{"type": "FeatureCollection", "features": [{"id": "10.1007/s00442-012-2578-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:25Z", "type": "Journal Article", "created": "2013-01-07", "title": "Effects Of Drought And N-Fertilization On N Cycling In Two Grassland Soils", "description": "Open AccessOecologia, 171 (3)", "keywords": ["[SDE] Environmental Sciences", "N2O fluxes", "550", "functional genes", "Nitrogen", "[SDV]Life Sciences [q-bio]", "Climate", "Climate Change", "Nitrification and denitrification", "enzyme activites", "Urine", "630", "10127 Institute of Evolutionary Biology and Environmental Studies", "Soil", "Quantitative PCR", "Climate change; Enzyme activities; Functional genes; Quantitative PCR; Nitrification and denitrification; N2O fluxes", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Animals", "Climate change", "Enzyme activities", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Ecosystem", "Soil Microbiology", "Functional genes", "Nitrogen Cycle", "Plants", "Archaea", "Droughts", "[SDV] Life Sciences [q-bio]", "1105 Ecology", " Evolution", " Behavior and Systematics", "climate change", "Genes", " Bacterial", "[SDE]Environmental Sciences", "quantitative PCR", "Denitrification", "570 Life sciences; biology", "590 Animals (Zoology)", "Cattle", "nitrification and denitrification"]}, "links": [{"href": "https://doi.org/10.1007/s00442-012-2578-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-012-2578-3", "name": "item", "description": "10.1007/s00442-012-2578-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-012-2578-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-01-08T00:00:00Z"}}, {"id": "10.1007/s10265-009-0294-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:30Z", "type": "Journal Article", "created": "2010-01-12", "title": "Taxonomic Identity, Phylogeny, Climate And Soil Fertility As Drivers Of Leaf Traits Across Chinese Grassland Biomes", "description": "Although broad-scale inter-specific patterns of leaf traits are influenced by climate, soil, and taxonomic identity, integrated assessments of these drivers remain rare. Here, we quantify these drivers in a field study of 171 plant species in 174 sites across Chinese grasslands, including the Tibetan Plateau, Inner Mongolia, and Xinjiang. General linear models were used to partition leaf trait variation. Of the total variation in leaf traits, on average 27% is due to taxonomic or phylogenetic differences among species within sites (pure species effect), 29% to variation among sites within species (pure site effect), 38% to joint effects of taxonomic and environmental factors (shared effect), and 6.2% to within-site and within-species variation. Examining the pure site effect, climate explained 7.8%, soil explained 7.4%, and climate and soil variables together accounted for 11%, leaving 18% of the inter-site variation due to factors other than climate or soil. The results do not support the hypothesis that soil fertility is the 'missing link' to explain leaf trait variation unexplained by climatic factors. Climate- and soil-induced leaf adaptations occur mostly among species, and leaf traits vary little within species in Chinese grassland plants, despite strongly varying climate and soil conditions.", "keywords": ["0106 biological sciences", "China", "Climate", "Soil fertility", "Poaceae", "01 natural sciences", "10127 Institute of Evolutionary Biology and Environmental Studies", "Soil", "Quantitative Trait", " Heritable", "Species Specificity", "1110 Plant Science", "Tibetan Plateau", "Leaf economics spectrum", "functional traits", "Photosynthesis", "Ecosystem", "Phylogeny", "2. Zero hunger", "photosynthesis", "soil fertility", "Inner Mongolia (China)", "15. Life on land", "Plant Leaves", "Inner Mongolia", "Linear Models", "leaf economics", "570 Life sciences; biology", "590 Animals (Zoology)", "Functional traits"]}, "links": [{"href": "https://doi.org/10.1007/s10265-009-0294-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Plant%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10265-009-0294-9", "name": "item", "description": "10.1007/s10265-009-0294-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10265-009-0294-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-01-13T00:00:00Z"}}, {"id": "10.1007/s11104-012-1248-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:14:44Z", "type": "Journal Article", "created": "2012-05-04", "title": "Effects Of Simulated Drought And Nitrogen Fertilizer On Plant Productivity And Nitrous Oxide (N2o) Emissions Of Two Pastures", "description": "Open AccessISSN:0032-079X", "keywords": ["Soil acidity", "Drought", "Soil microbial C and N", "04 agricultural and veterinary sciences", "15. Life on land", "Grassland", "Nitrification", "10127 Institute of Evolutionary Biology and Environmental Studies", "Grazing", "Greenhouse gases", "Summer drought", "13. Climate action", "1110 Plant Science", "Denitrification", "570 Life sciences; biology", "590 Animals (Zoology)", "0401 agriculture", " forestry", " and fisheries", "Compensatory growth; Denitrification; Drought; Grassland; Grazing; Greenhouse gases; Soil microbial C and N; Soil acidity; Nitrification; Summer drought", "Compensatory growth", "1111 Soil Science"]}, "links": [{"href": "https://doi.org/10.1007/s11104-012-1248-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-012-1248-x", "name": "item", "description": "10.1007/s11104-012-1248-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-012-1248-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-05-05T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2015.06.022", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:16:12Z", "type": "Journal Article", "created": "2015-07-05", "title": "Precipitation Modifies The Effects Of Warming And Nitrogen Addition On Soil Microbial Communities In Northern Chinese Grasslands", "description": "Terrestrial ecosystems experience simultaneous shifts in multiple drivers of global change, which can interactively affect various resources. The concept that different resources co-limit plant productivity has been well studied. However, co-limitation of soil microbial communities by multiple resources has not been as thoroughly investigated. Specifically, it is not clearly understood how microbial communities respond to shifts in multiple interacting resources such as water, temperature, and nitrogen (N), in the context of global change. To test the effects of these various resources on soil