{"type": "FeatureCollection", "features": [{"id": "10.5281/zenodo.8407642", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:24:15Z", "type": "Report", "title": "Shedding light on the genetic diversity and evolutionary dynamics of geographic populations of Wisteria vein mosaic virus: a case study for the spread of emerging potyviruses in Europe?", "description": "Wisteria vein mosaic virus (WVMV) is a member of the genus Potyvirus associated with Wisteria mosaic disease (WMD), the most serious disease affecting Wisteria spp. In 2022, severe symptoms of WMD were observed on the leaves of a Chinese wisteria (W. sinensis) tree growing in an urban area in Apulia (Italy). The presence of WVMV was ascertained by RT-PCR analysis. Although the occurrence of WVMV in Italy had been posited in the late 1960s, no molecular information had been reported for any Italian isolate prior to this study. Subsequent phylogenetic analyses based on NIb and CP genes placed the WVMV Italian isolate within a large clade identified in the genus Potyvirus as the BCMV supergroup. Based on the increasing number of reports of the virus worldwide, we attempted an exploratory analysis of its genetic diversity and possible mechanisms that may have shaped its geographic population structure. Relying on the N-terminus of the CP, available for twenty WVMV isolates from Europe, Asia, and Oceania, sixteen different haplotypes were identified. A high haplotype diversity was found, particularly relevant in the European population. The measured dN/dS ratio led to the assumption that the target region is under purifying selection. Tests evaluating the neutrality of nucleotide variability showed different results for the European and Asian groups. The estimation of inter-population genetic differentiation showed a high level of gene flow between the two populations. Overall, our results provide a possible approach to understanding the mechanisms of WVMV emergence in Europe and draw attention to its further spread and the increasing threat of this and other neglected potyvirus species to the ornamental nursery sector.", "keywords": ["WVMV; selection pressure; population genetics; genetic diversity; gene flow; haplotype diversity; neutrality tests; FastME phylogeny", "3. Good health"], "contacts": [{"organization": "G. D'Attoma, A. Minafra", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.8407642"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.8407642", "name": "item", "description": "10.5281/zenodo.8407642", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.8407642"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-09-18T00:00:00Z"}}, {"id": "10.7910/DVN/MIYBQE", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:24:57Z", "type": "Dataset", "title": "Ecogeographic land characterization map of the SADC region", "description": "With the aim of planning for the in situ and ex situ conservation of priority crop wild relatives (CWR) of the Southern African Development Community (SADC), a gap analysis at intra-specific level (i.e. ecogeographic diversity level used as a proxy of genetic diversity), was carried out. For this purpose, a generalist Ecogeographic Land Characterization (ELC) map for the SADC region was created using the ELC mapas tool of CAPFITOGEN (http://www.capfitogen.net/, Parra-Quijano et al., 2008, 2016) based on 16 ecogeographic variables from three different components (four geophysic variables, seven edaphic, and five bioclimatic; see the list below) at a resolution of 2.5 arc minutes (approximately 4.5 km at the equator). The Calinski-Harabasz (1974) criterion was applied to obtain an objective number of clusters for each bioclimatic, edaphic and geophysic multivariate analysis. The ELC map was then clipped to the SADC countries using ArcGIS 10.4.1 (ESRI, 2016). A total of 16 ecogeographic categories were identified in the SADC region with distinct ecogeographic characteristiscs (see file 'ELC_SADC_region_statistics.xlsx'). The files made available here include: the raster file of the ELC map of the SADC region (which is composed of 16 different files) and an Excel file which describes the statistics (i.e. average, median, maximum, minimum and standard deviation) of each ecogeographic category present in the map ('ELC_SADC_region_statistics.xlsx').<br> <br><b>Variables:</b> Geophysic: altitude (m) (WorldClim 1.4, http://worldclim.org), slope (\u00b0), latitude (decimal degrees), longitude (decimal degrees). Edaphic: topsoil organic carbon (% weight), topsoil pH (H2O) [-log(H+)], topsoil silt fraction (% weight), topsoil sand fraction (% weight), topsoil gravel content (% vol.), topsoil clay fraction (% weight), topsoil TEB (total exchangeable bases) (cmol/kg) (HWS Database, http://www.iiasa.ac.at/Research/LUC/External-World-soil-database/). Bioclimatic: annual precipitation (bio_12) (mm), precipitation seasonality (coefficient of variation) (bio_15) (mm), isothermality (bio_2/bio_7) (*100) (bio_3), max temperature of warmest month (bio_5) (\u00b0C), min temperature of coldest month (bio_6) (\u00b0C) (WorldClim 1.4, http://worldclim.org).<br> <br><b>References:</b> Calinski T and Harabasz J (1974) A dendrite method for cluster analysis. Communications in Statistics, 3(1): 1\u201227. ESRI (2016) ArcGIS Desktop release Version 10.4.1. Environmental Systems Research Institute. Redlands. CA. Parra-Quijano M, Draper D and Torres E (2008) Ecogeographical representativeness in crop wild relative ex situ collections. In: Maxted N, Ford\u2010Lloyd BV, Kell SP, Iriondo JM, Dulloo E and Turok J (eds), Crop wild relative conservation and use, pp. 249\u201373. Wallingford: CAB International. Parra-Quijano M, Torres E, Iriondo JM, L\u00f3pez F and Molina A (2016) CAPFITOGEN tools user manual, version 2.0. Rome, Italy: International Treaty on Plant Genetic Resources for Food and Agriculture, FAO. Available at: http://www.capfitogen.net/en/access/manuals/ [Accessed July 2021].", "keywords": ["Agricultural Sciences", "PLANNING", "PLANT GENETIC RESOURCES", "AGROBIODIVERSITY", "GENETIC DIVERSITY AS RESOURCE"], "contacts": [{"organization": "Magos Brehm, Joana", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.7910/DVN/MIYBQE"}, {"rel": "self", "type": "application/geo+json", "title": "10.7910/DVN/MIYBQE", "name": "item", "description": "10.7910/DVN/MIYBQE", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.7910/DVN/MIYBQE"}, {"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": "10.1007/s00122-021-03815-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:33Z", "type": "Journal Article", "created": "2021-03-25", "title": "Genomic prediction models trained with historical records enable populating the German ex situ genebank bio-digital resource center of barley (Hordeum\u00a0sp.) with information on resistances to soilborne barley mosaic viruses", "description": "Abstract Key message

Genomic prediction with special weight of major genes is a valuable tool to populate bio-digital resource centers.

Abstract

Phenotypic information of crop genetic resources is a prerequisite for an informed selection that aims to broaden the genetic base of the elite breeding pools. We investigated the potential of genomic prediction based on historical screening data of plant responses against the Barley yellow mosaic viruses for populating the bio-digital resource center of barley. Our study includes dense marker data for 3838 accessions of winter barley, and historical screening data of 1751 accessions for Barley yellow mosaic virus (BaYMV) and of 1771 accessions for Barley mild mosaic virus (BaMMV). Linear mixed models were fitted by considering combinations for the effects of genotypes, years, and locations. The best linear unbiased estimations displayed a broad spectrum of plant responses against BaYMV and BaMMV. Prediction abilities, computed as correlations between predictions and observed phenotypes of accessions, were low for the marker-assisted selection approach amounting to 0.42. In contrast, prediction abilities of genomic best linear unbiased predictions were high, with values of 0.62 for BaYMV and 0.64 for BaMMV. Prediction abilities of genomic prediction were improved by up to\uffe2\uff80\uff89~\uffe2\uff80\uff895% using W-BLUP, in which more weight is given to markers with significant major effects found by association mapping. Our results outline the utility of historical screening data and W-BLUP model to predict the performance of the non-phenotyped individuals in genebank collections. The presented strategy can be considered as part of the different approaches used in genebank genomics to valorize genetic resources for their usage in disease resistance breeding and research.

", "keywords": ["Genetic Markers", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Genotype", "Chromosome Mapping", "Genetic Variation", "Hordeum", "Genomics", "Potyviridae", "Linkage Disequilibrium", "Plant Breeding", "03 medical and health sciences", "Phenotype", "Databases", " Genetic", "Original Article", "Genetic Association Studies", "Disease Resistance", "Plant Diseases"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00122-021-03815-0.pdf"}, {"href": "https://doi.org/10.1007/s00122-021-03815-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Theoretical%20and%20Applied%20Genetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00122-021-03815-0", "name": "item", "description": "10.1007/s00122-021-03815-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00122-021-03815-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-25T00:00:00Z"}}, {"id": "10.1002/ajb2.1625", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:11Z", "type": "Journal Article", "created": "2021-03-19", "title": "Phylogeography of a gypsum endemic plant across its entire distribution range in the western Mediterranean", "description": "PREMISE

Gypsum soils in the Mediterranean Basin house large numbers of edaphic specialists that are adapted to stressful environments. The evolutionary history and standing genetic variation of these taxa have been influenced by the geological and paleoclimatic complexity of this area and the long\uffe2\uff80\uff90standing effect of human activities. However, little is known about the origin of Mediterranean gypsophiles and the factors affecting their genetic diversity and population structure.

