{"type": "FeatureCollection", "features": [{"id": "10.1007/s00248-007-9276-4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:14:30Z", "type": "Journal Article", "created": "2007-07-17", "title": "Comparison Of Soil Bacterial Communities Under Diverse Agricultural Land Management And Crop Production Practices", "description": "The composition and structure of bacterial communities were examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Five land management programs were initiated in July 2000: conventional, organic, continuous removal of vegetation (disk fallow), undisturbed (weed fallow), and bahiagrass pasture (Paspalum notatum var Argentine). Similar levels in the diversity of bacterial 16S rDNA amplicons were detected in soil samples collected from organically and conventionally managed plots 3 and 4 years after initiation of land management programs, whereas significantly lower levels of diversity were observed in samples collected from bahiagrass pasture. Differences in diversity were attributed to effects on how the relative abundance of individual amplicons were distributed (evenness) and not on the total numbers of bacterial 16S rDNA amplicons detected (richness). Similar levels of diversity were detected among all land management programs in soil samples collected after successive years of tomato (Lycopersicon esculentum) cultivation. A different trend was observed after a multivariate examination of the similarities in genetic composition among soil bacterial communities. After 3 years of land management, similarities in genetic composition of soil bacterial communities were observed in plots where disturbance was minimized (bahiagrass and weed fallow). The genetic compositions in plots managed organically were similar to each other and distinct from bacterial communities in other land management programs. After successive years of tomato cultivation and damage from two major hurricanes, only the composition of soil bacterial communities within organically managed plots continued to maintain a high degree of similarity to each other and remain distinct from other bacterial communities. This study reveals the effects of agricultural land management practices on soil bacterial community composition and diversity in a large-scale, long-term replicated study where the effect of soil type on community attributes was removed.", "keywords": ["Crops", " Agricultural", "DNA", " Bacterial", "2. Zero hunger", "Analysis of Variance", "Conservation of Natural Resources", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "DNA", " Ribosomal", "Polymerase Chain Reaction", "Solanum lycopersicum", "RNA", " Ribosomal", " 16S", "0401 agriculture", " forestry", " and fisheries", "Cloning", " Molecular", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-007-9276-4"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-007-9276-4", "name": "item", "description": "10.1007/s00248-007-9276-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-007-9276-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-07-07T00:00:00Z"}}, {"id": "10.1007/s00248-018-1305-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:14:30Z", "type": "Journal Article", "created": "2018-12-08", "title": "Soil Type and Cyanobacteria Species Influence the Macromolecular and Chemical Characteristics of the Polysaccharidic Matrix in Induced Biocrusts", "description": "Inoculation of soils with cyanobacteria is proposed as a sustainable biotechnological technique for restoration of degraded areas in drylands due to the important role that cyanobacteria and their exopolysaccharides (EPS) play in the environment. So far, few studies have analyzed the macromolecular and chemical characteristics of the polysaccharidic matrix in induced cyanobacterial biocrusts and the scarce existing studies have mainly focused on sandy soil textures. However, the characteristics of the cyanobacterial polysaccharidic matrix may greatly depend on soil type. The objective of this study was to examine the macromolecular distribution and monosaccharidic composition of the polysaccharidic matrix induced by inoculation of two cyanobacterial species common in arid environments, Phormidium ambiguum (non N-fixing) and Scytonema javanicum (N-fixing) in different soil types. S. javanicum promoted a higher release in the soil of the more soluble and less condensed EPS fraction (i.e., the loosely bound EPS fraction, LB-EPS), while P. ambiguum showed a higher release of the less soluble and more condensed EPS fraction (i.e., the tightly bound EPS fraction, TB-EPS). LB-EPSs were mainly composed of low MW molecules (<\u200950\u00a0kDa), while TB-EPSs were mainly composed of high MW molecules (1100-2000\u00a0kDa). The two EPS fractions showed a complex monosaccharidic composition (from 11 to 12 different types of monosaccharides), with glucose as the most abundant monosaccharide, in particular in the poorer soils characterized by lower organic C contents. In more C-rich soils, high abundances of galactose, mannose, and xylose were also found. Low abundance of uronic acids and hydrophobic monosaccharides, such as fucose and rhamnose, was found in the EPS extracted from the inoculated soils. Our results point to the influence of soil type on the macromolecular distribution and monosaccharide composition of the polysaccharidic matrix in induced biocrusts, which is likely to affect biocrust development and their role in soil structure and nutrient cycling in restored dryland soils.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Cyanobacteria inoculation", "Tightly bound EPS", "Polysaccharides", " Bacterial", "Biological soil crust; Cyanobacteria inoculation; Loosely bound EPS; Molecular weight; Monosaccharide composition; Tightly bound EPS; Ecology; Evolution; Behavior and Systematics; Ecology; Soil Science", "Biological soil crust", "Monosaccharide composition", "15. Life on land", "Cyanobacteria", "Molecular weight", "Biological soil crust; Cyanobacteria inoculation; Loosely bound EPS; Molecular weight; Monosaccharide composition; Tightly bound EPS; Ecology", " Evolution", " Behavior and Systematics; Ecology; Soil Science", "Soil", "03 medical and health sciences", "13. Climate action", "Loosely bound EPS", "Desert Climate", "Soil Microbiology"]}, "links": [{"href": "https://iris.unive.it/bitstream/10278/5089943/1/s00248-018-1305-y.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1007/s00248-018-1305-y.pdf"}, {"href": "https://doi.org/10.1007/s00248-018-1305-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-018-1305-y", "name": "item", "description": "10.1007/s00248-018-1305-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-018-1305-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-08T00:00:00Z"}}, {"id": "10.1007/s00253-019-09689-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:14:30Z", "type": "Journal Article", "created": "2019-02-20", "title": "Distribution of Oenococcus oeni populations in natural habitats", "description": "Oenococcus oeni is the lactic acid bacteria species most commonly encountered in wine, where it develops after the alcoholic fermentation and achieves the malolactic fermentation that is needed to improve the quality of most wines. O. oeni is abundant in the oenological environment as well as in apple cider and kombucha, whereas it is a minor species in the natural environment. Numerous studies have shown that there is a great diversity of strains in each wine region and in each product or type of wine. Recently, genomic studies have shed new light on the species diversity, population structure, and environmental distribution. They revealed that O. oeni has unique genomic features that have contributed to its fast evolution and adaptation to the enological environment. They have also unveiled the phylogenetic diversity and genomic properties of strains that develop in different regions or different products. This review explores the distribution of O. oeni and the diversity of strains in natural habitats.", "keywords": ["0106 biological sciences", "0301 basic medicine", "570", "Evolution", "[SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering", "590", "Wine", "01 natural sciences", "Domestication", "Evolution", " Molecular", "03 medical and health sciences", "[SDV.IDA]Life Sciences [q-bio]/Food engineering", "MD Multidisciplinary", "[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering", "Ecosystem", "Oenococcus", "Phylogeny", "0303 health sciences", "Malolactic fermentation", "Genetic Variation", "Genomics", "[SDV.IDA] Life Sciences [q-bio]/Food engineering", "Mini-Review", "Fermentation", "Oenococcus oeni", "Biotechnology"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s00253-019-09689-z.pdf"}, {"href": "https://doi.org/10.1007/s00253-019-09689-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-019-09689-z", "name": "item", "description": "10.1007/s00253-019-09689-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-019-09689-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-20T00:00:00Z"}}, {"id": "10.1007/s00425-017-2647-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:14:39Z", "type": "Journal Article", "created": "2017-01-04", "title": "The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis", "description": "Different nitrogen forms affect different metabolic pathways in lichens. In particular, the most relevant changes in protein expression were observed in the fungal partner, with NO 3- mostly affecting the energetic metabolism and NH 4+ affecting transport and regulation of proteins and the energetic metabolism much more than NO 3- did. Excess deposition of reactive nitrogen is a well-known agent of stress for lichens, but which symbiont is most affected and how, remains a mystery. Using proteomics can expand our understanding of stress effects on lichens. We investigated the effects of different doses and forms of reactive nitrogen, with and without supplementary phosphorus and potassium, on the proteome of the lichen Cladonia portentosa growing in a 'real-world' simulation of nitrogen deposition. Protein expression changed with the nitrogen treatments but mostly in the fungal partner, with NO3- mainly affecting the energetic metabolism and NH4+ also affecting the protein synthesis machinery. The photobiont mainly responded overexpressing proteins involved in energy production. This suggests that in response to nitrogen stress, the photobiont mainly supports the defensive mechanisms initiated by the mycobiont with an increased energy production. Such surplus energy is then used by the cell to maintain functionality in the presence of NO3-, while a futile cycle of protein production can be hypothesized to be induced by NH4+ excess. External supply of potassium and phosphorus influenced differently the responses of particular enzymes, likely reflecting the many processes in which potassium exerts a regulatory function.", "keywords": ["Chlorophyll", "Proteomics", "0301 basic medicine", "570", "mycobiont", "Lichens", "Nitrogen", "Cell Respiration", "Nitrate", "Mass Spectrometry", "Molecular mechanism", "03 medical and health sciences", "nitrate", "Ammonia", "Electrophoresis", " Gel", " Two-Dimensional", "Photosynthesis", "Ammonium", " Molecular mechanism", " Mycobiont", " Nitrate", " Photobiont", " Stress response", "Ammonium; Molecular mechanism; Mycobiont; Nitrate; Photobiont; Stress response; Genetics; Plant Science", "0303 health sciences", "Nitrates", "Stress response", "Chlorophyll A", "stress response", "Mycobiont", "ammonium", "Photobiont", "photobiont", "molecular mechanism", "Energy Metabolism", "Ammonium"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s00425-017-2647-2.pdf"}, {"href": "https://doi.org/10.1007/s00425-017-2647-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Planta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00425-017-2647-2", "name": "item", "description": "10.1007/s00425-017-2647-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00425-017-2647-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-04T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2022.108918", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:25Z", "type": "Journal Article", "created": "2022-12-22", "title": "Litter chemistry of common European tree species drives the feeding preference and consumption rate of soil invertebrates, and shapes the diversity and structure of gut and faecal microbiomes", "description": "Open AccessTerrestrial isopods and millipedes are key drivers of a litter decomposition in terrestrial ecosystems but the effects of litter chemistry on feeding preference and litter consumption rate as well as on the diversity and composition of gut and faecal microbiome still entails several challenges. We established a mesocosm experiment with terrestrial isopods (Oniscus asellus) and millipedes (Glomeris marginata) fed by leaf litter from six common European tree species (ash, maple, lime, beech, oak and Norway spruce) to reveal the effect of litter chemistry on consumption rate and feeding preference as well as on the compositions of gut and faecal microbiomes. The total percentage of consumed litter showed that O. asellus preferred nutrient-rich and labile-C litter of ash over more recalcitrant litter of oak, beech, and Norway spruce, while G. marginata preferred calcium-rich ash, maple and lime litter over beech and Norway spruce. Consumption of litter by O. asellus and G. marginata increased with concentrations of magnesium, sulphur and potassium but decreased with concentrations of iron, phosphorus, lignin, cellulose and TOC. The millipede G. marginata harboured higher bacterial OTU richness (73.5 \u00b1 12.5) than the isopod O. asellus (49.1 \u00b1 15.9), but fungal OTU richness was similar with 25.8 \u00b1 6.7 in O. asellus and 25.7 \u00b1 2.7 in G. marginata. In total, faeces of both animals hosted higher diversity than gut. In gut and faeces of O. asellus, the fungal OTU richness was highest for individuals fed by litter of Norway spruce, while lowest OTU richness was recorded for individuals fed by litter of more palatable ash. In contrast, the highest diversity of the fungal community in gut and faeces of G. marginata was recorded for individuals fed by palatable lime litter, while the lowest OTUs richness was recorded when millipedes were fed by maple and spruce. The structures of bacterial and fungal communities generally separated between O. asellus and G. marginata. The fungal community structure in gut and faeces differed between animals fed by different foliar litters, while the bacterial community structure mainly differed between gut and faeces regardless of the offered type of litter. The fungal community structure in gut and faeces of O. asellus and G. marginata were shaped by concentrations of magnesium, sulphur, lignin and cellulose. The bacterial communities in gut and faeces of both O. asellus and G. marginata were dominated by copiotrophic bacteria, while fungal communities were dominated by unspecified saprotrophs. Our study suggest that litter quality is a strong driver of feeding preference and consumption rates as well as composition of bacterial and fungal communities in gut and faeces of two species representing the main groups of litter feeding soil fauna in European forests.", "keywords": ["0301 basic medicine", "Genomic Insights into Social Insects and Symbiosis", "Plant Science", "Plant litter", "Agricultural and Biological Sciences", "03 medical and health sciences", "Biochemistry", " Genetics and Molecular Biology", "Litter", "Genetics", "Ecological Niche", "Biology", "Ecosystem", "Beech", "0303 