{"type": "FeatureCollection", "features": [{"id": "10.1007/s00442-012-2578-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:14:23Z", "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": "10.1002/ecy.2137", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:13:54Z", "type": "Journal Article", "created": "2018-01-10", "title": "Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere", "description": "Abstract<p>The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co\uffe2\uff80\uff90occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co\uffe2\uff80\uff90occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.</p", "keywords": ["0301 basic medicine", "Terrestrial Ecosystems", "archaea", "Evolution", "Eukaryotes", "Antarctic Regions", "1105 Ecology", "Biodiversity; Terrestrial Ecosystems; Archaea; Bacteria; Eukaryotes; Australia; Antarctica.", "Terrestrial ecosystems", "Soil", "03 medical and health sciences", "eukaryotes", "Behavior and Systematics", "XXXXXX - Unknown", "14. Life underwater", "bacteria", "Phylogeny", "Soil Microbiology", "biodiversity", "2. Zero hunger", "0303 health sciences", "Bacteria", "Australia", "terrestrial ecosystems", "Biodiversity", "15. Life on land", "archaebacteria", "Archaea", "soil ecology", "13. Climate action", "eukaryotic cells", "Antarctica"]}, "links": [{"href": "https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2137"}, {"href": "https://doi.org/10.1002/ecy.2137"}, {"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": "10.1002/ecy.2137", "name": "item", "description": "10.1002/ecy.2137", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecy.2137"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-12T00:00:00Z"}}, {"id": "10.1038/s41559-022-01756-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:40Z", "type": "Journal Article", "created": "2022-05-09", "title": "Phylotype diversity within soil fungal functional groups drives ecosystem stability", "description": "Soil fungi are fundamental to plant productivity, yet their influence on the temporal stability of global terrestrial ecosystems, and their capacity to buffer plant productivity against extreme drought events, remain uncertain. Here we combined three independent global field surveys of soil fungi with a satellite-derived temporal assessment of plant productivity, and report that phylotype richness within particular fungal functional groups drives the stability of terrestrial ecosystems. The richness of fungal decomposers was consistently and positively associated with ecosystem stability worldwide, while the opposite pattern was found for the richness of fungal plant pathogens, particularly in grasslands. We further demonstrated that the richness of soil decomposers was consistently positively linked with higher resistance of plant productivity in response to extreme drought events, while that of fungal plant pathogens showed a general negative relationship with plant productivity resilience/resistance patterns. Together, our work provides evidence supporting the critical role of soil fungal diversity to secure stable plant production over time in global ecosystems, and to buffer against extreme climate events.", "keywords": ["0301 basic medicine", "Evolution", "Resistance", "580 Plants (Botany)", "Soil", "03 medical and health sciences", "10126 Department of Plant and Microbial Biology", "Behavior and Systematics", "Soil fungal", "XXXXXX - Unknown", "10211 Zurich-Basel Plant Science Center", "Phylotype diversity", "Ecosystem", "Soil Microbiology", "Productivity", "2. Zero hunger", "0303 health sciences", "Ecology", "Biodiversity", "Ecolog\u00eda", "Plants", "15. Life on land", "Protect", " restore and promote sustainable use of terrestrial ecosystems", " sustainably manage forests", " combat\u00a0desertification", " and halt and reverse land degradation and halt biodiversity loss", "Droughts", "1105 Ecology", " Evolution", " Behavior and Systematics", "13. Climate action", "Ecosystem stability", "http://metadata.un.org/sdg/15", "2303 Ecology"]}, "links": [{"href": "https://www.nature.com/articles/s41559-022-01756-5.pdf"}, {"href": "https://doi.org/10.1038/s41559-022-01756-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Ecology%20%26amp%3B%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41559-022-01756-5", "name": "item", "description": "10.1038/s41559-022-01756-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41559-022-01756-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-09T00:00:00Z"}}, {"id": "10.1071/bt04154", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:55Z", "type": "Journal Article", "created": "2005-11-30", "title": "Changes In Soil Carbon And Soil Nitrogen After Tree Clearing In The Semi-Arid Rangelands Of Queensland", "description": "<p>  Changes in soil carbon (C) and nitrogen (N) stocks following tree clearing were estimated at 32 rangeland sites in central and southern Queensland by using paired-site sampling. When corrected for soil bulk-density differences