction zone as previously measured via XCT.</p>  <p>The fact that these changes are colocated near the root and the compaction zone suggests that decreased permeability as a result of soil structural changes acts as a barrier creating a zone with increased rhizosphere chemical interactions via surface\uffe2\uff80\uff90mediated processes, microbial activity and acidification.</p>  </p>", "keywords": ["2. Zero hunger", "550", "Iron", "Hordeum", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Plant Roots", "Soil", "Microscopy", " Fluorescence", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Tomography", " X-Ray Computed", "Sulfur", "Synchrotrons"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16242"}, {"href": "https://doi.org/10.1111/nph.16242"}, {"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.16242", "name": "item", "description": "10.1111/nph.16242", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.16242"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-12T00:00:00Z"}}, {"id": "10.1139/as-2022-0006", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:09Z", "type": "Journal Article", "created": "2022-07-04", "title": "Monitoring guidelines for polymer identification, quality assurance/quality control (QA/QC) and data reporting for monitoring of microplastics in the Arctic environment", "description": "<p> The pollution of the environment with plastics is of growing concern worldwide, including the Arctic region. While larger plastic pieces are a visible pollution issue, smaller microplastics are not visible with the naked eye. These particles are available for interaction by Arctic biota and have become a concern for animal and human health. The determination of microplastic properties includes several methodological steps, i.e., sampling, extraction, quantification, and chemical identification. This review discusses suitable analytical tools for the identification, quantification, and characterization of microplastics in the context of monitoring in the Arctic. It further addresses quality assurance and quality control (QA/QC), which is particularly important for the determination of microplastic in the Arctic, as both contamination and analyte losses can occur. It presents specific QA/QC measures for sampling procedures and for the handling of samples in the laboratory, either on land or on ship, and considering the small size of microplastics as well as the high risk of contamination. The review depicts which data should be mandatory to report, thereby supporting a framework for harmonized data reporting. </p>", "keywords": [":Analytisk kjemi: 445 [VDP]", "0211 other engineering and technologies", "Environmental engineering", "QA/QC", "02 engineering and technology", "Massespektrografi", "01 natural sciences", "[SDU] Sciences of the Universe [physics]", ":Analytical chemistry: 445 [VDP]", "Arctic", "VDP::Analytical chemistry: 445", "GE1-350", "14. Life underwater", "QA", "Raman", "QC", "0105 earth and related environmental sciences", "reporting", "Mass spectrometry", "TED-GC/MS", "TED-GC", "py-GC/MS", "Microplastic", "py-GC", "Fourier transform infrared spectroscopy", "MS", "VDP::Analytisk kjemi: 445", "TA170-171", "Microplast", "620", "Environmental sciences", "[SDV] Life Sciences [q-bio]", "monitoring", "FTIR", "13. Climate action", "microscopy", "microplastic"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/536963/1/primpke-et-al-2022-monitoring-of-microplastic-pollution-in-the-arctic-recent-developments-in-polymer-identification.pdf"}, {"href": "https://cdnsciencepub.com/doi/pdf/10.1139/as-2022-0006"}, {"href": "https://doi.org/10.1139/as-2022-0006"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Arctic%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1139/as-2022-0006", "name": "item", "description": "10.1139/as-2022-0006", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1139/as-2022-0006"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-01T00:00:00Z"}}, {"id": "10.1186/s13007-019-0523-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:18Z", "type": "Journal Article", "created": "2019-12-18", "title": "Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity", "description": "Abstract                 Background                 <p>Plant feeding, free-living nematodes cause extensive damage to plant roots by direct feeding and, in the case of some trichodorid and longidorid species, through the transmission of viruses. Developing more environmentally friendly, target-specific nematicides is currently impeded by slow and laborious methods of toxicity testing. Here, we developed a bioactivity assay based on the dynamics of light \uffe2\uff80\uff98speckle\uffe2\uff80\uff99 generated by living cells and we demonstrate its application by assessing chemicals\uffe2\uff80\uff99 toxicity to different nematode trophic groups.</p>                                Results                 <p>Free-living nematode populations extracted from soil were exposed to methanol and phenyl isothiocyanate (PEITC). Biospeckle analysis revealed differing behavioural responses as a function of nematode feeding groups. Trichodorus nematodes were less sensitive than were bacterial feeding nematodes or non-trichodorid plant feeding nematodes. Following 24\uffc2\uffa0h of exposure to PEITC, bioactivity significantly decreased for plant and bacterial feeders but not for Trichodorus nematodes. Decreases in movement for plant and bacterial feeders in the presence of PEITC also led to measurable changes to the morphology of biospeckle patterns.</p>                                Conclusions                 <p>Biospeckle analysis can be used to accelerate the screening of nematode bioactivity, thereby providing a fast way of testing the specificity of potential nematicidal compounds. With nematodes\uffe2\uff80\uff99 distinctive movement and activity levels being visible in the biospeckle pattern, the technique has potential to screen the behavioural responses of diverse trophic nematode communities. The method discriminates both behavioural responses, morphological traits and activity levels and hence could be used to assess the specificity of nematicidal compounds.</p>", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "Selective plane illumination microscopy (SPIM)", "Nematodes", "QH301-705.5", "Methodology", "Plant culture", "630", "SB1-1110", "Dynamic speckle", "03 medical and health sciences", "Isothiocyanate", "Biology (General)", "Selective plan illumination microscopy (SPIM)"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s13007-019-0523-8.pdf"}, {"href": "https://doi.org/10.1186/s13007-019-0523-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Methods", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s13007-019-0523-8", "name": "item", "description": "10.1186/s13007-019-0523-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s13007-019-0523-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-01T00:00:00Z"}}, {"id": "10.21203/rs.3.rs-4951965/v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:58Z", "type": "Journal Article", "created": "2024-10-15", "title": "All black: a microplastic extraction combined with colour-based analysis allows identification and characterisation of tire wear particles (TWP) in soils", "description": "<title>Abstract</title>         <p>While tire wear particles (TWP) have been estimated to represent more than 90% of the total microplastic (MP) emitted in European countries and may have environmental health effects, only few data about TWP concentrations and characteristics are available today. The lack of data stems from the fact that no standardized, cost efficient or accessible extraction and identification method is available yet. We present a method allowing the extraction of TWP from soil, performing analysis with a conventional optical microscope and a machine learning approach to identify TWP in soil based on their colour. The lowest size of TWP which could be measured reliably with an acceptable recovery using our experimental set-up was 35 \u00b5m. Further improvements would be possible given more advanced technical infrastructure (higher optical magnification and image quality). Our method showed a mean recovery of 85% in the 35-2000 \u00b5m particle size range and no blank contamination. We tested for possible interference from charcoal (as another black soil component with similar properties) in the soils and found a reduction of the interference from charcoal by 92% during extraction. We applied our method to a highway adjacent soil at 1 m, 2 m, 5 m, and 10 m and detected TWP in all samples with a tendency to higher concentrations at 1 m and 2 m from the road compared to 10 m from the road. The observed TWP concentrations were in the same order of magnitude as what was previously reported in literature in highway adjacent soils. These results demonstrate the potential of the method to provide quantitative data on the occurrence and characteristics of TWP in the environment. The method can be easily implemented in many labs, and help to address our knowledge gap regarding TWP concentrations in soils.