health sciences", "Species Distribution Modeling and Climate Change Impacts", "Ecology", "Ecological Modeling", "Botany", "Life Sciences", "15. Life on land", "Plant-Parasitic Nematodes in Molecular Plant Pathology", "Detritus", "FOS: Biological sciences", "Detritivore", "Environmental Science", "Physical Sciences", "Species richness"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2022.108918"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2022.108918", "name": "item", "description": "10.1016/j.soilbio.2022.108918", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2022.108918"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-01T00:00:00Z"}}, {"id": "10.1111/brv.12949", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:16Z", "type": "Journal Article", "created": "2023-03-14", "title": "Trade\u2010offs in carbon\u2010degrading enzyme activities limit long\u2010term soil carbon sequestration with biochar addition", "description": "ABSTRACT<p>Biochar amendment is one of the most promising agricultural approaches to tackle climate change by enhancing soil carbon (C) sequestration. Microbial\uffe2\uff80\uff90mediated decomposition processes are fundamental for the fate and persistence of sequestered C in soil, but the underlying mechanisms are uncertain. Here, we synthesise 923 observations regarding the effects of biochar addition (over periods ranging from several weeks to several years) on soil C\uffe2\uff80\uff90degrading enzyme activities from 130 articles across five continents worldwide. Our results showed that biochar addition increased soil ligninase activity targeting complex phenolic macromolecules by 7.1%, but suppressed cellulase activity degrading simpler polysaccharides by 8.3%. These shifts in enzyme activities explained the most variation of changes in soil C sequestration across a wide range of climatic, edaphic and experimental conditions, with biochar\uffe2\uff80\uff90induced shift in ligninase:cellulase ratio correlating negatively with soil C sequestration. Specifically, short\uffe2\uff80\uff90term (&lt;1\uffc2\uffa0year) biochar addition significantly reduced cellulase activity by 4.6% and enhanced soil organic C sequestration by 87.5%, whereas no significant responses were observed for ligninase activity and ligninase:cellulase ratio. However, long\uffe2\uff80\uff90term (\uffe2\uff89\uffa51\uffc2\uffa0year) biochar addition significantly enhanced ligninase activity by 5.2% and ligninase:cellulase ratio by 36.1%, leading to a smaller increase in soil organic C sequestration (25.1%). These results suggest that shifts in enzyme activities increased ligninase:cellulase ratio with time after biochar addition, limiting long\uffe2\uff80\uff90term soil C sequestration with biochar addition. Our work provides novel evidence to explain the diminished soil C sequestration with long\uffe2\uff80\uff90term biochar addition and suggests that earlier studies may have overestimated soil C sequestration with biochar addition by failing to consider the physiological acclimation of soil microorganisms over time.</p", "keywords": ["Carbon Sequestration", "Supplementary Data", "QH301 Biology", "General Biochemistry", "Genetics and Molecular Biology", "soil microorganism", "551", "QH301", "Soil", "soil carbon sequestration", "SDG 13 - Climate Action", "Cellulases", "Biochar addition", "European Commission", "2. Zero hunger", "GE", "15. Life on land", "Carbon", "enzyme activity", "meta-analysis", "enzyme activities", "13. Climate action", "experimental duration", "839806", "Other", "figshare", "General Agricultural and Biological Sciences", "biochar addition", "GE Environmental Sciences", "European Research Council"]}, "links": [{"href": "https://doi.org/10.1111/brv.12949"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biological%20Reviews", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/brv.12949", "name": "item", "description": "10.1111/brv.12949", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/brv.12949"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-13T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2024.105383", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:54Z", "type": "Journal Article", "created": "2024-03-23", "title": "Long-term restoration with organic amendments is clearer evidenced by soil organic matter composition than by changes in microbial taxonomy and functionality", "description": "Open AccessPeer reviewed", "keywords": ["2. Zero hunger", "Organic residues", "Circular economy", "SOM molecular composition", "13. Climate action", "11. Sustainability", "Soil recovery", "Climate change", "Microbiome", "15. Life on land", "6. Clean water", "12. Responsible consumption"]}, "links": [{"href": "https://doi.org/10.1016/j.apsoil.2024.105383"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2024.105383", "name": "item", "description": "10.1016/j.apsoil.2024.105383", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2024.105383"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-06-01T00:00:00Z"}}, {"id": "10.1016/j.cell.2021.04.024", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:03Z", "type": "Journal Article", "created": "2021-05-18", "title": "Innovation, conservation, and repurposing of gene function in root cell type development", "description": "Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.", "keywords": ["root development", "translatomes", "General Biochemistry", "Genetics and Molecular Biology", "Green Fluorescent Proteins", "Meristem", "Arabidopsis", "cell types; evolution; exodermis; gene regulation; rice; root development; tomato; translatomes; xylem", "tomato", "xylem", "Genes", " Plant", "Plant Roots", "Inventions", "Solanum lycopersicum", "Species Specificity", "Gene Expression Regulation", " Plant", "Xylem", "evolution", "Gene Regulatory Networks", "Promoter Regions", " Genetic", "Plant Proteins", "2. Zero hunger", "exodermis", "rice", "15. Life on land", "Protein Biosynthesis", "cell types", "gene regulation", "Transcription Factors"]}, "links": [{"href": "https://www.research.unipd.it/bitstream/11577/3392826/2/PIIS0092867421005043.pdf"}, {"href": "https://doi.org/10.1016/j.cell.2021.04.024"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Cell", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.cell.2021.04.024", "name": "item", "description": "10.1016/j.cell.2021.04.024", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.cell.2021.04.024"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-01T00:00:00Z"}}, {"id": "10.1016/j.coisb.2021.100379", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:06Z", "type": "Journal Article", "created": "2021-09-09", "title": "Approaches for completing metabolic networks through metabolite damage and repair discovery", "description": "Metabolites are prone to damage, either via enzymatic side reactions, which collectively form the underground metabolism, or via spontaneous chemical reactions. The resulting non-canonical metabolites that can be toxic, are mended by dedicated 'metabolite repair enzymes.' Deficiencies in the latter can cause severe disease in humans, whereas inclusion of repair enzymes in metabolically engineered systems can improve the production yield of value-added chemicals. The metabolite damage and repair loops are typically not yet included in metabolic reconstructions and it is likely that many remain to be discovered. Here, we review strategies and associated challenges for unveiling non-canonical metabolites and metabolite repair enzymes, including systematic approaches based on high-resolution mass spectrometry, metabolome-wide side-activity prediction, as well as high-throughput substrate and phenotypic screens.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", ": Biochemistry", " biophysics & molecular biology [F05] [Life sciences]", ": Biochimie", " biophysique & biologie mol\u00e9culaire [F05] [Sciences du vivant]", "Article"]}, "links": [{"href": "https://doi.org/10.1016/j.coisb.2021.100379"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Opinion%20in%20Systems%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.coisb.2021.100379", "name": "item", "description": "10.1016/j.coisb.2021.100379", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.coisb.2021.100379"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-01T00:00:00Z"}}, {"id": "10.1016/j.cub.2020.09.063", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:07Z", "type": "Journal Article", "created": "2020-10-15", "title": "Newly explored\u00a0Faecalibacterium\u00a0diversity is connected to age, lifestyle, geography, and disease.", "description": "Faecalibacterium is prevalent in the human gut and a promising microbe for the development of next-generation probiotics (NGPs) or biotherapeutics. Analyzing reference Faecalibacterium genomes and almost 3,000 Faecalibacterium-like metagenome-assembled genomes (MAGs) reconstructed from 7,907 human and 203 non-human primate gut metagenomes, we identified the presence of 22 different Faecalibacterium-like species-level genome bins (SGBs), some further divided in different strains according to the subject geographical origin. Twelve SGBs are globally spread in the human gut and show different genomic potential in the utilization of complex polysaccharides, suggesting that higher SGB diversity may be related with increased utilization of plant-based foods. Moreover, up to 11 different species may co-occur in the same subject, with lower diversity in Western populations, as well as intestinal inflammatory states and obesity. The newly explored Faecalibacterium diversity will be able to support the choice of strains suitable as NGPs, guided by the consideration of the differences existing in their functional potential.", "keywords": ["Adult", "0301 basic medicine", "pangenome", "Adolescent", "gut microbiome", "Datasets as Topic", "General Biochemistry", " Genetics and Molecular Biology", "Innovation action", "Feces", "03 medical and health sciences", "Animals", "Humans", "biotherapeutics", "European Commission", "Child", "Life Style", "Faecalibacterium", "Aged", "Aurora Universities Network", "Horizon 2020", "0303 health sciences", "EC", "Geography", "Faecalibacterium prausnitzii", "H2020", "Age Factors", "Infant", "Middle Aged", "Gastrointestinal Microbiome", "Faecalibacterium prausnitzii", " gut microbiome", " strain diversity", " pangenome", " novel probiotics", " biotherapeutics", "Child", " Preschool", "novel probiotics", "Dysbiosis", "Macaca", "Metagenome", "strain diversity", "Metagenomics", "General Agricultural and Biological Sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/819607/1/PIIS0960982220314330.pdf"}, {"href": "https://doi.org/10.1016/j.cub.2020.09.063"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.cub.2020.09.063", "name": "item", "description": "10.1016/j.cub.2020.09.063", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.cub.2020.09.063"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-01T00:00:00Z"}}, {"id": "10.1016/j.envres.2024.118880", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:22Z", "type": "Journal Article", "created": "2024-04-04", "title": "Unveiling the capacity of bioaugmentation application, in comparison with biochar and rhamnolipid for TPHs degradation in aged hydrocarbons polluted soil", "description": "Persistent, aged hydrocarbons in soil hinder remediation, posing a significant environmental threat. While bioremediation offers an environmentally friendly and cost-effective approach, its efficacy for complex contaminants relies on enhancing pollutant bioavailability. This study explores the potential of immobilized bacterial consortia combined with biochar and rhamnolipids to accelerate bioremediation of aged total petroleum hydrocarbon (TPH)-contaminated soil. Previous research indicates that biochar and biosurfactants can increase bioremediation rates, while mixed consortia offer sequential degradation and higher hydrocarbon mineralization. The present investigation aimed to assess whether combining these strategies could further enhance degradation in aged, complex soil matrices. The bioaugmentation (BA) with bacterial consortium increased the TPHs degradation in aged soil (over 20% compared to natural attenuation - NA). However, co-application of BA with biochar and rhamnolipid higher did not show a statistically prominent synergistic effect. While biochar application facilitated the maintenance of hydrocarbon degrading bacterial consortium in soil, the present study did not identify a direct influence in TPHs degradation. The biochar application in contaminated soil contributed to TPHs adsorption. Rhamnolipid alone slightly increased the TPHs biodegradation with NA, while the combined bioaugmentation treatment with rhamnolipid and biochar increased the degradation between 27.5 and 29.8%. These findings encourage further exploration of combining bioaugmentation with amendment, like biochar and rhamnolipid, for remediating diverse environmental matrices contaminated with complex and aged hydrocarbons.", "keywords": ["Qu\u00edmica agr\u00edcola", "Bioqu\u00edmica", "Biolog\u00eda molecular", "Rhamnolipids", "Molecular biology", "Chemistry", " Inorganic", "Biochemistry", "Qu\u00edmica inorg\u00e1nica", "Hydrocarbons", "Inorganic", "Chemistry", "Biochar", "Soil", "Bioaugmentation", "Agricultural chemistry", "Biodegradation", " Environmental", "Petroleum", "Recalcitrant hydrocarbons", "Charcoal", "Biodegradation", "Soil Pollutants", "TPHs polluted soils", "Glycolipids", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.envres.2024.118880"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envres.2024.118880", "name": "item", "description": "10.1016/j.envres.2024.118880", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envres.2024.118880"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-01T00:00:00Z"}}, {"id": "10.1016/j.ijbiomac.2018.12.270", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:45Z", "type": "Journal Article", "created": "2019-01-03", "title": "Improving polyhydroxyalkanoates production in phototrophic mixed cultures by optimizing accumulator reactor operating conditions", "description": "Open AccessPolyhydroxyalkanoates (PHAs) production with phototrophic mixed cultures (PMCs) has been recently proposed. These cultures can be selected under the permanent presence of carbon and the PHA production can be enhanced in subsequent accumulation steps. To optimize the PHA production in accumulator reactors, this work evaluated the impact of 1) initial acetate concentration, 2) light intensity, 3) removal of residual nitrogen on the culture performance. Results indicate that low acetate concentration (&lt;30CmM) and specific light intensities around 20W/gX are optimal operating conditions that lead to high polyhydroxybutyrate (PHB) storage yields (0.83+-0.07 Cmol-PHB/Cmol-Acet) and specific PHB production rates of 2.21+-0.07 Cmol-PHB/Cmol X d. This rate is three times higher than previously registered in non-optimized accumulation tests and enabled a PHA content increase from 15 to 30% in less than 4h. Also, it was shown for the first time, the capability of a PMC to use a real waste, fermented cheese whey, to produce PHA with a hydroxyvalerate (HV) content of 12%. These results confirm that fermented wastes can be used as substrates for PHA production with PMCs and that the energy levels in sunlight that lead to specific light intensities from 10 to 20W/gX are sufficient to drive phototrophic PHA production processes.", "keywords": ["0106 biological sciences", "1303 