{"type": "FeatureCollection", "features": [{"id": "10.1038/s41598-018-27781-8", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:19:26Z", "type": "Journal Article", "created": "2018-06-15", "title": "Characterization of a community-acquired-MRSA USA300 isolate from a river sample in Austria and whole genome sequence based comparison to a diverse collection of USA300 isolates", "description": "Abstract

The increasing emergence of multi-resistant bacteria in healthcare settings, in the community and in the environment represents a major health threat worldwide. In 2016, we started a pilot project to investigate antimicrobial resistance in surface water. Bacteria were enriched, cultivated on selective chromogenic media and species identification was carried out by MALDI-TOF analysis. From a river in southern Austria a methicillin resistant Staphylococcus aureus (MRSA) was isolated. Whole genome sequence analysis identified the isolate as ST8, spa type t008, SCCmecIV, PVL and ACME positive, which are main features of CA-MRSA USA300. Whole genome based cgMLST of the water isolate and comparison to 18 clinical MRSA USA300 isolates from the Austrian national reference laboratory for coagulase positive staphylococci originating from 2004, 2005 and 2016 and sequences of 146 USA300 isolates arbitrarily retrieved from the Sequence Read Archive revealed a close relatedness to a clinical isolate from Austria. The presence of a CA-MRSA USA300 isolate in an aquatic environment might pose a public health risk by serving as a potential source of infection or a source for emergence of new pathogenic MRSA clones.

", "keywords": ["Methicillin-Resistant Staphylococcus aureus", "0301 basic medicine", "METHICILLIN-RESISTANT", "GENES", "TRANSMISSION", "Article", "Applied microbiology", "EMERGENCE", "03 medical and health sciences", "106005 Bioinformatik", "SDG 3 - Good Health and Well-being", "Rivers", "Sequence Homology", " Nucleic Acid", "Infectious-disease epidemiology", "ENVIRONMENT", "0303 health sciences", "ANTIMICROBIAL RESISTANCE", "RESISTANT STAPHYLOCOCCUS-AUREUS", "ANTIBIOTIC-RESISTANCE", "EVOLUTION", "3. Good health", "Community-Acquired Infections", "SDG 3 \u2013 Gesundheit und Wohlergehen", "Austria", "VIRULENCE", "Bacterial infection", "106005 Bioinformatics", "Genome", " Bacterial"]}, "links": [{"href": "https://www.nature.com/articles/s41598-018-27781-8.pdf"}, {"href": "https://doi.org/10.1038/s41598-018-27781-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-018-27781-8", "name": "item", "description": "10.1038/s41598-018-27781-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-018-27781-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-21T00:00:00Z"}}, {"id": "10.1038/ismej.2010.3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:17Z", "type": "Journal Article", "created": "2010-02-04", "title": "Shifts In Microbial Community Structure Along An Ecological Gradient Of Hypersaline Soils And Sediments", "description": "Abstract

Studies of hypersaline ecosystems often yield novel organisms and contribute to our understanding of extreme environments. Soils and sediments from La Sal del Rey, a previously uncharacterized, hypersaline lake located in southern Texas, USA, were surveyed to characterize the structure and diversity of their microbial communities. Samples were collected along a transect that spanned vegetated uplands, exposed lakebed sediments, and water-logged locations, capturing a wide range of environments and physical and chemical gradients. Community quantitative PCR (qPCR) was used in combination with tag-encoded pyrosequencing, 16S rRNA gene cloning, and Sanger sequencing to characterize the lake's soil and sediment microbial communities. Further, we used multivariate statistics to identify the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa, and sharing significant correlations with site water content, phosphorus and total organic carbon concentrations, and pH. Some individual populations, especially of Archaea, also correlated with sodium concentration and electrical conductivity salinity. Across the transect, Bacteria were numerically dominant relative to Archaea, and among them, three phyla\uffe2\uff80\uff94the Proteobacteria, Bacteroidetes, and Firmicutes\uffe2\uff80\uff94accounted for the majority of taxa detected. Although these taxa were detected with similar abundances to those described in other hypersaline ecosystems, the greater depth of sequencing achieved here resulted in the detection of taxa not described previously in hypersaline sediments. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems.

", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Geologic Sediments", "Salinity", "0303 health sciences", "Bacteria", "Genes", " rRNA", "Sequence Analysis", " DNA", "15. Life on land", "Archaea", "Polymerase Chain Reaction", "Texas", "6. Clean water", "Soil", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Water Microbiology", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2010.3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2010.3", "name": "item", "description": "10.1038/ismej.2010.3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2010.3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-02-04T00:00:00Z"}}, {"id": "10.1038/nature02053", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-06-26T16:19:18Z", "type": "Journal Article", "created": "2003-10-22", "title": "Genome-Scale Approaches To Resolving Incongruence In Molecular Phylogenies", "description": "One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.", "keywords": ["0301 basic medicine", "Saccharomyces", "0303 health sciences", "03 medical and health sciences", "Genes", " Fungal", "Regression Analysis", "Reproducibility of Results", "Genomics", "Genome", " Fungal", "Phylogeny"]}, "links": [{"href": "https://doi.org/10.1038/nature02053"}, {"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/nature02053", "name": "item", "description": "10.1038/nature02053", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/nature02053"}, {"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/s41396-022-01225-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:20Z", "type": "Journal Article", "created": "2022-03-30", "title": "Cross-biome antibiotic resistance decays after millions of years of soil development", "description": "Abstract

Soils harbor the most diverse naturally evolved antibiotic resistance genes (ARGs) on Earth, with implications for human health and ecosystem functioning. How ARGs evolve as soils develop over centuries, to millennia (i.e., pedogenesis), remains poorly understood, which introduces uncertainty in predictions of the dynamics of ARGs under changing environmental conditions. Here we investigated changes in the soil resistome by analyzing 16 globally distributed soil chronosequences, from centuries to millennia, spanning a wide range of ecosystem types and substrate age ranges. We show that ARG abundance and diversity decline only after millions of years of soil development as observed in very old chronosequences. Moreover, our data show increases in soil organic carbon content and microbial biomass as soil develops that were negatively correlated with the abundance and diversity of soil ARGs. This work reveals natural dynamics of soil ARGs during pedogenesis and suggests that such ecological patterns are predictable, which together advances our understanding of the environmental drivers of ARGs in terrestrial environments.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.Greenspaces are important for sustaining healthy urban environments and their human populations. Yet their capacity to support multiple ecosystem services simultaneously (multiservices) compared with nearby natural ecosystems remains virtually unknown. We conducted a global field survey in 56 urban areas to investigate the influence of urban greenspaces on 23 soil and plant attributes and compared them with nearby natural environments. We show that, in general, urban greenspaces and nearby natural areas support similar levels of soil multiservices, with only six of 23 attributes (available phosphorus, water holding capacity, water respiration, plant cover, arbuscular mycorrhizal fungi (AMF), and arachnid richness) significantly greater in greenspaces, and one (available ammonium) greater in natural areas. Further analyses showed that, although natural areas and urban greenspaces delivered a similar number of services at low (>25% threshold) and moderate (>50%) levels of functioning, natural systems supported significantly more functions at high (>75%) levels of functioning. Management practices (mowing) played an important role in explaining urban ecosystem services, but there were no effects of fertilisation or irrigation. Some services declined with increasing site size, for both greenspaces and natural areas. Our work highlights the fact that urban greenspaces are more similar to natural environments than previously reported and underscores the importance of managing urban greenspaces not only for their social and recreational values, but for supporting multiple ecosystem services on which soils and human well-being depends.Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM) and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Biota", "Article", "6. Clean water", "Genes", " Archaeal", "03 medical and health sciences", "Ammonia", "Genes", " Bacterial", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep28981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep28981", "name": "item", "description": "10.1038/srep28981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep28981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-30T00:00:00Z"}}, {"id": "10.1111/gcb.16042", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:38Z", "type": "Journal Article", "created": "2021-12-19", "title": "Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N2O emission", "description": "Abstract

Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N2O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N\uffe2\uff80\uff90induced changes in soil N2O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N2O emission by 261%, whereas there was no clear relationship between changes in soil N2O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field\uffe2\uff80\uff90based results challenge the laboratory\uffe2\uff80\uff90based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N2O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N\uffe2\uff80\uff90induced changes in soil N2O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N2O emission.Analysis of focal copy number variations (CNVs) is highly relevant for cancer research, as they pinpoint driver genes. More specifically, due to selective pressure oncogenes and tumor suppressor genes are more often affected by these events than neighboring passengers. In cases where multiple candidates co-reside in a genomic locus, careful comparison is required to either identify multigenic minimally deleted regions of synergistic co-mutations, or the true single driver gene. The study of focal CNVs in large cancer genome cohorts requires specialized visualization and statistical analysis.

Results

We developed the GenomeTornadoPlot R-package which generates gene-centric visualizations of CNV types, locations and lengths from cohortwise NGS data. Furthermore, the software enables the pairwise comparison of proximate genes to identify co-mutation patterns or driver-passenger hierarchies. The visual examination provided by GenomeTornadoPlot is further supported by adaptable local and global focality scoring. Integrated into the GenomeTornadoPlot R-Package is the comprehensive PCAWG database of CNVs, comprising 2976 cancer genome entities from 46 cohorts of the Pan-cancer Analysis of Whole Genomes project. The GenomeTornadoPlot R-package can be used to perform exploratory or hypothesis-driven analyses on the basis of the PCAWG data or in combination with data provided by the user.

Availability and implementation

GenomeTornadoPlot is written in R script and released via github: <https://github.com/chenhong-dkfz/GenomeTornadoPlot/>. The package is under the license of GPL-3.0.

", "keywords": ["570", "DNA Copy Number Variations", "ddc-570", "Genomics", "Oncogenes", "004 Data processing Computer science", "Software", "ddc-004", "570 Life sciences", "004", "3. Good health"]}, "links": [{"href": "https://archiv.ub.uni-heidelberg.de/volltextserver/34483/1/btac037.pdf"}, {"href": "https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/34483/1/btac037.pdf"}, {"href": "https://academic.oup.com/bioinformatics/article-pdf/38/7/2036/49009547/btac037.pdf"}, {"href": "https://doi.org/10.1093/bioinformatics/btac037"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/bioinformatics/btac037", "name": "item", "description": "10.1093/bioinformatics/btac037", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/bioinformatics/btac037"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-31T00:00:00Z"}}, {"id": "10.1093/femsec/fiaa058", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:20:07Z", "type": "Journal Article", "created": "2020-03-27", "title": "Persistence of wastewater antibiotic resistant bacteria and their genes in human fecal material", "description": "ABSTRACT

Domestic wastewater is a recognized source of antibiotic resistant bacteria and antibiotic resistance genes (ARB&ARGs), whose risk of transmission to humans cannot be ignored. The fitness of wastewater ARB in the complex fecal microbiota of a healthy human was investigated in feces-based microcosm assays (FMAs). FMAs were inoculated with two wastewater isolates, Escherichia coli strain A2FCC14 (MLST ST131) and Enterococcus faecium strain H1EV10 (MLST ST78), harboring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The FMAs, incubated in the presence or absence of oxygen or in the presence or absence of the antibiotics cefotaxime or vancomycin, were monitored based on cultivation, ARGs quantification and bacterial community analysis. The fecal bacterial community was dominated by members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The ARGs harbored by the wastewater isolates could be quantified after one week, in FMAs incubated under both aerobic and anaerobic conditions. These observations were not significantly different in FMAs incubated anaerobically, supplemented with sub-inhibitory concentrations of cefotaxime or vancomycin. The observation that ARGs of wastewater ARB persisted in presence of the human fecal microbiota for at least one week supports the hypothesis of a potential transmission to humans, a topic that deserves further investigation.