</p>", "keywords": ["TP1080-1185", "Segmentation", "TD172-193.5", "Tire wear", "Soil pollution", "Machine learning", "Microplastic", "Methodology", "Polymers and polymer manufacture", "Optical microscopy", "Environmental pollution"]}, "links": [{"href": "https://doi.org/10.21203/rs.3.rs-4951965/v1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microplastics%20and%20Nanoplastics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.21203/rs.3.rs-4951965/v1", "name": "item", "description": "10.21203/rs.3.rs-4951965/v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.21203/rs.3.rs-4951965/v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-10-15T00:00:00Z"}}, {"id": "10261/401806", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:36Z", "type": "Journal Article", "created": "2025-09-15", "title": "Unveiling single-particle composition, size, shape, and mixing state of freshly emitted Icelandic dust via electron microscopy analysis", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Abstract. Iceland is a significant high-latitude dust source area. Airborne Icelandic dust influences the climate system by interacting with radiation, clouds, and biogeochemical cycles; it also affects snow and ice albedo and air quality. These impacts are sensitive to the dust\u2019s mineralogical, chemical, and physical properties. However, comprehensive measurements and analyses of Icelandic dust particles remain limited. This study examines dust samples collected during a field campaign in the Dyngjusandur desert (August\u2013September 2021) using active and passive aerosol sampling. Over 190\u2009000 individual particles, ranging from 0.1 to 120\u2009\u00b5m, were analyzed for their chemical and physical properties using computer-controlled scanning electron microscopy/energy-dispersive X-ray spectroscopy (ccSEM/EDX). Results show heterogeneity in particle size, shape, and composition. The most abundant particle type was medium-Al mixed particles, likely glass-like, comprising 35\u2009%\u201392\u2009% of the aerosol volume. Sulfate particles, suggesting volcanic contributions, were detected in some samples. Iron (Fe)- and titanium (Ti)-rich particles made up 3.3\u2009% and 6\u2009% of the aerosol volume, respectively, mainly in the size fraction &lt;\u20091\u2009\u00b5m. The median aspect ratio ranged from 1.37 to 1.53, increasing with particle size. Our findings highlight key differences in Icelandic dust compared to Saharan dust, including higher iron and titanium content and a lack of potassium in Icelandic dust. Additionally, Icelandic dust shows a size-dependent increase in aspect ratio, unlike Saharan dust, which remains constant. These observations can improve model simulations that account for the effect of high-latitude dust in the Earth system.</p></article>", "keywords": ["Climate system", "info:eu-repo/classification/ddc/550", "Radiation", "550", "electron microscopy analysis", "ddc:550", "Icelandic dust", "Geowissenschaften", "http://metadata.un.org/sdg/3", "http://metadata.un.org/sdg/9", "Earth sciences", "Make cities and human settlements inclusive", " safe", " resilient and sustainable", "Build resilient infrastructure", " promote inclusive and sustainable industrialization and foster innovation", "http://metadata.un.org/sdg/11", "Ensure healthy lives and promote well-being for all at all ages", "single-particle composition"]}, "links": [{"href": "https://doi.org/10261/401806"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Atmospheric%20Chemistry%20and%20Physics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10261/401806", "name": "item", "description": "10261/401806", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10261/401806"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-03-12T00:00:00Z"}}, {"id": "10.2527/2001.7971892x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:20:32Z", "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": "10.26434/chemrxiv-2022-cr5ws-v2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:20:35Z", "type": "Journal Article", "created": "2023-04-10", "title": "Quantitative image analysis of microplastics in bottled water using Artificial Intelligence", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The ubiquitous occurrence of microplastics (MPs) in the environment and the use of plastics in packaging materials result in the presence of MPs in the food chain and the exposure of consumers. Yet, no fully validated analytical method is available for microplastic (MP) quantification, thereby preventing the reliable estimation of the level of exposure and, ultimately, the assessment of the food safety risks associated with MP contamination. In this study, a novel approach is presented that exploits interactive artificial intelligence tools to enable the automation of MP analysis. An integrated method for the analysis of MPs in bottled water based on Nile Red staining and fluorescent microscopy was developed and validated, featuring a partial interrogation of the filter and a fully automated image processing workflow based on a Random Forest classifier, thereby boosting the analysis speed. The image analysis provided particle count, size and size distribution of the MPs. From these data, a rough estimation of the mass of the individual MPs, and consequently of the MP mass concentration in the sample, could be obtained as well. Critical materials, method performance characteristics, and final applicability were studied in detail. The method showed to be highly sensitive in sizing MPs down to 10 \u00b5m, with a particle count limit of detection and quantification of 28 and 85 items/500 mL, respectively. Linearity of mass concentration determined between 10 ppb and 1.5 ppm showed a regression coefficient of (R2) of 0.99. Method precision was demonstrated by repeatability of 9 - 16% RSD (n = 7) and within-laboratory reproducibility of 15 - 27 % RSD (n = 21). Accuracy based on recovery was 92 \u00b1 15 % and 98 \u00b1 23 % at a level of 0.1 and 1.0 ppm, respectively. The quantitative performance characteristics thus obtained complied with regulatory requirements. Finally, the method was successfully applied to the analysis of twenty commercial samples of bottled water, with and without gas and flavor additives, yielding results ranging from values below the limit of detection to 7237 (95% CI [6456, 8088]) items/500 mL.</p></article>", "keywords": ["Fluorescence microscopy", "Artificial intelligence", "Bottled water", "Method validation", "Artificial Intelligence", "Microplastics", "Drinking Water", "Microplastic", "Nile red", "Reproducibility of Results", "Plastics", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.26434/chemrxiv-2022-cr5ws-v2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Talanta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.26434/chemrxiv-2022-cr5ws-v2", "name": "item", "description": "10.26434/chemrxiv-2022-cr5ws-v2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.26434/chemrxiv-2022-cr5ws-v2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-10T00:00:00Z"}}, {"id": "10.3389/fbioe.2019.00378", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:20:39Z", "type": "Journal Article", "created": "2019-12-04", "title": "Thickness of Polyelectrolyte Layers of Separately Confined Bacteria Alters Key Physiological Parameters on a Single Cell Level", "description": "Confinement of bacterial cells in a matrix or in capsules is an integral part of many biotechnological applications. Here, the well-known layer-by-layer method of deposition of a polyelectrolyte film a few nanometers in thickness to confine separated bacterial cells in permeable and physically durable shells has been examined. Due to the physical properties of such a confinement, we found that this method enables investigation of effects of physical barriers against mass gain and cell division. Using the method of time-lapse confocal microscopy, we observed a prolonged lag phase, dependent on the number of polyelectrolyte layers. In the confinement, both the GFP fluorescent signal from the leaking T7 promoter and the cell size were increased by factors of more than five and two, respectively. This creates a paradigm shift that enables use of mechanical entrapment for control of bacterial cell physiology and opens possibilities of controlling the division rate as well as gene expression. These effects can be attributed to the perturbation of the sensing of the cell size, which results in disproportional synthesis of a cell envelope impinging the intracellular material and compels cells to grow rapidly. In addition, the charged surface of cells enables prolonged intercellular physical interaction and results in spherically shaped microcolonies.", "keywords": ["polyelectrolytes", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "layer-by-layer encapsulation", "time-lapse confocal microscopy", " polyelectrolytes", " layer-by-layer encapsulation", " electrostatic interactions", " cell surface modification", "cell surface modification", "Bioengineering and Biotechnology", "electrostatic interactions", "time-lapse confocal microscopy", "TP248.13-248.65", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.3389/fbioe.2019.00378"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Bioengineering%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fbioe.2019.00378", "name": "item", "description": "10.3389/fbioe.2019.00378", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fbioe.2019.00378"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-04T00:00:00Z"}}, {"id": "10.3390/ma11060957", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:20:56Z", "type": "Journal Article", "created": "2018-06-05", "title": "The Biological Fate of Silver Nanoparticles from a Methodological Perspective", "description": "<p>We analyzed the performance and throughput of currently available analytical techniques for quantifying body burden and cell internalization/distribution of silver nanoparticles (Ag NPs). Our review of Ag NP biological fate data shows that most of the evidence gathered for Ag NPs body burden actually points to total Ag and not only Ag NPs. On the other hand, Ag NPs were found inside the cells and tissues of some organisms, but comprehensive explanation of the mechanism(s) of NP entry and/or in situ formation is usually lacking. In many cases, the methods used to detect NPs inside the cells could not discriminate between ions and particles. There is currently no single technique that would discriminate between the metals species, and at the same time enable localization and quantification of NPs down to the cellular level. This paper serves as an orientation towards selection of the appropriate method for studying the fate of Ag NPs in line with their properties and the specific question to be addressed in the study. Guidance is given for method selection for quantification of NP uptake, biodistribution, precise tissue and cell localization, bioaccumulation, food chain transfer and modeling studies regarding the optimum combination of methods and key factors to consider.