Biochemistry", "Light", "Nitrogen", "Polyhydroxyalkanoates (PHA)", "Fermented cheese whey (FCW)", "Phototrophic mixed cultures (PMCs)", "Acetates", "7. Clean energy", "01 natural sciences", "1315 Structural Biology", "Bioreactors", "Cheese", "Whey", "1312 Molecular Biology", "0105 earth and related environmental sciences", "Polyhydroxyalkanoates", "Volatile fatty acids (VFAs)", "Other Quantitative Biology (q-bio.OT)", "Quantitative Biology - Other Quantitative Biology", "Purple phototrophic bacteria (PPB)", "Kinetics", "Phototrophic Processes", "13. Climate action", "FOS: Biological sciences", "Fermentation"]}, "links": [{"href": "https://doi.org/10.1016/j.ijbiomac.2018.12.270"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Biological%20Macromolecules", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ijbiomac.2018.12.270", "name": "item", "description": "10.1016/j.ijbiomac.2018.12.270", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ijbiomac.2018.12.270"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-01T00:00:00Z"}}, {"id": "10.1016/j.jafr.2023.100732", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:47Z", "type": "Journal Article", "created": "2023-08-07", "title": "Aeromycological studies in the crops of the main cereals: A systematic review", "description": "Open AccessLes \u00e9tudes a\u00e9romycologiques sur les cultures c\u00e9r\u00e9ali\u00e8res permettent de d\u00e9terminer la variation temporelle des agents pathog\u00e8nes des plantes affectant la culture et de d\u00e9terminer le moment appropri\u00e9 pour appliquer les fongicides. Cependant, ce sujet n'a pas \u00e9t\u00e9 syst\u00e9matiquement revu. L'objectif de ce travail \u00e9tait d'analyser syst\u00e9matiquement toutes les \u00e9tudes a\u00e9romycologiques r\u00e9alis\u00e9es sur le ma\u00efs, le bl\u00e9, le riz, l'avoine, l'orge, le seigle, le sorgho et le millet. Une recherche syst\u00e9matique a \u00e9t\u00e9 effectu\u00e9e dans Scopus depuis le d\u00e9but de la base de donn\u00e9es jusqu'au 1er ao\u00fbt 2022. Les crit\u00e8res d'inclusion \u00e9taient qu'il s'agissait d'\u00e9tudes a\u00e9romycologiques sur le bl\u00e9 ou le riz ou le ma\u00efs ou l'avoine ou le sorgho ou le seigle ou l'orge ou le millet et d'\u00e9tudes publi\u00e9es dans des revues \u00e0 comit\u00e9 de lecture index\u00e9es dans Journal Citation Reports et r\u00e9dig\u00e9es en anglais ou en espagnol. Quarante-trois \u00e9tudes (21 sur le bl\u00e9, 15 sur le riz, 5 sur le ma\u00efs, 1 sur le sorgho et 2 sur l'orge) r\u00e9pondant \u00e0 tous les crit\u00e8res d'\u00e9ligibilit\u00e9 ont \u00e9t\u00e9 incluses (une des \u00e9tudes sur le ma\u00efs a \u00e9galement \u00e9t\u00e9 men\u00e9e sur le bl\u00e9). Aucune \u00e9tude a\u00e9romycologique n'a \u00e9t\u00e9 trouv\u00e9e chez l'avoine, le seigle et le millet. Il a \u00e9t\u00e9 not\u00e9 que la plupart des recherches a\u00e9romycologiques ont \u00e9t\u00e9 men\u00e9es sur les cultures de bl\u00e9 et principalement dans les pays des Am\u00e9riques. De plus, les propagules fongiques sont principalement collect\u00e9es par des m\u00e9thodes non viables, en utilisant divers types de collecteurs. En g\u00e9n\u00e9ral, les \u00e9tudes visaient \u00e0 identifier un agent pathog\u00e8ne sp\u00e9cifique et non \u00e0 la diversit\u00e9 des agents pathog\u00e8nes qui peuvent \u00eatre trouv\u00e9s. La relation des champignons identifi\u00e9s avec les param\u00e8tres m\u00e9t\u00e9orologiques \u00e9tait variable dans les diff\u00e9rentes \u00e9tudes. Cette revue syst\u00e9matique permet de r\u00e9sumer les \u00e9tudes a\u00e9romycologiques qui ont \u00e9t\u00e9 men\u00e9es sur les cultures de bl\u00e9, de riz, de ma\u00efs, de sorgho et d'orge. Il sugg\u00e8re \u00e9galement o\u00f9 les futures \u00e9tudes dans ce domaine devraient \u00eatre dirig\u00e9es, en fonction des limites rencontr\u00e9es.", "keywords": ["Impacts of Elevated CO2 and Ozone on Plant Physiology", "Agriculture (General)", "Health", " Toxicology and Mutagenesis", "Plant Science", "Crop", "S1-972", "Agricultural and Biological Sciences", "Barley", "Biochemistry", " Genetics and Molecular Biology", "TX341-641", "10. No inequality", "Biology", "Sorghum", "2. Zero hunger", "Corn", "Airborne spores", "Nutrition. Foods and food supply", "Life Sciences", "Phylogenetic Analysis", "Cell Biology", "15. Life on land", "2414.06 Hongos", "Agronomy", "3. Good health", "Wheat", "Environmental Science", "Physical Sciences", "Rice", "Indoor Air Quality and Health Effects", "Diversity and Evolution of Fungal Pathogens", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.jafr.2023.100732"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Agriculture%20and%20Food%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jafr.2023.100732", "name": "item", "description": "10.1016/j.jafr.2023.100732", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jafr.2023.100732"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "10.1016/j.nbt.2023.12.003", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:58Z", "type": "Journal Article", "created": "2023-12-19", "title": "Phytostabilization of metal(loid)s by ten emergent macrophytes following a 90-day exposure to industrially contaminated groundwater", "description": "Better understanding of macrophyte tolerance under long exposure times in real environmental matrices is crucial for phytoremediation and phytoattenuation strategies for aquatic systems. The metal(loid) attenuation ability of 10 emergent macrophyte species (Carex riparia, Cyperus longus, Cyperus rotundus, Iris pseudacorus, Juncus effusus, Lythrum salicaria, Menta aquatica, Phragmites australis, Scirpus holoschoenus, and Typha angustifolia) was investigated using real groundwater from an industrial site, over a 90-day exposure period. A 'phytobial' treatment was included, with 3 plant growth-promoting rhizobacterial strains. Plants exposed to the polluted water generally showed similar or reduced aerial biomass compared to the controls, except for C. riparia. This species, along with M. aquatica, exhibited improved biomass after bioaugmentation. Phytoremediation mechanisms accounted for more than 60% of As, Cd, Cu, Ni, and Pb removal, whilst abiotic mechanisms contributed to \u223c80% removal of Fe and Zn. Concentrations of metal(loid)s in the roots were generally between 10-100 times higher than in the aerial parts. The macrophytes in this work can be considered 'underground attenuators', more appropriate for rhizostabilization strategies, especially L. salicaria, M. aquatica, S. holoschoenus, and T. angustifolia. For I. pseudacorus, C. longus, and C. riparia; harvesting the aerial parts could be a complementary phytoextraction approach to further remove Pb and Zn. Of all the plants, S. holoschoenus showed the best balance between biomass production and uptake of multiple metal(loid)s. Results also suggest that multiple phytostrategies may be possible for the same plant depending on the final remedial aim. Phytobial approaches need to be further assessed for each macrophyte species.", "keywords": ["Rhizostabilization", "Metalloid", "Biotecnolog\u00eda", "Biolog\u00eda molecular", "Emergent macrophyte", "Metal", "Molecular biology", "Plants", "15. Life on land", "Poaceae", "6. Clean water", "Biodegradation", " Environmental", "Lead", "13. Climate action", "Metals", " Heavy", "Plant growth promoting bacteria", "Biomass", "Groundwater", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.nbt.2023.12.003"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.nbt.2023.12.003", "name": "item", "description": "10.1016/j.nbt.2023.12.003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.nbt.2023.12.003"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-03-01T00:00:00Z"}}, {"id": "10.1016/j.pbi.2021.102120", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:58Z", "type": "Journal Article", "created": "2021-11-30", "title": "Fighting salt or enemies: shared perception and signaling strategies", "description": "Plants react to a myriad of biotic and abiotic environmental signals through specific cellular mechanisms required for survival under stress. Although pathogen perception has been widely studied and characterized, salt stress perception and signaling remain largely elusive. Recent observations, obtained in the model plant Arabidopsis thaliana, show that perception of specific features of pathogens also allows plants to mount salt stress resilience pathways, highlighting the possibility that salt sensing and pathogen perception mechanisms partially overlap. We discuss these overlapping strategies and examine the emerging role of A.\u00a0thaliana cell wall and plasma membrane components in activating both salt- and pathogen-induced responses, as part of exquisite mechanisms underlying perception of damage and danger. This knowledge helps understanding the complexity of plant responses to pathogens and salinity, leading to new hypotheses that could explain why plants evolved similar strategies to respond to these, at first sight, very different types of stimuli.", "keywords": ["0301 basic medicine", "Salinity", "0303 health sciences", "Pathogen elicitors", "Arabidopsis Proteins", "Arabidopsis", "Plants", "15. Life on land", "Salt Stress", "03 medical and health sciences", "Cell wall sensing", "Plant immune responses", "Damage-associated molecular patterns (DAMPs)", "Gene Expression Regulation", " Plant", "Stress", " Physiological", "Perception", "Danger signals"]}, "links": [{"href": "https://doi.org/10.1016/j.pbi.2021.102120"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Opinion%20in%20Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.pbi.2021.102120", "name": "item", "description": "10.1016/j.pbi.2021.102120", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.pbi.2021.102120"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-01T00:00:00Z"}}, {"id": "10.1038/s41467-018-05980-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:11Z", "type": "Journal Article", "created": "2018-08-29", "title": "Land use driven change in soil pH affects microbial carbon cycling processes", "description": "Abstract<p>Soil microorganisms act as gatekeepers for soil\uffe2\uff80\uff93atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates.</p", "keywords": ["572 Biochemistry", "BACTERIAL", "ILLUMINA SEQUENCING PLATFORM", "550", "Supplementary Data", "QH301 Biology", "General Physics and Astronomy", "microbial ecology", "Soil", "Biomass", "Soil Microbiology", "SDG 15 - Life on Land", "FUNGAL", "2. Zero hunger", "Carbon Isotopes", "Environmental microbiology", "Ecology", "Q", "ecosystem ecology", "Agriculture", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Grassland", "soil microbiology", "6. Clean water", "COMMUNITY", "GROWTH", "TURNOVER", "570", "PIPELINE", "Science", "Culture and Communities", "General Biochemistry", "Genetics and Molecular Biology", "Microbial Consortia", "General Biochemistry", " Genetics and Molecular Biology", "Article", "Applied microbiology", "QH301", "carbon cycle", "USE EFFICIENCY", "PHYSIOLOGY", "QD415-436 Biochemistry", "Natural Environment Research Council (NERC)", "NE/M017125/1", "General Chemistry", "Carbon Dioxide", "15. Life on land", "Carbon", "United Kingdom", "CLIMATE", "13. Climate action", "0401 agriculture", " forestry", " and fisheries"]}, "links": [{"href": "https://centaur.reading.ac.uk/78980/8/s41467-018-05980-1.pdf"}, {"href": "https://doi.org/10.1038/s41467-018-05980-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-018-05980-1", "name": "item", "description": "10.1038/s41467-018-05980-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-018-05980-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-09-04T00:00:00Z"}}, {"id": "10.1038/s41467-019-09448-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:11Z", "type": "Journal Article", "created": "2019-03-29", "title": "Multiple plant diversity components drive consumer communities across ecosystems", "description": "Abstract<p>Humans modify ecosystems and biodiversity worldwide, with negative consequences for ecosystem functioning. Promoting plant diversity is increasingly suggested as a mitigation strategy. However, our mechanistic understanding of how plant diversity affects the diversity of heterotrophic consumer communities remains limited. Here, we disentangle the relative importance of key components of plant diversity as drivers of herbivore, predator, and parasitoid species richness in experimental forests and grasslands. We find that plant species richness effects on consumer species richness are consistently positive and mediated by elevated structural and functional diversity of the plant communities. The importance of these diversity components differs across trophic levels and ecosystems, cautioning against ignoring the fundamental ecological complexity of biodiversity effects. Importantly, plant diversity effects on higher trophic-level species richness are in many cases mediated by modifications of consumer abundances. In light of recently reported drastic declines in insect abundances, our study identifies important pathways connecting plant diversity and consumer diversity across ecosystems.</p>", "keywords": ["0106 biological sciences", "2. Zero hunger", "570", "/dk/atira/pure/core/keywords/nachhaltigkeitswissenschaft; name=Sustainability Science", "Science", "/dk/atira/pure/subjectarea/asjc/1600; name=Chemistry(all)", "Q", "/dk/atira/pure/subjectarea/asjc/1300; name=Biochemistry", " Genetics and Molecular Biology(all)", "634", "Biodiversity", "/dk/atira/pure/core/keywords/biology; name=Ecosystems Research", "Plants", "15. Life on land", "/dk/atira/pure/subjectarea/asjc/1000; name=General", "01 natural sciences", "Article", "ddc:", "/dk/atira/pure/subjectarea/asjc/3100; name=Physics and Astronomy(all)", "Species Specificity", "Animals", "14. Life underwater", "Arthropods"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-09448-8.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-09448-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-09448-8", "name": "item", "description": "10.1038/s41467-019-09448-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-09448-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-29T00:00:00Z"}}, {"id": "10.1038/s41467-018-05824-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:11Z", "type": "Journal Article", "created": "2018-08-20", "title": "Biogenic volatile release from permafrost thaw is determined by the soil microbial sink", "description": "Abstract<p>Warming in the Arctic accelerates thawing of permafrost-affected soils, which leads to a release of greenhouse gases to the atmosphere. We do not know whether permafrost thaw also releases non-methane volatile organic compounds that can contribute to both negative and positive radiative forcing on climate. Here we show using proton transfer reaction\uffe2\uff80\uff93time of flight\uffe2\uff80\uff93mass spectrometry that substantial amounts of ethanol and methanol and in total 316 organic ions were released from Greenlandic permafrost soils upon thaw in laboratory incubations. We demonstrate that the majority of this release is taken up in the active layer above. In an experiment using 14C-labeled ethanol and methanol, we demonstrate that these compounds are consumed by microorganisms. Our findings highlight that the thawing permafrost soils are not only a considerable source of volatile organic compounds but also that the active layer regulates their release into the atmosphere.