{"type": "FeatureCollection", "features": [{"id": "10.1002/sae2.12031", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:14:16Z", "type": "Journal Article", "created": "2022-11-12", "title": "Frontiers in soil ecology\u2014Insights from the World Biodiversity Forum 2022", "description": "Abstract<p>Global change is affecting soil biodiversity and functioning across all terrestrial ecosystems. Still, much is unknown about how soil biodiversity and function will change in the future in response to simultaneous alterations in climate and land use, as well as other environmental drivers. It is crucial to understand the direct, indirect\uffc2\uffa0and interactive effects of global change drivers on soil communities and ecosystems across environmental contexts, not only today but also in the near future. This is particularly relevant for international efforts to tackle climate change like the Paris Agreement, and considering the failure to achieve the 2020 biodiversity targets, especially the target of halting soil degradation. Here, we outline the main frontiers related to soil ecology that were presented and discussed at the thematic sessions of the World Biodiversity Forum 2022 in Davos, Switzerland. We highlight multiple frontiers of knowledge associated with data integration, causal inference, soil biodiversity and function scenarios, critical soil biodiversity facets, underrepresented drivers, global collaboration, knowledge application and transdisciplinarity, as well as policy and public communication. These identified research priorities are not only of immediate interest to the scientific community but may also be considered in research priority programmes and calls for funding.</p", "keywords": ["[SDE] Environmental Sciences", "0301 basic medicine", "570", "Agriculture (General)", "577", "soil biodiversity", "scenario modelling", "580 Plants (Botany)", "S1-972", "03 medical and health sciences", "10126 Department of Plant and Microbial Biology", "11. Sustainability", "Life Science", "GE1-350", "10211 Zurich-Basel Plant Science Center", "Biology", "soil macroecology", "Biodiversity change", "2. Zero hunger", "Soil macroecology", "0303 health sciences", "15. Life on land", "Scenario modelling", "Soil biodiversity", "6. Clean water", "Environmental sciences", "biodiversity change", "13. Climate action", "ecosystem functioning", "[SDE]Environmental Sciences", "Ecosystem functioning", "ta1181"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/sae2.12031"}, {"href": "https://doi.org/10.1002/sae2.12031"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Sustainable%20Agriculture%20and%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/sae2.12031", "name": "item", "description": "10.1002/sae2.12031", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/sae2.12031"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-11T00:00:00Z"}}, {"id": "10.1007/s11104-008-9853-4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:05Z", "type": "Journal Article", "created": "2008-12-19", "title": "White Lupin Leads To Increased Maize Yield Through A Soil Fertility-Independent Mechanism: A New Candidate For Fighting Striga Hermonthica Infestation?", "description": "Open AccessISSN:0032-079X", "keywords": ["2. Zero hunger", "Lupinus albus; Desmodium uncinatum; Striga hermonthica; Zea mays; Soil fertility; Cluster roots", "04 agricultural and veterinary sciences", "580 Plants (Botany)", "15. Life on land", "Soil fertility", "Zea mays", "Cluster roots", "10126 Department of Plant and Microbial Biology", "Lupinus albus", "Desmodium uncinatum", "1110 Plant Science", "Striga hermonthica", "0401 agriculture", " forestry", " and fisheries", "1111 Soil Science"]}, "links": [{"href": "https://doi.org/10.1007/s11104-008-9853-4"}, {"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/s11104-008-9853-4", "name": "item", "description": "10.1007/s11104-008-9853-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-008-9853-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-12-20T00:00:00Z"}}, {"id": "10.1093/femsec/fiv066", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:57Z", "type": "Journal Article", "created": "2015-06-20", "title": "Effects Of Warming And Drought On Potential N2o Emissions And Denitrifying Bacteria Abundance In Grasslands With Different Land-Use", "description": "Increased warming in spring and prolonged summer drought may alter soil microbial denitrification. We measured potential denitrification activity and denitrifier marker gene abundances (nirK, nirS, nosZ) in grasslands soils in three geographic regions characterized by site-specific land-use indices (LUI) after warming in spring, at an