microorganisms, we established a field experiment with temperature and N manipulation in three grasslands of northern China, where there is a decrease in precipitation from east to west across the region. We found that microbial responses to temperature depended upon seasonal water regimes in these temperate steppes. When there was sufficient water present, warming had positive effects on soil microorganisms, suggesting an interaction between water and increases in temperature enhanced local microbial communities. When drought or alternating wet\u2013dry stress occurred, warming had detrimental effects on soil microbial communities. Our results also provide clear evidence for serial co-limitation of microorganisms by water and N at the functional group and community levels, where water is a primary limiting factor and N addition positively affects soil microorganisms only when water is sufficient. We predict that future microbial responses to changes in temperature and N availability could be seasonal or exist only in non-drought years, and will strongly rely on future precipitation regimes.", "keywords": ["2. Zero hunger", "10127 Institute of Evolutionary Biology and Environmental Studies", "13. Climate action", "2404 Microbiology", "570 Life sciences; biology", "590 Animals (Zoology)", "Soil Science", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "Microbiology", "1111 Soil Science", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2015.06.022"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2015.06.022", "name": "item", "description": "10.1016/j.soilbio.2015.06.022", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2015.06.022"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-10-01T00:00:00Z"}}, {"id": "10.1038/srep15550", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:16:51Z", "type": "Journal Article", "created": "2015-10-27", "title": "Soil Restoration With Organic Amendments: Linking Cellular Functionality And Ecosystem Processes", "description": "Abstract<p>A hot topic in recent decades, the application of organic amendments to arid-degraded soils has been shown to benefit microbially-mediated processes. However, despite the importance of soils for global sustainability, a gap has not been addressed yet in soil science: is there any connection between ecosystem-community processes, cellular functionality and microbial lifestyles (i.e. oligotrophy-copiotrophy) in restored soils? Together with classical ecosystem indicators (fatty-acids, extracellular-enzyme activities, basal respiration), state-of-the-art metaproteomics was applied to fill this gap in a model-restoration experiment initiated 10-years ago by the addition of sewage-sludge and compost. Organic amendment strongly impacted ecosystem processes. Furthermore, the type of material used induced differences in the cellular functionalities through variations in the percentages of proteins involved in translation, transcription, energy production and C-fixation. We conclude that the long-term impact of organic restoration goes beyond ecosystem processes and affects cellular functionalities and phyla-lifestyles coupled with differences in microbial-community structures.</p>", "keywords": ["Proteomics", "2. Zero hunger", "0301 basic medicine", "1000 Multidisciplinary", "Sewage", "610 Medicine & health", "10071 Functional Genomics Center Zurich", "04 agricultural and veterinary sciences", "15. Life on land", "Article", "6. Clean water", "Enzymes", "Environmental sciences", "Soil", "03 medical and health sciences", "Soil microbiology", "13. Climate action", "11. Sustainability", "570 Life sciences; biology", "0401 agriculture", " forestry", " and fisheries", "Soil microbiology; Environmental sciences", "Ecosystem", "Environmental Restoration and Remediation", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep15550"}, {"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/srep15550", "name": "item", "description": "10.1038/srep15550", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep15550"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-10-27T00:00:00Z"}}, {"id": "10.1093/bioinformatics/btac037", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:14Z", "type": "Journal Article", "created": "2022-01-26", "title": "GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis", "description": "Abstract                                   Motivation                   <p>Analysis of focal copy number variations (CNVs) is highly relevant for cancer research, as they pinpoint driver genes. More specifically, due to selective pressure oncogenes and tumor suppressor genes are more often affected by these events than neighboring passengers. In cases where multiple candidates co-reside in a genomic locus, careful comparison is required to either identify multigenic minimally deleted regions of synergistic co-mutations, or the true single driver gene. The study of focal CNVs in large cancer genome cohorts requires specialized visualization and statistical analysis.</p>                                                   Results                   <p>We developed the GenomeTornadoPlot R-package which generates gene-centric visualizations of CNV types, locations and lengths from cohortwise NGS data. Furthermore, the software enables the pairwise comparison of proximate genes to identify co-mutation patterns or driver-passenger hierarchies. The visual examination provided by GenomeTornadoPlot is further supported by adaptable local and global focality scoring. Integrated into the GenomeTornadoPlot R-Package is the comprehensive PCAWG database of CNVs, comprising 2976 cancer genome entities from 46 cohorts of the Pan-cancer Analysis of Whole Genomes project. The GenomeTornadoPlot R-package can be used to perform exploratory or hypothesis-driven analyses on the basis of the PCAWG data or in combination with data provided by the user.</p>                                                   Availability and implementation                   <p>GenomeTornadoPlot is written in R script and released via github: &amp;lt;https://github.com/chenhong-dkfz/GenomeTornadoPlot/&amp;gt;. The package is under the license of GPL-3.0.