</p>", "keywords": ["0301 basic medicine", "Ethanol", "Science", "Climate", "Methanol", "General Biochemistry", "Genetics and Molecular Biology", "Q", "General Physics and Astronomy", "Permafrost", "General Chemistry", "15. Life on land", "01 natural sciences", "Article", "03 medical and health sciences", "13. Climate action", "11. Sustainability", "SDG 13 - Climate Action", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.nature.com/articles/s41467-018-05824-y.pdf"}, {"href": "https://doi.org/10.1038/s41467-018-05824-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-018-05824-y", "name": "item", "description": "10.1038/s41467-018-05824-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-018-05824-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-08-24T00:00:00Z"}}, {"id": "10.1038/s41467-019-14197-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:12Z", "type": "Journal Article", "created": "2020-01-24", "title": "High-quality genome sequence of white lupin provides insight into soil exploration and seed quality", "description": "Abstract<p>White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n\uffe2\uff80\uff89=\uffe2\uff80\uff8950, 451\uffe2\uff80\uff89Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.</p>", "keywords": ["Repetitive Sequences", " Nucleic Acid/genetics", "0301 basic medicine", "[SDV]Life Sciences [q-bio]", "Plant Roots/genetics", "Gene Dosage", "Plant Science", "Crop", "Alkaloids/chemistry", "Plant Roots", "Gene", "Repetitive Sequences", "630", "Agricultural and Biological Sciences", "Domestication", "Soil", "Models", "Symbiotic Nitrogen Fixation in Legumes", "Gene Duplication", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_3224", "Plant Proteins/metabolism", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Genome", "Q", "http://aims.fao.org/aos/agrovoc/c_27583", "Life Sciences", "Transcriptome/genetics", "http://aims.fao.org/aos/agrovoc/c_92382", "Polymorphism", " Single Nucleotide/genetics", "Lupinus", "[SDV] Life Sciences [q-bio]", "Protein Crop", "Seeds", "http://aims.fao.org/aos/agrovoc/c_5956", "White (mutation)", "Single Nucleotide/genetics", "Sequence Analysis", "Genome", " Plant", "expression des g\u00e8nes", "http://aims.fao.org/aos/agrovoc/c_4464", "Synteny/genetics", "Evolution", "Lupin Seeds", "Science", "Centromere", "Lupinus/genetics", "Polymorphism", " Single Nucleotide", "Article", "g\u00e9nomique", "Evolution", " Molecular", "Evolution and Nutritional Properties of Lupin Seeds", "physiologie v\u00e9g\u00e9tale", "03 medical and health sciences", "Alkaloids", "Genetic", "Nucleic Acid/genetics", "Seeds/physiology", "Centromere/genetics", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Polymorphism", "Biology", "Ecology", " Evolution", " Behavior and Systematics", "Repetitive Sequences", " Nucleic Acid", "Sequence assembly", "http://aims.fao.org/aos/agrovoc/c_25189", "Ecotype", "Models", " Genetic", "g\u00e9nome", "Botany", "Molecular", "Genetic Variation", "Molecular Sequence Annotation", "Plant", "DNA", "Sequence Analysis", " DNA", "s\u00e9quence nucl\u00e9otidique", "15. Life on land", "http://aims.fao.org/aos/agrovoc/c_27527", "Agronomy", "Plant Leaves", "Evolution and Ecology of Endophyte-Grass Symbiosis", "Lupinus albus", "FOS: Biological sciences", "Genomic Structural Variation", "Plant Leaves/metabolism", "Gene expression", "Transcriptome", "am\u00e9lioration des plantes"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-14197-9.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-14197-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-14197-9", "name": "item", "description": "10.1038/s41467-019-14197-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-14197-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-24T00:00:00Z"}}, {"id": "10.1038/s41467-020-15622-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:12Z", "type": "Journal Article", "created": "2020-05-05", "title": "Sustained fluvial deposition recorded in Mars\u2019 Noachian stratigraphic record", "description": "Abstract<p>Orbital observation has revealed a rich record of fluvial landforms on Mars, with much of this record dating 3.6\uffe2\uff80\uff933.0 Ga. Despite widespread geomorphic evidence, few analyses of Mars\uffe2\uff80\uff99 alluvial sedimentary-stratigraphic record exist, with detailed studies of alluvium largely limited to smaller sand-bodies amenable to study in-situ by rovers. These typically metre-scale outcrop dimensions have prevented interpretation of larger scale channel-morphology and long-term basin evolution, vital for understanding the past Martian climate. Here we give an interpretation of a large sedimentary succession at Izola mensa within the NW Hellas Basin rim. The succession comprises channel and barform packages which together demonstrate that river deposition was already well established &gt;3.7 Ga. The deposits mirror terrestrial analogues subject to low-peak discharge variation, implying that river deposition at Izola was subject to sustained, potentially perennial, fluvial flow. Such conditions would require an environment capable of maintaining large volumes of water for extensive time-periods, necessitating a precipitation-driven hydrological cycle.</p>", "keywords": ["550", "Science", "General Biochemistry", "Genetics and Molecular Biology", "Q", "500", "General Physics and Astronomy", "Geomorphology", "General Chemistry", "15. Life on land", "01 natural sciences", "Article", "12. Responsible consumption", "Sedimentology", " Stratigraphy", " Fluvial Deposits", " Mars", " Sedimentary Deposits", "[SDU.STU.PL]Sciences of the Universe [physics]/Earth Sciences/Planetology", "13. Climate action", "Inner planets", "[SDU.STU.PL] Sciences of the Universe [physics]/Earth Sciences/Planetology", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://oro.open.ac.uk/70442/1/70442.pdf"}, {"href": "https://www.nature.com/articles/s41467-020-15622-0.pdf"}, {"href": "https://doi.org/10.1038/s41467-020-15622-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-020-15622-0", "name": "item", "description": "10.1038/s41467-020-15622-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-020-15622-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-05T00:00:00Z"}}, {"id": "10.1038/s41467-022-29161-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:12Z", "type": "Journal Article", "created": "2022-03-17", "title": "Structure and function of the soil microbiome underlying N2O emissions from global wetlands", "description": "Abstract<p>Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.</p", "keywords": ["0301 basic medicine", "570", "571", "Supplementary Data", "QH301 Biology", "Science", "General Biochemistry", "Genetics and Molecular Biology", "Nitrous Oxide", "General Physics and Astronomy", "Soil Science", "551", "852993", "Article", "DH150187", "QH301", "Greenhouse Gases", "Soil", "03 medical and health sciences", "948219", "General", "Soil Microbiology", "0303 health sciences", "Microbiota", "Q", "General Chemistry", "15. Life on land", "6. Clean water", "BBS/e/F/000Pr10355", "13. Climate action", "BB/r012490/1", "Wetlands", "Biotechnology and Biological Sciences Research Council (BBSRC)", "Other", "European Research Council"]}, "links": [{"href": "https://pub.epsilon.slu.se/27540/1/bahram-m-et-al-220412.pdf"}, {"href": "https://ueaeprints.uea.ac.uk/id/eprint/84269/1/Published_Version.pdf"}, {"href": "https://www.nature.com/articles/s41467-022-29161-3.pdf"}, {"href": "https://doi.org/10.1038/s41467-022-29161-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-022-29161-3", "name": "item", "description": "10.1038/s41467-022-29161-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-022-29161-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-17T00:00:00Z"}}, {"id": "10.1038/s41467-022-32464-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:12Z", "type": "Journal Article", "created": "2022-08-22", "title": "Global systematic review with meta-analysis reveals yield advantage of legume-based rotations and its drivers", "description": "Abstract<p>Diversified cropping systems, especially those including legumes, have been proposed to enhance food production with reduced inputs and environmental impacts. However, the impact of legume pre-crops on main crop yield and its drivers has never been systematically investigated in a global context. Here, we synthesize 11,768 yield observations from 462 field experiments comparing legume-based and non-legume cropping systems and show that legumes enhanced main crop yield by 20%. These yield advantages decline with increasing N fertilizer rates and crop diversity of the main cropping system. The yield benefits are consistent among main crops (e.g., rice, wheat, maize) and evident across pedo-climatic regions. Moreover, greater yield advantages (32% vs. 7%) are observed in low- vs. high-yielding environments, suggesting legumes increase crop production with low inputs (e.g., in Africa or organic agriculture). In conclusion, our study suggests that legume-based rotations offer a critical pathway for enhancing global crop production, especially when integrated into low-input and low-diversity agricultural systems.</p", "keywords": ["Crops", " Agricultural", "0106 biological sciences", "Supplementary Information", "330", "QH301 Biology", "Science", "General Biochemistry", "Genetics and Molecular Biology", "General Physics and Astronomy", "Crops", "01 natural sciences", "Article", "QH301", "Vegetables", "SDG 2 - Zero Hunger", "General", "Fertilizers", "Fertilizers/analysis", "2. Zero hunger", "Agricultural", "Q", "Agriculture", "Fabaceae", "General Chemistry", "04 agricultural and veterinary sciences", "15. Life on land", "Crop Production", "https://doi.org/10.1038/s41467-022-32464-0", "0401 agriculture", " forestry", " and fisheries"]}, "links": [{"href": "https://doi.org/10.1038/s41467-022-32464-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-022-32464-0", "name": "item", "description": "10.1038/s41467-022-32464-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-022-32464-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-08-22T00:00:00Z"}}, {"id": "10.1038/s41598-017-07305-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:16Z", "type": "Journal Article", "created": "2017-07-26", "title": "Theoretical isotopic fractionation of magnesium between chlorophylls", "description": "Abstract<p>Magnesium is the metal at the center of all types of chlorophyll and is thus crucial to photosynthesis. When an element is involved in a biosynthetic pathway its isotopes are fractionated based on the difference of vibrational frequency between the different molecules. With the technical advance of multi-collectors plasma-mass-spectrometry and improvement in analytical precision, it has recently been found that two types of chlorophylls (a and b) are isotopically distinct. These results have very significant implications with regards to the use of Mg isotopes to understand the biosynthesis of chlorophyll. Here we present theoretical constraints on the origin of these isotopic fractionations through ab initio calculations. We present the fractionation factor for chlorphyll a, b, d, and f. We show that the natural isotopic variations among chlorophyll a and b are well explained by isotopic fractionation under equilibrium, which implies exchanges of Mg during the chlorophyll cycle. We predict that chlorophyll d and f should be isotopically fractionated compared to chlorophyll a and that this could be used in the future to understand the biosynthesis of these molecules.</p>", "keywords": ["Chlorophyll", "0301 basic medicine", "0303 health sciences", "RELEVANT", "Molecular Structure", "PHOTOSYNTHESIS", "Science", "Q", "POTENTIALS", "R", "Chemical Fractionation", "Fe", "Article", "3. Good health", "[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry", "[CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry", "03 medical and health sciences", "Isotopes", "Zn", "Medicine", "PLANTS", "Magnesium", "[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry", " Molecular Biology/Biochemistry [q-bio.BM]", "GEOCHEMISTRY", "[SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry", " Molecular Biology/Biochemistry [q-bio.BM]"], "contacts": [{"organization": "Fr\u00e9d\u00e9ric Moynier, Fr\u00e9d\u00e9ric Moynier, Toshiyuki Fujii,", "roles": ["creator"]}]}, "links": [{"href": "https://www.nature.com/articles/s41598-017-07305-6.pdf"}, {"href": "https://doi.org/10.1038/s41598-017-07305-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-017-07305-6", "name": "item", "description": "10.1038/s41598-017-07305-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-017-07305-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-08-01T00:00:00Z"}}, {"id": "10.1038/s41598-023-49194-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:17Z", "type": "Journal Article", "created": "2023-12-13", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "description": "Abstract<p>Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.</p", "keywords": ["0301 basic medicine", "Bacillus", "Gene", "Agricultural and Biological Sciences", "https://purl.org/becyt/ford/1.6", "Phylogeny", "GC-content", "2. Zero hunger", "0303 health sciences", "Genome", "Acinetobacter", "soil bacteria", "Q", "Probiotics and Prebiotics", "R", "Life Sciences", "Anti-Bacterial Agents", "3. Good health", "Ribosomal RNA", "Medicine", "Microbial genetics", "metagenomics assembly", "Biotechnology", "Bacteriocin", "Science", ".", "Synteny", "Microbiology", "Article", "Applied microbiology", "Lipopeptides", "03 medical and health sciences", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "https://purl.org/becyt/ford/1", "Molecular Biology", "Biology", "genetic engineering", "Bacteria", "Secondary metabolites", "In silico", "bacterial genomes", "Whole genome sequencing", "FOS: Biological sciences", "Microbial Enzymes and Biotechnological Applications", "Antibacterial activity", "Genome", " Bacterial", "Food Science", "Phylogenetic tree"]}, "links": [{"href": "https://www.nature.com/articles/s41598-023-49194-y.pdf"}, {"href": "https://doi.org/10.1038/s41598-023-49194-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-023-49194-y", "name": "item", "description": "10.1038/s41598-023-49194-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-023-49194-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-13T00:00:00Z"}}, {"id": "10.1039/d0mt00043d", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:22Z", "type": "Journal Article", "created": "2020-05-20", "title": "Biomolecular approaches to understanding metal tolerance and hyperaccumulation in plants", "description": "Abstract<p>Trace metal elements are essential for plant growth but become toxic at high concentrations, while some non-essential elements, such as Cd and As, show toxicity even in traces. Thus, metal homeostasis is tightly regulated in plants. Plant species colonising metalliferous soils have evolved mechanisms to hypertolerate metals and, in rare cases, can hyperaccumulate them in excess amounts in their shoots. The molecular mechanisms of metal hypertolerance and hyperaccumulation are likely derived from alterations in the basic mechanisms involved in general metal homeostasis. Genes involved in metal transport, synthesis of metal chelators and oxidative stress responses are constitutively and highly expressed in metal hypertolerant and hyperaccumulator species. Plant specialized metabolites and cell wall components have been proposed as major players in these mechanisms. In addition, the high intra-specific natural variation of metal hypertolerance and hyperaccumulation suggests that various molecular mechanisms might be involved in the evolution of these traits. To date, the potential of wild plant populations as systems to study metal tolerance and hyperaccumulation has not been fully exploited. The advent of next-generation sequencing (NGS) has enabled the study of non-model species, providing an opportunity to study natural populations and new tolerant and/or hyperaccumulating species, and will provide new insights into metal tolerance and hyperaccumulation. In this review we highlight background knowledge about metal tolerance and hyperaccumulation in plants and the current state-of-the-art techniques to study and identify the underlying mechanisms of metal hypertolerance and hyperaccumulation. We also outline for the reader the importance of the multidisciplinarity of this research field and how the integration of multiomic approaches will benefit facing the future scientific challenges.