intermediate sampling and after summer drought. Potential denitrification was significantly increased by warming, but did not persist over the intermediate sampling. At the intermediate sampling, the relevance of grassland land-use intensity was reflected by increased potential N2O production at sites with higher LUI. Abundances of total bacteria did not respond to experimental warming or drought treatments, displaying resilience to minor and short-term effects of climate change. In contrast, nirS- and nirK-type denitrifiers were more influenced by drought in combination with LUI and pH, while the nosZ abundance responded to the summer drought manipulation. Land-use was a strong driver for potential denitrification as grasslands with higher LUI also had greater potentials for N2O emissions. We conclude that both warming and drought affected the denitrifying communities and the potential denitrification in grassland soils. However, these effects are overruled by regional and site-specific differences in soil chemical and physical properties which are also related to grassland land-use intensity.", "keywords": ["0301 basic medicine", "570", "UFSP13-8 Global Change and Biodiversity", "Climate Change", "Microbial Consortia", "580 Plants (Botany)", "Nitric Oxide", "142-005 142-005", "Soil", "03 medical and health sciences", "potential N2O emissions", "RNA", " Ribosomal", " 16S", "2402 Applied Microbiology and Biotechnology", "use index", "Soil Microbiology", "2. Zero hunger", "Biodiversity Exploratories", "denitrification", "Bacteria", "2404 Microbiology", "04 agricultural and veterinary sciences", "15. Life on land", "Grassland", "6. Clean water", "Droughts", "land", "climate change", "Genes", " Bacterial", "13. Climate action", "8. Economic growth", "Denitrification", "0401 agriculture", " forestry", " and fisheries", "grassland", "microbial community", "2303 Ecology"]}, "links": [{"href": "https://doi.org/10.1093/femsec/fiv066"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiv066", "name": "item", "description": "10.1093/femsec/fiv066", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiv066"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-06-19T00:00:00Z"}}, {"id": "10.1038/s41477-023-01583-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:13Z", "type": "Journal Article", "created": "2023-12-04", "title": "Subtilase-mediated biogenesis of the expanded family of SERINE RICH ENDOGENOUS PEPTIDES", "description": "Plant signalling peptides are typically released from larger precursors by proteolytic cleavage to regulate plant growth, development and stress responses. Recent studies reported the characterization of a divergent family of Brassicaceae-specific peptides, SERINE RICH ENDOGENOUS PEPTIDES (SCOOPs), and their perception by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2). Here, we reveal that the SCOOP family is highly expanded, containing at least 50 members in the Columbia-0 reference Arabidopsis thaliana genome. Notably, perception of these peptides is strictly MIK2-dependent. How bioactive SCOOP peptides are produced, and to what extent their perception is responsible for the multiple physiological roles associated with MIK2 are currently unclear. Using N-terminomics, we validate the N-terminal cleavage site of representative PROSCOOPs. The cleavage sites are determined by conserved motifs upstream of the minimal SCOOP bioactive epitope. We identified subtilases necessary and sufficient to process PROSCOOP peptides at conserved cleavage motifs. Mutation of these subtilases, or their recognition motifs, suppressed PROSCOOP cleavage and associated overexpression phenotypes. Furthermore, we show that higher-order mutants of these subtilases show phenotypes reminiscent of mik2 null mutant plants, consistent with impaired PROSCOOP biogenesis, and demonstrating biological relevance of SCOOP perception by MIK2. Together, this work provides insights into the molecular mechanisms underlying the functions of the recently identified SCOOP peptides and their receptor MIK2.", "keywords": ["570", "Arabidopsis Proteins", "[SDV]Life Sciences [q-bio]", "Arabidopsis", "Receptors", " Cell Surface", "580 Plants (Botany)", "[SDV] Life Sciences [q-bio]", "10126 Department of Plant and Microbial Biology", "1110 Plant Science", "Taverne", "Brassicaceae", "Serine", "Life Science", "10211 Zurich-Basel Plant Science Center", "Peptides", "Protein