{"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": "10.1038/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": "10.1111/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": "10.21769/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": "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=10126+Department+of+Plant+and+Microbial+Biology&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=10126+Department+of+Plant+and+Microbial+Biology&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=10126+Department+of+Plant+and+Microbial+Biology&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=10126+Department+of+Plant+and+Microbial+Biology&offset=12", "hreflang": "en-US"}], "numberMatched": 12, "numberReturned": 12, "distributedFeatures": [], "timeStamp": "2026-04-16T01:41:05.385880Z"}