</p", "keywords": ["[SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry", "580", "2. Zero hunger", "0301 basic medicine", "Molecular Biology/Genomics [q-bio.GN]", "570", "0303 health sciences", "Molecular Biology/Molecular Networks [q-bio.MN]", "[SDV.BBM]Life Sciences [q-bio]/Biochemistry", "High-Throughput Nucleotide Sequencing", "[SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry", " Molecular Biology/Molecular Networks [q-bio.MN]", "[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry", "[SDV.BID]Life Sciences [q-bio]/Biodiversity", "15. Life on land", "3. Good health", "[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding", "03 medical and health sciences", "Biodegradation", " Environmental", "Metals", "[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry", " Molecular Biology/Genomics [q-bio.GN]", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Soil Pollutants", "[SDV.BBM]Life Sciences [q-bio]/Biochemistry", " Molecular Biology", "Molecular Biology", "Cadmium"]}, "links": [{"href": "https://academic.oup.com/metallomics/article-pdf/12/6/840/41702193/d0mt00043d.pdf"}, {"href": "https://doi.org/10.1039/d0mt00043d"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Metallomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1039/d0mt00043d", "name": "item", "description": "10.1039/d0mt00043d", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1039/d0mt00043d"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-20T00:00:00Z"}}, {"id": "10.1039/d2cp00325b", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:22Z", "type": "Journal Article", "created": "2022-05-13", "title": "Taming non-radiative recombination in Si nanocrystals interlinked in a porous network", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>It is possible to control the source of recombination in the same sample of porous silicon by applying a cyclic sequence of hydrogenation\u2013oxidation\u2013hydrogenation processes and, consequently, switching on-demand between Shockley\u2013Read\u2013Hall and Auger recombinations.</p></article>", "keywords": ["Science & Technology", "Chemical Physics", "02 Physical Sciences", "Chemistry", " Physical", "Physics", "ELECTRON-PHONON", "IMPURITIES", "Physics", " Atomic", " Molecular & Chemical", "Atomic", "Molecular & Chemical", "530", "09 Engineering", "620", "Chemistry", "MATRIX-ELEMENTS", "Physical Sciences", "Physical", "SILICON", "03 Chemical Sciences"]}, "links": [{"href": "http://pubs.rsc.org/en/content/articlepdf/2022/CP/D2CP00325B"}, {"href": "https://doi.org/10.1039/d2cp00325b"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Physical%20Chemistry%20Chemical%20Physics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1039/d2cp00325b", "name": "item", "description": "10.1039/d2cp00325b", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1039/d2cp00325b"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10.1093/bioinformatics/btad407", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:56Z", "type": "Journal Article", "created": "2023-06-24", "title": "enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways", "description": "Abstract                                   Motivation                   <p>Transformation products (TPs) of man-made chemicals, formed through microbially mediated transformation in the environment, can have serious adverse environmental effects, yet the analytical identification of TPs is challenging. Rule-based prediction tools are successful in predicting TPs, especially in environmental chemistry applications that typically have to rely on small datasets, by imparting the existing knowledge on enzyme-mediated biotransformation reactions. However, the rules extracted from biotransformation reaction databases usually face the issue of being over/under-generalized and are not flexible to be updated with new reactions.</p>                                                   Results                   <p>We developed an automatic rule extraction tool called enviRule. It clusters biotransformation reactions into different groups based on the similarities of reaction fingerprints, and then automatically extracts and generalizes rules for each reaction group in SMARTS format. It optimizes the genericity of automatic rules against the downstream TP prediction task. Models trained with automatic rules outperformed the models trained with manually curated rules by 30% in the area under curve (AUC) scores. Moreover, automatic rules can be easily updated with new reactions, highlighting enviRule\uffe2\uff80\uff99s strengths for both automatic extraction of optimized reactions rules and automated updating thereof.</p>                                                   Availability and implementation                   <p>enviRule code is freely available at https://github.com/zhangky12/enviRule.</p>", "keywords": ["10120 Department of Chemistry", "Statistics and Probability", "Original Paper", "1303 Biochemistry", "Computational Biology", "Biochemistry", "Computer Science Applications", "Computational Mathematics", "Computational Theory and Mathematics", "13. Climate action", "540 Chemistry", "1312 Molecular Biology", "1706 Computer Science Applications", "2613 Statistics and Probability", "2605 Computational Mathematics", "Molecular Biology", "Biotransformation", "1703 Computational Theory and Mathematics"]}, "links": [{"href": "https://doi.org/10.1093/bioinformatics/btad407"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/bioinformatics/btad407", "name": "item", "description": "10.1093/bioinformatics/btad407", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/bioinformatics/btad407"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-24T00:00:00Z"}}, {"id": "10.1093/femsle/fnab100", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:57Z", "type": "Journal Article", "created": "2021-07-30", "title": "Transcriptomic markers of fungal growth, respiration and carbon-use efficiency", "description": "ABSTRACT                <p>Fungal metabolic carbon acquisition and its subsequent partitioning between biomass production and respiration, i.e. the carbon-use efficiency (CUE), are central parameters in biogeochemical modeling. However, current available techniques for estimating these parameters are all associated with practical and theoretical shortcomings, making assessments unreliable. Gene expression analyses hold the prospect of phenotype prediction by indirect means, providing new opportunities to obtain information about metabolic priorities. We cultured four different fungal isolates (Chalara longipes, Laccaria bicolor, Serpula lacrymans and Trichoderma harzianum) in liquid media with contrasting nitrogen availability and measured growth rates and respiration to calculate CUE. By relating gene expression markers to measured carbon fluxes, we identified genes coding for 1,3-\uffce\uffb2-glucan synthase and 2-oxoglutarate dehydrogenase as suitable markers for growth and respiration, respectively, capturing both intraspecific variation as well as within-strain variation dependent on growth medium. A transcript index based on these markers correlated significantly with differences in CUE between the fungal isolates. Our study paves the way for the use of these markers to assess differences in growth, respiration and CUE in natural fungal communities, using metatranscriptomic or the RT-qPCR approach.</p", "keywords": ["0301 basic medicine", "growth", "Fungal Proteins", "Laccaria", "03 medical and health sciences", "Ascomycota", "Research Letter", "Biologiska vetenskaper", "Trichoderma", "0303 health sciences", "metatranscriptomics", "Ecology", "Basidiomycota", "Biochemistry and Molecular Biology", "Fungi", "Biological Sciences", "Carbon", "Microbiology (Microbiology in the medical area to be 30109)", "Hypocreales", "carbon-use efficiency", "gene markers", "fungi", "Transcriptome", "respiration", "Biomarkers"]}, "links": [{"href": "https://pub.epsilon.slu.se/26755/1/hasby_f_a_et_al_220119.pdf"}, {"href": "http://academic.oup.com/femsle/article-pdf/368/15/fnab100/39805403/fnab100.pdf"}, {"href": "https://doi.org/10.1093/femsle/fnab100"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Letters", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsle/fnab100", "name": "item", "description": "10.1093/femsle/fnab100", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsle/fnab100"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-01T00:00:00Z"}}, {"id": "10.1098/rstb.2020.0169", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:05Z", "type": "Journal Article", "created": "2021-08-08", "title": "The role of soils in delivering Nature's Contributions to People", "description": "<p>             This theme issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). The papers in this issue show that soils can contribute positively to the delivery of all NCP. These contributions can be maximized through careful soil management to provide healthy soils, but poorly managed, degraded or polluted soils may contribute negatively to the delivery of NCP. Soils are also shown to contribute positively to the UN Sustainable Development Goals. Papers in the theme issue emphasize the need for careful soil management. Priorities for soil management must include: (i) for healthy soils in natural ecosystems,             protect             them from conversion and degradation, (ii) for managed soils,             manage             in a way to protect and enhance soil biodiversity, health, productivity and sustainability and to prevent degradation, and (iii) for degraded soils,             restore             to full soil health. Our knowledge of what constitutes sustainable soil management is mature enough to implement best management practices, in order to maintain and improve soil health. The papers in this issue show the vast potential of soils to contribute to NCP. This is not only desirable, but essential to sustain a healthy planet and if we are to deliver sustainable development in the decades to come.           </p>           <p>This article is part of the theme issue \uffe2\uff80\uff98The role of soils in delivering Nature\uffe2\uff80\uff99s Contributions to People\uffe2\uff80\uff99.</p", "keywords": ["Conservation of Natural Resources", "Biomedical and clinical sciences", "330", "Life on Land", "QH301 Biology", "General Biochemistry", "Genetics and Molecular Biology", "Medical and Health Sciences", "soil", "12. Responsible consumption", "QH301", "Soil", "11. Sustainability", "774378", "Humans", "European Commission", "Ecosystem", "2. Zero hunger", "Evolutionary Biology", "Biomedical and Clinical Sciences", "soil health", "Biodiversity", "04 agricultural and veterinary sciences", "Biological Sciences", "15. Life on land", "Biological sciences", "Nature's Contributions to People", "13. Climate action", "NCP", "0401 agriculture", " forestry", " and fisheries", "General Agricultural and Biological Sciences"]}, "links": [{"href": "https://escholarship.org/content/qt2ht9h1mh/qt2ht9h1mh.pdf"}, {"href": "https://doi.org/10.1098/rstb.2020.0169"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Philosophical%20Transactions%20of%20the%20Royal%20Society%20B%3A%20Biological%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1098/rstb.2020.0169", "name": "item", "description": "10.1098/rstb.2020.0169", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1098/rstb.2020.0169"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-04T00:00:00Z"}}, {"id": "10.1101/2024.05.03.592357", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:07Z", "type": "Journal Article", "created": "2025-06-27", "title": "The evolutionary history and functional specialization of microRNA genes inArabidopsis halleriandA. lyrata", "description": "Abstract                <p>MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in plant genomes. While some miRNA genes are deeply conserved, the majority appear to be species-specific, raising the question of how they emerge and integrate into cellular regulatory networks. To address this question, we first performed a detailed annotation of miRNA genes in the closely related Arabidopsis halleri and A. lyrata, then evaluated their phylogenetic conservation across 87 plant species. We then characterized the process by which newly emerged miRNA genes progressively acquire the properties of \uffe2\uff80\uff9ccanonical\uffe2\uff80\uff9d miRNA genes, in terms of size and stability of the hairpin precursor, loading of their cleavage products into Argonaute proteins, and potential to regulate downstream target genes. Analysis of nucleotide polymorphism distribution along the hairpin sequence (stem, mature miRNA, terminal loop) revealed that the selective constraints on recently emerged miRNA genes were initially weak, gradually increasing toward evolutionarily conserved miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary progression toward canonical miRNAs by which a small fraction of de novo formed miRNA genes eventually integrate into \uffe2\uff80\uff9ccore\uffe2\uff80\uff9d biological processes.</p", "keywords": ["[SDV] Life Sciences [q-bio]", "0301 basic medicine", "arabidopsis", "0303 health sciences", "03 medical and health sciences", "microRNA", "evolution", "species-specific genes", "[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry", " Molecular Biology/Genomics [q-bio.GN]", "15. Life on land", "polymorphism", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics"]}, "links": [{"href": "https://doi.org/10.1101/2024.05.03.592357"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Plant%20Cell", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2024.05.03.592357", "name": "item", "description": "10.1101/2024.05.03.592357", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2024.05.03.592357"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-05-05T00:00:00Z"}}, {"id": "10.1111/1462-2920.13954", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:14Z", "type": "Journal Article", "created": "2022-10-18", "title": "Application of stable-isotope labelling techniques for the detection of active diazotrophs", "description": "Summary<p>Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N\uffe2\uff80\uff90based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to 15N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting 15N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.