Kinases"]}, "links": [{"href": "https://www.nature.com/articles/s41477-023-01583-x.pdf"}, {"href": "https://hal.science/hal-04394015/file/NaturePlants_subtilase_scoop_2023_revised.pdf"}, {"href": "https://doi.org/10.1038/s41477-023-01583-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Plants", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41477-023-01583-x", "name": "item", "description": "10.1038/s41477-023-01583-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41477-023-01583-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-04T00:00:00Z"}}, {"id": "10.1038/s41559-022-01756-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:14Z", "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": "10.1073/pnas.2309881120", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:39Z", "type": "Journal Article", "created": "2024-01-08", "title": "Extreme drought impacts have been underestimated in grasslands and shrublands globally", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Climate change is increasing the frequency and severity of short-term (~1 y) drought events\u2014the most common duration of drought\u2014globally. Yet the impact of this intensification of drought on ecosystem functioning remains poorly resolved. This is due in part to the widely disparate approaches ecologists have employed to study drought, variation in the severity and duration of drought studied, and differences among ecosystems in vegetation, edaphic and climatic attributes that can mediate drought impacts. To overcome these problems and better identify the factors that modulate drought responses, we used a coordinated distributed experiment to quantify the impact of short-term drought on grassland and shrubland ecosystems. With a standardized approach, we imposed ~a single year of drought at 100 sites on six continents. Here we show that loss of a foundational ecosystem function\u2014aboveground net primary production (ANPP)\u2014was 60% greater at sites that experienced statistically extreme drought (1-in-100-y event) vs. those sites where drought was nominal (historically more common) in magnitude (35% vs. 21%, respectively). This reduction in a key carbon cycle process with a single year of extreme drought greatly exceeds previously reported losses for grasslands and shrublands. Our global experiment also revealed high variability in drought response but that relative reductions in ANPP were greater in drier ecosystems and those with fewer plant species. Overall, our results demonstrate with unprecedented rigor that the global impacts of projected increases in drought severity have been significantly underestimated and that drier and less diverse sites are likely to be most vulnerable to extreme drought.</p></article>", "keywords": ["[SDE] Environmental Sciences", "Medical Sciences", "Drought Severity", "550", "580 Plants (Botany)", "551", "Tierras de Matorral", "Medical Specialties", "Medicine and Health Sciences", "SDG 13 - Climate Action", "climate extreme | Drought-Net | International Drought Experiment | productivity", "Productividad Primaria Neta", "Net Primary Productivity", "Productivity", "2. Zero hunger", "Praderas", "Productividad", "Life Sciences", "Biological Sciences", "Grassland", "6. Clean water", "Droughts", "Grasslands", "[SDE]Environmental Sciences", "Drought-Net", "Public Health", "International Drought Experiment", "Ciclo del Carbono", "Severidad de la Sequ\u00eda", "Global Impacts", "productivity", "Climate Change", "climate extreme", "333", "Carbon Cycle", "Environmental Public Health", "XXXXXX - Unknown", "Impacto Global", "Scrublands", "General", "Biology", "Ecosystem", "Experimento internacional de Sequ\u00eda", "500", "Receptor Protein-Tyrosine Kinases", "15. Life on land", "Clima Extremo", "Climate Science", "13. Climate action", "Cambio Clim\u00e1tico", "Extreme Climate", "Climate extreme", "Klimatvetenskap"]}, "links": [{"href": "https://boris.unibe.ch/191349/1/smith-et-al-2024-extreme-drought-impacts-have-been-underestimated-in-grasslands-and-shrublands-globally.pdf"}, {"href": "https://escholarship.org/content/qt9b707158/qt9b707158.pdf"}, {"href": "https://doi.org/10.1073/pnas.2309881120"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.2309881120", "name": "item", "description": "10.1073/pnas.2309881120", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.2309881120"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-08T00:00:00Z"}}, {"id": "10.1111/gcb.16989", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:24Z", "type": "Journal Article", "created": "2023-10-27", "title": "Shifts in soil ammonia\u2010oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions", "description": "Abstract<p>Anthropogenic nitrogen (N) loading alters soil ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize\uffc2\uffa068 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N\uffe2\uff80\uff90stimulation of nitrification, but does so via climate\uffe2\uff80\uff90related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N\uffe2\uff80\uff90availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate\uffe2\uff80\uff90related shifts in soil ammonia\uffe2\uff80\uff90oxidizing community maintain the N\uffe2\uff80\uff90stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.