</p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "spectroscopy", "Review", "01 natural sciences", "quantification", "body burden", "internalization", "03 medical and health sciences", "bioaccumulation", "microscopy", "silver nanoparticles review", "info:eu-repo/classification/udc/620.3", "biodistribution", "throughput", "performance", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://www.mdpi.com/1996-1944/11/6/957/pdf"}, {"href": "https://doi.org/10.3390/ma11060957"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/ma11060957", "name": "item", "description": "10.3390/ma11060957", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/ma11060957"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-05T00:00:00Z"}}, {"id": "10.3390/v11070611", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:21:06Z", "type": "Journal Article", "created": "2019-06-12", "title": "Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum\u2014A Novel Lineage of Lactobacillus Phages Comprising Five New Members", "description": "<p>Lactobacillus plantarum is a bacterium with promising applications to the food industry and agriculture and probiotic properties. So far, bacteriophages of this bacterium have been moderately addressed. We examined the diversity of five new L. plantarum phages via whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. These analyses revealed a high degree of similarity among the five phages, which extended to the vast majority of predicted virion-associated proteins. Based on these, we selected one of the phages as a representative and performed transmission electron microscopy and structural protein sequencing tests. Overall, the results suggested that the five phages belong to the family Myoviridae, they have a long genome of 137.973-141.344 bp, a G/C content of 36,3-36,6% that is quite distinct from their host&amp;rsquo;s, and, surprisingly, seven to 15 tRNAs. Only an average 41/174 of their predicted genes were assigned a function. The comparative analyses unraveled considerable genetic diversity for the five L. plantarum phages of this study. Hence, the new genus &amp;ldquo;Semelevirus&amp;rdquo; was proposed, which comprises exclusively the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp.. The five new Lactobacillus phages have a potential value for the development of more robust starters through, for example, the selection of mutants insensitive to phage infections. The five phages could also form part of phage cocktails, which producers would apply in different stages of L. plantarum fermentations in order to create a range of organoleptic outputs.</p>", "keywords": ["0301 basic medicine", "Annotation", "comparative genomics", "Genome", " Viral", "<i>Lactobacillus plantarum</i>", "Microbiology", "Article", "Isolation", "diversity", "03 medical and health sciences", "Microscopy", " Electron", " Transmission", "DNA Packaging", "phage", "Bacteriophages", "Phylogeny", "Viral Structural Proteins", "2. Zero hunger", "Diversity", "Base Composition", "0303 health sciences", "Comparative genomics", "new genus", "Genomics", "Sequence Analysis", " DNA", "QR1-502", "virology", "Phylogenetics", "phylogenetics", "Lactobacillus", "annotation", "Myoviridae", "Phage", "New genus", "isolation", "Lactobacillus plantarum"]}, "links": [{"href": "http://www.mdpi.com/1999-4915/11/7/611/pdf"}, {"href": "https://www.mdpi.com/1999-4915/11/7/611/pdf"}, {"href": "https://doi.org/10.3390/v11070611"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Viruses", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/v11070611", "name": "item", "description": "10.3390/v11070611", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/v11070611"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-11T00:00:00Z"}}, {"id": "10.5194/acp-2022-742", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:21:35Z", "type": "Journal Article", "created": "2022-11-07", "title": "Insights into the single particle composition, size, mixing state and aspect ratio of freshly emitted mineral dust from field measurements in the Moroccan Sahara using electron microscopy", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Abstract. The chemical and morphological properties of mineral dust aerosols emitted by wind erosion from arid and semi-arid regions influence climate, ocean and land ecosystems, air quality, and multiple socio-economic sectors. However, there is an incomplete understanding of the emitted dust particle size distribution (PSD) in terms of its constituent minerals that typically result from the fragmentation of soil aggregates during wind erosion. The emitted dust PSD affects the duration of particle transport and thus each mineral\u2019s global distribution, along with its specific effect upon climate. This lack of understanding is largely due to the scarcity of relevant in situ measurements in dust sources. To advance our understanding of the physicochemical properties of the emitted dust PSD, we present insights into the elemental composition and morphology of individual dust particles collected during the FRontiers in dust minerAloGical coMposition and its Effects upoN climaTe (FRAGMENT) field campaign in the Moroccan Sahara in September 2019. We analyzed more than 300,000 freshly emitted individual particles by performing offline analysis in the laboratory using Scanning Electron Microscopy (SEM) coupled with Energy-Dispersive X-ray Spectrometry (EDX). Eight major particle-type classes were identified where clay minerals make up the majority of the analyzed particles by number, with carbonates and quartz contributing to a lesser extent. We provide an exhaustive analysis of the size distribution and potential mixing state of different particle types, focusing largely on iron-rich (Fe-oxi/hydroxides) and feldspar particles, which are key to the effects of dust upon radiation and clouds. Nearly pure or externally mixed Fe-oxi/hydroxides are present only in diameters smaller than 2 \u00b5m and mainly below 1 \u00b5m. Fe-oxi/hydroxides tend to be increasingly internally mixed with other minerals, especially clays, as particle size increases, i.e., the volume fraction of Fe-oxi/hydroxides in aggregates decreases with particle size. Pure (externally-mixed) feldspar grains represented 3.7 % of all the particles, of which we estimated about a quarter to be K-feldspar. The externally-mixed total feldspar and K-feldspar abundances are relatively invariant with particle size, in contrast to the increasing abundance of feldspar-like (internally-mixed) aggregates with particle size. We also found that overall the median aspect ratio is rather constant across particle size and mineral groups, although we obtain slightly higher aspect ratios for internally-mixed particles. The detailed information on the composition of freshly emitted individual dust particles along with the quantitative analysis of their mixing state presented here can be used to constrain climate models including mineral species in their representation of the dust cycle.                         </p></article>", "keywords": ["Atmospheric chemistry", "550", "QC1-999", "http://metadata.un.org/sdg/3", "Mineral dust", "01 natural sciences", "Climate models", "\u00c0rees tem\u00e0tiques de la UPC::Enginyeria agroaliment\u00e0ria::Ci\u00e8ncies de la terra i de la vida::Climatologia i meteorologia", "Aerosols Measurement", "Pols minerals", "QD1-999", "Ensure healthy lives and promote well-being for all at all ages", "0105 earth and related environmental sciences", "mineral dust", "info:eu-repo/classification/ddc/550", "electron microscopy", "ddc:550", "Physics", "15. Life on land", "info:eu-repo/classification/udc/502.3/.7", "Pollution", "Moroccan Sahara", "Earth sciences", "Chemistry", "13. Climate action", "Mineral dust particles", "Air quality", "Desert dust"]}, "links": [{"href": "https://acp.copernicus.org/articles/23/3861/2023/acp-23-3861-2023.pdf"}, {"href": "https://acp.copernicus.org/articles/23/3861/2023/acp-23-3861-2023-supplement.pdf"}, {"href": "https://doi.org/10.5194/acp-2022-742"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Atmospheric%20Chemistry%20and%20Physics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.5194/acp-2022-742", "name": "item", "description": "10.5194/acp-2022-742", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5194/acp-2022-742"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-07T00:00:00Z"}}, {"id": "10.5281/zenodo.6572473", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:23:22Z", "type": "Report", "title": "Micro Raman analysis of micro and nanoplastics in drinking water: from number to mass", "description": "Works focusing on micro- and