</p>", "keywords": ["Spectrum Analysis", " Raman", "BIOLOGICAL SOIL CRUSTS", "106005 Bioinformatik", "106023 Molekularbiologie", "Nitrogen Fixation", "REVEALS", "FLUORESCENCE", "Research Articles", "Soil Microbiology", "106022 Mikrobiologie", "SPECTROSCOPY", "Bacteria", "Nitrogen Isotopes", "106003 Biodiversity research", "106023 Molecular biology", "GENETIC-REGULATION", "Archaea", "6. Clean water", "SURFACE-ENHANCED RAMAN", "COMMUNITY", "106003 Biodiversit\u00e4tsforschung", "13. Climate action", "Isotope Labeling", "106022 Microbiology", "NITROGEN-FIXATION", "106005 Bioinformatics", "RIBOSOMAL-RNA", "N-2 FIXATION"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13954"}, {"href": "https://doi.org/10.1111/1462-2920.13954"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.13954", "name": "item", "description": "10.1111/1462-2920.13954", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13954"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-12-15T00:00:00Z"}}, {"id": "10.1111/1462-2920.16213", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:14Z", "type": "Journal Article", "created": "2022-10-18", "title": "Application of stable\u2010isotope labelling techniques for the detection of active diazotrophs", "description": "Summary<p>Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N\uffe2\uff80\uff90based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to 15N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting 15N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.</p", "keywords": ["Spectrum Analysis", " Raman", "BIOLOGICAL SOIL CRUSTS", "106005 Bioinformatik", "106023 Molekularbiologie", "Nitrogen Fixation", "REVEALS", "FLUORESCENCE", "Research Articles", "Soil Microbiology", "106022 Mikrobiologie", "SPECTROSCOPY", "Bacteria", "Nitrogen Isotopes", "106003 Biodiversity research", "106023 Molecular biology", "GENETIC-REGULATION", "Archaea", "6. Clean water", "SURFACE-ENHANCED RAMAN", "COMMUNITY", "106003 Biodiversit\u00e4tsforschung", "13. Climate action", "Isotope Labeling", "106022 Microbiology", "NITROGEN-FIXATION", "106005 Bioinformatics", "RIBOSOMAL-RNA", "N-2 FIXATION"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13954"}, {"href": "https://doi.org/10.1111/1462-2920.16213"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.16213", "name": "item", "description": "10.1111/1462-2920.16213", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.16213"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-12-15T00:00:00Z"}}, {"id": "10.1111/ecog.05478", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:16Z", "type": "Journal Article", "created": "2021-05-07", "title": "Multi\u2010taxa colonisation along the foreland of a vanishing equatorial glacier", "description": "<p>Retreating glaciers, icons of climate change, release new potential habitats for both aquatic and terrestrial organisms. High\uffe2\uff80\uff90elevation species are threatened by temperature increases and the upward migration of lowlands species. Improving our understanding of successional processes after glacier retreat becomes urgent, especially in the tropics, where glacier shrinkage is particularly fast. We examined the successional patterns of aquatic invertebrates, ground beetles, terrestrial plants, soil eukaryotes (algae, invertebrates, plants) in an equatorial glacier foreland (Carihuairazo, Ecuador). Based on both taxonomical identification and eDNA metabarcoding, we analysed the effects of both environmental conditions and age of deglacierization on community composition. Except for algae, diversity increased with time since deglacierization, especially among passive dispersers, suggesting that dispersal was a key driver structuring the glacier foreland succession. Spatial \uffce\uffb2\uffe2\uff80\uff90diversity was mainly attributed to nestedness for aquatic invertebrates, terrestrial plants and soil algae, likely linked to low environmental variability within the studied glacier foreland; and to turnover for soil invertebrates, suggesting competition exclusion at the oldest successional stage. Pioneer communities were dominated by species exhibiting flexible feeding strategies and high dispersal ability (mainly transported by wind), probably colonising from lower altitudes, or from the glacier in the case of algae. Overall, glacier foreland colonisation in the tropics exhibit common characteristics to higher latitudes. High\uffe2\uff80\uff90elevation species are nevertheless threatened, as the imminent extinction of many tropical glaciers will affect species associated to glacier\uffe2\uff80\uff90influenced habitats but also prevent cold\uffe2\uff80\uff90adapted and hygrophilous species from using these habitats as refuges in a warming world.</p>", "keywords": ["Colonization", "[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", "550", "Early succession", "glacier retreat", "Sociology", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "Environmental DNA Sequencing", "Glacier", "Ecology", "Geography", "early succession", "Life Sciences", "Phylogenetics and taxonomy", "Biodiversity", "[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics", "Threatened species", "FOS: Sociology", "Multiple-taxa", "multiple-taxa", "Habitat", "[SDE]Environmental Sciences", "Physical Sciences", "environment/Ecosystems", "570", "Physical geography", "Population", "Global Diversity of Microbial Eukaryotes and Their Evolution", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics", "Ecological succession", "Biochemistry", " Genetics and Molecular Biology", "Biological dispersal", "[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "equatorial glacier foreland", "Equatorial glacier foreland", "Glacier retreat", "Molecular Biology", "Biology", "Demography", "Marine Microbial Diversity and Biogeography", "Colonisation", "South America", "15. Life on land", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "13. Climate action", "FOS: Biological sciences", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "Environmental Science", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "early succession; equatorial glacier foreland; glacier retreat; multiple-taxa", "Environmental DNA in Biodiversity Monitoring"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/851699/2/rosero%202021.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.05478"}, {"href": "https://doi.org/10.1111/ecog.05478"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecography", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/ecog.05478", "name": "item", "description": "10.1111/ecog.05478", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/ecog.05478"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-05-06T00:00:00Z"}}, {"id": "10.1111/gcb.15420", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:23Z", "type": "Journal Article", "created": "2021-03-04", "title": "Microbial inputs at the litter layer translate climate into altered organic matter properties", "description": "<p>&amp;lt;p&amp;gt;Plant litter chemistry is altered during decomposition but it remains unknown if these alterations, and thus the composition of residual litter, will change in response to climate. Selective microbial mineralization of litter components and the accumulation of microbial necromass can drive litter compositional change, but the extent to which these mechanisms respond to climate remains poorly understood. We addressed this knowledge gap by studying needle litter decomposition along a boreal forest climate transect. Specifically, we investigated how the composition and/or metabolism of the decomposer community varies with climate, and if that variation is associated with distinct modifications of litter chemistry during decomposition. We analyzed the composition of microbial phospholipid fatty acids (PLFAs) in the litter layer and measured natural abundance &amp;amp;#948;&amp;lt;sup&amp;gt;13&amp;lt;/sup&amp;gt;C&amp;lt;sub&amp;gt;PLFA&amp;lt;/sub&amp;gt; values as an integrated measure of microbial metabolisms. Changes in litter chemistry and &amp;amp;#948;&amp;lt;sup&amp;gt;13&amp;lt;/sup&amp;gt;C values were measured in litterbag experiments conducted at each transect site. A warmer climate was associated with higher litter nitrogen concentrations as well as altered microbial community structure (lower fungi:bacteria ratios) and microbial metabolism (higher &amp;amp;#948;&amp;lt;sup&amp;gt;13&amp;lt;/sup&amp;gt;C&amp;lt;sub&amp;gt;PLFA&amp;lt;/sub&amp;gt;). Litter in warmer transect regions accumulated less aliphatic&amp;amp;#8208;C (lipids, waxes) and retained more O&amp;amp;#8208;alkyl&amp;amp;#8208;C (carbohydrates), consistent with enhanced &amp;lt;sup&amp;gt;13&amp;lt;/sup&amp;gt;C&amp;amp;#8208;enrichment in residual litter, than in colder regions. These results suggest that chemical changes during litter decomposition will change with climate, driven primarily by indirect climate effects (e.g., greater nitrogen availability and decreased fungi:bacteria ratios) rather than direct temperature effects. A positive correlation between microbial biomass &amp;amp;#948;&amp;lt;sup&amp;gt;13&amp;lt;/sup&amp;gt;C values and &amp;lt;sup&amp;gt;13&amp;lt;/sup&amp;gt;C&amp;amp;#8208;enrichment during decomposition suggests that change in litter chemistry is driven more by distinct microbial necromass inputs than differences in the selective removal of litter components. Our study highlights the role that microbial inputs during early litter decomposition can play in shaping surface litter contribution to soil organic matter as it responds to climate warming effects such as greater nitrogen availability.&amp;lt;/p&amp;gt;</p>", "keywords": ["DECOMPOSITION", "C-13", "CP&#8208", "necromass", "litter decomposition", "COMMUNITY COMPOSITION", "Soil", "CARBON SEQUESTRATION", "Taiga", "boreal forest", "bacteria", "C-13 NMR", "TEMPERATURE", "Biochemistry", " cell and molecular biology", "Soil Microbiology", "FUNGAL", "2. Zero hunger", "MAS C-13&#8208", "Fungi", "04 agricultural and veterinary sciences", "15. Life on land", "NMR", "6. Clean water", "climate transect", "Plant Leaves", "13. Climate action", "FOREST SOILS", "PLFA", "0401 agriculture", " forestry", " and fisheries", "fungi", "FATTY-ACIDS", "BULK CARBON", "LIGNIN"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15420"}, {"href": "https://doi.org/10.1111/gcb.15420"}, {"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.15420", "name": "item", "description": "10.1111/gcb.15420", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.15420"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-16T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:55Z", "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": "10.1111/ppl.12714", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:50Z", "type": "Journal Article", "created": "2018-03-01", "title": "Anatomical and hormonal description of rootlet primordium development along white lupin cluster root", "description": "<p>Cluster root (CR) is one of the most spectacular plant developmental adaptations to hostile environment. It can be found in a few species from a dozen botanical families, including white lupin (Lupinus albus) in the Fabaceae family. These amazing structures are produced in phosphate\uffe2\uff80\uff90deprived conditions and are made of hundreds of short roots also known as rootlets. White lupin is the only crop bearing CRs and is considered as the model species for CR studies. However, little information is available on CRs atypical development, including the molecular events that trigger their formation. To provide insights on CR formation, we performed an anatomical and cellular description of rootlet development in white lupin. Starting with a classic histological approach, we described rootlet primordium development and defined eight developmental stages from rootlet initiation to their emergence. Due to the major role of hormones in the developmental program of root system, we next focussed on auxin\uffe2\uff80\uff90related mechanisms. We observed the establishment of an auxin maximum through rootlet development in transgenic roots expressing the DR5:GUS auxin reporter. Expression analysis of the main auxin\uffe2\uff80\uff90related genes [TIR, Auxin Response Factor (ARF) and AUX/IAA] during a detailed time course revealed specific expression associated with the formation of the rootlet primordium. We showed that L. albus TRANSPORT INHIBITOR RESPONSE 1b is expressed during rootlet primordium formation and that L. albus AUXIN RESPONSE FACTOR 5 is expressed in the vasculature but absent in the primordium itself. Altogether, our results describe the very early cellular events leading to CR formation and reveal some of the auxin\uffe2\uff80\uff90related mechanisms.</p>", "keywords": ["0301 basic medicine", "racine laterale", "Plant Roots", "inhibiteur de transport d'auxine", "physiologie v\u00e9g\u00e9tale", "03 medical and health sciences", "Gene Expression Regulation", " Plant", "http://aims.fao.org/aos/agrovoc/c_16034", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Cloning", " Molecular", "Promoter Regions", " Genetic", "Plant Proteins", "580", "http://aims.fao.org/aos/agrovoc/c_25189", "0303 health sciences", "syst\u00e8me racinaire", "Vegetal Biology", "interaction sol racine", "Indoleacetic Acids", "Plants", " Genetically Modified", "http://aims.fao.org/aos/agrovoc/c_27527", "Lupinus", "Lupinus albus", "lupinus albus", "phosphate inorganique", "Biologie v\u00e9g\u00e9tale", "expression des g\u00e8nes", "http://aims.fao.org/aos/agrovoc/c_4464"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.12714"}, {"href": "https://doi.org/10.1111/ppl.12714"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Physiologia%20Plantarum", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/ppl.12714", "name": "item", "description": "10.1111/ppl.12714", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/ppl.12714"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-26T00:00:00Z"}}, {"id": "10.1126/sciadv.adj8016", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:53Z", "type": "Journal Article", "created": "2023-11-29", "title": "Connecting the multiple dimensions of global soil fungal diversity", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.