METHODS

Using phylogenetic and phylogeographic approaches based on microsatellites and sequence data from nuclear and chloroplast regions, we evaluated the divergence time, genetic diversity, and population structure of 27 different populations of the widespread Iberian gypsophile Lepidium subulatum throughout its entire geographic range.

RESULTS

Lepidium subulatum diverged from its nearest relatives ~3 million years ago, and ITS and psbA/matK trees supported the monophyly of the species. These results suggest that both geological and climatic changes in the region around the Plio\uffe2\uff80\uff90Pleistocene promoted its origin, compared to other evolutionary processes. We found high genetic diversity in both nuclear and chloroplast markers, but a greater population structure in the chloroplast data. These results suggest that while seed dispersal is limited, pollen flow may be favored by the presence of numerous habitat patches that enhance the movement of pollinators.

CONCLUSIONS

Despite being an edaphic endemic, L. subulatum possesses high genetic diversity probably related to its relatively old age and high population sizes across its range. Our study highlights the value of using different markers to fully understand the phylogeographic history of plant species.Tropical forests exchange large amounts of greenhouse gases (GHGs: carbon dioxide, CO2; methane, CH4; and nitrous oxide, N2O) with the atmosphere. Forest soils and stems can be either sources or sinks for CH4 and N2O, but little is known about what determines the sign and magnitude of these fluxes. Here, we aimed to study how stem and soil GHG fluxes vary along a topographic gradient in a tropical forest.

Methods
Fluxes of GHG from 56 individual tree stems and adjacent soils were measured with manual static chambers. The topographic gradient was characterized by a soil moisture gradient, with one end in a wetland area (\u201cseasonally flooded\u201d; SF), the other end in an upland area (\u201cterra firme\u201d; TF) and in between a transitional area on the slope (SL).

Results
Tree stems and soils were always sources of CO2 with higher fluxes in SF compared to TF and SL. Fluxes of CH4 and N2O were more variable, even within one habitat. Results showed that, in TF, soils acted as sinks for N2O whereas, in SF and SL, they acted as sources. In contrast, tree stems which were predominantly sources of N2O in SF and TF, were sinks in SL. In the soil, N2O fluxes were significantly influenced by both temperature and soil water content, whereas CH4 fluxes were only significantly correlated with soil water content.

Conclusion
SF areas were major sources of the three gases, whereas SL and TF soils and tree stems acted as either sources or sinks for CH4 and N2O. Our results indicate that tree stems represent overlooked sources of CH4 and N2O in tropical forests that need to be further studied to refine GHG budgets.", "keywords": ["[SDV.SA.AGRO] Life Sciences [q-bio]/Agricultural sciences/Agronomy", "106022 Mikrobiologie", "550", "source", "Spatial variation", "Sink", "[SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy", "spatial variation", "Source", "15. Life on land", "Stem", "630", "soil", "[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics", "Soil", "Greenhouse gas (GHG) exchange", "13. Climate action", "106026 \u00d6kosystemforschung", "[SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics", "106022 Microbiology", "stem", "sink", "106026 Ecosystem research", "Biology", "greenhouse gas (GHG) exchange"]}, "links": [{"href": "https://doi.org/10.1007/s11104-023-05991-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-023-05991-y", "name": "item", "description": "10.1007/s11104-023-05991-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-023-05991-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-05-09T00:00:00Z"}}, {"id": "10.1016/j.cub.2020.09.063", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:02Z", "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.cell.2021.04.024", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:58Z", "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.envexpbot.2024.105986", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:12Z", "type": "Journal Article", "created": "2024-10-04", "title": "From landraces to haplotypes, exploiting a genomic and phenomic approach to identify heat tolerant genotypes within durum wheat landraces", "description": "Dry and hot climates severely impact wheat yields, necessitating the development of innovative solutions to accelerate the breeding and selection of more adaptable durum wheat genotypes. The aim of this study was to identify new wheat ecotypes that can bridge the gap between commercial varieties and adaptability to ongoing climate change. In this study, advanced genomic and phenomic techniques were combined to characterize a set of durum wheat landraces derived from single seed descent (SSD). This approach enabled the identification of novel variability in the TdHsp26-A1 and-B1 genes. As a result, 38 durum wheat genotypes were analyzed using targeted enrichment PCR, leading to the identification of 17 novel haplotype combinations with SNPs in the TdHsp26 genes. The response of these SSD haplotypes to heat stress was characterized at both the seedling and tillering growth stages. Phenotypic analysis of contrasting genotypes led to the selection of two distinct genotypes: SSD69 and SSD397. During heat stress, SSD69 exhibited altered accumulation of H2O2 2 O 2 and MDA content under both growth conditions, providing new insights into the oxidative response to heat stress. Additionally, this work identifies phenotypic traits that are suitable for detecting differences between variants. The geographic distribution of the different alleles aligned with the spread of durum wheat from its center of origin.", "keywords": ["Natural germplasm", "Phenotyping", "Settore AGRI-06/A - Genetica agraria", "Heat stre", "Durum wheat", " Natural germplasm", " sHsp26", " Heat stress", " Phenotyping", " SNPs", "Durum wheat", "sHsp26", "630", "SNPs"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/526470/1/From%20landraces%20to%20haplotypes%2c%20exploiting%20a%20genomic%20and%20phenomic%20approach%20to%20identify%20heat%20tolerant%20genotypes%20within%20durum%20wheat%20landraces.pdf"}, {"href": "https://doi.org/10.1016/j.envexpbot.2024.105986"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20and%20Experimental%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envexpbot.2024.105986", "name": "item", "description": "10.1016/j.envexpbot.2024.105986", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envexpbot.2024.105986"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-12-01T00:00:00Z"}}, {"id": "10.1016/j.isci.2019.10.043", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:38Z", "type": "Journal Article", "created": "2019-10-25", "title": "Genetic Loci Associated with Early Salt Stress Responses of Roots", "description": "Salinity is a devastating abiotic stress accounting for major crop losses yearly. Plant roots can strikingly grow away from high-salt patches. This response is termed halotropism and occurs through auxin redistribution in roots in response to a salt gradient. Here, a natural variation screen for the early and NaCl-specific halotropic response of 333 Arabidopsis accessions revealed quantitative differences in the first 24 h. These data were successfully used to identify genetic components associated with the response through Genome-Wide Association Study (GWAS). Follow-up characterization of knockout mutants in Col-0 background confirmed the role of transcription factor WRKY25, cation-proton exchanger CHX13, and a gene of unknown function DOB1 (Double Bending 1) in halotropism. In chx13 and dob1 mutants, ion accumulation and shoot biomass under salt stress were also affected. Thus, our GWAS has identified genetic components contributing to main root halotropism that provide insight into the genetic architecture underlying plant salt responses.", "keywords": ["580", "2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "Science", "Q", "Plant Biology", "Biological Sciences", "15. Life on land", "Plant Genetics", "Article", "03 medical and health sciences", "Plant Physiology"]}, "links": [{"href": "https://doi.org/10.1016/j.isci.2019.10.043"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/iScience", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.isci.2019.10.043", "name": "item", "description": "10.1016/j.isci.2019.10.043", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.isci.2019.10.043"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-01T00:00:00Z"}}, {"id": "10.1016/j.jafr.2023.100732", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:39Z", "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.soilbio.2022.108918", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:15Z", "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": "10.1017/s0021859618000084", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:34Z", "type": "Journal Article", "created": "2018-02-28", "title": "Forecasting potential evapotranspiration by combining numerical weather predictions and visible and near-infrared satellite images: an application in southern Italy", "description": "Abstract

Irrigation according to reliable estimates of crop water requirements (CWR) is one of the key strategies to ensure long-term sustainability of irrigated agriculture. In southern Mediterranean regions, during the irrigation season, CWR is almost totally controlled by the potential evapotranspiration of the irrigated crop. An innovative system for forecasting crop potential evapotranspiration (ETp) has been implemented recently in the Campania region (southern Italy). The system produces ETp forecasts with a lead time of up to 5 days, by coupling the visible and near-infrared crop imagery with numerical weather prediction outputs of a limited area model. The forecasts are delivered to farmers with a simple and intuitive web app interface, which makes daily real-time ETp maps accessible from desktop computers, tablets and smartphones. Forecast performances were evaluated for maize fields of two farms in two irrigation seasons (2014\uffe2\uff80\uff932015). The mean absolute bias of the forecasted ETp was <0.3 mm/day and the RMSE was <0.6 mm/day, both for lead times up to 5 days.