nanoplastics analysis in drinking water by means of Raman microscopy have been raising in recent years, however a standardised protocol is still lacking. Moreover, at the best of our knowledge, no paper among them proposed a reliable way to calculating the particles masses. The current research aims to fill this gap by presenting a new analytical method employing Raman microscopy, applied to drinking water samples from a Danish facility. This work supports the above mentioned view and offers a comprehensive application of such principles, with the authors stressing the pivotal role of method validation when dealing with micro- and nanoplastics analysis.", "keywords": ["microplastics", "Raman microscopy", "drinking water", "water quality", "6. Clean water", "nanoplastics"], "contacts": [{"organization": "Luca Maurizi, Lucian Iordachescu, Inga Vanessa Kirstein, Jes Vollertsen, Asbj\u00f8rn Haaning Nielsen,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.6572473"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.6572473", "name": "item", "description": "10.5281/zenodo.6572473", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.6572473"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-23T00:00:00Z"}}, {"id": "10.5281/zenodo.6572474", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:23:22Z", "type": "Report", "title": "Micro Raman analysis of micro and nanoplastics in drinking water: from number to mass", "description": "Works focusing on micro- and nanoplastics analysis in drinking water by means of Raman microscopy have been raising in recent years, however a standardised protocol is still lacking. Moreover, at the best of our knowledge, no paper among them proposed a reliable way to calculating the particles masses. The current research aims to fill this gap by presenting a new analytical method employing Raman microscopy, applied to drinking water samples from a Danish facility. This work supports the above mentioned view and offers a comprehensive application of such principles, with the authors stressing the pivotal role of method validation when dealing with micro- and nanoplastics analysis.", "keywords": ["microplastics", "Raman microscopy", "drinking water", "water quality", "6. Clean water", "nanoplastics"], "contacts": [{"organization": "Luca Maurizi, Lucian Iordachescu, Inga Vanessa Kirstein, Jes Vollertsen, Asbj\u00f8rn Haaning Nielsen,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.6572474"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.6572474", "name": "item", "description": "10.5281/zenodo.6572474", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.6572474"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-23T00:00:00Z"}}, {"id": "11585/634154", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:53Z", "type": "Journal Article", "created": "2018-03-28", "title": "Poisoning histories in the Italian renaissance: The case of Pico Della Mirandola and Angelo Poliziano", "description": "Giovanni Pico della Mirandola and Angelo Poliziano were two of the most important humanists of the Italian Renaissance. They died suddenly in 1494 and their deaths have been for centuries a subject of debate. The exhumation of their remains offered the opportunity to study the cause of their death through a multidisciplinary research project. Anthropological analyses, together with documentary evidences, radiocarbon dating and ancient DNA analysis supported the identification of the remains attributed to Pico. Macroscopic examination did not reveal paleopathological lesions or signs related to syphilis. Heavy metals analysis, carried out on bones and mummified tissues, showed that in Pico's remains there were potentially lethal levels of arsenic, supporting the philosopher's poisoning theory reported by documentary sources. The arsenic concentrations obtained from analysis of Poliziano's remains, are probably more related to an As chronic exposure or diagenetic processes rather than poisoning.", "keywords": ["Male", "Microscopy", "Spectrum Analysis", "Environmental Exposure", "Mummies", "06 humanities and the arts", "Bone and Bones", "Arsenic", "Forensic Toxicology", "03 medical and health sciences", "0302 clinical medicine", "Italy", "Arsenic Poisoning", "Microscopy", " Electron", " Scanning", "Humans", "0601 history and archaeology", "Carbon Radioisotopes", "Ancient DNA; Angelo Poliziano; Arsenic poisoning; Girolamo benivieni; Pico della Mirandola; Radiocarbon dating", "DNA", " Ancient", "History", " 15th Century"]}, "links": [{"href": "https://doi.org/11585/634154"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Forensic%20and%20Legal%20Medicine", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11585/634154", "name": "item", "description": "11585/634154", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11585/634154"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-05-01T00:00:00Z"}}, {"id": "1983/ee301c22-7b50-46dd-9d94-2cb7973a0a60", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:08Z", "type": "Journal Article", "created": "2023-02-06", "title": "Competitive incorporation of Mn and Mg in vivianite at varying salinity and effects on crystal structure and morphology", "description": "Open AccessVivianite, a ferrous phosphate mineral, can be an important phosphorus (P) sink in non-sulfidic, reducing coastal sediments. The Fe in the crystal structure of vivianite can be substituted by other divalent metal cations such as Mn2+ or Mg2+. Since Mg is much more abundant in coastal porewaters than Mn, the more frequent reports of Mn substitution in vivianites of coastal sediments has been suggested to indicate a preferential incorporation of Mn over Mg into the crystal structure of vivianite. However, although both Mn and Mg substitution in vivianite are environmentally relevant, it is yet unknown whether Mn or Mg is preferentially incorporated and how these isomorphic substitutions alter the crystal structure and morphology of vivianite, parameters which may influence vivianite reactivity. Here, we studied the incorporation of Mn and/or Mg in vivianites formed by co-precipitation at pH 7 in the presence of varying dissolved Mn and/or Mg concentrations and solution salinities resembling an estuarine gradient from 0 to 9 psu. In total, 19 different vivianites were synthesized, with up to 50% of Fe substituted by Mn and Mg. Thermodynamic equilibrium calculations showed that aqueous Mg speciation was altered with increasing salinity, while Mn speciation was less affected, likely explaining the preferential incorporation of Mn in the vivianite structure at higher salinities. 57Fe-M\u00f6ssbauer spectroscopy revealed that both Mn and Mg were preferentially incorporated in the double-octahedral Fe position, at which intervalence charge transfer is possible during the oxidation of vivianite. In contrast to Mg, which is redox inactive, incorporated Mn can participate in heteronuclear intervalence charge transfer with Fe. Thus, incorporation of either cation may impact the reactivity of vivianite under oxidizing conditions in element specific ways. Results of complementary analyses including X-ray diffraction, electron microscopy and Fe K-edge X-ray absorption spectroscopy further showed that incorporation of Mn and/or Mg led to smaller particle size, increased crystal roughness and thinner crystals, as well as systematic changes in unit cell parameters. These observed changes in crystal morphology might impact the reactivity of vivianite in natural environments and thus the effect of cation incorporation in vivianite should be considered when studying Fe and P cycling in coastal sediments.", "keywords": ["M\u00f6ssbauer Spectroscopy", "550", "Isomorphic substitution", "13. Climate action", "Ferrous phosphate minerals", "Electron microscopy", "Ferrous phosphate minerals; Phosphorus burial; Isomorphic substitution; M\u00f6ssbauer Spectroscopy; Electron microscopy", "Phosphorus burial", "01 natural sciences", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/1983/ee301c22-7b50-46dd-9d94-2cb7973a0a60"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Geochimica%20et%20Cosmochimica%20Acta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1983/ee301c22-7b50-46dd-9d94-2cb7973a0a60", "name": "item", "description": "1983/ee301c22-7b50-46dd-9d94-2cb7973a0a60", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1983/ee301c22-7b50-46dd-9d94-2cb7973a0a60"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-01T00:00:00Z"}}, {"id": "20.500.12556/RUNG-9073", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:17Z", "type": "Journal Article", "created": "2022-11-07", "title": "Insights into the single particle composition, size, mixing state and aspect ratio of freshly emitted mineral dust from field measurements in the Moroccan Sahara using electron microscopy", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Abstract. The chemical and morphological properties of mineral dust aerosols emitted by wind erosion from arid and semi-arid regions influence climate, ocean and land ecosystems, air quality, and multiple socio-economic sectors. However, there is an incomplete understanding of the emitted dust particle size distribution (PSD) in terms of its constituent minerals that typically result from the fragmentation of soil aggregates during wind erosion. The emitted dust PSD affects the duration of particle transport and thus each mineral\u2019s global distribution, along with its specific effect upon climate. This lack of understanding is largely due to the scarcity of relevant in situ measurements in dust sources. To advance our understanding of the