</p></article>", "keywords": ["Supplementary Data", "biodiversity", " fungi", " ecology", "QH301 Biology", "Diversity (politics)", "Plant Science", "Biodiversity conservation", "Fungal Diversity", "Agricultural and Biological Sciences", "Soil", "Life", "Sociology", "WATER", "Global biodiversity distribution", "Fungal diversity", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Multidisciplinary", "Earth", " Environmental", " Ecological", " and Space Sciences", "Geography", "Ecology", "soil fungal diversity", "4. Education", "SPECIES RICHNESS", "Life Sciences", "https://www.science.org/doi/suppl/10.1126/sciadv.adj8016/suppl_file/sciadv.adj8016_sm.pdf", "Biodiversity", "FOS: Sociology", "global biodiversity distribution", "sienet", "https://www.science.org/doi/suppl/10.1126/sciadv.adj8016/suppl_file/sciadv.adj8016_tables_s1_to_s13.zip", "Diversity and Evolution of Fungal Pathogens", "570", "Supplementary Information", "DNA markers", "QH301", "Sequencing high-resolution DNA", "Biochemistry", " Genetics and Molecular Biology", "monimuotoisuus", "Mycorrhizal Fungi and Plant Interactions", "Life Science", "Humans", "14. Life underwater", "General", "Global ecological processes", "Biology", "Ecosystem", "Ecology", " Evolution", " Behavior and Systematics", "global ecological processes", "Soil fungal diversity", "microbiology", "Fungi", "Water", "Cell Biology", "15. Life on land", "luonnon monimuotoisuus", "Agronomy", "biodiversiteetti", "LIFE", "ekosysteemit (ekologia)", "Evolution and Ecology of Endophyte-Grass Symbiosis", "13. Climate action", "Ecology", " evolutionary biology", "Earth and Environmental Sciences", "FOS: Biological sciences", "Anthropology", "ta1181", "biodiversity conservation", "Species richness"]}, "links": [{"href": "https://www.science.org/doi/epdf/10.1126/sciadv.adj8016"}, {"href": "https://www.science.org/doi/pdf/10.1126/sciadv.adj8016"}, {"href": "https://doi.org/10.1126/sciadv.adj8016"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20Advances", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1126/sciadv.adj8016", "name": "item", "description": "10.1126/sciadv.adj8016", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1126/sciadv.adj8016"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "10.1155/2018/9736547", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:20:01Z", "type": "Journal Article", "created": "2018-05-09", "title": "Chronological Classification of Ancient Mortars Employing Spectroscopy and Spectrometry Techniques: Sagunto (Valencia, Spain) Case", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Forty-two mortar samples, from two archaeological excavations located in Sagunto (Valencian Community, Spain), were analysed by both portable energy dispersive X-ray fluorescence spectroscopy (pED-XRF) and inductively coupled plasma mass spectrometry (ICP-MS) to determine major and minor elements and traces including rare earth elements (REEs). Collected data were crossed with those previously obtained from Sagunto Castle mortars, and principal component analysis (PCA) was applied to discriminate the construction phases of the unearthed buildings. REE permitted to ascribe most of the masonries to the Roman Imperial period. Moreover, a statistical model was built by employing partial least squares discriminant analysis (PLS-DA) in order to classify the mortars from Roman Imperial period and from Islamic period due to the problematic overlapping between these two phases. Results confirmed the effectiveness of the developed indirect chronology method, based on REE data, to discriminate among historic mortars from different construction periods on a wide scale including different Sagunto archaeological sites.</p></article>", "keywords": ["2. Zero hunger", "0601 history and archaeology", "QC350-467", "06 humanities and the arts", "Optics. Light", "energy dispersive X-ray fluorescence spectroscopy (pED-XRF); inductively coupled plasma mass spectrometry (ICP-MS)", "Analytical Chemistry; Atomic and Molecular Physics", " and Optics; Spectroscopy"]}, "links": [{"href": "https://eprints.whiterose.ac.uk/130462/1/9736547.pdf"}, {"href": "https://iris.unica.it/bitstream/11584/248342/2/Ramacciotti%20et%20al%202018.pdf"}, {"href": "https://arpi.unipi.it/bitstream/11568/935316/1/P101%20Chronological%20Classification%20of%20Ancient%20Mortars.pdf"}, {"href": "https://doi.org/10.1155/2018/9736547"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Spectroscopy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1155/2018/9736547", "name": "item", "description": "10.1155/2018/9736547", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1155/2018/9736547"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-01-01T00:00:00Z"}}, {"id": "10.1371/journal.pone.0029642", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:20:14Z", "type": "Journal Article", "created": "2012-01-04", "title": "Carbon Stocks And Fluxes In Tropical Lowland Dipterocarp Rainforests In Sabah, Malaysian Borneo", "description": "Deforestation in the tropics is an important source of carbon C release to the atmosphere. To provide a sound scientific base for efforts taken to reduce emissions from deforestation and degradation (REDD+) good estimates of C stocks and fluxes are important. We present components of the C balance for selectively logged lowland tropical dipterocarp rainforest in the Malua Forest Reserve of Sabah, Malaysian Borneo. Total organic C in this area was 167.9 Mg C ha\u207b\u00b9\u00b13.8 (SD), including: Total aboveground (TAGC: 55%; 91.9 Mg C ha\u207b\u00b9\u00b12.9 SEM) and belowground carbon in trees (TBGC: 10%; 16.5 Mg C ha\u207b\u00b9\u00b10.5 SEM), deadwood (8%; 13.2 Mg C ha\u207b\u00b9\u00b13.5 SEM) and soil organic matter (SOM: 24%; 39.6 Mg C ha\u207b\u00b9\u00b10.9 SEM), understory vegetation (3%; 5.1 Mg C ha\u207b\u00b9\u00b11.7 SEM), standing litter (<1%; 0.7 Mg C ha\u207b\u00b9\u00b10.1 SEM) and fine root biomass (<1%; 0.9 Mg C ha\u207b\u00b9\u00b10.1 SEM). Fluxes included litterfall, a proxy for leaf net primary productivity (4.9 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b10.1 SEM), and soil respiration, a measure for heterotrophic ecosystem respiration (28.6 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b11.2 SEM). The missing estimates necessary to close the C balance are wood net primary productivity and autotrophic respiration.Twenty-two years after logging TAGC stocks were 28% lower compared to unlogged forest (128 Mg C ha\u207b\u00b9\u00b113.4 SEM); a combined weighted average mean reduction due to selective logging of -57.8 Mg C ha\u207b\u00b9 (with 95% CI -75.5 to -40.2). Based on the findings we conclude that selective logging decreased the dipterocarp stock by 55-66%. Silvicultural treatments may have the potential to accelerate the recovery of dipterocarp C stocks to pre-logging levels.", "keywords": ["0106 biological sciences", "1000 Multidisciplinary", "Tropical Climate", "Science", "Rain", "Q", "R", "1100 General Agricultural and Biological Sciences", "Biodiversity", "15. Life on land", "01 natural sciences", "Carbon", "Dipterocarpaceae", "Trees", "10127 Institute of Evolutionary Biology and Environmental Studies", "Soil", "1300 General Biochemistry", " Genetics and Molecular Biology", "Borneo", "Seedlings", "13. Climate action", "570 Life sciences; biology", "590 Animals (Zoology)", "Medicine", "Biomass", "Research Article"], "contacts": [{"organization": "Saner, Philippe, Loh, Yen Yee, Ong, Robert C., Hector, Andy,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0029642"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0029642", "name": "item", "description": "10.1371/journal.pone.0029642", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0029642"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-01-03T00:00:00Z"}}, {"id": "10.1890/0012-96152003073[0377:rataip]2.0.co,2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:20:44Z", "type": "Journal Article", "created": "2004-10-30", "description": "Abstract   The noise free 300 MHz 1H NMR spectra of \u03b2-DPN+, recorded in the Fourier mode at 12\u00b0 and 68\u00b0C have been completely analysed by extensive computer simulation. It is shown, whether the coenzyme exists as an equilibrium mixture of folded \u21c4 extended forms (12\u00b0C) or in overwhelminghly extended forms (68\u00b0C), the backbone of both the nicotinamide and adenine fragments preferentially exist in       2   E-gg-g\u2032g\u2032    conformation. This orientation is significantly different from those reported in the solid state for the extended species in contact with the enzyme where       2   E-tg-g\u2032g\u2032    and       3   E-tg-g\u2032g\u2032    orientations have been observed. It is suggested that specific interactions of the backbone with the various amino acid residues in the enzyme induces conformational aberrations in the backbone. Intimate details of the backbone conformation of the extended forms of AcPy-DPN+ and \u03b2-TPN+ are also presented.", "keywords": ["Models", " Molecular", "0301 basic medicine", "Structure-Activity Relationship", "03 medical and health sciences", "Magnetic Resonance Spectroscopy", "Fourier Analysis", "Molecular Conformation", "Temperature", "NAD", "01 natural sciences", "NADP", "0104 chemical sciences"], "contacts": [{"organization": "Kurethara S. Bose, Ramaswamy H. Sarma,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1890/0012-96152003073[0377:rataip]2.0.co,2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biochemical%20and%20Biophysical%20Research%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1890/0012-96152003073[0377:rataip]2.0.co,2", "name": "item", "description": "10.1890/0012-96152003073[0377:rataip]2.0.co,2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1890/0012-96152003073[0377:rataip]2.0.co,2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1975-10-01T00:00:00Z"}}, {"id": "20864344", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:26:56Z", "type": "Journal Article", "created": "2010-09-08", "title": "Discovery and optimization of adamantyl carbamate inhibitors of 11\u03b2-HSD1", "description": "Synthesis of 2-adamantyl carbamate derivatives of piperidines and pyrrolidines led to the discovery of 9a with an IC(50) of 15.2 nM against human 11\u03b2-HSD1 in adipocytes. Optimization for increased adipocyte potency, metabolic stability and selectivity afforded 11k and 11l, both of which were >25% orally bioavailable in rat.", "keywords": ["Models", " Molecular", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "11-beta-Hydroxysteroid Dehydrogenase Type 1", "Drug Discovery", "Animals", "Adamantane", "Enzyme Inhibitors", "Rats", "3. Good health"]}, "links": [{"href": "https://doi.org/20864344"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioorganic%20%26amp%3B%20Medicinal%20Chemistry%20Letters", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20864344", "name": "item", "description": "20864344", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20864344"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-11-01T00:00:00Z"}}, {"id": "10.3389/fmicb.2020.568224", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:21:42Z", "type": "Journal Article", "created": "2020-10-27", "title": "Exopolysaccharide Features Influence Growth Success in Biocrust-forming Cyanobacteria, Moving From Liquid Culture to Sand Microcosms", "description": "Land degradation in drylands is a drawback of the combined action of climate change and human activities. New techniques have been developed to induce artificial biocrusts formation as a tool for restoration of degraded drylands, and among them soils inoculation with cyanobacteria adapted to environmental stress. Improvement of soil properties by cyanobacteria inoculation is largely related to their ability to synthesize exopolysaccharides (EPS). However, cyanobacterial EPS features [amount, molecular weight (MW), composition] can change from one species to another or when grown in different conditions. We investigated the differences in growth and polysaccharidic matrix features among three common biocrust-forming cyanobacteria (Nostoc commune, Scytonema javanicum, and Phormidium ambiguum), when grown in liquid media and on sandy soil microcosms under optimal nutrient and water, in controlled laboratory conditions. We extracted and analyzed the released EPS (RPS) and sheath for the liquid cultures, and the more soluble or loosely-bound (LB) and the more condensed or tightly-bound (TB) soil EPS fractions for the sandy soil microcosms. In liquid culture, P. ambiguum showed the greatest growth and EPS release. In contrast, on the sandy soil, S. javanicum showed the highest growth and highest LB-EPS content. N. commune showed no relevant growth after its inoculation of the sandy soil. A difference was observed in terms of MW distribution, showing that the higher MW of the polymers produced by P. ambiguum and S. javanicum compared to the polymers produced by N. commune, could have had a positive effect on growth for the first two organisms when inoculated on the sandy soil. We also observed how both RPS and sheath fractions reflected in the composition of the soil TB-EPS fraction, indicating the role in soil stabilization of both the released and the cell attached EPS. Our results indicate that the features of the polysaccharidic matrix produced by different cyanobacteria can influence their growth success in soil. These results are of great relevance when selecting suitable candidates for large-scale cyanobacteria applications in soil restoration.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "EPS monosaccharidic composition", "15. Life on land", "sand inoculation", "semiarid soil", "Microbiology", "QR1-502", "6. Clean water", "03 medical and health sciences", "EPS molecular weight distribution", "13. Climate action", "cyanobacteria liquid culture", "cyanobacteria liquid culture", " sand inoculation", " sandy soil microcosms", " EPS monosaccharidic composition", " EPS molecular weight distribution", " semiarid soil", "sandy soil microcosms"]}, "links": [{"href": "https://flore.unifi.it/bitstream/2158/1215077/2/fmicb-11-568224.pdf"}, {"href": "https://doi.org/10.3389/fmicb.2020.568224"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2020.568224", "name": "item", "description": "10.3389/fmicb.2020.568224", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2020.568224"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-27T00:00:00Z"}}, {"id": "10.2139/ssrn.4173912", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:21:19Z", "type": "Journal Article", "created": "2022-07-28", "title": "How the Structure of Per- and Polyfluoroalkyl Substances (Pfas) Influences Their Binding Potency to the Peroxisome Proliferator-Activated and Thyroid Hormone Receptors \u2013 an in Silico Screening Study", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>In this study, we investigated PFAS (per- and polyfluoroalkyl substances) binding potencies to nuclear hormone receptors (NHRs): peroxisome proliferator-activated receptors (PPARs) \u03b1, \u03b2, and \u03b3 and thyroid hormone receptors (TRs) \u03b1 and \u03b2. We have simulated the docking scores of 43 perfluoroalkyl compounds and based on these data developed QSAR (Quantitative Structure-Activity Relationship) models for predicting the binding probability to five receptors. In the next step, we implemented the developed QSAR models for the screening approach of a large group of compounds (4464) from the NORMAN Database. The in silico analyses indicated that the probability of PFAS binding to the receptors depends on the chain length, the number of fluorine atoms, and the number of branches in the molecule. According to the findings, the considered PFAS group bind to the PPAR\u03b1, \u03b2, and \u03b3 only with low or moderate probability, while in the case of TR \u03b1 and \u03b2 it is similar except that those chemicals with longer chains show a moderately high probability of binding.