", "keywords": ["2. Zero hunger", "Earth observation", "Crop water requirements", "0207 environmental engineering", "forecasting", "02 engineering and technology", "15. Life on land", "01 natural sciences", "numerical weather predictions", "13. Climate action", "potential evapotranspiration", "11. Sustainability", "Genetics", "Animal Science and Zoology", "Agronomy and Crop Science", "Crop water requirements; Earth observation; forecasting; numerical weather predictions; potential evapotranspiration; Animal Science and Zoology; Agronomy and Crop Science; Genetics", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1017/s0021859618000084"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Journal%20of%20Agricultural%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1017/s0021859618000084", "name": "item", "description": "10.1017/s0021859618000084", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1017/s0021859618000084"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-28T00:00:00Z"}}, {"id": "10.1021/acs.jafc.3c04532", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:37Z", "type": "Journal Article", "created": "2023-10-05", "title": "Ultra-high Performance Liquid Chromatography\u2013Ion Mobility\u2013High-Resolution Mass Spectrometry to Evaluate the Metabolomic Response of Durum Wheat to Sustainable Treatments", "description": "Sustainable agriculture aims at achieving a healthy food production while reducing the use of fertilizers and greenhouse gas emissions using biostimulants and soil amendments. Untargeted metabolomics by ultra-high performance liquid chromatography-ion mobility-high-resolution mass spectrometry, operating in a high-definition MSE mode, was applied to investigate the metabolome of durum wheat in response to sustainable treatments, i.e., the addition of biochar, commercial plant growth promoting microbes, and their combination. Partial least squares-discriminant analysis provided a good discrimination among treatments with sensitivity, specificity, and a non-error rate close to 1. A total of 88 and 45 discriminant compounds having biological, nutritional, and technological implications were tentatively identified in samples grown in 2020 and 2021. The addition of biochar-biostimulants produced the highest up-regulation of lipids and flavonoids, with the glycolipid desaturation being the most impacted pathway, whereas carbohydrates were mostly down-regulated. The findings achieved suggest the safe use of the combined biochar-biostimulant treatment for sustainable wheat cultivation.", "keywords": ["2. Zero hunger", "Settore CHEM-01/A - Chimica analitica", "630", "Mass Spectrometry", "12. Responsible consumption", "ultra-high performance liquid chromatography\u2212high-resolution mass spectrometry ion mobility untargeted metabolomics multivariate data analysis durum wheat biostimulants soil amendments", "13. Climate action", "Settore AGRI-06/A - Genetica agraria", "615", "Metabolomics", "ultra-high performance liquid chromatography\u2013high-resolution mass spectrometry ion mobility untargeted metabolomics multivariate data analysis durum wheat biostimulants soil amendments", "Settore BIOS-10/A - Biologia cellulare e applicata", "Chromatography", " High Pressure Liquid", "Triticum"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.jafc.3c04532"}, {"href": "https://doi.org/10.1021/acs.jafc.3c04532"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Agricultural%20and%20Food%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.jafc.3c04532", "name": "item", "description": "10.1021/acs.jafc.3c04532", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.jafc.3c04532"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-05T00:00:00Z"}}, {"id": "10.1371/journal.pone.0076447", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:50Z", "type": "Journal Article", "created": "2013-09-26", "title": "The Arbuscular Mycorrhizal Fungal Community Response To Warming And Grazing Differs Between Soil And Roots On The Qinghai-Tibetan Plateau", "description": "Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most plant species in terrestrial ecosystems, and are affected by environmental variations. To reveal the impact of disturbance on an AM fungal community under future global warming, we examined the abundance and community composition of AM fungi in both soil and mixed roots in an alpine meadow on the Qinghai-Tibetan Plateau, China. Warming and grazing had no significant effect on AM root colonization, spore density and extraradical hyphal density. A total of 65 operational taxonomic units (OTUs) of AM fungi were identified from soil and roots using molecular techniques. AM fungal OTU richness was higher in soil (54 OTUs) than in roots (34 OTUs), and some AM fungi that differed between soil and roots, showed significantly biased occurrence to warming or grazing. Warming and grazing did not significantly affect AM fungal OTU richness in soil, but warming with grazing significantly increased AM fungal OTU richness in roots compared to the grazing-only treatment. Non-metric multidimensional scaling analysis showed that the AM fungal community composition was significantly different between soil and roots, and was significantly affected by grazing in roots, whereas in soil it was significantly affected by warming and plant species richness. The results suggest that the AM fungal community responds differently to warming and grazing in soil compared with roots. This study provides insights into the role of AM fungi under global environmental change scenarios in alpine meadows of the Qinghai-Tibetan Plateau.", "keywords": ["0106 biological sciences", "Hot Temperature", "Science", "Molecular Sequence Data", "Population Dynamics", "Global Warming", "Plant Roots", "Polymerase Chain Reaction", "01 natural sciences", "Species Specificity", "Mycorrhizae", "Herbivory", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Analysis of Variance", "Base Sequence", "Models", " Genetic", "Altitude", "Q", "R", "Bayes Theorem", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Spores", " Fungal", "15. Life on land", "Biota", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Polymorphism", " Restriction Fragment Length", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0076447"}, {"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.0076447", "name": "item", "description": "10.1371/journal.pone.0076447", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0076447"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-09-26T00:00:00Z"}}, {"id": "10.1038/nature02052", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:54Z", "type": "Journal Article", "created": "2003-10-08", "title": "Loss Of Omi Mitochondrial Protease Activity Causes The Neuromuscular Disorder Of Mnd2 Mutant Mice", "description": "The mouse mutant mnd2 (motor neuron degeneration 2) exhibits muscle wasting, neurodegeneration, involution of the spleen and thymus, and death by 40 days of age. Degeneration of striatal neurons, with astrogliosis and microglia activation, begins at around 3 weeks of age, and other neurons are affected at later stages. Here we have identified the mnd2 mutation as the missense mutation Ser276Cys in the protease domain of the nuclear-encoded mitochondrial serine protease Omi (also known as HtrA2 or Prss25). Protease activity of Omi is greatly reduced in tissues of mnd2 mice but is restored in mice rescued by a bacterial artificial chromosome transgene containing the wild-type Omi gene. Deletion of the PDZ domain partially restores protease activity to the inactive recombinant Omi protein carrying the Ser276Cys mutation, suggesting that the mutation impairs substrate access or binding to the active site pocket. Loss of Omi protease activity increases the susceptibility of mitochondria to induction of the permeability transition, and increases the sensitivity of mouse embryonic fibroblasts to stress-induced cell death. The neurodegeneration and juvenile lethality in mnd2 mice result from this defect in mitochondrial Omi protease.", "keywords": ["Male", "0301 basic medicine", "0303 health sciences", "Binding Sites", "Cell Death", "Science", "Homozygote", "Molecular Sequence Data", "Caseins", "Chromosome Mapping", "Mice", " Transgenic", "High-Temperature Requirement A Serine Peptidase 2", "Mitochondria", "Mitochondrial Proteins", "Mice", "Mice", " Neurologic Mutants", "03 medical and health sciences", "Animals", "Humans", "Calcium", "Female", "Amino Acid Sequence", "Cells", " Cultured", "Crosses", " Genetic"]}, "links": [{"href": "https://doi.org/10.1038/nature02052"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/nature02052", "name": "item", "description": "10.1038/nature02052", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/nature02052"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-10-01T00:00:00Z"}}, {"id": "10.1038/s41467-018-05980-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:56Z", "type": "Journal Article", "created": "2018-08-29", "title": "Land use driven change in soil pH affects microbial carbon cycling processes", "description": "Abstract

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.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.

", "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/s41467-019-14197-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:57Z", "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

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.

", "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/s41467-020-16438-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:57Z", "type": "Journal Article", "created": "2020-05-25", "title": "Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome", "description": "Abstract

Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.