</p", "keywords": ["550", "Nitrogen", "2306 Global and Planetary Change", "ammonia oxidizers", "580 Plants (Botany)", "nitrogen addition", "333", "Nitrogen/analysis", "2300 General Environmental Science", "Soil", "10126 Department of Plant and Microbial Biology", "Ammonia", "Climate change", "10211 Zurich-Basel Plant Science Center", "Soil Microbiology", "Phylogeny", "Soil/chemistry", "2. Zero hunger", "Nitrogen addition", "info:eu-repo/classification/ddc/550", "ddc:550", "Microbial community structure", "15. Life on land", "Nitrification", "Archaea", "6. Clean water", "nitrification", "Ammonia oxidizers", "Earth sciences", "climate change", "13. Climate action", "microbial community structure", "2304 Environmental Chemistry", "soil properties", "Soil properties", "2303 Ecology", "Oxidation-Reduction"]}, "links": [{"href": "https://doi.org/10.1111/gcb.16989"}, {"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.16989", "name": "item", "description": "10.1111/gcb.16989", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.16989"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-27T00:00:00Z"}}, {"id": "10.1371/journal.pone.0051818", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:20:14Z", "type": "Journal Article", "created": "2012-12-20", "title": "Calcium Induces Long-Term Legacy Effects In A Subalpine Ecosystem", "description": "Human activities have transformed a significant proportion of the world's land surface, with profound effects on ecosystem processes. Soil applications of macronutrients such as nitrate, phosphorus, potassium or calcium are routinely used in the management of croplands, grasslands and forests to improve plant health or increase productivity. However, while the effects of continuous fertilization and liming on terrestrial ecosystems are well documented, remarkably little is known about the legacy effect of historical fertilization and liming events in terrestrial ecosystems and of the mechanisms involved. Here, we show that more than 70 years after the last application of lime on a subalpine grassland, all major soil and plant calcium pools were still significantly larger in limed than in unlimed plots, and that the resulting shift in the soil calcium/aluminium ratio continues to affect ecosystem services such as primary production. The difference in the calcium content of the vegetation and the topmost 10 cm of the soil in limed vs. unlimed plots amounts to approximately 19.5 g m(-2), equivalent to 16.3% of the amount that was added to the plots some 70 years ago. In contrast, plots that were treated with nitrogen-phosphorus-potassium fertilizer in the 1930s did not differ from unfertilized plots in any of the soil and vegetation characteristics measured. Our findings suggest that the long-term legacy effect of historical liming is due to long-term storage of added calcium in stable soil pools, rather than a general increase in nutrient availability. Our results demonstrate that single applications of calcium in its carbonated form can profoundly and persistently alter ecosystem processes and services in mountain ecosystems.", "keywords": ["EFFET SUR VEGETAL", "[SDE] Environmental Sciences", "0301 basic medicine", "Nitrogen", "Science", "580 Plants (Botany)", "CALCIUM", "Time", "Soil", "03 medical and health sciences", "ECOSYSTEME MONTAGNARD", "Humans", "Fertilizers", "Ecosystem", "Plant Physiological Phenomena", "2. Zero hunger", "0303 health sciences", "Q", "R", "Phosphorus", "Calcium Compounds", "15. Life on land", "6. Clean water", "FERTILISATION", "13. Climate action", "[SDE]Environmental Sciences", "Medicine", "Research Article"]}, "links": [{"href": "https://boris.unibe.ch/91277/1/journal.pone.0051818.PDF"}, {"href": "https://hal.science/hal-00778782/file/gr2012-pub00036992.pdf"}, {"href": "https://doi.org/10.1371/journal.pone.0051818"}, {"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.0051818", "name": "item", "description": "10.1371/journal.pone.0051818", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0051818"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-12-20T00:00:00Z"}}, {"id": "10.21769/bioprotoc.3799", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:21:21Z", "type": "Journal Article", "created": "2020-10-19", "title": "Low-cost and High-throughput RNA-seq Library Preparation for Illumina Sequencing from Plant