</p>", "keywords": ["570", "DNA Copy Number Variations", "ddc-570", "Genomics", "Oncogenes", "004 Data processing Computer science", "Software", "ddc-004", "570 Life sciences", "004", "3. Good health"]}, "links": [{"href": "https://archiv.ub.uni-heidelberg.de/volltextserver/34483/1/btac037.pdf"}, {"href": "https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/34483/1/btac037.pdf"}, {"href": "https://academic.oup.com/bioinformatics/article-pdf/38/7/2036/49009547/btac037.pdf"}, {"href": "https://doi.org/10.1093/bioinformatics/btac037"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/bioinformatics/btac037", "name": "item", "description": "10.1093/bioinformatics/btac037", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/bioinformatics/btac037"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-31T00:00:00Z"}}, {"id": "10.1111/1365-2745.13504", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:24Z", "type": "Journal Article", "created": "2020-09-25", "title": "Invasive earthworms reduce chemical defense and increase herbivory and pathogen infection in native trees", "description": "Abstract<p>   <p>Recent research shows that earthworms can alter defense traits of plants against herbivores and pathogens by affecting soil biochemistry. Yet, the effects of invasive earthworms on defense traits of native plants from previously earthworm\uffe2\uff80\uff90free ecosystems as well as the consequences for multitrophic interactions are virtually unknown.</p>  <p>Here we use a combination of an observational study and a complementary experimental study to investigate the effects of invasive earthworms on leaf defense traits, herbivore damage and pathogen infection in two poplar tree species (Populus balsamifera and Populus tremuloides) native to North American boreal forests.</p>  <p>Our observational study showed that earthworm invasion was associated with enhanced leaf herbivory (by leaf\uffe2\uff80\uff90chewing insects) in saplings of both tree species. However, we only detected significant shifts in the concentration of chemical defense compounds in response to earthworm invasion for P. balsamifera. Specifically, leaf phenolic concentrations, including salicinoids and catechin, were lower in P. balsamifera from earthworm\uffe2\uff80\uff90invaded sites.</p>  <p>Our experimental study confirmed an earthworm\uffe2\uff80\uff90induced reduction in leaf defense levels in P. balsamifera for one of the defense compounds, tremulacin. The experimental study additionally showed that invasive earthworms reduced leaf dry matter content, potentially increasing leaf palatability, and enhanced susceptibility of trees to infection by a fungal pathogen, but not to aphid infestation, in the same tree species.</p>  <p>Synthesis. Our results show that invasive earthworms can decrease the concentrations of some chemical defense compounds in P. balsamifera, which could make them susceptible to leaf\uffe2\uff80\uff90chewing insects. Such potential impacts of invasive earthworms are likely to have implications for tree survival and competition, native tree biodiversity and ecosystem functioning.</p>  </p>", "keywords": ["0106 biological sciences", "multi-trophic interactions", "secondary metabolites", "15. Life on land", "01 natural sciences", "invasion ecology", "plant\u2013herbivore interactions", "13. Climate action", "international", "physical defense", "570 Life sciences; biology", "boreal forests", "Plan_S-Compliant_TA", "Research Articles", "belowground invasion"]}, "links": [{"href": "https://boris.unibe.ch/152111/1/1365-2745.13504.pdf"}, {"href": "https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.13504"}, {"href": "https://doi.org/10.1111/1365-2745.13504"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1365-2745.13504", "name": "item", "description": "10.1111/1365-2745.13504", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1365-2745.13504"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-09T00:00:00Z"}}, {"id": "10.1111/ddi.13146", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:26Z", "type": "Journal Article", "created": "2020-09-02", "title": "Shifting aspect or elevation? The climate change response of ectotherms in a complex mountain topography", "description": "AbstractAim<p>Climate change is expected to cause mountain species to shift their ranges to higher elevations. Due to the decreasing amounts of habitats with increasing elevation, such shifts are likely to increase their extinction risk. Heterogeneous mountain topography, however, may reduce this risk by providing microclimatic conditions that can buffer macroclimatic warming or provide nearby refugia. As aspect strongly influences the local microclimate, we here assess whether shifts from warm south\uffe2\uff80\uff90exposed aspects to cool north\uffe2\uff80\uff90exposed aspects in response to climate change can compensate for an upward shift into cooler elevations.</p>Location<p>Switzerland, Swiss Alps.</p>Methods<p>We built ensemble distribution models using high\uffe2\uff80\uff90resolution climate data for two mountain\uffe2\uff80\uff90dwelling viviparous ectotherms, the Alpine salamander and the Common lizard, and projected them into various future scenarios to gain insights into distributional changes. We further compared elevation and aspect (northness) of current and predicted future locations to analyse preferences and future shifts.</p>Results<p>Future ranges were consistently decreasing for the lizard, but for the salamander they were highly variable, depending on the climate scenario and threshold rule. Aspect preferences were elevation\uffe2\uff80\uff90dependent: warmer, south\uffe2\uff80\uff90exposed microclimates were clearly preferred at higher compared to lower elevations. In terms of presence and future locations, we observed both elevational upward shifts and northward shifts in aspect. Under future conditions, the shift to cooler north\uffe2\uff80\uff90exposed aspects was particularly pronounced at already warmer lower elevations.</p>Main conclusions<p>For our study species, shifts in aspect and elevation are complementary strategies to mitigate climatic warming in the complex mountain topography. This complements the long\uffe2\uff80\uff90standing view of elevational upward shift being their only option to move into areas with suitable future climate. High\uffe2\uff80\uff90resolution climate data are critical in heterogeneous environments to identify microrefugia and thereby improving future impact assessments of climate change.