", "keywords": ["Primates", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Science", "Probiotics", "Q", "gut microbiome", "Article", "Gastrointestinal Microbiome", "lactic acid bacteria", "Lactococcus lactis", "03 medical and health sciences", "Lactobacillales", "Databases", " Genetic", "Food Microbiology", "Animals", "Humans", "Metagenome", "Streptococcus thermophilus", "Fermented Foods", "[PHYS.ASTR] Physics [physics]/Astrophysics [astro-ph]", "Life Style", "genome analysis"]}, "links": [{"href": "https://iris.unitn.it/bitstream/11572/269813/1/s41467-020-16438-8.pdf"}, {"href": "https://www.iris.unina.it/bitstream/11588/811717/2/NatComm%2c2020_LABfoodgut.pdf"}, {"href": "https://www.nature.com/articles/s41467-020-16438-8.pdf"}, {"href": "https://doi.org/10.1038/s41467-020-16438-8"}, {"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/s41467-020-16438-8", "name": "item", "description": "10.1038/s41467-020-16438-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-020-16438-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-25T00:00:00Z"}}, {"id": "10.1038/s41467-024-51515-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:58Z", "type": "Journal Article", "created": "2024-08-23", "title": "A NAC triad modulates plant immunity by negatively regulating N-hydroxy pipecolic acid biosynthesis", "description": "N-hydroxy\u00a0pipecolic acid (NHP) plays an important role in plant immunity. In contrast to its biosynthesis, our current knowledge with respect to the transcriptional regulation of the NHP pathway is limited. This study commences with the engineering of Arabidopsis plants that constitutively produce high NHP levels and display enhanced immunity. Label-free proteomics reveals a NAC-type transcription factor (NAC90) that is strongly induced in these plants. We find that NAC90 is a target gene of SAR DEFICIENT 1 (SARD1) and induced by pathogen, salicylic acid (SA), and NHP. NAC90 knockout mutants exhibit constitutive immune activation, earlier senescence, higher levels of NHP and SA, as well as increased expression of NHP and SA biosynthetic genes. In contrast, NAC90 overexpression lines are compromised in disease resistance and accumulated reduced levels of NHP and SA. NAC90 could interact with NAC61 and NAC36 which are also induced by pathogen, SA, and NHP. We next discover that this protein triad directly represses expression of the NHP and SA biosynthetic genes AGD2-LIKE DEFENSE RESPONSE PROTEIN 1 (ALD1), FLAVIN MONOOXYGENASE 1 (FMO1), and ISOCHORISMATE SYNTHASE 1 (ICS1). Constitutive immune response in nac90 is abolished once blocking NHP biosynthesis in the fmo1 background, signifying that NAC90 negative regulation of immunity is mediated via NHP biosynthesis. Our findings expand the currently documented NHP regulatory network suggesting a model that together with NHP glycosylation, NAC repressors take part in a 'gas-and-brake' transcriptional mechanism to control NHP production and the plant growth and defense trade-off.", "keywords": ["Proteomics", "0301 basic medicine", "0303 health sciences", "Arabidopsis Proteins", "Science", "Q", "Arabidopsis", "Plants", " Genetically Modified", "Article", "03 medical and health sciences", "Gene Expression Regulation", " Plant", "Pipecolic Acids", "Plant Immunity", "Salicylic Acid", "Transcription Factors", "Plant Diseases", "Disease Resistance"]}, "links": [{"href": "https://doi.org/10.1038/s41467-024-51515-2"}, {"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/s41467-024-51515-2", "name": "item", "description": "10.1038/s41467-024-51515-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-024-51515-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-22T00:00:00Z"}}, {"id": "10.1038/s41586-023-05791-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:00Z", "type": "Journal Article", "created": "2023-03-08", "title": "The giant diploid faba genome unlocks variation in a global protein crop", "description": "Abstract

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia fabaL.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13\uffe2\uff80\uff89Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the\uffc2\uffa0improvement of sustainable protein production across the\uffc2\uffa0Mediterranean, subtropical and northern temperate agroecological zones.In this study we used meteorological parameters and predictive modelling interpreted by model explanation to develop stress metrics that indicate the presence of drought and heat stress at the specific environment. We started from the extreme temperature and precipitation indices, modified some of them and introduced additional drought indices relevant to the analysis. Based on maize\uffe2\uff80\uff99s sensitivity to stress, the growing season was divided into four stages. The features were calculated throughout the growing season and split in two groups, one for the drought and the other for heat stress. Generated meteorological features were combined with soil features and fed to random forest regression model for the yield prediction. Model explanation gave us the contribution of features to yield decrease, from which we estimated total amount of stress at the environments, which represents new environmental index. Using this index we ranked the environments according to the level of stress. More than 2400 hybrids were tested across the environments where they were grown and based on the yield stability they were marked as either tolerant or susceptible to heat, drought or combined heat and drought stress. Presented methodology and results were produced within the Syngenta Crop Challenge 2019.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.A dramatic evolution of fruit size has accompanied the domestication and improvement of fruit-bearing crop species. In tomato (Solanum lycopersicum), naturally occurring cis-regulatory mutations in the genes of the CLAVATA-WUSCHEL signaling pathway have led to a significant increase in fruit size generating enlarged meristems that lead to flowers with extra organs and bigger fruits. In this work, by combining mapping-by-sequencing and CRISPR/Cas9 genome editing methods, we isolatedEXCESSIVE NUMBER OF FLORAL ORGANS(ENO), an AP2/ERF transcription factor which regulates floral meristem activity. Thus, theENOgene mutation gives rise to plants that yield larger multilocular fruits due to an increased size of the floral meristem. Genetic analyses indicate thatenoexhibits synergistic effects with mutations at theLOCULE NUMBER(encodingSlWUS) andFASCIATED(encodingSlCLV3) loci, two central players in the evolution of fruit size in the domestication of cultivated tomatoes. Our findings reveal that anenomutation causes a substantial expansion ofSlWUSexpression domains in a flower-specific manner. In vitro binding results show that ENO is able to interact with the GGC-box cis-regulatory element within theSlWUSpromoter region, suggesting that ENO directly regulatesSlWUSexpression domains to maintain floral stem-cell homeostasis. Furthermore, the study of natural allelic variation of theENOlocus proved that a cis-regulatory mutation in the promoter ofENOhad been targeted by positive selection during the domestication process, setting up the background for significant increases in fruit locule number and fruit size in modern tomatoes.

", "keywords": ["0301 basic medicine", "570", "Floral meristem", "[SPI] Engineering Sciences [physics]", "[SDV]Life Sciences [q-bio]", "Meristem", "Quantitative Trait Loci", "Genes", " Plant", "CLAVATA/WUSCHEL regulatory network", "Domestication", "[SPI]Engineering Sciences [physics]", "03 medical and health sciences", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "AP2/ERF transcription factor", "Promoter Regions", " Genetic", "Cell Proliferation", "Plant Proteins", "580", "Homeodomain Proteins", "2. Zero hunger", "Tomato (Solanum lycopersicum)", "0303 health sciences", "Stem Cells", "Biological Sciences", "15. Life on land", "fruit size", "Crop Production", "[SDV] Life Sciences [q-bio]", "CLAVATA-WUSCHEL regulatory network", "GENETICA", "Fruit", "Mutation", "Fruit size", "floral meristem", "Transcription Factors"]}, "links": [{"href": "https://pnas.org/doi/pdf/10.1073/pnas.1913688117"}, {"href": "https://doi.org/10.1073/pnas.1913688117"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.1913688117", "name": "item", "description": "10.1073/pnas.1913688117", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.1913688117"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-16T00:00:00Z"}}, {"id": "10.1093/pcp/pcae113", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:41Z", "type": "Journal Article", "created": "2024-11-06", "title": "Population Genomics Reveals Demographic History and Climate Adaptation in Japanese Arabidopsis halleri", "description": "Abstract

Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge (\uffe2\uff88\uffbc50, 000 years ago). The ecological niche modeling predicted the geographic or distribution range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.During nutrient scarcity, plants can adapt their developmental strategy to maximize their chance of survival. Such plasticity in development is underpinned by hormonal regulation, which mediates the relationship between environmental cues and developmental outputs. In legumes, endosymbiosis with nitrogen-fixing bacteria (rhizobia) is a key adaptation for supplying the plant with nitrogen in the form of ammonium. Rhizobia are housed in lateral root-derived organs termed nodules that maintain an environment conducive to Nitrogenase in these bacteria. Several phytohormones are important for regulating the formation of nodules, with both positive and negative roles proposed for gibberellin (GA). In this study, we determine the cellular location and function of bioactive GA during nodule organogenesis using a genetically encoded second-generation GA biosensor, GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula. We find endogenous bioactive GA accumulates locally at the site of nodule primordia, increasing dramatically in the cortical cell layers, persisting through cell divisions, and maintaining accumulation in the mature nodule meristem. We show, through misexpression of GA-catabolic enzymes that suppress GA accumulation, that GA acts as a positive regulator of nodule growth and development. Furthermore, increasing or decreasing GA through perturbation of biosynthesis gene expression can increase or decrease the size of nodules, respectively. This is unique from lateral root formation, a developmental program that shares common organogenesis regulators. We link GA to a wider gene regulatory program by showing that nodule-identity genes induce and sustain GA accumulation necessary for proper nodule formation.Pseudomonas species have become reliable platforms for bioproduction due to their capability to tolerate harsh conditions imposed by large\uffe2\uff80\uff90scale bioprocesses and their remarkable resistance to diverse physicochemical stresses. The last few years have brought forth a variety of synthetic biology tools for the genetic manipulation of pseudomonads, but most of them are either applicable only to obtain certain types of mutations, lack efficiency, or are not easily accessible to be used in different Pseudomonas species (e.g. natural isolates). In this work, we describe a versatile, robust and user\uffe2\uff80\uff90friendly procedure that facilitates virtually any kind of genomic manipulation in Pseudomonas species in 3\uffe2\uff80\uff935\uffc2\uffa0days. The protocol presented here is based on DNA recombination forced by double\uffe2\uff80\uff90stranded DNA cuts (through the activity of the I\uffe2\uff80\uff90SceI homing meganuclease from yeast) followed by highly efficient counterselection of mutants (aided by a synthetic CRISPR\uffe2\uff80\uff90Cas9 device). The individual parts of the genome engineering toolbox, tailored for knocking genes in and out, have been standardized to enable portability and easy exchange of functional gene modules as needed. The applicability of the procedure is illustrated both by eliminating selected genomic regions in the platform strain P.\uffc2\uffa0putida KT2440 (including difficult\uffe2\uff80\uff90to\uffe2\uff80\uff90delete genes) and by integrating different reporter genes (comprising novel variants of fluorescent proteins) into a defined landing site in the target chromosome.

", "keywords": ["Gene Editing", "Recombination", " Genetic", "0301 basic medicine", "03 medical and health sciences", "Pseudomonas putida", "Brief Reports", "Clustered Regularly Interspaced Short Palindromic Repeats", "CRISPR-Cas Systems", "TP248.13-248.65", "Biotechnology", "3. Good health"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.13396"}, {"href": "https://doi.org/10.1111/1751-7915.13396"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1751-7915.13396", "name": "item", "description": "10.1111/1751-7915.13396", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1751-7915.13396"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-12T00:00:00Z"}}, {"id": "10.1111/1751-7915.13383", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:54Z", "type": "Journal Article", "created": "2019-03-13", "title": "Physical decoupling of XylS/ Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida", "description": "Summary

Most of the gene expression systems available for Gram\uffe2\uff80\uff90negative bacteria are afflicted by relatively high levels of basal (i.e. leaky) expression of the target gene(s). This occurrence affects the system dynamics, ultimately reducing the output and productivity of engineered pathways and synthetic circuits. In order to circumvent this problem, we have designed a novel expression system based on the well\uffe2\uff80\uff90known XylS/Pm transcriptional regulator/promoter pair from the soil bacterium Pseudomonas putida mt\uffe2\uff80\uff902, in which the key functional elements are physically decoupled. By integrating the xylS gene into the chromosome of the platform strain KT2440, while placing the Pm promoter into a set of standard plasmid vectors, the inducibility of the system (i.e. the output difference between the induced and uninduced state) improved up to 170\uffe2\uff80\uff90fold. We further combined this modular system with an extra layer of post\uffe2\uff80\uff90translational control by means of conditional proteolysis. In this setup, the target gene is tagged with a synthetic motif dictating protein degradation. When the system features were characterized using the monomeric superfolder GFP as a model protein, the basal levels of fluorescence were brought down to zero (i.e. below the limit of detection). In all, these novel expression systems constitute an alternative tool to altogether suppress leaky gene expression, and they can be easily adapted to other vector formats and plugged\uffe2\uff80\uff90in into different Gram\uffe2\uff80\uff90negative bacterial species at the user's will.

", "keywords": ["0301 basic medicine", "0303 health sciences", "Pseudomonas putida", "Gene Expression", "Gene Expression Regulation", " Bacterial", "03 medical and health sciences", "Bacterial Proteins", "Proteolysis", "Trans-Activators", "Brief Reports", "Promoter Regions", " Genetic", "TP248.13-248.65", "Biotechnology", "Plasmids"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.13383"}, {"href": "https://doi.org/10.1111/1751-7915.13383"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1751-7915.13383", "name": "item", "description": "10.1111/1751-7915.13383", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1751-7915.13383"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-12T00:00:00Z"}}, {"id": "10.1111/1755-0998.12949", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:54Z", "type": "Journal Article", "created": "2018-09-29", "title": "Conditionally autoregressive models improve occupancy analyses of autocorrelated data: An example with environmental DNA", "description": "Abstract

Site occupancy\uffe2\uff80\uff90detection models (SODMs) are statistical models widely used for biodiversity surveys where imperfect detection of species occurs. For instance, SODMs are increasingly used to analyse environmental DNA (eDNA) data, taking into account the occurrence of both false\uffe2\uff80\uff90positive and false\uffe2\uff80\uff90negative errors. However, species occurrence data are often characterized by spatial and temporal autocorrelation, which might challenge the use of standard SODMs. Here we reviewed the literature of eDNA biodiversity surveys and found that most of studies do not take into account spatial or temporal autocorrelation. We then demonstrated how the analysis of data with spatial or temporal autocorrelation can be improved by using a conditionally autoregressive SODM, and show its application to environmental DNA data. We tested the autoregressive model on both simulated and real data sets, including chronosequences with different degrees of autocorrelation, and a spatial data set on a virtual landscape. Analyses of simulated data showed that autoregressive SODMs perform better than traditional SODMs in the estimation of key parameters such as true\uffe2\uff80\uff90/false\uffe2\uff80\uff90positive rates and show a better discrimination capacity (e.g., higher true skill statistics). The usefulness of autoregressive SODMs was particularly high in data sets with strong autocorrelation. When applied to real eDNA data sets (eDNA from lake sediment cores and freshwater), autoregressive SODM provided more precise estimation of true\uffe2\uff80\uff90/false\uffe2\uff80\uff90positive rates, resulting in more reasonable inference of occupancy states. Our results suggest that analyses of occurrence data, such as many applications of eDNA, can be largely improved by applying conditionally autoregressive specifications to SODMs.

", "keywords": ["0106 biological sciences", "Genetics", " Population", "Spatio-Temporal Analysis", "330", "DNA", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "Biostatistics", "15. Life on land", "Biota", "01 natural sciences", "conditionally autoregressive model; sedimentary DNA; spatial autocorrelation; species occupancy-detection model; temporal autocorrelation; true skill statistics; Biostatistics; DNA; Spatio-Temporal Analysis; Biota; Genetics", " Population; Biotechnology; Ecology", " Evolution", " Behavior and Systematics; Genetics"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/635968/2/Chen_et_al-2019-Molecular_Ecology_Resources.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12949"}, {"href": "https://doi.org/10.1111/1755-0998.12949"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecular%20Ecology%20Resources", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1755-0998.12949", "name": "item", "description": "10.1111/1755-0998.12949", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1755-0998.12949"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-01T00:00:00Z"}}, {"id": "10.1111/ecog.05478", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:55Z", "type": "Journal Article", "created": "2021-05-07", "title": "Multi\u2010taxa colonisation along the foreland of a vanishing equatorial glacier", "description": "

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.