physicochemical properties of the emitted dust PSD, we present insights into the elemental composition and morphology of individual dust particles collected during the FRontiers in dust minerAloGical coMposition and its Effects upoN climaTe (FRAGMENT) field campaign in the Moroccan Sahara in September 2019. We analyzed more than 300,000 freshly emitted individual particles by performing offline analysis in the laboratory using Scanning Electron Microscopy (SEM) coupled with Energy-Dispersive X-ray Spectrometry (EDX). Eight major particle-type classes were identified where clay minerals make up the majority of the analyzed particles by number, with carbonates and quartz contributing to a lesser extent. We provide an exhaustive analysis of the size distribution and potential mixing state of different particle types, focusing largely on iron-rich (Fe-oxi/hydroxides) and feldspar particles, which are key to the effects of dust upon radiation and clouds. Nearly pure or externally mixed Fe-oxi/hydroxides are present only in diameters smaller than 2 \u00b5m and mainly below 1 \u00b5m. Fe-oxi/hydroxides tend to be increasingly internally mixed with other minerals, especially clays, as particle size increases, i.e., the volume fraction of Fe-oxi/hydroxides in aggregates decreases with particle size. Pure (externally-mixed) feldspar grains represented 3.7 % of all the particles, of which we estimated about a quarter to be K-feldspar. The externally-mixed total feldspar and K-feldspar abundances are relatively invariant with particle size, in contrast to the increasing abundance of feldspar-like (internally-mixed) aggregates with particle size. We also found that overall the median aspect ratio is rather constant across particle size and mineral groups, although we obtain slightly higher aspect ratios for internally-mixed particles. The detailed information on the composition of freshly emitted individual dust particles along with the quantitative analysis of their mixing state presented here can be used to constrain climate models including mineral species in their representation of the dust cycle.</p></article>", "keywords": ["Atmospheric chemistry", "550", "QC1-999", "http://metadata.un.org/sdg/3", "Mineral dust", "01 natural sciences", "Climate models", "\u00c0rees tem\u00e0tiques de la UPC::Enginyeria agroaliment\u00e0ria::Ci\u00e8ncies de la terra i de la vida::Climatologia i meteorologia", "Aerosols Measurement", "Pols minerals", "QD1-999", "Ensure healthy lives and promote well-being for all at all ages", "0105 earth and related environmental sciences", "mineral dust", "info:eu-repo/classification/ddc/550", "electron microscopy", "ddc:550", "Physics", "15. Life on land", "info:eu-repo/classification/udc/502.3/.7", "Pollution", "Moroccan Sahara", "Earth sciences", "Chemistry", "13. Climate action", "Mineral dust particles", "Air quality", "Desert dust"]}, "links": [{"href": "https://acp.copernicus.org/articles/23/3861/2023/acp-23-3861-2023.pdf"}, {"href": "https://acp.copernicus.org/articles/23/3861/2023/acp-23-3861-2023-supplement.pdf"}, {"href": "https://doi.org/20.500.12556/RUNG-9073"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Atmospheric%20Chemistry%20and%20Physics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.12556/RUNG-9073", "name": "item", "description": "20.500.12556/RUNG-9073", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.12556/RUNG-9073"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-07T00:00:00Z"}}, {"id": "2992753670", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:46Z", "type": "Journal Article", "created": "2019-12-04", "title": "Thickness of Polyelectrolyte Layers of Separately Confined Bacteria Alters Key Physiological Parameters on a Single Cell Level", "description": "Confinement of bacterial cells in a matrix or in capsules is an integral part of many biotechnological applications. Here, the well-known layer-by-layer method of deposition of a polyelectrolyte film a few nanometers in thickness to confine separated bacterial cells in permeable and physically durable shells has been examined. Due to the physical properties of such a confinement, we found that this method enables investigation of effects of physical barriers against mass gain and cell division. Using the method of time-lapse confocal microscopy, we observed a prolonged lag phase, dependent on the number of polyelectrolyte layers. In the confinement, both the GFP fluorescent signal from the leaking T7 promoter and the cell size were increased by factors of more than five and two, respectively. This creates a paradigm shift that enables use of mechanical entrapment for control of bacterial cell physiology and opens possibilities of controlling the division rate as well as gene expression. These effects can be attributed to the perturbation of the sensing of the cell size, which results in disproportional synthesis of a cell envelope impinging the intracellular material and compels cells to grow rapidly. In addition, the charged surface of cells enables prolonged intercellular physical interaction and results in spherically shaped microcolonies.", "keywords": ["polyelectrolytes", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "layer-by-layer encapsulation", "time-lapse confocal microscopy", " polyelectrolytes", " layer-by-layer encapsulation", " electrostatic interactions", " cell surface modification", "cell surface modification", "Bioengineering and Biotechnology", "electrostatic interactions", "time-lapse confocal microscopy", "TP248.13-248.65", "Biotechnology"]}, "links": [{"href": "https://doi.org/2992753670"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Bioengineering%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2992753670", "name": "item", "description": "2992753670", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2992753670"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-04T00:00:00Z"}}, {"id": "3130873339", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:58Z", "type": "Journal Article", "created": "2021-02-13", "title": "Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere", "description": "Abstract<p>Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.</p", "keywords": ["0301 basic medicine", "570", "Microscopy", "Silicon", "0303 health sciences", "Temperature", "root-microbe interactions", "Equipment Design", "Biological Sciences", "Environment", "15. Life on land", "Plant Roots", "630", "Fluorescence", "Soil", "03 medical and health sciences", "Seedlings", "Calibration", "Rhizosphere", "Image Processing", " Computer-Assisted", "environmental imaging", "rhizosphere", "Soil Microbiology", "Bacillus subtilis", "Lactuca"]}, "links": [{"href": "https://eprints.whiterose.ac.uk/178939/18/e2109176118.full.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.2109176118"}, {"href": "https://doi.org/3130873339"}, {"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": "3130873339", "name": "item", "description": "3130873339", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3130873339"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-13T00:00:00Z"}}, {"id": "2980155975", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:45Z", "type": "Journal Article", "created": "2019-10-08", "title": "Root\u2010induced soil deformation influences Fe, S and P: rhizosphere chemistry investigated using synchrotron XRF and XANES", "description": "Summary<p>   <p>Rhizosphere soil has distinct physical and chemical properties from bulk soil. However, besides root\uffe2\uff80\uff90induced physical changes, chemical changes have not been extensively measured in situ on the pore scale.</p>  <p>In this study, we couple structural information, previously obtained using synchrotron X\uffe2\uff80\uff90ray computed tomography (XCT), with synchrotron X\uffe2\uff80\uff90ray fluorescence microscopy (XRF) and X\uffe2\uff80\uff90ray absorption near\uffe2\uff80\uff90edge structure (XANES) to unravel chemical changes induced by plant roots.</p>  <p>Our results suggest that iron (Fe) and sulfur (S) increase notably in the direct vicinity of the root via solubilization and microbial activity. XANES further shows that Fe is slightly reduced, S is increasingly transformed into sulfate (SO42\uffe2\uff88\uff92) and phosphorus (P) is increasingly adsorbed to humic substances in this enrichment zone. In addition, the ferrihydrite fraction decreases drastically, suggesting the preferential dissolution and the formation of more stable Fe oxides. Additionally, the increased transformation of organic S to sulfate indicates that the microbial activity in this zone is increased. These changes in soil chemistry correspond to the soil compaction zone as previously measured via XCT.</p>  <p>The fact that these changes are colocated near the root and the compaction zone suggests that decreased permeability as a result of soil structural changes acts as a barrier creating a zone with increased rhizosphere chemical interactions via surface\uffe2\uff80\uff90mediated processes, microbial activity and acidification.