</p>", "keywords": ["0106 biological sciences", "0301 basic medicine", "570", "4290733-0", "elevation", "aspect", "Modellierung", "4077275-5", "ddc:900", "01 natural sciences", "4128128-7", "10127 Institute of Evolutionary Biology and Environmental Studies", "03 medical and health sciences", "4170297-9", "Schweizer Alpen", "Anthropogene Klima\u00e4nderung", "Wechselwarme", "aspect; climate change; ectotherms; microrefugia; mountain topography; Salamandra atra; species distribution modelling; Switzerland; thresholds; Zootoca vivipara", "4189352-9", "shift", "15. Life on land", "reptile", "1105 Ecology", " Evolution", " Behavior and Systematics", "climate change", "Geschichte und Geografie", "900", "13. Climate action", "Anpassung", "570 Life sciences; biology", "590 Animals (Zoology)", "amphibian", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/785568/2/feldmeier%202020%20divers%20distrib.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/ddi.13146"}, {"href": "https://doi.org/10.1111/ddi.13146"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Diversity%20and%20Distributions", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/ddi.13146", "name": "item", "description": "10.1111/ddi.13146", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/ddi.13146"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-26T00:00:00Z"}}, {"id": "10.1111/gcb.12666", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:29Z", "type": "Journal Article", "created": "2014-06-21", "title": "Interactive Effects Of Elevated Co2 And Nitrogen Deposition On Fatty Acid Molecular And Isotope Composition Of Above- And Belowground Tree Biomass And Forest Soil Fractions", "description": "Abstract<p>Atmospheric carbon dioxide (CO2) and reactive nitrogen (N) concentrations have been increasing due to human activities and impact the global carbon (C) cycle by affecting plant photosynthesis and decomposition processes in soil. Large amounts of C are stored in plants and soils, but the mechanisms behind the stabilization of plant\uffe2\uff80\uff90 and microbial\uffe2\uff80\uff90derived organic matter (OM) in soils are still under debate and it is not clear how N deposition affects soil OM dynamics. Here, we studied the effects of 4\uffc2\uffa0years of elevated (13C\uffe2\uff80\uff90depleted) CO2 and N deposition in forest ecosystems established in open\uffe2\uff80\uff90top chambers on composition and turnover of fatty acids (FAs) in plants and soils. FAs served as biomarkers for plant\uffe2\uff80\uff90 and microbial\uffe2\uff80\uff90derived OM in soil density fractions. We analyzed above\uffe2\uff80\uff90 and belowground plant biomass of beech and spruce trees as well as soil density fractions for the total organic C and FA molecular and isotope (\uffce\uffb413C) composition. FAs did not accumulate relative to total organic C in fine mineral fractions, showing that FAs are not effectively stabilized by association with soil minerals. The \uffce\uffb413C values of FAs in plant biomass increased under high N deposition. However, the N effect was only apparent under elevated CO2 suggesting a N limitation of the system. In soil fractions, only isotope compositions of short\uffe2\uff80\uff90chain FAs (C16+18) were affected. Fractions of \uffe2\uff80\uff98new\uffe2\uff80\uff99 (experimental\uffe2\uff80\uff90derived) FAs were calculated using isotope depletion in elevated CO2 plots and decreased from free light to fine mineral fractions. \uffe2\uff80\uff98New\uffe2\uff80\uff99 FAs were higher in short\uffe2\uff80\uff90chain compared to long\uffe2\uff80\uff90chain FAs (C20\uffe2\uff88\uff9230), indicating a faster turnover of short\uffe2\uff80\uff90chain compared to long\uffe2\uff80\uff90chain FAs. Increased N deposition did not significantly affect the quantity of \uffe2\uff80\uff98new\uffe2\uff80\uff99 FAs in soil fractions, but showed a tendency of increased amounts of \uffe2\uff80\uff98old\uffe2\uff80\uff99 (pre\uffe2\uff80\uff90experimental) C suggesting that decomposition of \uffe2\uff80\uff98old\uffe2\uff80\uff99 C is retarded by high N inputs.</p>", "keywords": ["UFSP13-8 Global Change and Biodiversity", "2306 Global and Planetary Change", "Chemical Fractionation", "Forests", "2300 General Environmental Science", "Soil", "Fagus", "Environmental Chemistry", "Biomass", "Photosynthesis", "Picea", "General Environmental Science", "2. Zero hunger", "Global and Planetary Change", "Analysis of Variance", "Carbon Isotopes", "Ecology", "Atmosphere", "Fatty Acids", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "Reactive Nitrogen Species", "13. Climate action", "2304 Environmental Chemistry", "570 Life sciences; biology", "0401 agriculture", " forestry", " and fisheries", "2303 Ecology"]}, "links": [{"href": "https://doi.org/10.1111/gcb.12666"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/gcb.12666", "name": "item", "description": "10.1111/gcb.12666", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.12666"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-07-08T00:00:00Z"}}, {"id": "10.1111/j.1365-2486.2012.02798.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:38Z", "type": "Journal Article", "created": "2012-07-28", "title": "Increasing Soil Methane Sink Along A 120-Year Afforestation Chronosequence Is Driven By Soil Moisture", "description": "Abstract<p>Upland soils are important sinks for atmospheric methane (CH4), a process essentially driven by methanotrophic bacteria. Soil CH4 uptake often depends on land use, with afforestation generally increasing the soil CH4 sink. However, the mechanisms driving these changes are not well understood to date. We measured soil CH4 and N2O fluxes along an afforestation chronosequence with Norway spruce (Picea abies L.) established on an extensively grazed subalpine pasture. Our experimental design included forest stands with ages ranging from 25 to &gt;120\uffc2\uffa0years and included a factorial cattle urine addition treatment to test for the sensitivity of soil CH4 uptake to N application. Mean CH4 uptake significantly increased with stand age on all sampling dates. In contrast, CH4 oxidation by sieved soils incubated in the laboratory did not show a similar age dependency. Soil CH4 uptake was unrelated to soil N status (but cattle urine additions stimulated N2O emission). Our data indicated that soil CH4 uptake in older forest stands was driven by reduced soil water content, which resulted in a facilitated diffusion of atmospheric CH4 into soils. The lower soil moisture likely resulted from increased interception and/or evapotranspiration in the older forest stands. This mechanism contrasts alternative explanations focusing on nitrogen dynamics or the composition of methanotrophic communities, although these factors also might be at play. Our findings further imply that the current dramatic increase in forested area increases CH4 uptake in alpine regions.