at each site, average soil C across all sites decreased after tree clearing by 8.0% for 0\uffe2\uff80\uff930.3-m soil depth, and by 5.4% for 0\uffe2\uff80\uff931.0-m depth; there were corresponding declines in soil C of 2.5 and 3.5tha\uffe2\uff80\uff931, respectively. Mean soil C stocks (excluding surface litter, extractable roots and coarse charcoal) at uncleared sites were 29.5tha\uffe2\uff80\uff931 for 0\uffe2\uff80\uff930.3-m soil depth, and 62.5tha\uffe2\uff80\uff931 for 0\uffe2\uff80\uff931.0-m depth. Mean soil C stocks (0\uffe2\uff80\uff930.3m) were 41% of the mean total C for the soil\uffe2\uff80\uff93plant system (soil + litter/woody debris + stand biomass) at uncleared sites. Soil C decline (0\uffe2\uff80\uff930.3m) accounted for approximately 7% of the average total C lost because of land clearing across all sites. Soil C stocks at uncleared sites were correlated with tree basal area, clay content and soil phosphorus (P) content. Changes in soil C after tree clearing were strongly correlated to initial soil C contents at the uncleared sites, and were associated with particular vegetation groups and soil types. Changes in soil N were strongly correlated with changes in soil C; however, the average change in soil N across all sites was not significant. Given the size of the C and N pools in rangeland soils, the factors that influence soil C and soil N dynamics in rangeland systems need to be better understood for the effective management of C stocks in these soils. </p>", "keywords": ["Ecology", "Behavior and Systematics", "Evolution", "1110 Plant Science", "0401 agriculture", " forestry", " and fisheries", "Plant Science", "04 agricultural and veterinary sciences", "15. Life on land", "1105 Ecology"]}, "links": [{"href": "https://doi.org/10.1071/bt04154"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Australian%20Journal%20of%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1071/bt04154", "name": "item", "description": "10.1071/bt04154", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1071/bt04154"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-01-01T00:00:00Z"}}, {"id": "10.1111/1365-2745.12959", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:31Z", "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", "bacteria", " bryophytes", " competition hierarchy", " coexistence", " functional traits", " protists", " rock-paper-scissors", " saprobic fungi", " vascular plants", "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/10.1111/1365-2745.12959"}, {"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": "10.1111/1365-2745.12959", "name": "item", "description": "10.1111/1365-2745.12959", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1365-2745.12959"}, {"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": "10.1111/ddi.13146", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:33Z", "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": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:09Z", "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": "10.1890/06-2100.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:52Z", "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": "10.5194/bg-19-3505-2022", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:21:38Z", "type": "Journal Article", "created": "2022-07-28", "title": "Reviews and syntheses: The promise of big diverse soil data, moving current practices towards future potential", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Abstract. In the age of big data, soil data are more available and richer than ever, but \u2013 outside of a few large soil survey resources \u2013 they remain largely unusable for informing soil management and understanding Earth system processes beyond the original study. Data science has promised a fully reusable research pipeline where data from past studies are used to contextualize new findings and reanalyzed for new insight. Yet synthesis projects encounter challenges at all steps of the data reuse pipeline, including unavailable data, labor-intensive transcription of datasets, incomplete metadata, and a lack of communication between collaborators. Here, using insights from a diversity of soil, data, and climate scientists, we summarize current practices in soil data synthesis across all stages of database creation: availability, input, harmonization, curation, and publication. We then suggest new soil-focused semantic tools to improve existing data pipelines, such as ontologies, vocabulary lists, and community practices. Our goal is to provide the soil data community with an overview of current practices in soil data and where we need to go to fully leverage big data to solve soil problems in the next century.                     </p></article>", "keywords": ["FOS: Computer and information sciences", "0301 basic medicine", "Data Sharing", "Information Systems and Management", "literature review", "1904 Earth-Surface Processes", "Social Sciences", "data set", "01 natural sciences", "Decision Sciences", "Data science", "Life", "QH501-531", "910 Geography & travel", "soil analysis", "database", "QH540-549.5", "2. Zero hunger", "QE1-996.5", "000", "Ecology", "communication", "Physics", "Earth", "Geology", "[SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces", " environment", "World Wide Web", "10122 Institute of Geography", "soil survey", "Physical Sciences", "Data Reuse", "environment", "Information Systems", "Evolution", "future prospect", "Data management", "Data Sharing and Stewardship in Science", "Database", "Big data", "03 medical and health sciences", "Behavior and Systematics", "Data mining", "0105 earth and related environmental sciences", "[SDU.OCEAN]Sciences of the Universe [physics]/Ocean", "Management and Reproducibility of Scientific Workflows", "Metadata", "Data curation", "Atmosphere", "[SDU.OCEAN] Sciences of the Universe [physics]/Ocean", " Atmosphere", "Acoustics", "15. Life on land", "Computer science", "1105 Ecology", " Evolution", " Behavior and Systematics", "Surface Processes", "Harmonization", "FOS: Biological sciences", "Computer Science", "Environmental Science", "[SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces", "soil management", "Research Data", "Environmental DNA in Biodiversity Monitoring"]}, "links": [{"href": "https://doi.org/10.5194/bg-19-3505-2022"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biogeosciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.5194/bg-19-3505-2022", "name": "item", "description": "10.5194/bg-19-3505-2022", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5194/bg-19-3505-2022"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-28T00:00:00Z"}}, {"id": "10045/75093", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:24:24Z", "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": "1959.7/uws:68562", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:07Z", "type": "Journal Article", "created": "2022-05-09", "title": "Phylotype diversity within soil fungal functional groups drives ecosystem stability", "description": "Soil fungi are fundamental to plant productivity, yet their influence on the temporal stability of global terrestrial ecosystems, and their capacity to buffer plant productivity against extreme drought events, remain uncertain. Here we combined three independent global field surveys of soil fungi with a satellite-derived temporal assessment of plant productivity, and report that phylotype richness within particular fungal functional groups drives the stability of terrestrial ecosystems. The richness of fungal decomposers was consistently and positively associated with ecosystem stability worldwide, while the opposite pattern was found for the richness of fungal plant pathogens, particularly in grasslands. We further demonstrated that the richness of soil decomposers was consistently positively linked with higher resistance of plant productivity in response to extreme drought events, while that of fungal plant pathogens showed a general negative relationship with plant productivity resilience/resistance patterns. Together, our work provides evidence supporting the critical role of soil fungal diversity to secure stable plant production over time in global ecosystems, and to buffer against extreme climate events.", "keywords": ["0301 basic medicine", "Evolution", "Resistance", "580 Plants (Botany)", "Soil", "03 medical and health sciences", "10126 Department of Plant and Microbial Biology", "Behavior and Systematics", "Soil fungal", "XXXXXX - Unknown", "10211 Zurich-Basel Plant Science Center", "Phylotype diversity", "Ecosystem", "Soil Microbiology", "Productivity", "2. Zero hunger", "0303 health sciences", "Ecology", "Biodiversity", "Ecolog\u00eda", "Plants", "15. Life on land", "Droughts", "Protect", " restore and promote sustainable use of terrestrial ecosystems", " sustainably manage forests", " combat desertification", " and halt and reverse land degradation and halt biodiversity loss", "1105 Ecology", " Evolution", " Behavior and Systematics", "13. Climate action", "Ecosystem stability", "http://metadata.un.org/sdg/15", "2303 Ecology"]}, "links": [{"href": "https://www.nature.com/articles/s41559-022-01756-5.pdf"}, {"href": "https://doi.org/1959.7/uws:68562"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Ecology%20%26amp%3B%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1959.7/uws:68562", "name": "item", "description": "1959.7/uws:68562", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1959.7/uws:68562"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-09T00:00:00Z"}}, {"id": "20.500.11850/562259", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:14Z", "type": "Journal Article", "created": "2022-07-28", "title": "Reviews and syntheses: The promise of big diverse soil data, moving current practices towards future potential", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Abstract. In the age of big data, soil data are more available and richer than ever, but \u2013 outside