</p>  </p", "keywords": ["2. Zero hunger", "550", "Iron", "Hordeum", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Plant Roots", "Soil", "Microscopy", " Fluorescence", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Tomography", " X-Ray Computed", "Sulfur", "Synchrotrons"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16242"}, {"href": "https://doi.org/2980155975"}, {"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": "2980155975", "name": "item", "description": "2980155975", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2980155975"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-12T00:00:00Z"}}, {"id": "2995832821", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:46Z", "type": "Journal Article", "created": "2019-12-18", "title": "Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity", "description": "Abstract                 Background                 <p>Plant feeding, free-living nematodes cause extensive damage to plant roots by direct feeding and, in the case of some trichodorid and longidorid species, through the transmission of viruses. Developing more environmentally friendly, target-specific nematicides is currently impeded by slow and laborious methods of toxicity testing. Here, we developed a bioactivity assay based on the dynamics of light \uffe2\uff80\uff98speckle\uffe2\uff80\uff99 generated by living cells and we demonstrate its application by assessing chemicals\uffe2\uff80\uff99 toxicity to different nematode trophic groups.</p>                                Results                 <p>Free-living nematode populations extracted from soil were exposed to methanol and phenyl isothiocyanate (PEITC). Biospeckle analysis revealed differing behavioural responses as a function of nematode feeding groups. Trichodorus nematodes were less sensitive than were bacterial feeding nematodes or non-trichodorid plant feeding nematodes. Following 24\uffc2\uffa0h of exposure to PEITC, bioactivity significantly decreased for plant and bacterial feeders but not for Trichodorus nematodes. Decreases in movement for plant and bacterial feeders in the presence of PEITC also led to measurable changes to the morphology of biospeckle patterns.</p>                                Conclusions                 <p>Biospeckle analysis can be used to accelerate the screening of nematode bioactivity, thereby providing a fast way of testing the specificity of potential nematicidal compounds. With nematodes\uffe2\uff80\uff99 distinctive movement and activity levels being visible in the biospeckle pattern, the technique has potential to screen the behavioural responses of diverse trophic nematode communities. The method discriminates both behavioural responses, morphological traits and activity levels and hence could be used to assess the specificity of nematicidal compounds.</p>", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "Selective plane illumination microscopy (SPIM)", "Nematodes", "QH301-705.5", "Methodology", "Plant culture", "630", "SB1-1110", "Dynamic speckle", "03 medical and health sciences", "Isothiocyanate", "Biology (General)", "Selective plan illumination microscopy (SPIM)"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s13007-019-0523-8.pdf"}, {"href": "https://doi.org/2995832821"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Methods", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2995832821", "name": "item", "description": "2995832821", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2995832821"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-01T00:00:00Z"}}, {"id": "31591727", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:26:01Z", "type": "Journal Article", "created": "2019-10-08", "title": "Root\u2010induced soil deformation influences Fe, S and P: rhizosphere chemistry investigated using synchrotron XRF and XANES", "description": "Summary<p>   <p>Rhizosphere soil has distinct physical and chemical properties from bulk soil. However, besides root\uffe2\uff80\uff90induced physical changes, chemical changes have not been extensively measured in situ on the pore scale.</p>  <p>In this study, we couple structural information, previously obtained using synchrotron X\uffe2\uff80\uff90ray computed tomography (XCT), with synchrotron X\uffe2\uff80\uff90ray fluorescence microscopy (XRF) and X\uffe2\uff80\uff90ray absorption near\uffe2\uff80\uff90edge structure (XANES) to unravel chemical changes induced by plant roots.</p>  <p>Our results suggest that iron (Fe) and sulfur (S) increase notably in the direct vicinity of the root via solubilization and microbial activity. XANES further shows that Fe is slightly reduced, S is increasingly transformed into sulfate (SO42\uffe2\uff88\uff92) and phosphorus (P) is increasingly adsorbed to humic substances in this enrichment zone. In addition, the ferrihydrite fraction decreases drastically, suggesting the preferential dissolution and the formation of more stable Fe oxides. Additionally, the increased transformation of organic S to sulfate indicates that the microbial activity in this zone is increased. These changes in soil chemistry correspond to the soil compaction zone as previously measured via XCT.</p>  <p>The fact that these changes are colocated near the root and the compaction zone suggests that decreased permeability as a result of soil structural changes acts as a barrier creating a zone with increased rhizosphere chemical interactions via surface\uffe2\uff80\uff90mediated processes, microbial activity and acidification.</p>  </p", "keywords": ["2. Zero hunger", "550", "Iron", "Hordeum", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Plant Roots", "Soil", "Microscopy", " Fluorescence", "Rhizosphere", "0401 agriculture", " forestry", " and fisheries", "Tomography", " X-Ray Computed", "Sulfur", "Synchrotrons"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16242"}, {"href": "https://doi.org/31591727"}, {"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": "31591727", "name": "item", "description": "31591727", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/31591727"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-12T00:00:00Z"}}, {"id": "3199163144", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:26:04Z", "type": "Journal Article", "created": "2021-07-16", "title": "High-resolution 3D mapping of rhizosphere glycan patterning using molecular probes in a transparent soil system", "description": "Rhizospheres are microecological zones at the interface of roots and soils. Interactions between bacteria and roots are critical for maintaining plant and soil health but are difficult to study because of constraints inherent in working with underground systems. We have developed an in-situ rhizosphere imaging system based on transparent soils and molecular probes that can be imaged using confocal microscopy. We observed spatial patterning of polysaccharides along roots and on cells deposited into the rhizosphere and also co-localised fluorescently tagged soil bacteria. These studies provide insight into the complex glycan landscape of rhizospheres and suggest a means by which root / rhizobacteria interactions can be non-disruptively studied.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "QH573-671", "15. Life on land", "630", "Article", "Transparent Soil", "03 medical and health sciences", "Fluorescence Microscopy", "Rhizosphere", "Rhizobacteria", "Polysaccharide", "Cytology"]}, "links": [{"href": "https://eprints.ncl.ac.uk/fulltext.aspx?url=279778/5D67D23B-DAA5-4CF5-A60A-16112D9E3664.pdf&pub_id=279778"}, {"href": "https://doi.org/3199163144"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Cell%20Surface", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3199163144", "name": "item", "description": "3199163144", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3199163144"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-01T00:00:00Z"}}, {"id": "37487270", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:26:16Z", "type": "Journal Article", "created": "2023-04-10", "title": "Quantitative image analysis of microplastics in bottled water using Artificial Intelligence", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The ubiquitous occurrence of microplastics (MPs) in the environment and the use of plastics in packaging materials result in the presence of MPs in the food chain and the exposure of consumers. Yet, no fully validated analytical method is available for microplastic (MP) quantification, thereby preventing the reliable estimation of the level of exposure and, ultimately, the assessment of the food safety risks associated with MP contamination. In this study, a novel approach is presented that exploits interactive artificial intelligence tools to enable the automation of MP analysis. An integrated method for the analysis of MPs in bottled water based on Nile Red staining and fluorescent microscopy was developed and validated, featuring a partial interrogation of the filter and a fully automated image processing workflow based on a Random Forest classifier, thereby boosting the analysis speed. The image analysis provided particle count, size and size distribution of the MPs. From these data, a rough estimation of the mass of the individual MPs, and consequently of the MP mass concentration in the sample, could be obtained as well. Critical materials, method performance characteristics, and final applicability were studied in detail. The method showed to be highly sensitive in sizing MPs down to 10 \u00b5m, with a particle count limit of detection and quantification of 28 and 85 items/500 mL, respectively. Linearity of mass concentration determined between 10 ppb and 1.5 ppm showed a regression coefficient of (R2) of 0.99. Method precision was demonstrated by repeatability of 9 - 16% RSD (n = 7) and within-laboratory reproducibility of 15 - 27 % RSD (n = 21). Accuracy based on recovery was 92 \u00b1 15 % and 98 \u00b1 23 % at a level of 0.1 and 1.0 ppm, respectively. The quantitative performance characteristics thus obtained complied with regulatory requirements. Finally, the method was successfully applied to the analysis of twenty commercial samples of bottled water, with and without gas and flavor additives, yielding results ranging from values below the limit of detection to 7237 (95% CI [6456, 8088]) items/500 mL.