</p>", "keywords": ["2300 General Environmental Science", "2. Zero hunger", "10127 Institute of Evolutionary Biology and Environmental Studies", "13. Climate action", "2304 Environmental Chemistry", "570 Life sciences; biology", "590 Animals (Zoology)", "2306 Global and Planetary Change", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "2303 Ecology", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1111/j.1365-2486.2012.02798.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1365-2486.2012.02798.x", "name": "item", "description": "10.1111/j.1365-2486.2012.02798.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-2486.2012.02798.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-09-07T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:51Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACT                                     <p>               Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s               V               = 0.857, and Theil\uffe2\uff80\uff99s               U               = 0.316). For species-level community profiling, we found strong correlations (               r                                s                              &gt; 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average               r                                s                              = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.             </p>                            IMPORTANCE               <p>A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.</p>", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/10.1128/msystems.00859-24"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00859-24", "name": "item", "description": "10.1128/msystems.00859-24", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00859-24"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "10.1371/journal.pone.0029642", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:18:03Z", "type": "Journal Article", "created": "2012-01-04", "title": "Carbon Stocks And Fluxes In Tropical Lowland Dipterocarp Rainforests In Sabah, Malaysian Borneo", "description": "Deforestation in the tropics is an important source of carbon C release to the atmosphere. To provide a sound scientific base for efforts taken to reduce emissions from deforestation and degradation (REDD+) good estimates of C stocks and fluxes are important. We present components of the C balance for selectively logged lowland tropical dipterocarp rainforest in the Malua Forest Reserve of Sabah, Malaysian Borneo. Total organic C in this area was 167.9 Mg C ha\u207b\u00b9\u00b13.8 (SD), including: Total aboveground (TAGC: 55%; 91.9 Mg C ha\u207b\u00b9\u00b12.9 SEM) and belowground carbon in trees (TBGC: 10%; 16.5 Mg C ha\u207b\u00b9\u00b10.5 SEM), deadwood (8%; 13.2 Mg C ha\u207b\u00b9\u00b13.5 SEM) and soil organic matter (SOM: 24%; 39.6 Mg C ha\u207b\u00b9\u00b10.9 SEM), understory vegetation (3%; 5.1 Mg C ha\u207b\u00b9\u00b11.7 SEM), standing litter (<1%; 0.7 Mg C ha\u207b\u00b9\u00b10.1 SEM) and fine root biomass (<1%; 0.9 Mg C ha\u207b\u00b9\u00b10.1 SEM). Fluxes included litterfall, a proxy for leaf net primary productivity (4.9 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b10.1 SEM), and soil respiration, a measure for heterotrophic ecosystem respiration (28.6 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b11.2 SEM). The missing estimates necessary to close the C balance are wood net primary productivity and autotrophic respiration.Twenty-two years after logging TAGC stocks were 28% lower compared to unlogged forest (128 Mg C ha\u207b\u00b9\u00b113.4 SEM); a combined weighted average mean reduction due to selective logging of -57.8 Mg C ha\u207b\u00b9 (with 95% CI -75.5 to -40.2). Based on the findings we conclude that selective logging decreased the dipterocarp stock by 55-66%. Silvicultural treatments may have the potential to accelerate the recovery of dipterocarp C stocks to pre-logging levels.", "keywords": ["0106 biological sciences", "1000 Multidisciplinary", "Tropical Climate", "Science", "Rain", "Q", "R", "1100 General Agricultural and Biological Sciences", "Biodiversity", "15. Life on land", "01 natural sciences", "Carbon", "Dipterocarpaceae", "Trees", "10127 Institute of Evolutionary Biology and Environmental Studies", "Soil", "1300 General Biochemistry", " Genetics and Molecular Biology", "Borneo", "Seedlings", "13. Climate action", "570 Life sciences; biology", "590 Animals (Zoology)", "Medicine", "Biomass", "Research Article"], "contacts": [{"organization": "Saner, Philippe, Loh, Yen Yee, Ong, Robert C., Hector, Andy,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0029642"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0029642", "name": "item", "description": "10.1371/journal.pone.0029642", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0029642"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-01-03T00:00:00Z"}}, {"id": "10.1890/06-2100.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:18:23Z", "type": "Journal Article", "created": "2007-12-11", "title": "Interactive Effects Of Plant Species Diversity And Elevated Co2 On Soil Biota And Nutrient Cycling", "description": "Terrestrial ecosystems consist of mutually dependent producer and decomposer subsystems, but not much is known on how their interactions are modified by plant diversity and elevated atmospheric CO2 concentrations. Factorially manipulating grassland plant species diversity and atmospheric CO2 concentrations for five years, we tested whether high diversity or elevated CO2 sustain larger or more active soil communities, affect soil aggregation, water dynamics, or nutrient cycling, and whether plant diversity and elevated CO2 interact. Nitrogen (N) and phosphorus (P) pools, symbiotic N2 fixation, plant litter quality, soil moisture, soil physical structure, soil nematode, collembola and acari communities, soil microbial biomass and microflora community structure (phospholipid fatty acid [PLFA] profiles), soil enzyme activities, and rates of C fluxes to soils were measured. No increases in soil C fluxes or the biomass, number, or activity of soil organisms were detected at high plant diversity; soil H2O and aggregation remained unaltered. Elevated CO2 affected the ecosystem primarily by improving plant and soil