", "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/j.1399-3054.2008.01138.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:14Z", "type": "Journal Article", "created": "2008-05-26", "title": "Adjustments Of Water Use Efficiency By Stomatal Regulation During Drought And Recovery In The Drought-Adaptedvitishybrid Richter-110 (V.\u2003Berlandieri\u2003\u00d7\u2003V.\u2003Rupestris)", "description": "

The hybrid Richter\uffe2\uff80\uff90110 (Vitis berlandieri\uffe2\uff80\uff83\uffc3\uff97\uffe2\uff80\uff83Vitis rupestris) (R\uffe2\uff80\uff90110) has the reputation of being a genotype strongly adapted to drought. A study was performed with plants of R\uffe2\uff80\uff90110 subjected to water withholding followed by re\uffe2\uff80\uff90watering. The goal was to analyze how stomatal conductance (gs) is regulated with respect to different physiological variables under water stress and recovery, as well as how water stress affects adjustments of water use efficiency (WUE) at the leaf level. Water stress induced a substantial stomatal closure and an increase in WUE, which persisted many days after re\uffe2\uff80\uff90watering. The gs during water stress was mainly related to the content of ABA in the xylem and partly related to plant hydraulic conductivity but not to leaf water potential. By contrast, low gs during re\uffe2\uff80\uff90watering did not correlate with ABA contents and was only related to a sustained decreased hydraulic conductivity. In addition to a complex physiological regulation of stomatal closure, gs and rate of transpiration (E) were strongly affected by leaf\uffe2\uff80\uff90to\uffe2\uff80\uff90air vapor pressure deficit (VPD) in a way dependent of the treatment. Interestingly, E increased with increasing VPD in control plants, but decreased with increasing VPD in severely stressed plants. All together, the fine stomatal regulation in R\uffe2\uff80\uff90110 resulted in very high WUE at the leaf level. This genotype is revealed to be very interesting for further studies on the physiological mechanisms leading to regulation of stomatal responsiveness and WUE in response to drought.

", "keywords": ["0106 biological sciences", "Picea abies", "Stomatal conductance; water use efficiency; water stress; drought; water potential; water relations; plant hydraulics; abscisic acid; vapour pressure deficit", "Water", "Plant Transpiration", "svinec", "info:eu-repo/classification/udc/581", "15. Life on land", "sadike", "Adaptation", " Physiological", "01 natural sciences", "6. Clean water", "Droughts", "Plant Leaves", "Plant Stomata", "Hybridization", " Genetic", "Vitis", "citokinin"]}, "links": [{"href": "https://doi.org/10.1111/j.1399-3054.2008.01138.x"}, {"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/j.1399-3054.2008.01138.x", "name": "item", "description": "10.1111/j.1399-3054.2008.01138.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1399-3054.2008.01138.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-09-15T00:00:00Z"}}, {"id": "10.1126/sciadv.aar3599", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:29Z", "type": "Journal Article", "created": "2018-09-12", "title": "Nitrogen isotope signature evidences ammonium deprotonation as a common transport mechanism for the AMT-Mep-Rh protein superfamily", "description": "

Natural nitrogen isotopic signature reveals deprotonation during ammonium transport across living organisms.

", "keywords": ["0301 basic medicine", "570", "Potassium Channels", "Saccharomyces cerevisiae Proteins", "Nitrogen", "Ammonium deprotonation", "Saccharomyces cerevisiae", "Biochemistry", "630", "03 medical and health sciences", "Ammonia", "Ammonium Compounds", "Cation Transport Proteins", "Research Articles", "Plant Proteins", "AMT-Mep-Rh membrane proteins", "0303 health sciences", "Ion Transport", "Nitrogen Isotopes", "Arabidopsis Proteins", "Sciences bio-m\u00e9dicales et agricoles", "AMT-Mep-Rh proteins", "Hydrogen-Ion Concentration", "3. Good health", "Ammonium transport", "N isotope fractionation", "PH control", "Potassium", "Microorganisms", " Genetically-Modified", "Nitrogen (N)", "Ammonium"]}, "links": [{"href": "https://dipot.ulb.ac.be/dspace/bitstream/2013/277241/4/doi_260868.pdf"}, {"href": "https://doi.org/10.1126/sciadv.aar3599"}, {"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.aar3599", "name": "item", "description": "10.1126/sciadv.aar3599", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1126/sciadv.aar3599"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-09-07T00:00:00Z"}}, {"id": "10.1111/ppl.12714", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:26Z", "type": "Journal Article", "created": "2018-03-01", "title": "Anatomical and hormonal description of rootlet primordium development along white lupin cluster root", "description": "

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.

", "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": "10.1111/nph.18387", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:25Z", "type": "Journal Article", "created": "2020-04-18", "title": "RootPainter: deep learning segmentation of biological images with corrective annotation", "description": "

We present RootPainter, a GUI-based software tool for the rapid training of deep neural networks for use in biological image analysis. RootPainter facilitates both fully-automatic and semi-automatic image segmentation. We investigate the effectiveness of RootPainter using three plant image datasets, evaluating its potential for root length extraction from chicory roots in soil, biopore counting and root nodule counting from scanned roots. We also use RootPainter to compare dense annotations to corrective ones which are added during the training based on the weaknesses of the current model.

", "keywords": ["Buildings and machinery", "0301 basic medicine", "phenotyping", "root nodule", "biopore", "interactive machine learning", "Research", "segmentation", "deep learning", "rhizotron", "Breeding and genetics", "Machine Learning", "Soil", "03 medical and health sciences", "Deep Learning", "GUI", "Farm nutrient management", "Image Processing", " Computer-Assisted", "Neural Networks", " Computer"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/2020.04.16.044461v1.full.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18387"}, {"href": "https://doi.org/10.1111/nph.18387"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.18387", "name": "item", "description": "10.1111/nph.18387", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.18387"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-18T00:00:00Z"}}, {"id": "10.1126/sciadv.adj8016", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:29Z", "type": "Journal Article", "created": "2023-11-29", "title": "Connecting the multiple dimensions of global soil fungal diversity", "description": "

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.

", "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": "10.1128/genomeA.01256-17", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-04T16:19:31Z", "type": "Journal Article", "created": "2017-11-10", "title": "Draft Genome Sequences of Three Terrestrial Isoprene-Degrading Rhodococcus Strains", "description": "ABSTRACT

Isoprene is produced in abundance by plants and constitutes a carbon source for microbes. The genomes of three isoprene degraders isolated from tree leaves or soil from the campus of the University of East Anglia were sequenced. These high-GC-content isolates are actinobacteria belonging to the genus Rhodococcus .

", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "QH426 Genetics", "Prokaryotes", "630"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/65487/1/Published_manuscript.pdf"}, {"href": "https://journals.asm.org/doi/pdf/10.1128/genomeA.01256-17"}, {"href": "https://repository.essex.ac.uk/20656/1/Genome%20Announc.-2017-Crombie-.pdf"}, {"href": "https://doi.org/10.1128/genomeA.01256-17"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genome%20Announcements", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/genomeA.01256-17", "name": "item", "description": "10.1128/genomeA.01256-17", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/genomeA.01256-17"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-11-09T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:31Z", "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

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 > 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.

IMPORTANCE

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.

", "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": "10.1186/s12870-019-1831-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:41Z", "type": "Journal Article", "created": "2019-05-30", "title": "Construction of a high-density genetic map and identification of loci controlling purple sepal trait of flower head in Brassica oleracea L. italica", "description": "Some broccoli (Brassica oleracea L. italic) accessions have purple sepals and cold weather would deepen the purple color, while the sepals of other broccoli lines are always green even in cold winter. The related locus or gene is still unknown. In this study, a high-density genetic map was constructed based on specific locus amplified fragment (SLAF) sequencing in a doubled-haploid segregation population with 127 individuals. And mapping of the purple sepal trait in flower heads based on phenotypic data collected during three seasons was performed.A genetic map was constructed, which contained 6694 SLAF markers with an average sequencing depth of 81.37-fold in the maternal line, 84-fold in the paternal line, and 15.76-fold in each individual population studied. In all of the annual data recorded, three quantitative trait loci (QTLs) were identified that were all distributed within the linkage group (LG) 1. Among them, a major locus, qPH.C01-2, located at 36.393\u2009cM LG1, was consistently detected in all analysis. Besides this locus, another two minor loci, qPH.C01-4 and qPH.C01-5, were identified near qPH.C01-2, based on the phenotypic data from spring of 2018.The purple sepal trait could be controlled by a major single locus and two minor loci. The genetic map and location of the purple sepal trait of flower heads provide an important foundation for mapping other compound traits and the identification of the genes related to purple sepal trait in broccoli.", "keywords": ["0301 basic medicine", "0303 health sciences", "QTL", "Pigmentation", "Broccoli", "Quantitative Trait Loci", "Botany", "Chromosome Mapping", "Brassica", "03 medical and health sciences", "Genetic map", "QK1-989", "Broccoli; Genetic map; Purple sepal; QTL; SLAF; Brassica; Chromosome Mapping; Inflorescence; Pigmentation; Quantitative Trait Loci", "Purple sepal", "Inflorescence", "SLAF", "Research Article"]}, "links": [{"href": "https://www.iris.unict.it/bitstream/20.500.11769/378740/2/Construction.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1186/s12870-019-1831-x.pdf"}, {"href": "https://doi.org/10.1186/s12870-019-1831-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BMC%20Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s12870-019-1831-x", "name": "item", "description": "10.1186/s12870-019-1831-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s12870-019-1831-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-30T00:00:00Z"}}, {"id": "10.1186/s40168-022-01405-w", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:42Z", "type": "Journal Article", "created": "2022-12-12", "title": "The global distribution and environmental drivers of the soil antibiotic resistome", "description": "Abstract Background

Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth\uffe2\uff80\uff99s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs.