</p></article>", "keywords": ["Fluorescence microscopy", "Artificial intelligence", "Bottled water", "Method validation", "Artificial Intelligence", "Microplastics", "Drinking Water", "Microplastic", "Nile red", "Reproducibility of Results", "Plastics", "6. Clean water"]}, "links": [{"href": "https://doi.org/37487270"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Talanta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "37487270", "name": "item", "description": "37487270", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/37487270"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-10T00:00:00Z"}}, {"id": "PMC11044595", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:27:59Z", "type": "Journal Article", "created": "2024-04-10", "title": "Plastic Fruit Stickers in Industrial Composting\u2500Surface and Structural Alterations Revealed by Electron Microscopy and Computed Tomography", "description": "Often large quantities of plastics are found in compost, with price look-up stickers being a major but little-explored component in the contamination path. Stickers glued to fruit or vegetable peels usually remain attached to the organic material despite sorting processes in the composting plant. Here, we investigated the effects of industrial composting on the structural alterations of these stickers. Commercial polypropylene (PP) stickers on banana peels were added to a typical organic material mixture for processing in an industrial composting plant and successfully resampled after a prerotting (11 days) and main rotting step (25 days). Afterward, both composted and original stickers were analyzed for surface and structural changes via scanning electron microscopy, Fourier-transform infrared spectroscopy, and micro- and nano-X-ray computed tomography (CT) combined with deep learning approaches. The composting resulted in substantial surface changes and degradation in the form of microbial colonization, deformation, and occurrence of cracks in all stickers. Their pore volumes increased from 16.7% in the original sticker to 26.3% at the end of the compost process. In a similar way, the carbonyl index of the stickers increased. Micro-CT images additionally revealed structural changes in the form of large adhesions that penetrated the surface of the sticker. These changes were accompanied by delamination after 25 days of composting, thus overall hinting at the degradation of the stickers and the subsequent formation of smaller microplastic pieces.", "keywords": ["Technology", "ddc:600", "ddc:550", "Composting", "600", "02 engineering and technology", "540", "Polypropylenes", "01 natural sciences", "620", "Soil", "Fruit", "Microscopy", " Electron", " Scanning", "info:eu-repo/classification/ddc/600", "Tomography", " X-Ray Computed", "0210 nano-technology", "Plastics", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.3c08734"}, {"href": "https://doi.org/PMC11044595"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11044595", "name": "item", "description": "PMC11044595", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11044595"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-10T00:00:00Z"}}, {"id": "PMC10866023", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-25T16:27:59Z", "type": "Journal Article", "created": "2023-06-29", "title": "Construction and Characterisation of a Structured, Tuneable, and Transparent 3D Culture Platform for Soil Bacteria", "description": "2.Abstract<p>We have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the metabolic profile of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms,Bacillus subtilisandStreptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of other difficult-to-culture bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as interaction, competition, and warfare.</p>3.Graphical Abstract<p>A step-by-step method for creating a tailored 3D culture medium for study of soil microbes.</p><p>The complete workflow can be split into three parts: Growth and observation, metabolic profiling to provide a stable refractive index matching solution, and production of the 3D soil environment. The 3D culture scaffold was created by cryomilling Nafion\uffe2\uff84\uffa2 resin pellets and size filtration. Chemical processing altered the surface chemistry of Nafion\uffe2\uff84\uffa2 particles and facilitated nutrient binding by titration of a defined liquid culture medium. Metabolic profiling determined non-metabolisable sugars and provided an inert refractive index matching substrate, which was added to the final nutrient titration. Inoculation and growth of the test strain allowed for downstream assessment of colonisation behaviours and community dynamicsin situby, for example, optical microscopy.</p", "keywords": ["2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "Plant Microbiology and Soil Health (formerly Environmental Biology)", "15. Life on land", "Microbiology", "Carbon", "620", "Soil", "03 medical and health sciences", "Microscopy", " Fluorescence", "Microbial Interactions", "Bacillus subtilis"]}, "links": [{"href": "https://strathprints.strath.ac.uk/87995/7/Rooney-etal-Microbiology-2024-Construction-and-characterisation-of-a-structured-tuneable-and-transparent-3D-culture-platform.pdf"}, {"href": "https://doi.org/PMC10866023"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC10866023", "name": "item", "description": "PMC10866023", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC10866023"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-28T00:00:00Z"}}, {"id": "PMC11525289", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:00Z", "type": "Journal Article", "created": "2024-10-15", "title": "All black: a microplastic extraction combined with colour-based analysis allows identification and characterisation of tire wear particles (TWP) in soils", "description": "<title>Abstract</title>         <p>While tire wear particles (TWP) have been estimated to represent more than 90% of the total microplastic (MP) emitted in European countries and may have environmental health effects, only few data about TWP concentrations and characteristics are available today. The lack of data stems from the fact that no standardized, cost efficient or accessible extraction and identification method is available yet. We present a method allowing the extraction of TWP from soil, performing analysis with a conventional optical microscope and a machine learning approach to identify TWP in soil based on their colour. The lowest size of TWP which could be measured reliably with an acceptable recovery using our experimental set-up was 35 \u00b5m. Further improvements would be possible given more advanced technical infrastructure (higher optical magnification and image quality). Our method showed a mean recovery of 85% in the 35-2000 \u00b5m particle size range and no blank contamination. We tested for possible interference from charcoal (as another black soil component with similar properties) in the soils and found a reduction of the interference from charcoal by 92% during extraction. We applied our method to a highway adjacent soil at 1 m, 2 m, 5 m, and 10 m and detected TWP in all samples with a tendency to higher concentrations at 1 m and 2 m from the road compared to 10 m from the road. The observed TWP concentrations were in the same order of magnitude as what was previously reported in literature in highway adjacent soils. These results demonstrate the potential of the method to provide quantitative data on the occurrence and characteristics of TWP in the environment. The method can be easily implemented in many labs, and help to address our knowledge gap regarding TWP concentrations in soils.</p>", "keywords": ["TP1080-1185", "Segmentation", "TD172-193.5", "Tire wear", "Soil pollution", "Machine learning", "Microplastic", "Methodology", "Polymers and polymer manufacture", "Optical microscopy", "Environmental pollution"]}, "links": [{"href": "https://doi.org/PMC11525289"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microplastics%20and%20Nanoplastics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11525289", "name": "item", "description": "PMC11525289", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11525289"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-10-15T00:00:00Z"}}, {"id": "PMC6904277", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:04Z", "type": "Journal Article", "created": "2019-12-04", "title": "Thickness of Polyelectrolyte Layers of Separately Confined Bacteria Alters Key Physiological Parameters on a Single Cell Level", "description": "Confinement of bacterial cells in a matrix or in capsules is an integral part of many biotechnological applications. Here, the well-known layer-by-layer method of deposition of a polyelectrolyte film a few nanometers in thickness to confine separated bacterial cells in permeable and physically durable shells has been examined. Due to the physical properties of such a confinement, we found that this method enables investigation of effects of physical barriers against mass gain and cell division. Using the method of time-lapse confocal microscopy, we observed a prolonged lag phase, dependent on the number of polyelectrolyte layers. In the confinement, both the GFP fluorescent signal from the leaking T7 promoter and the cell size were increased by factors of more than five and two, respectively. This creates a paradigm shift that enables use of mechanical entrapment for control of bacterial cell physiology and opens possibilities