of a few large soil survey resources \u2013 they remain largely unusable for informing soil management and understanding Earth system processes beyond the original study. Data science has promised a fully reusable research pipeline where data from past studies are used to contextualize new findings and reanalyzed for new insight. Yet synthesis projects encounter challenges at all steps of the data reuse pipeline, including unavailable data, labor-intensive transcription of datasets, incomplete metadata, and a lack of communication between collaborators. Here, using insights from a diversity of soil, data, and climate scientists, we summarize current practices in soil data synthesis across all stages of database creation: availability, input, harmonization, curation, and publication. We then suggest new soil-focused semantic tools to improve existing data pipelines, such as ontologies, vocabulary lists, and community practices. Our goal is to provide the soil data community with an overview of current practices in soil data and where we need to go to fully leverage big data to solve soil problems in the next century.</p></article>", "keywords": ["FOS: Computer and information sciences", "0301 basic medicine", "Data Sharing", "Information Systems and Management", "literature review", "1904 Earth-Surface Processes", "Social Sciences", "data set", "01 natural sciences", "Decision Sciences", "Data science", "Life", "QH501-531", "910 Geography & travel", "soil analysis", "database", "QH540-549.5", "2. Zero hunger", "QE1-996.5", "000", "Ecology", "communication", "Physics", "Earth", "Geology", "[SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces", " environment", "World Wide Web", "10122 Institute of Geography", "soil survey", "Physical Sciences", "Data Reuse", "environment", "Information Systems", "Evolution", "future prospect", "Data management", "Data Sharing and Stewardship in Science", "Database", "Big data", "03 medical and health sciences", "Behavior and Systematics", "Data mining", "0105 earth and related environmental sciences", "[SDU.OCEAN]Sciences of the Universe [physics]/Ocean", "Management and Reproducibility of Scientific Workflows", "Metadata", "Data curation", "Atmosphere", "[SDU.OCEAN] Sciences of the Universe [physics]/Ocean", " Atmosphere", "Acoustics", "15. Life on land", "Computer science", "1105 Ecology", " Evolution", " Behavior and Systematics", "Surface Processes", "Harmonization", "FOS: Biological sciences", "Computer Science", "Environmental Science", "[SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces", "soil management", "Research Data", "Environmental DNA in Biodiversity Monitoring"]}, "links": [{"href": "https://doi.org/20.500.11850/562259"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biogeosciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.11850/562259", "name": "item", "description": "20.500.11850/562259", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.11850/562259"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-28T00:00:00Z"}}, {"id": "2440/132742", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:25:32Z", "type": "Journal Article", "created": "2018-01-10", "title": "Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere", "description": "Abstract<p>The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co\uffe2\uff80\uff90occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co\uffe2\uff80\uff90occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.</p", "keywords": ["0301 basic medicine", "Terrestrial Ecosystems", "archaea", "Evolution", "Eukaryotes", "Antarctic Regions", "1105 Ecology", "Terrestrial ecosystems", "Soil", "03 medical and health sciences", "eukaryotes", "Behavior and Systematics", "XXXXXX - Unknown", "14. Life underwater", "bacteria", "Phylogeny", "Soil Microbiology", "biodiversity", "2. Zero hunger", "0303 health sciences", "Bacteria", "Australia", "terrestrial ecosystems", "Biodiversity", "15. Life on land", "archaebacteria", "Archaea", "soil ecology", "13. Climate action", "eukaryotic cells", "Antarctica"]}, "links": [{"href": "https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2137"}, {"href": "https://doi.org/2440/132742"}, {"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": "2440/132742", "name": "item", "description": "2440/132742", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2440/132742"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-12T00:00:00Z"}}, {"id": "PMC11494973", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:28:00Z", "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"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=1105+Ecology&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=1105+Ecology&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=1105+Ecology&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=1105+Ecology&offset=14", "hreflang": "en-US"}], "numberMatched": 14, "numberReturned": 14, "distributedFeatures": [], "timeStamp": "2026-05-26T06:21:03.577186Z"}