Results

We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs.

Conclusions

Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome.

", "keywords": ["Ecolog\u00eda (Biolog\u00eda)", "0301 basic medicine", "SDG-03: Good health and well-being", "550", "Antibiotic resistance", "Edafolog\u00eda (Biolog\u00eda)", "Antibiotic resistance genes (ARGs)", "910", "http://metadata.un.org/sdg/3", "631.4", "Microbial ecology", "2417.14 Gen\u00e9tica Vegetal", "Soil", "03 medical and health sciences", "XXXXXX - Unknown", "Global scale", "Humans", "Global change", "SCALE", "Ensure healthy lives and promote well-being for all at all ages", "2. Zero hunger", "0303 health sciences", "Ecology", "Research", "QR100-130", "Human health", "15. Life on land", "Gen\u00e9tica", "Anti-Bacterial Agents", "3. Good health", "Phenotype", "Mobile genetic elements", "13. Climate action", "BACTERIA", "2511.02 Biolog\u00eda de Suelos", "RESISTANCE GENES"]}, "links": [{"href": "https://doi.org/10.1186/s40168-022-01405-w"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-022-01405-w", "name": "item", "description": "10.1186/s40168-022-01405-w", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-022-01405-w"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-11T00:00:00Z"}}, {"id": "10.12688/openreseurope.13987.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:43Z", "type": "Journal Article", "created": "2022-09-05", "title": "Chromosome-scale assembly of the yellow mealworm genome", "description": "Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.", "keywords": ["2. Zero hunger", "0301 basic medicine", "chromosome-scale assembly", "0206 medical engineering", "Articles", "[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics", "02 engineering and technology", "Yellow Mealworm;Tenebrio molitor;genomics;chromosome-scale assembly", "12. Responsible consumption", "03 medical and health sciences", "Yellow Mealworm", "genomics", "Tenebrio molitor", "Research Article"]}, "links": [{"href": "https://doi.org/10.12688/openreseurope.13987.1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Open%20Research%20Europe", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.12688/openreseurope.13987.1", "name": "item", "description": "10.12688/openreseurope.13987.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.12688/openreseurope.13987.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-17T00:00:00Z"}}, {"id": "10.1371/journal.pone.0200979", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:53Z", "type": "Journal Article", "created": "2019-04-11", "title": "Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR", "description": "Abstract

Soil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition.

To address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer\uffc2\uffae, marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers between 1.00 and 2.20 m below ground level.

Importantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition.

Finally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier.

These outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.

", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Science", "Microbial Consortia", "DIVERSITY", "SOFTWARE", "Real-Time Polymerase Chain Reaction", "BACILLUS-SUBTILIS", "BIOMASS", "03 medical and health sciences", "BIOAUGMENTATION", "DNA", " Bacterial/chemistry", "MICROBIAL COMMUNITIES", "Soil Microbiology", "2. Zero hunger", "0303 health sciences", "16S RIBOSOMAL-RNA", "Q", "R", "PROFILES", "ACIDS", "TRANSFORMATION", "6. Clean water", "Microbial Consortia/genetics", "Enhancer Elements", " Genetic", "13. Climate action", "Medicine", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/365395v1.full.pdf"}, {"href": "https://doi.org/10.1371/journal.pone.0200979"}, {"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.0200979", "name": "item", "description": "10.1371/journal.pone.0200979", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0200979"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-09T00:00:00Z"}}, {"id": "10.1371%2fjournal.pone.0044697", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:48Z", "type": "Journal Article", "created": "2012-09-11", "title": "A Novel Stress-Induced Sugarcane Gene Confers Tolerance To Drought, Salt And Oxidative Stress In Transgenic Tobacco Plants", "description": "Drought is a major abiotic stress that affects crop productivity worldwide. Sugarcane can withstand periods of water scarcity during the final stage of culm maturation, during which sucrose accumulation occurs. Meanwhile, prolonged periods of drought can cause severe plant losses.In a previous study, we evaluated the transcriptome of drought-stressed plants to better understand sugarcane responses to drought. Among the up-regulated genes was Scdr1 (sugarcane drought-responsive 1). The aim of the research reported here was to characterize this gene. Scdr1 encodes a putative protein containing 248 amino acids with a large number of proline (19%) and cysteine (13%) residues. Phylogenetic analysis showed that ScDR1is in a clade with homologs from other monocotyledonous plants, separate from those of dicotyledonous plants. The expression of Scdr1 in different varieties of sugarcane plants has not shown a clear association with drought tolerance.The overexpression of Scdr1 in transgenic tobacco plants increased their tolerance to drought, salinity and oxidative stress, as demonstrated by increased photosynthesis, water content, biomass, germination rate, chlorophyll content and reduced accumulation of ROS. Physiological parameters, such as transpiration rate (E), net photosynthesis (A), stomatal conductance (gs) and internal leaf CO(2) concentration, were less affected by abiotic stresses in transgenic Scdr1 plants compared with wild-type plants. Overall, our results indicated that Scdr1 conferred tolerance to multiple abiotic stresses, highlighting the potential of this gene for biotechnological applications.", "keywords": ["Chlorophyll", "Nicotiana", "0301 basic medicine", "Sucrose", "Science", "Molecular Sequence Data", "03 medical and health sciences", "Amino Acid Sequence", "Biomass", "Transgenes", "Photosynthesis", "Phylogeny", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Base Sequence", "Sequence Homology", " Amino Acid", "Q", "R", "Water", "15. Life on land", "Plants", " Genetically Modified", "6. Clean water", "Droughts", "Saccharum", "Oxidative Stress", "Medicine", "Salts", "Reactive Oxygen Species", "Research Article", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1371%2fjournal.pone.0044697"}, {"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%2fjournal.pone.0044697", "name": "item", "description": "10.1371%2fjournal.pone.0044697", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371%2fjournal.pone.0044697"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-09-11T00:00:00Z"}}, {"id": "10.1371/journal.pone.0012346", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:49Z", "type": "Journal Article", "created": "2010-09-01", "title": "Fruit And Soil Quality Of Organic And Conventional Strawberry Agroecosystems", "description": "Sale of organic foods is one of the fastest growing market segments within the global food industry. People often buy organic food because they believe organic farms produce more nutritious and better tasting food from healthier soils. Here we tested if there are significant differences in fruit and soil quality from 13 pairs of commercial organic and conventional strawberry agroecosystems in California.At multiple sampling times for two years, we evaluated three varieties of strawberries for mineral elements, shelf life, phytochemical composition, and organoleptic properties. We also analyzed traditional soil properties and soil DNA using microarray technology. We found that the organic farms had strawberries with longer shelf life, greater dry matter, and higher antioxidant activity and concentrations of ascorbic acid and phenolic compounds, but lower concentrations of phosphorus and potassium. In one variety, sensory panels judged organic strawberries to be sweeter and have better flavor, overall acceptance, and appearance than their conventional counterparts. We also found the organically farmed soils to have more total carbon and nitrogen, greater microbial biomass and activity, and higher concentrations of micronutrients. Organically farmed soils also exhibited greater numbers of endemic genes and greater functional gene abundance and diversity for several biogeochemical processes, such as nitrogen fixation and pesticide degradation.Our findings show that the organic strawberry farms produced higher quality fruit and that their higher quality soils may have greater microbial functional capability and resilience to stress. These findings justify additional investigations aimed at detecting and quantifying such effects and their interactions.", "keywords": ["570", "Plant Extracts - analysis", "Nitrogen", "Science", "Agriculture - methods", "Fragaria - growth & development", "910", "Ante-disciplinary", "Soil - analysis", "Fragaria", "630", "Inclusive", "Carbon - analysis", "Open Access", "Soil", "Engineering", "Fruit - chemistry", "Interdisciplinary", "Biology", "PLOS", "2. Zero hunger", "Organic Agriculture", "Nitrogen - analysis", "Plant Extracts", "Research", "Physics", "Q", "R", "Agriculture", "04 agricultural and veterinary sciences", "15. Life on land", "Fragaria - genetics", "Peer-review", "Carbon", "Open-Access", "Chemistry", "Public Library of Science", "Fruit - growth & development", "Fruit", "Fragaria - chemistry", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0012346"}, {"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.0012346", "name": "item", "description": "10.1371/journal.pone.0012346", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0012346"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-09-01T00:00:00Z"}}, {"id": "10.1371/journal.pone.0029642", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:49Z", "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": "10.2134/jeq2006.0540", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:20:33Z", "type": "Journal Article", "created": "2008-02-12", "title": "Impact Of Glyphosate-Tolerant Soybean And Glufosinate-Tolerant Corn Production On Herbicide Losses In Surface Runoff", "description": "Abstract