Tissue", "description": "Transcriptome analysis can provide clues to biological processes affected in different genetic backgrounds or/and under various conditions. The price of RNA sequencing (RNA-seq) has decreased enough so that medium- to large-scale transcriptome analyses in a range of conditions are feasible. However, the price and variety of options for library preparation of RNA-seq can still be daunting to those who would like to use RNA-seq for their first time or for a single experiment. Among the criteria for selecting a library preparation protocol are the method of RNA isolation, nucleotide fragmentation to obtain desired size range, and library indexing to pool sequencing samples for multiplexing. Here, we present a high-quality and a high-throughput option for preparing libraries from polyadenylated mRNA for transcriptome analysis. Both high-quality and high-throughput protocol options include steps of mRNA enrichment through magnetic bead-enabled precipitation of the poly-A tail, cDNA synthesis, and then fragmentation and adapter addition simultaneously through Tn5-mediated 'tagmentation'. All steps of the protocols have been validated with Arabidopsis thaliana leaf and seedling tissues and streamlined to work together, with minimal cost in money and time, thus intended to provide a beginner-friendly start-to-finish RNA-seq library preparation for transcriptome analysis.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "Arabidopsis thaliana", "QH301-705.5", "Plant", "580 Plants (Botany)", "Multiplexing", "Tagmentation", "03 medical and health sciences", "10126 Department of Plant and Microbial Biology", "10211 Zurich-Basel Plant Science Center", "RNA-seq", "Biology (General)", "Transcriptomics"]}, "links": [{"href": "https://escholarship.org/content/qt44f1027m/qt44f1027m.pdf"}, {"href": "https://doi.org/10.21769/bioprotoc.3799"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BIO-PROTOCOL", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.21769/bioprotoc.3799", "name": "item", "description": "10.21769/bioprotoc.3799", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.21769/bioprotoc.3799"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "10141/623078", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:25:53Z", "type": "Journal Article", "created": "2022-11-12", "title": "Frontiers in soil ecology\u2014Insights from the World Biodiversity Forum 2022", "description": "Abstract<p>Global change is affecting soil biodiversity and functioning across all terrestrial ecosystems. Still, much is unknown about how soil biodiversity and function will change in the future in response to simultaneous alterations in climate and land use, as well as other environmental drivers. It is crucial to understand the direct, indirect\uffc2\uffa0and interactive effects of global change drivers on soil communities and ecosystems across environmental contexts, not only today but also in the near future. This is particularly relevant for international efforts to tackle climate change like the Paris Agreement, and considering the failure to achieve the 2020 biodiversity targets, especially the target of halting soil degradation. Here, we outline the main frontiers related to soil ecology that were presented and discussed at the thematic sessions of the World Biodiversity Forum 2022 in Davos, Switzerland. We highlight multiple frontiers of knowledge associated with data integration, causal inference, soil biodiversity and function scenarios, critical soil biodiversity facets, underrepresented drivers, global collaboration, knowledge application and transdisciplinarity, as well as policy and public communication. These identified research priorities are not only of immediate interest to the scientific community but may also be considered in research priority programmes and calls for funding.</p", "keywords": ["[SDE] Environmental Sciences", "0301 basic medicine", "570", "Agriculture (General)", "577", "soil biodiversity", "scenario modelling", "580 Plants (Botany)", "S1-972", "03 medical and health sciences", "10126 Department of Plant and Microbial Biology", "11. Sustainability", "Life Science", "GE1-350", "10211 Zurich-Basel Plant Science Center", "Biology", "soil macroecology", "Biodiversity change", "2. Zero hunger", "Soil macroecology", "0303 health sciences", "15. Life on land", "Scenario modelling", "Soil biodiversity", "6. Clean water", "Environmental sciences", "biodiversity change", "13. Climate action", "ecosystem functioning", "[SDE]Environmental Sciences", "Ecosystem