water status by reducing leaf conductance, whereas changes in C cycling appeared to be of subordinate importance. Slowed-down soil drying cycles resulted in lower soil aggregation under elevated CO2. Collembola benefited from extra soil moisture under elevated CO2, whereas other faunal groups did not respond. Diversity effects and interactions with elevated CO2 may have been absent because soil responses were mainly driven by community-level processes such as rates of organic C input and water use; these drivers were not changed by plant diversity manipulations, possibly because our species diversity gradient did not extend below five species and because functional type composition remained unaltered. Our findings demonstrate that global change can affect soil aggregation, and we advocate that soil aggregation should be considered as a dynamic property that may respond to environmental changes and feed back on other ecosystem functions.", "keywords": ["2. Zero hunger", "Ecology", "Evolution", "Nitrogen", "Water", "Phosphorus", "Biodiversity", "04 agricultural and veterinary sciences", "Carbon Dioxide", "Plants", "15. Life on land", "Carbon", "10127 Institute of Evolutionary Biology and Environmental Studies", "Soil", "1105 Ecology", " Evolution", " Behavior and Systematics", "Oxygen Consumption", "Behavior and Systematics", "Species Specificity", "13. Climate action", "570 Life sciences; biology", "590 Animals (Zoology)", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1890/06-2100.1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1890/06-2100.1", "name": "item", "description": "10.1890/06-2100.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1890/06-2100.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-12-01T00:00:00Z"}}, {"id": "10.17169/refubium-31202", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:18:18Z", "type": "Journal Article", "created": "2021-05-21", "title": "Global data on earthworm abundance, biomass, diversity and corresponding environmental properties", "description": "Abstract<p>Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change.</p>", "keywords": ["2401.17 Invertebrados", "0301 basic medicine", "592", "Data Descriptor", "Ecology and Evolutionary Biology", "earthworms", "Data Descriptor ; Biodiversity ; Biogeography ; Community ecology", "Plan_S-Compliant-OA", "https://purl.org/becyt/ford/1.6", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "Diversity data", "Biomass", "S Agriculture (General)", "Ekologia ja evoluutiobiologia", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "biodiversity", "2. Zero hunger", "maaper\u00e4", "abundance", "Data", "Diversity", "0303 health sciences", "Ecology", "Q", "eli\u00f6yhteis\u00f6t", "Biodiversity", "maaper\u00e4eli\u00f6st\u00f6", "ddc:", "Computer Science Applications", "Biogeography", "2401.06 Ecolog\u00eda animal", "international", "Statistics", " Probability and Uncertainty", "environment/Ecosystems", "Information Systems", "Statistics and Probability", "Ecolog\u00eda (Biolog\u00eda)", "570", "lierot", "Science", "Invertebrados", "577", "Global database", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "Library and Information Sciences", "574", "333", "soil", "eli\u00f6maantiede", "Education", "diversity", "03 medical and health sciences", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "BIODIVERSITY CHANGE", "Life Science", "Earthworms", "Datasets", "Animals", "Community ecology", "Oligochaeta", "https://purl.org/becyt/ford/1", "eartworm", "biogeography", "Ecosystem", "LAND-USE", "biomass", "500", "Biology and Life Sciences", "PLATFORM", "Global dataset", "Oligochaeta/classification", "500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie", "Ecolog\u00eda", "15. Life on land", "biodiversiteetti", "Environmental sciences", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "maaper\u00e4el\u00e4imist\u00f6", "Ecology", " evolutionary biology", "13. Climate action", "Earthworm", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "570 Life sciences; biology", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "eartworm ; abundance ; biomass ; diversity", "COMMUNITIES", "community ecology"]}, "links": [{"href": "https://www.nature.com/articles/s41597-021-00912-z.pdf"}, {"href": "https://pub.epsilon.slu.se/25868/1/phillips_h_r_p_et_al_211019.pdf"}, {"href": "https://boris.unibe.ch/165726/1/48.__Global_data_on_earthworm_abundance__biomass__diversity_and_corresponding_environmental_properties.pdf"}, {"href": "https://www.iris.unict.it/bitstream/20.500.11769/509583/1/SCIENTIFIC%20DATA%20%282021%29%20GLOBAL%20DATA%20ON%20EARTHWORMS.pdf"}, {"href": "https://rau.repository.guildhe.ac.uk/id/eprint/16454/1/Phillips_et_al-2021-Scientific_Data.pdf"}, {"href": "https://doi.org/10.17169/refubium-31202"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Data", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.17169/refubium-31202", "name": "item", "description": "10.17169/refubium-31202", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.17169/refubium-31202"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-05-21T00:00:00Z"}}, {"id": "10.3390/su16031308", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:19:14Z", "type": "Journal Article", "created": "2024-02-05", "title": "Natural/Small Water Retention Measures: Their Contribution to Ecosystem-Based Concepts", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The increasing incidence of droughts and heavy rainfall events is exacerbating conflicts between human and environmental demands for water. However, through providing multiple water-related ecosystem services and benefits simultaneously, Natural/Small Water Retention Measures (NSWRM) can mitigate such competing claims. Thus, they also contribute to the achievement of various Sustainable Development Goals and environmental targets set out in water- and agriculture-related policies of the European Union. In particular, NSWRM provide for the sound management of watersheds, which can significantly contribute to improved water quality and availability\u2014as well as improving the resilience of agriculture and society. This paper demonstrates how NSWRM fit into the framework of ecosystem-based concepts, including Natural Water Retention Measures (NWRM), Green Infrastructure (GI), Sustainable Land Management (SLM), Ecosystem-based Adaptation (EbA), and Nature-based Solutions (NbS). NSWRM, as a distinct concept, bring added value to the other concepts by focussing on easy-to-implement, modestly sized, localised technical solutions to problems associated with water management, sediment, and nutrient loss. Through experience under the EU Horizon 2020 project OPTAIN (\u201cOPtimal strategies to retAIN and re-use water and nutrients in small agricultural catchments across different soil-climatic regions in Europe\u201d), we show what NSWRM are, how they are linked to each of the ecosystem-based concepts, and how they can help add value to these concepts. Fourteen case studies are drawn upon from diverse countries across Europe. As a result of this analysis, we present the potential for the application of NSWRM in the context of these concepts, while helping to identify planning tools, the expertise required, and potential funding mechanisms.