of controlling the division rate as well as gene expression. These effects can be attributed to the perturbation of the sensing of the cell size, which results in disproportional synthesis of a cell envelope impinging the intracellular material and compels cells to grow rapidly. In addition, the charged surface of cells enables prolonged intercellular physical interaction and results in spherically shaped microcolonies.", "keywords": ["polyelectrolytes", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "layer-by-layer encapsulation", "cell surface modification", "Bioengineering and Biotechnology", "electrostatic interactions", "time-lapse confocal microscopy", "TP248.13-248.65", "Biotechnology"]}, "links": [{"href": "https://doi.org/PMC6904277"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Bioengineering%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC6904277", "name": "item", "description": "PMC6904277", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC6904277"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-04T00:00:00Z"}}, {"id": "PMC6921579", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:04Z", "type": "Journal Article", "created": "2019-12-18", "title": "Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity", "description": "Abstract                 Background                 <p>Plant feeding, free-living nematodes cause extensive damage to plant roots by direct feeding and, in the case of some trichodorid and longidorid species, through the transmission of viruses. Developing more environmentally friendly, target-specific nematicides is currently impeded by slow and laborious methods of toxicity testing. Here, we developed a bioactivity assay based on the dynamics of light \uffe2\uff80\uff98speckle\uffe2\uff80\uff99 generated by living cells and we demonstrate its application by assessing chemicals\uffe2\uff80\uff99 toxicity to different nematode trophic groups.</p>                                Results                 <p>Free-living nematode populations extracted from soil were exposed to methanol and phenyl isothiocyanate (PEITC). Biospeckle analysis revealed differing behavioural responses as a function of nematode feeding groups. Trichodorus nematodes were less sensitive than were bacterial feeding nematodes or non-trichodorid plant feeding nematodes. Following 24\uffc2\uffa0h of exposure to PEITC, bioactivity significantly decreased for plant and bacterial feeders but not for Trichodorus nematodes. Decreases in movement for plant and bacterial feeders in the presence of PEITC also led to measurable changes to the morphology of biospeckle patterns.</p>                                Conclusions                 <p>Biospeckle analysis can be used to accelerate the screening of nematode bioactivity, thereby providing a fast way of testing the specificity of potential nematicidal compounds. With nematodes\uffe2\uff80\uff99 distinctive movement and activity levels being visible in the biospeckle pattern, the technique has potential to screen the behavioural responses of diverse trophic nematode communities. The method discriminates both behavioural responses, morphological traits and activity levels and hence could be used to assess the specificity of nematicidal compounds.</p>", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "Selective plane illumination microscopy (SPIM)", "Nematodes", "QH301-705.5", "Methodology", "Plant culture", "630", "SB1-1110", "Dynamic speckle", "03 medical and health sciences", "Isothiocyanate", "Biology (General)", "Selective plan illumination microscopy (SPIM)"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s13007-019-0523-8.pdf"}, {"href": "https://doi.org/PMC6921579"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Methods", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC6921579", "name": "item", "description": "PMC6921579", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC6921579"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-01T00:00:00Z"}}, {"id": "PMC8445887", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:06Z", "type": "Journal Article", "created": "2021-07-16", "title": "High-resolution 3D mapping of rhizosphere glycan patterning using molecular probes in a transparent soil system", "description": "Rhizospheres are microecological zones at the interface of roots and soils. Interactions between bacteria and roots are critical for maintaining plant and soil health but are difficult to study because of constraints inherent in working with underground systems. We have developed an in-situ rhizosphere imaging system based on transparent soils and molecular probes that can be imaged using confocal microscopy. We observed spatial patterning of polysaccharides along roots and on cells deposited into the rhizosphere and also co-localised fluorescently tagged soil bacteria. These studies provide insight into the complex glycan landscape of rhizospheres and suggest a means by which root / rhizobacteria interactions can be non-disruptively studied.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "QH573-671", "15. Life on land", "630", "Article", "Transparent Soil", "03 medical and health sciences", "Fluorescence Microscopy", "Rhizosphere", "Rhizobacteria", "Polysaccharide", "Cytology"]}, "links": [{"href": "https://eprints.ncl.ac.uk/fulltext.aspx?url=279778/5D67D23B-DAA5-4CF5-A60A-16112D9E3664.pdf&pub_id=279778"}, {"href": "https://doi.org/PMC8445887"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Cell%20Surface", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC8445887", "name": "item", "description": "PMC8445887", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC8445887"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-01T00:00:00Z"}}, {"id": "PMC8640753", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:06Z", "type": "Journal Article", "created": "2021-02-13", "title": "Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere", "description": "Abstract<p>Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.</p", "keywords": ["0301 basic medicine", "570", "Silicon", "Environment", "Plant Roots", "630", "Fluorescence", "Soil", "03 medical and health sciences", "Image Processing", " Computer-Assisted", "Soil Microbiology", "root\u2013microbe interactions", "Microscopy", "0303 health sciences", "Temperature", "root-microbe interactions", "Equipment Design", "Biological Sciences", "15. Life on land", "Seedlings", "Calibration", "Rhizosphere", "environmental imaging", "rhizosphere", "Bacillus subtilis", "Lactuca"]}, "links": [{"href": "https://eprints.whiterose.ac.uk/178939/18/e2109176118.full.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.2109176118"}, {"href": "https://doi.org/PMC8640753"}, {"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": "PMC8640753", "name": "item", "description": "PMC8640753", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC8640753"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-13T00:00:00Z"}}, {"id": "PMC9478162", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:08Z", "type": "Journal Article", "created": "2022-07-07", "title": "Novel form of collective movement by soil bacteria", "description": "Abstract                <p>Although migrations are essential for soil microorganisms to exploit scarce and heterogeneously distributed resources, bacterial mobility in soil remains poorly studied due to experimental limitations. In this study, time-lapse images collected using live microscopy techniques captured collective and coordinated groups of B. subtilis cells exhibiting \uffe2\uff80\uff9ccrowd movement\uffe2\uff80\uff9d. Groups of B. subtilis cells moved through transparent soil (nafion polymer with particle size resembling sand) toward plant roots and re-arranged dynamically around root tips in the form of elongating and retracting \uffe2\uff80\uff9cflocks\uffe2\uff80\uff9d resembling collective behaviour usually associated with higher organisms (e.g., bird flocks or fish schools). Genetic analysis reveals B. subtilis flocks are likely driven by the diffusion of extracellular signalling molecules (e.g., chemotaxis, quorum sensing) and may be impacted by the physical obstacles and hydrodynamics encountered in the soil like environment. Our findings advance understanding of bacterial migration through soil matrices and expand known behaviours for coordinated bacterial movement.</p", "keywords": ["light sheet microscopy", "0301 basic medicine", "570", "0303 health sciences", "Bacteria", "transparent soil", "Evolution", "/dk/atira/pure/subjectarea/asjc/2400/2404", "Polymers", "Quorum Sensing", "Bacteria/genetics", "15. Life on land", "Soil", "03 medical and health sciences", "Behavior and Systematics", "root colonisation", "Sand", "collective movement", "name=Ecology", "name=Microbiology", "B. subtilis", "co-ordination", "bacterial flocculation", "/dk/atira/pure/subjectarea/asjc/1100/1105"]}, "links": [{"href": "https://www.nature.com/articles/s41396-022-01277-w.pdf"}, {"href": "https://doi.org/PMC9478162"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC9478162", "name": "item", "description": "PMC9478162", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC9478162"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-07T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microscopy&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microscopy&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microscopy&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Microscopy&offset=50", "hreflang": "en-US"}], "numberMatched": 50, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-05-26T03:55:36.478647Z"}