functioning", "ta1181"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/sae2.12031"}, {"href": "https://doi.org/10141/623078"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Sustainable%20Agriculture%20and%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10141/623078", "name": "item", "description": "10141/623078", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10141/623078"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-11T00:00:00Z"}}, {"id": "10871/134717", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:26:13Z", "type": "Journal Article", "created": "2023-10-27", "title": "Shifts in soil ammonia\u2010oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions", "description": "Abstract<p>Anthropogenic nitrogen (N) loading alters soil ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize\uffc2\uffa068 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N\uffe2\uff80\uff90stimulation of nitrification, but does so via climate\uffe2\uff80\uff90related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N\uffe2\uff80\uff90availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate\uffe2\uff80\uff90related shifts in soil ammonia\uffe2\uff80\uff90oxidizing community maintain the N\uffe2\uff80\uff90stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.</p", "keywords": ["550", "Nitrogen", "2306 Global and Planetary Change", "ammonia oxidizers", "580 Plants (Botany)", "nitrogen addition", "333", "Nitrogen/analysis", "2300 General Environmental Science", "Soil", "10126 Department of Plant and Microbial Biology", "Ammonia", "Climate change", "10211 Zurich-Basel Plant Science Center", "Soil Microbiology", "Phylogeny", "Soil/chemistry", "2. Zero hunger", "Nitrogen addition", "info:eu-repo/classification/ddc/550", "ddc:550", "Microbial community structure", "15. Life on land", "Nitrification", "Archaea", "6. Clean water", "nitrification", "Ammonia oxidizers", "Earth sciences", "climate change", "13. Climate action", "microbial community structure", "2304 Environmental Chemistry", "soil properties", "Soil properties", "2303 Ecology", "Oxidation-Reduction"]}, "links": [{"href": "https://doi.org/10871/134717"}, {"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": "10871/134717", "name": "item", "description": "10871/134717", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10871/134717"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-27T00:00:00Z"}}, {"id": "1959.7/uws:68562", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:26:39Z", "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": "1959.7/uws:76872", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:26:40Z", "type": "Journal Article", "created": "2024-01-08", "title": "Extreme drought impacts have been underestimated in grasslands and shrublands globally", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Climate change is increasing the frequency and severity of short-term (~1 y) drought events\u2014the most common duration of drought\u2014globally. Yet the impact of this intensification of drought on ecosystem functioning remains poorly resolved. This is due in part to the widely disparate approaches ecologists have employed to study drought, variation in the severity and duration of drought studied, and differences among ecosystems in vegetation, edaphic and climatic attributes that can mediate drought impacts. To overcome these problems and better identify the factors that modulate drought responses, we used a coordinated distributed experiment to quantify the impact of short-term drought on grassland and shrubland ecosystems. With a standardized approach, we imposed ~a single year of drought at 100 sites on six continents. Here we show that loss of a foundational ecosystem function\u2014aboveground net primary production (ANPP)\u2014was 60% greater at sites that experienced statistically extreme drought (1-in-100-y event) vs. those sites where drought was nominal (historically more common) in magnitude (35% vs. 21%, respectively). This reduction in a key carbon cycle process with a single year of extreme drought greatly exceeds previously reported losses for grasslands and shrublands. Our global experiment also revealed high variability in drought response but that relative reductions in ANPP were greater in drier ecosystems and those with fewer plant species. Overall, our results demonstrate with unprecedented rigor that the global impacts of projected increases in drought severity have been significantly underestimated and that drier and less diverse sites are likely to be most vulnerable to extreme drought.