</p></article>", "keywords": ["13. Climate action", "11. Sustainability", "570 Life sciences; biology", "15. Life on land", "01 natural sciences", "6. Clean water", "12. Responsible consumption", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://boris.unibe.ch/193071/1/Magnier_et-al_2024_Natural-Small_Water_Retention_Measures__Their_Contribution_to_Ecosystem-Based_Concepts.pdf"}, {"href": "https://doi.org/10.3390/su16031308"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sustainability", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/su16031308", "name": "item", "description": "10.3390/su16031308", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/su16031308"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-04T00:00:00Z"}}, {"id": "10.48350/193071", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:19:24Z", "type": "Journal Article", "created": "2024-02-05", "title": "Natural/Small Water Retention Measures: Their Contribution to Ecosystem-Based Concepts", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The increasing incidence of droughts and heavy rainfall events is exacerbating conflicts between human and environmental demands for water. However, through providing multiple water-related ecosystem services and benefits simultaneously, Natural/Small Water Retention Measures (NSWRM) can mitigate such competing claims. Thus, they also contribute to the achievement of various Sustainable Development Goals and environmental targets set out in water- and agriculture-related policies of the European Union. In particular, NSWRM provide for the sound management of watersheds, which can significantly contribute to improved water quality and availability\u2014as well as improving the resilience of agriculture and society. This paper demonstrates how NSWRM fit into the framework of ecosystem-based concepts, including Natural Water Retention Measures (NWRM), Green Infrastructure (GI), Sustainable Land Management (SLM), Ecosystem-based Adaptation (EbA), and Nature-based Solutions (NbS). NSWRM, as a distinct concept, bring added value to the other concepts by focussing on easy-to-implement, modestly sized, localised technical solutions to problems associated with water management, sediment, and nutrient loss. Through experience under the EU Horizon 2020 project OPTAIN (\u201cOPtimal strategies to retAIN and re-use water and nutrients in small agricultural catchments across different soil-climatic regions in Europe\u201d), we show what NSWRM are, how they are linked to each of the ecosystem-based concepts, and how they can help add value to these concepts. Fourteen case studies are drawn upon from diverse countries across Europe. As a result of this analysis, we present the potential for the application of NSWRM in the context of these concepts, while helping to identify planning tools, the expertise required, and potential funding mechanisms.</p></article>", "keywords": ["13. Climate action", "11. Sustainability", "570 Life sciences; biology", "15. Life on land", "01 natural sciences", "6. Clean water", "0105 earth and related environmental sciences", "12. Responsible consumption"]}, "links": [{"href": "https://boris.unibe.ch/193071/1/Magnier_et-al_2024_Natural-Small_Water_Retention_Measures__Their_Contribution_to_Ecosystem-Based_Concepts.pdf"}, {"href": "https://www.mdpi.com/2071-1050/16/3/1308/pdf"}, {"href": "https://doi.org/10.48350/193071"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sustainability", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.48350/193071", "name": "item", "description": "10.48350/193071", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.48350/193071"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-04T00:00:00Z"}}, {"id": "10045/75093", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:21:36Z", "type": "Journal Article", "created": "2018-04-16", "title": "Intransitive competition is common across five major taxonomic groups and is driven by productivity, competitive rank and functional traits", "description": "Abstract<p><p>Competition can be fully hierarchical or intransitive, and this degree of hierarchy is driven by multiple factors, including environmental conditions, the functional traits of the species involved or the topology of competition networks. Studies simultaneously analysing these drivers of competition hierarchy are rare. Additionally, organisms compete either directly or via interference competition for resources or space, within a local neighbourhood or across the habitat. Therefore, the drivers of competition could change accordingly and depend on the taxa studied.</p><p>We performed the first multi\uffe2\uff80\uff90taxon study on pairwise competition across major taxonomic groups, including experiments with vascular plants, mosses, saprobic fungi, aquatic protists and soil bacteria. We evaluated how general is competition intransitivity from the pairwise competition matrix including all species and also for each possible three\uffe2\uff80\uff90species combination (triplets). We then examined which species were likely to engage in competitive loops and the effects of environmental conditions, competitive rank and functional traits on intransitive competition.</p><p>We found some degree of competition intransitivity in all taxa studied, with 38% to 5% of triplets being intransitive. Variance in competitive rank between species and more fertile conditions strongly reduced intransitivity, with triplets composed of species differing widely in their competitive ranks much less likely to be intransitive.