</p></article>", "keywords": ["0301 basic medicine", "Fluorocarbons", "0303 health sciences", "Receptors", " Thyroid Hormone", "binding probability", "peroxisome proliferator-activated receptor", "QSAR", "PFAS", "H2020", "thyroid receptor", "Organic chemistry", "Quantitative Structure-Activity Relationship", "molecular docking", "virtual screening", "PROMISCES", "MLR", "Article", "03 medical and health sciences", "perfluoroalkyl compounds", "QD241-441", "in silico", "Peroxisome Proliferators", "perfluoroalkyl compounds; PFAS; peroxisome proliferator-activated receptor; thyroid receptor; QSAR; MLR; in silico; binding probability; molecular docking; virtual screening"]}, "links": [{"href": "http://www.mdpi.com/1420-3049/28/2/479/pdf"}, {"href": "https://www.mdpi.com/1420-3049/28/2/479/pdf"}, {"href": "https://doi.org/10.2139/ssrn.4173912"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/SSRN%20Electronic%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2139/ssrn.4173912", "name": "item", "description": "10.2139/ssrn.4173912", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2139/ssrn.4173912"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10.3389/fpls.2020.00274", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:21:44Z", "type": "Journal Article", "created": "2020-03-03", "title": "Editorial: Interactions of Plants With Bacteria and Fungi: Molecular and Epigenetic Plasticity of the Host", "description": "Interactions of Plants with Bacteria and Fungi:Molecular and Epigenetic Plasticity of the Host", "keywords": ["genotypes; molecular mechanisms; omics tools; plant-bacterial interactions; plant-fungal interactions", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "plant-bacterial interactions", "omics tools", "molecular mechanisms", "Plant culture", "Molecular mechanisms", "Plant Science", "SB1-1110", "Plant-fungal Interactions", "03 medical and health sciences", "plant-fungal interactions", "Plant-bacterial Interactions", "genotypes", "Omics Tools"]}, "links": [{"href": "https://doi.org/10.3389/fpls.2020.00274"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fpls.2020.00274", "name": "item", "description": "10.3389/fpls.2020.00274", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2020.00274"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-04T00:00:00Z"}}, {"id": "10.3389/fpls.2022.922982", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:21:45Z", "type": "Journal Article", "created": "2022-06-23", "title": "Molecular Mechanisms of Intercellular Rhizobial Infection: Novel Findings of an Ancient Process", "description": "<p>Establishment of the root-nodule symbiosis in legumes involves rhizobial infection of nodule primordia in the root cortex that is dependent on rhizobia crossing the root epidermal barrier. Two mechanisms have been described: either through root hair infection threads or through the intercellular passage of bacteria. Among the legume genera investigated, around 75% use root hair entry and around 25% the intercellular entry mode. Root-hair infection thread-mediated infection has been extensively studied in the model legumes Medicago truncatula and Lotus japonicus. In contrast, the molecular circuit recruited during intercellular infection, which is presumably an ancient and simpler pathway, remains poorly known. In recent years, important discoveries have been made to better understand the transcriptome response and the genetic components involved in legumes with obligate (Aeschynomene and Arachis spp.) and conditional (Lotus and Sesbania spp.) intercellular rhizobial infections. This review addresses these novel findings and briefly considers possible future research to shed light on the molecular players that orchestrate intercellular infection in legumes.</p", "keywords": ["580", "0106 biological sciences", "0301 basic medicine", "nodule", "Arachis", "legumes", "[SDV.BBM]Life Sciences [q-bio]/Biochemistry", "Plant culture", "Plant Science", "01 natural sciences", "[SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy", "SB1-1110", "intercellular symbiosis", "03 medical and health sciences", "Aeschynomene", "616", "Sesbania", "[SDV.BBM] Life Sciences [q-bio]/Biochemistry", " Molecular Biology", "Lotus", "Molecular Biology", "[SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy"], "contacts": [{"organization": "Johan Quilb\u00e9, Jes\u00fas Montiel, Jes\u00fas Montiel, Jean-Fran\u00e7ois Arrighi, Jens Stougaard,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3389/fpls.2022.922982"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fpls.2022.922982", "name": "item", "description": "10.3389/fpls.2022.922982", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2022.922982"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-06-23T00:00:00Z"}}, {"id": "10.3390/genes10010068", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:21:54Z", "type": "Journal Article", "created": "2019-01-22", "title": "Convergent Evolution of the Seed Shattering Trait", "description": "<p>Loss of seed shattering is a key trait in crop domestication, particularly for grain crops. For wild plants, seed shattering is a crucial mechanism to achieve greater fitness, although in the agricultural context, this mechanism reduces harvesting efficiency, especially under dry conditions. Loss of seed shattering was acquired independently in different monocotyledon and dicotyledon crop species by \uffe2\uff80\uff98convergent phenotypic evolution\uffe2\uff80\uff99, leading to similar low dehiscent and indehiscent phenotypes. Here, the main aim is to review the current knowledge about seed shattering in crops, in order to highlight the tissue modifications that underlie the convergent phenotypic evolution of reduced shattering in different types of fruit, from the silique of Brassicaceae species, to the pods of legumes and spikes of cereals. Emphasis is given to legumes, with consideration of recent data obtained for the common bean. The current review also discusses to what extent convergent phenotypes arose from parallel changes at the histological and/or molecular levels. For this reason, an overview is included of the main findings relating to the genetic control of seed shattering in the model species Arabidopsis thaliana and in other important crops.</p>", "keywords": ["QTL mapping", "common bean", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "legumes", "Quantitative Trait Loci", "Common bean; Crop domestication; Gene expression; Legumes; Pod anatomy; QTL mapping; Genetics; Genetics (clinical)", "legume", "Review", "QH426-470", "pod anatomy", "15. Life on land", "Evolution", " Molecular", "crop domestication", "Magnoliopsida", "03 medical and health sciences", "Seed Dispersal", "Seeds", "Genetics", "gene expression"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/1/68/pdf"}, {"href": "https://doi.org/10.3390/genes10010068"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10010068", "name": "item", "description": "10.3390/genes10010068", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10010068"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-19T00:00:00Z"}}, {"id": "10.3390/s21092980", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:22:06Z", "type": "Journal Article", "created": "2021-04-25", "title": "Towards the Development and Verification of a 3D-Based Advanced Optimized Farm Machinery Trajectory Algorithm", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Efforts related to minimizing the environmental burden caused by agricultural activities and increasing economic efficiency are key contemporary drivers in the precision agriculture domain. Controlled Traffic Farming (CTF) techniques are being applied against soil compaction creation, using the on-line optimization of trajectory planning for soil-sensitive field operations. The research presented in this paper aims at a proof-of-concept solution with respect to optimizing farm machinery trajectories in order to minimize the environmental burden and increase economic efficiency. As such, it further advances existing CTF solutions by including (1) efficient plot divisions in 3D, (2) the optimization of entry and exit points of both plot and plot segments, (3) the employment of more machines in parallel and (4) obstacles in a farm machinery trajectory. The developed algorithm is expressed in terms of unified modeling language (UML) activity diagrams as well as pseudo-code. Results were visualized in 2D and 3D to demonstrate terrain impact. Verifications were conducted at a fully operational commercial farm (Rost\u011bnice, the Czech Republic) against second-by-second sensor measurements of real farm machinery trajectories.</p></article>", "keywords": ["Agriculture and Food Sciences", "2. Zero hunger", "Technology and Engineering", "controlled traffic farming", "Chemical technology", "mission planning", "TP1-1185", "04 agricultural and veterinary sciences", "Biochemistry", "Article", "Analytical Chemistry", "soil compaction", "Atomic and Molecular Physics", "digital elevation model", "AGRICULTURAL ROBOTS", "0401 agriculture", " forestry", " and fisheries", "Electrical and Electronic Engineering", "and Optics", "coverage path planning", "controlled traffic farming; coverage path planning; digital elevation model; mission planning; soil compaction"]}, "links": [{"href": "http://www.mdpi.com/1424-8220/21/9/2980/pdf"}, {"href": "https://www.mdpi.com/1424-8220/21/9/2980/pdf"}, {"href": "https://doi.org/10.3390/s21092980"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sensors", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/s21092980", "name": "item", "description": "10.3390/s21092980", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/s21092980"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-23T00:00:00Z"}}, {"id": "10.3929/ethz-b-000278733", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:22:16Z", "type": "Journal Article", "created": "2018-07-06", "title": "Cost\u2013benefit optimization of structural health monitoring sensor networks", "description": "<p>Structural health monitoring (SHM) allows the acquisition of information on the structural integrity of any mechanical system by processing data, measured through a set of sensors, in order to estimate relevant mechanical parameters and indicators of performance. Herein we present a method to perform the cost\uffe2\uff80\uff93benefit optimization of a sensor network by defining the density, type, and positioning of the sensors to be deployed. The effectiveness (benefit) of an SHM system may be quantified by means of information theory, namely through the expected Shannon information gain provided by the measured data, which allows the inherent uncertainties of the experimental process (i.e., those associated with the prediction error and the parameters to be estimated) to be accounted for. In order to evaluate the computationally expensive Monte Carlo estimator of the objective function, a framework comprising surrogate models (polynomial chaos expansion), model order reduction methods (principal component analysis), and stochastic optimization methods is introduced. Two optimization strategies are proposed: the maximization of the information provided by the measured data, given the technological, identifiability, and budgetary constraints; and the maximization of the information\uffe2\uff80\uff93cost ratio. The application of the framework to a large-scale structural problem, the Pirelli tower in Milan, is presented, and the two comprehensive optimization methods are compared.</p>", "keywords": ["Stochastic Processes", "structural health monitoring", "structural health monitoring; Bayesian inference; cost\u2013benefit analysis; stochastic optimization; information theory; Bayesian experimental design; surrogate modeling; model order reduction", "Chemical technology", "Cost-Benefit Analysis", "Bayesian inference", "Bayesian experimental design", "Uncertainty", "Bayes Theorem", "TP1-1185", "02 engineering and technology", "stochastic optimization", "Bayesian experimental design; Bayesian inference; Benefit analysis; Cost; Information theory; Model order reduction; Stochastic optimization; Structural health monitoring; Surrogate modeling; Algorithms; Monte Carlo Method; Nonlinear Dynamics; Stochastic Processes; Uncertainty; Bayes Theorem; Cost-Benefit Analysis; Analytical Chemistry; Atomic and Molecular Physics", " and Optics; Biochemistry; Instrumentation; Electrical and Electronic Engineering", "Article", "surrogate modeling", "0201 civil engineering", "Nonlinear Dynamics", "model order reduction", "cost\u2013benefit analysis", "Monte Carlo Method", "Algorithms", "information theory"]}, "links": [{"href": "http://www.mdpi.com/1424-8220/18/7/2174/pdf"}, {"href": "https://re.public.polimi.it/bitstream/11311/1085132/1/Sensors_2018b.pdf"}, {"href": "https://doi.org/10.3929/ethz-b-000278733"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sensors", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3929/ethz-b-000278733", "name": "item", "description": "10.3929/ethz-b-000278733", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3929/ethz-b-000278733"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-06T00:00:00Z"}}, {"id": "10.5061/dryad.gxd2547hz", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:22:35Z", "type": "Dataset", "title": "Data from: Chemical structure predicts the effect of plant-derived low-molecular weight compounds on soil microbiome structure and pathogen suppression", "description": "1. Plant-derived low molecular weight compounds play a crucial role in  shaping soil microbiome functionality. While various compounds have been  demonstrated to affect soil microbes, most data are case-specific and do  not provide generalizable predictions on their effects. Here we show that  the chemical structural affiliation of low molecular weight compounds  typically secreted by plant roots \u2013 sugars, amino acids, organic acids and  phenolic acids \u2013 can predictably affect microbiome diversity, composition  and functioning in terms of plant disease suppression. 2. We amended soil  with single or mixtures of representative compounds, mimicking carbon  deposition by plants. We then assessed how different classes of compounds,  or their combinations, affected microbiome composition and the protection  of tomato plants from the soil-borne Ralstonia solanacearum bacterial  pathogen. 3. We found that chemical class predicted well the changes in  microbiome composition and diversity. Organic and amino acids generally  decreased the microbiome diversity compared to sugars and phenolic acids.  These changes were also linked to disease incidence, with amino acids and  nitrogen-containing compound mixtures inducing more severe disease  symptoms connected with a reduction in bacterial community diversity. 4.  Together, our results demonstrate that low molecular weight compounds can  predictably steer rhizosphere microbiome functioning providing guidelines  to engineer microbiomes based on root exudation patterns by specific plant  cultivars or crop regimes.", "keywords": ["2. Zero hunger", "Chemical structure", "13. Climate action", "Plant-derived low molecular weight compounds", "soil suppressiveness", "soil microbiome", "15. Life on land"], "contacts": [{"organization": "Gu, Yian, Wang, Xiaofang, Yang, Tianjie, Friman, Ville Petri, Geisen, Stefan, Wei, Zhong, Xu, Yangchun, Jousset, Alexandre, Shen, Qirong,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.gxd2547hz"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.gxd2547hz", "name": "item", "description": "10.5061/dryad.gxd2547hz", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.gxd2547hz"}, {"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": "10.5194/bg-2021-323", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:22:46Z", "type": "Report", "created": "2021-12-15", "title": "Reviews and syntheses: The promise of big 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 than ever, but -outside of a few large soil survey resources- remain largely unusable for informing soil management and understanding Earth system processes outside of 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 global relevance. 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: data discovery, 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", "Data Sharing", "Biomedical Ontologies and Text Mining", "Data management", "Leverage (statistics)", "01 natural sciences", "Data science", "Data Sharing and Stewardship in Science", "Database", "Big data", "Biochemistry", " Genetics and Molecular Biology", "Machine learning", "Molecular Biology", "Data mining", "0105 earth and related environmental sciences", "2. Zero hunger", "Metadata", "Ecology", "Data curation", "Physics", "Life Sciences", "Acoustics", "15. Life on land", "Computer science", "World Wide Web", "Harmonization", "13. 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