</p></article>", "keywords": ["[SDE] Environmental Sciences", "Medical Sciences", "Drought Severity", "550", "580 Plants (Botany)", "551", "Tierras de Matorral", "Medical Specialties", "Medicine and Health Sciences", "SDG 13 - Climate Action", "climate extreme | Drought-Net | International Drought Experiment | productivity", "Productividad Primaria Neta", "Net Primary Productivity", "Productivity", "2. Zero hunger", "Praderas", "Productividad", "Life Sciences", "Biological Sciences", "Grassland", "6. Clean water", "Droughts", "Grasslands", "[SDE]Environmental Sciences", "Drought-Net", "Public Health", "International Drought Experiment", "Ciclo del Carbono", "Severidad de la Sequ\u00eda", "Global Impacts", "productivity", "Climate Change", "climate extreme", "333", "Carbon Cycle", "Environmental Public Health", "XXXXXX - Unknown", "Impacto Global", "Scrublands", "General", "Biology", "Ecosystem", "Experimento internacional de Sequ\u00eda", "500", "Receptor Protein-Tyrosine Kinases", "15. Life on land", "Clima Extremo", "Climate Science", "13. Climate action", "Cambio Clim\u00e1tico", "Extreme Climate", "Climate extreme", "Klimatvetenskap"]}, "links": [{"href": "https://boris.unibe.ch/191349/1/smith-et-al-2024-extreme-drought-impacts-have-been-underestimated-in-grasslands-and-shrublands-globally.pdf"}, {"href": "https://escholarship.org/content/qt9b707158/qt9b707158.pdf"}, {"href": "https://doi.org/1959.7/uws:76872"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1959.7/uws:76872", "name": "item", "description": "1959.7/uws:76872", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1959.7/uws:76872"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-08T00:00:00Z"}}, {"id": "3093542655", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:27:38Z", "type": "Journal Article", "created": "2020-10-19", "title": "Low-cost and High-throughput RNA-seq Library Preparation for Illumina Sequencing from Plant Tissue", "description": "Transcriptome analysis can provide clues to biological processes affected in different genetic backgrounds or/and under various conditions. The price of RNA sequencing (RNA-seq) has decreased enough so that medium- to large-scale transcriptome analyses in a range of conditions are feasible. However, the price and variety of options for library preparation of RNA-seq can still be daunting to those who would like to use RNA-seq for their first time or for a single experiment. Among the criteria for selecting a library preparation protocol are the method of RNA isolation, nucleotide fragmentation to obtain desired size range, and library indexing to pool sequencing samples for multiplexing. Here, we present a high-quality and a high-throughput option for preparing libraries from polyadenylated mRNA for transcriptome analysis. Both high-quality and high-throughput protocol options include steps of mRNA enrichment through magnetic bead-enabled precipitation of the poly-A tail, cDNA synthesis, and then fragmentation and adapter addition simultaneously through Tn5-mediated 'tagmentation'. All steps of the protocols have been validated with Arabidopsis thaliana leaf and seedling tissues and streamlined to work together, with minimal cost in money and time, thus intended to provide a beginner-friendly start-to-finish RNA-seq library preparation for transcriptome analysis.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "Arabidopsis thaliana", "QH301-705.5", "Plant", "580 Plants (Botany)", "Multiplexing", "Tagmentation", "03 medical and health sciences", "10126 Department of Plant and Microbial Biology", "10211 Zurich-Basel Plant Science Center", "RNA-seq", "Biology (General)", "Transcriptomics"]}, "links": [{"href": "https://escholarship.org/content/qt44f1027m/qt44f1027m.pdf"}, {"href": "https://doi.org/3093542655"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BIO-PROTOCOL", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3093542655", "name": "item", "description": "3093542655", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3093542655"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "38049516", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:28:02Z", "type": "Journal Article", "created": "2023-12-04", "title": "Subtilase-mediated biogenesis of the expanded family of SERINE RICH ENDOGENOUS PEPTIDES", "description": "Plant signalling peptides are typically released from larger precursors by proteolytic cleavage to regulate plant growth, development and stress responses. Recent studies reported the characterization of a divergent family of Brassicaceae-specific peptides, SERINE RICH ENDOGENOUS PEPTIDES (SCOOPs), and their perception by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2). Here, we reveal that the SCOOP family is highly expanded, containing at least 50 members in the Columbia-0 reference Arabidopsis thaliana genome. Notably, perception of these peptides is strictly MIK2-dependent. How