</p><p>Including functional traits of the species involved more than doubled the variation explained compared to models including competitive rank only. Both trait means and variance within triplets affected the odds of them being intransitive. However, the traits responsible and the direction of trait effects varied widely between taxa, suggesting that traits can have a wide variety of effects on competition.</p><p>Synthesis. We evaluated the drivers of competition across multiple taxa and showed that productivity and competitive rank are fundamental drivers of intransitivity. We also showed that not only the functional traits of each species, but also those of the accompanying species, determine competition intransitivity. Intransitive competition is common across multiple taxa but can dampen under fertile conditions or for those species with large variance in their competitive abilities. This provides a first step towards predicting the prevalence of intransitive competition in natural communities.</p></p", "keywords": ["saprobic fungi", "0106 biological sciences", "01 natural sciences", "10127 Institute of Evolutionary Biology and Environmental Studies", "bryophytes", "XXXXXX - Unknown", "Competition hierarchy", "1110 Plant Science", "competition hierarchy", "functional traits", "vascular plants", "bacteria", "580", "protists", "Bacteria", "Vascular plants", "Bryophytes", "Saprobic fungi", "rock\u2013paper\u2013scissors", "Protists", "Ecolog\u00eda", "15. Life on land", "1105 Ecology", " Evolution", " Behavior and Systematics", "570 Life sciences; biology", "590 Animals (Zoology)", "competition", "Rock\u2013paper\u2013scissors", "2303 Ecology", "Functional traits"]}, "links": [{"href": "https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.12959"}, {"href": "https://doi.org/10045/75093"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10045/75093", "name": "item", "description": "10045/75093", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10045/75093"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-16T00:00:00Z"}}, {"id": "PMC11494973", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:24:20Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACT                                                             <p>                       Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s                       V                       = 0.857, and Theil\uffe2\uff80\uff99s                       U                       = 0.316). For species-level community profiling, we found strong correlations (                       r                                                s                                              &gt; 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average                       r                                                s                                              = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.                     </p>                                            IMPORTANCE                       <p>A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.</p>", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/PMC11494973"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11494973", "name": "item", "description": "PMC11494973", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11494973"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "PMC8963283", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-09-20T16:24:25Z", "type": "Journal Article", "created": "2022-01-26", "title": "GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis", "description": "Abstract                                   Motivation                   <p>Analysis of focal copy number variations (CNVs) is highly relevant for cancer research, as they pinpoint driver genes. More specifically, due to selective pressure oncogenes and tumor suppressor genes are more often affected by these events than neighboring passengers. In cases where multiple candidates co-reside in a genomic locus, careful comparison is required to either identify multigenic minimally deleted regions of synergistic co-mutations, or the true single driver gene. The study of focal CNVs in large cancer genome cohorts requires specialized visualization and statistical analysis.</p>                                                   Results                   <p>We developed the GenomeTornadoPlot R-package which generates gene-centric visualizations of CNV types, locations and lengths from cohortwise NGS data. Furthermore, the software enables the pairwise comparison of proximate genes to identify co-mutation patterns or driver-passenger hierarchies. The visual examination provided by GenomeTornadoPlot is further supported by adaptable local and global focality scoring. Integrated into the GenomeTornadoPlot R-Package is the comprehensive PCAWG database of CNVs, comprising 2976 cancer genome entities from 46 cohorts of the Pan-cancer Analysis of Whole Genomes project. The GenomeTornadoPlot R-package can be used to perform exploratory or hypothesis-driven analyses on the basis of the PCAWG data or in combination with data provided by the user.</p>                                                   Availability and implementation                   <p>GenomeTornadoPlot is written in R script and released via github: &amp;lt;https://github.com/chenhong-dkfz/GenomeTornadoPlot/&amp;gt;. The package is under the license of GPL-3.0.</p>", "keywords": ["570", "DNA Copy Number Variations", "ddc-570", "Genomics", "Oncogenes", "004 Data processing Computer science", "Software", "004", "570 Life sciences", "ddc-004", "3. Good health"]}, "links": [{"href": "https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/34483/1/btac037.pdf"}, {"href": "https://archiv.ub.uni-heidelberg.de/volltextserver/34483/1/btac037.pdf"}, {"href": "https://academic.oup.com/bioinformatics/article-pdf/38/7/2036/49009547/btac037.pdf"}, {"href": "https://doi.org/PMC8963283"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC8963283", "name": "item", "description": "PMC8963283", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC8963283"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-31T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=570+Life+sciences&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=570+Life+sciences&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=570+Life+sciences&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=570+Life+sciences&offset=19", "hreflang": "en-US"}], "numberMatched": 19, "numberReturned": 19, "distributedFeatures": [], "timeStamp": "2026-09-21T03:49:18.383482Z"}