Residual herbicides used in the production of soybean [Glycine max (L.) Merr] and corn (Zea mays L.) are often detected in surface runoff at concentrations exceeding their maximum contaminant levels (MCL) or health advisory levels (HAL). With the advent of transgenic, glyphosate\uffe2\uff80\uff90tolerant soybean and glufosinate\uffe2\uff80\uff90tolerant corn this concern might be reduced by replacing some of the residual herbicides with short half\uffe2\uff80\uff90life, strongly sorbed, contact herbicides. We applied both herbicide types to two chiseled and two no\uffe2\uff80\uff90till watersheds in a 2\uffe2\uff80\uff90yr corn\uffe2\uff80\uff93soybean rotation and at half rates to three disked watersheds in a 3\uffe2\uff80\uff90yr corn/soybean/wheat (Triticum aestivum L.)\uffe2\uff80\uff90red clover (Trifolium pratense L.) rotation and monitored herbicide losses in runoff water for four crop years. In soybean years, average glyphosate loss (0.07%) was \uffe2\uff88\uffbc1/7 that of metribuzin (0.48%) and about one\uffe2\uff80\uff90half that of alachlor (0.12%), residual herbicides it can replace. Maximum, annual, flow\uffe2\uff80\uff90weighted concentration of glyphosate (9.2 \uffce\uffbcg L\uffe2\uff88\uff921) was well below its 700 \uffce\uffbcg L\uffe2\uff88\uff921 MCL and metribuzin (9.5 \uffce\uffbcg L\uffe2\uff88\uff921) was well below its 200 \uffce\uffbcg L\uffe2\uff88\uff921 HAL, whereas alachlor (44.5 \uffce\uffbcg L\uffe2\uff88\uff921) was well above its 2 \uffce\uffbcg L\uffe2\uff88\uff921 MCL. In corn years, average glufosinate loss (0.10%) was similar to losses of alachlor (0.07%) and linuron (0.15%), but about one\uffe2\uff80\uff90fourth that of atrazine (0.37%). Maximum, annual, flow\uffe2\uff80\uff90weighted concentration of glufosinate (no MCL) was 3.5 \uffce\uffbcg L\uffe2\uff88\uff921, whereas atrazine (31.5 \uffce\uffbcg L\uffe2\uff88\uff921) and alachlor (9.8 \uffce\uffbcg L\uffe2\uff88\uff921) substantially exceeded their MCLs of 3 and 2 \uffce\uffbcg L\uffe2\uff88\uff921, respectively. Regardless of tillage system, flow\uffe2\uff80\uff90weighted atrazine and alachlor concentrations exceeded their MCLs in at least one crop year. Replacing these herbicides with glyphosate and glufosinate can reduce the occurrence of dissolved herbicide concentrations in runoff exceeding drinking water standards.

", "keywords": ["2. Zero hunger", "Glyphosate", "Glycine max", "Herbicides", "Rain", "Glycine", "Agriculture", "Drug Tolerance", "04 agricultural and veterinary sciences", "15. Life on land", "Plants", " Genetically Modified", "Zea mays", "6. Clean water", "Water Supply", "13. Climate action", "Water Movements", "0401 agriculture", " forestry", " and fisheries", "Water Pollutants", " Chemical", "Environmental Monitoring", "Ohio"]}, "links": [{"href": "https://doi.org/10.2134/jeq2006.0540"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Environmental%20Quality", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2134/jeq2006.0540", "name": "item", "description": "10.2134/jeq2006.0540", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2134/jeq2006.0540"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-03-01T00:00:00Z"}}, {"id": "10.25387/g3.11522544", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:01Z", "type": "Dataset", "created": "2020-01-09", "title": "Supplemental Material for Susi\u010d et al., 2020", "description": "Supplemental data corresponding to the manuscript titled: Whole genome sequencing and comparative genomics of two nematicidal Bacillus strains reveals a wide range of possible virulence factors. The data include the morphological characteristics of the two studied strains; 16S analysis; detailed phylogenetic positioning of the two strains within the genus Bacillus; detailed ANI, Tetra and TCS scores; strain-specific homologous clusters and their GO-term affiliations; BLASTP hits for putative nematode-virulent proteases; putative chitinase sequences analysis; and predicted/putative secondary metabolite clusters (antiSMASH analysis).
", "keywords": ["FOS: Computer and information sciences", "60503 Microbial Genetics", "FOS: Biological sciences", "60408 Genomics", "Microbiology", "60501 Bacteriology", "60102 Bioinformatics"], "contacts": [{"organization": "Susi\u010d, Nik, Jane\u017ei\u010d, Sandra, Rupnik, Maja, Stare, Barbara Geri\u010d,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.25387/g3.11522544"}, {"rel": "self", "type": "application/geo+json", "title": "10.25387/g3.11522544", "name": "item", "description": "10.25387/g3.11522544", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.25387/g3.11522544"}, {"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": "10.25387/g3.11522544.v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:01Z", "type": "Dataset", "created": "2020-01-09", "title": "Supplemental Material for Susi\u010d et al., 2020", "description": "Supplemental data corresponding to the manuscript titled: Whole genome sequencing and comparative genomics of two nematicidal Bacillus strains reveals a wide range of possible virulence factors. The data include the morphological characteristics of the two studied strains; 16S analysis; detailed phylogenetic positioning of the two strains within the genus Bacillus; detailed ANI, Tetra and TCS scores; strain-specific homologous clusters and their GO-term affiliations; BLASTP hits for putative nematode-virulent proteases; putative chitinase sequences analysis; and predicted/putative secondary metabolite clusters (antiSMASH analysis).
", "keywords": ["FOS: Computer and information sciences", "60503 Microbial Genetics", "FOS: Biological sciences", "60408 Genomics", "Microbiology", "60501 Bacteriology", "60102 Bioinformatics"], "contacts": [{"organization": "Susi\u010d, Nik, Jane\u017ei\u010d, Sandra, Rupnik, Maja, Stare, Barbara Geri\u010d,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.25387/g3.11522544.v1"}, {"rel": "self", "type": "application/geo+json", "title": "10.25387/g3.11522544.v1", "name": "item", "description": "10.25387/g3.11522544.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.25387/g3.11522544.v1"}, {"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": "10.3389/fpls.2019.00045", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:11Z", "type": "Journal Article", "created": "2019-01-29", "title": "Construction of a High-Density Genetic Map and Identification of Loci Related to Hollow Stem Trait in Broccoli (Brassic oleracea L. italica)", "description": "A high-quality genetic map is important for mapping of compound traits. In this study, a genetic map was constructed based on the reference genome TO1000 after specific locus amplified fragment (SLAF) sequencing in a double-haploid segregation population of broccoli, and loci controlling hollow stem trait were identified in the genetic map. The genetic map contains 4,787 SLAF markers, with a mean marker distance of 0.22 cM and the mean sequencing depths of 91.14-fold in the maternal line, 88.97-fold in the paternal line and 17.11-fold in each DH progeny. A locus controlling the hollow stem trait, QHS.C09-2, which could explain 14.1% of the phenotypic variation, was steadily detected on the linkage group nine in the indicated data of 3 years' trials and BLUE analysis. The genetic map could lay an important foundation for mapping of compound traits, and mapping of hollow stem trait would be basis to clone the genes related to hollow stems in broccoli.", "keywords": ["broccoli", "0301 basic medicine", "locus", "0303 health sciences", "Locus", "Broccoli; Genetic map; Hollow stems; Locus; SLAF; Plant Science", "Broccoli", "Plant culture", "Plant Science", "hollow stems", "SB1-1110", "03 medical and health sciences", "Genetic map", "Hollow stems", "genetic map", "SLAF"]}, "links": [{"href": "https://www.iris.unict.it/bitstream/20.500.11769/361610/5/fpls-10-00045.pdf"}, {"href": "https://doi.org/10.3389/fpls.2019.00045"}, {"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.2019.00045", "name": "item", "description": "10.3389/fpls.2019.00045", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2019.00045"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-29T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Genetic&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Genetic&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Genetic&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=+Genetic&offset=50", "hreflang": "en-US"}], "numberMatched": 99, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-04-05T04:12:34.440266Z"}