bioactive SCOOP peptides are produced, and to what extent their perception is responsible for the multiple physiological roles associated with MIK2 are currently unclear. Using N-terminomics, we validate the N-terminal cleavage site of representative PROSCOOPs. The cleavage sites are determined by conserved motifs upstream of the minimal SCOOP bioactive epitope. We identified subtilases necessary and sufficient to process PROSCOOP peptides at conserved cleavage motifs. Mutation of these subtilases, or their recognition motifs, suppressed PROSCOOP cleavage and associated overexpression phenotypes. Furthermore, we show that higher-order mutants of these subtilases show phenotypes reminiscent of mik2 null mutant plants, consistent with impaired PROSCOOP biogenesis, and demonstrating biological relevance of SCOOP perception by MIK2. Together, this work provides insights into the molecular mechanisms underlying the functions of the recently identified SCOOP peptides and their receptor MIK2.", "keywords": ["570", "Arabidopsis Proteins", "[SDV]Life Sciences [q-bio]", "Arabidopsis", "Receptors", " Cell Surface", "580 Plants (Botany)", "[SDV] Life Sciences [q-bio]", "10126 Department of Plant and Microbial Biology", "1110 Plant Science", "Taverne", "Brassicaceae", "Serine", "Life Science", "10211 Zurich-Basel Plant Science Center", "Peptides", "Protein Kinases"]}, "links": [{"href": "https://www.nature.com/articles/s41477-023-01583-x.pdf"}, {"href": "https://hal.science/hal-04394015/file/NaturePlants_subtilase_scoop_2023_revised.pdf"}, {"href": "https://doi.org/38049516"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Plants", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "38049516", "name": "item", "description": "38049516", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/38049516"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-04T00:00:00Z"}}, {"id": "PMC7842799", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:30:08Z", "type": "Journal Article", "created": "2020-10-19", "title": "Low-cost and High-throughput RNA-seq Library Preparation for Illumina Sequencing from Plant Tissue", "description": "Transcriptome analysis can provide clues to biological processes affected in different genetic backgrounds or/and under various conditions. The price of RNA sequencing (RNA-seq) has decreased enough so that medium- to large-scale transcriptome analyses in a range of conditions are feasible. However, the price and variety of options for library preparation of RNA-seq can still be daunting to those who would like to use RNA-seq for their first time or for a single experiment. Among the criteria for selecting a library preparation protocol are the method of RNA isolation, nucleotide fragmentation to obtain desired size range, and library indexing to pool sequencing samples for multiplexing. Here, we present a high-quality and a high-throughput option for preparing libraries from polyadenylated mRNA for transcriptome analysis. Both high-quality and high-throughput protocol options include steps of mRNA enrichment through magnetic bead-enabled precipitation of the poly-A tail, cDNA synthesis, and then fragmentation and adapter addition simultaneously through Tn5-mediated 'tagmentation'. All steps of the protocols have been validated with Arabidopsis thaliana leaf and seedling tissues and streamlined to work together, with minimal cost in money and time, thus intended to provide a beginner-friendly start-to-finish RNA-seq library preparation for transcriptome analysis.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "Arabidopsis thaliana", "QH301-705.5", "Plant", "580 Plants (Botany)", "Multiplexing", "Tagmentation", "03 medical and health sciences", "10126 Department of Plant and Microbial Biology", "10211 Zurich-Basel Plant Science Center", "RNA-seq", "Biology (General)", "Transcriptomics"]}, "links": [{"href": "https://escholarship.org/content/qt44f1027m/qt44f1027m.pdf"}, {"href": "https://doi.org/PMC7842799"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BIO-PROTOCOL", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC7842799", "name": "item", "description": "PMC7842799", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC7842799"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=580+Plants+%28Botany%29&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=580+Plants+%28Botany%29&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=580+Plants+%28Botany%29&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=580+Plants+%28Botany%29&offset=16", "hreflang": "en-US"}], "numberMatched": 16, "numberReturned": 16, "distributedFeatures": [], "timeStamp": "2026-04-16T01:44:03.989944Z"}