", "keywords": ["0301 basic medicine", "Microcosm assays", "0303 health sciences", "Bacteria", "Angiotensin-Converting Enzyme Inhibitors", "Wastewater", "Human fecal microbiota", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "Angiotensin Receptor Antagonists", "Feces", "03 medical and health sciences", "Antibiotic resistance genes", "Antibiotic resistant bacteria", "Genes", " Bacterial", "11. Sustainability", "Humans", "Antibiotic resistance transmission", "Microcosm effect", "Multilocus Sequence Typing"]}, "links": [{"href": "http://academic.oup.com/femsec/article-pdf/96/6/fiaa058/33327470/fiaa058.pdf"}, {"href": "https://doi.org/10.1093/femsec/fiaa058"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiaa058", "name": "item", "description": "10.1093/femsec/fiaa058", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiaa058"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-02T00:00:00Z"}}, {"id": "10.1093/femsec/fiad145", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:20:07Z", "type": "Journal Article", "created": "2023-11-09", "title": "Vegetation type, not the legacy of warming, modifies the response of microbial functional genes and greenhouse gas fluxes to drought in Oro-Arctic and alpine regions", "description": "Abstract

Climate warming and summer droughts alter soil microbial activity, affecting greenhouse gas (GHG) emissions in Arctic and alpine regions. However, the long-term effects of warming, and implications for future microbial resilience, are poorly understood. Using one alpine and three Arctic soils subjected to in situ long-term experimental warming, we simulated drought in laboratory incubations to test how microbial functional-gene abundance affects fluxes in three GHGs: carbon dioxide, methane, and nitrous oxide. We found that responses of functional gene abundances to drought and warming are strongly associated with vegetation type and soil carbon. Our sites ranged from a wet, forb dominated, soil carbon-rich systems to a drier, soil carbon-poor alpine site. Resilience of functional gene abundances, and in turn methane and carbon dioxide fluxes, was lower in the wetter, carbon-rich systems. However, we did not detect an effect of drought or warming on nitrous oxide fluxes. All gene\uffe2\uff80\uff93GHG relationships were modified by vegetation type, with stronger effects being observed in wetter, forb-rich soils. These results suggest that impacts of warming and drought on GHG emissions are linked to a complex set of microbial gene abundances and may be habitat-specific.Research on wood phenology has mainly focused on reactivation of the cambium in spring. In this study we investigated if summer drought advances cessation of wood formation and if it has any influence on wood structure in late successional forest trees of the temperate zone. The end of xylogenesis was monitored between August and November in stands of European beech and pedunculate oak in Belgium for two consecutive years, 2017 and 2018, with the latter year having experienced an exceptional summer drought. Wood formation in oak was affected by the drought, with oak trees ceasing cambial activity and wood maturation about 3\uffc2\uffa0weeks earlier in 2018 compared with 2017. Beech ceased wood formation before oak, but its wood phenology did not differ between years. Furthermore, between the 2\uffc2\uffa0years, no significant difference was found in ring width, percentage of mature fibers in the late season, vessel size and density. In 2018, beech did show thinner fiber walls, whereas oak showed thicker walls. In this paper, we showed that summer drought can have an important impact on late season wood phenology xylem development. This will help to better understand forest ecosystems and improve forest models.

", "keywords": ["580", "0106 biological sciences", "xylogenesis", "beech cessation of wood formation drought oak xylogenesis", "634", "drought", "15. Life on land", "cessation of wood formation", "Wood", "01 natural sciences", "6. Clean water", "Droughts", "Trees", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "Xylem", "13. Climate action", "oak", "Seasons", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "beech", "Biology", "Ecosystem"]}, "links": [{"href": "https://doi.org/10.1093/treephys/tpaa175"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Tree%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/treephys/tpaa175", "name": "item", "description": "10.1093/treephys/tpaa175", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/tpaa175"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-22T00:00:00Z"}}, {"id": "10.1099/mic.0.000931", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:20:16Z", "type": "Journal Article", "created": "2020-05-22", "title": "Microbial metabolism of isoprene: a much-neglected climate-active gas", "description": "

The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.

", "keywords": ["0301 basic medicine", "0303 health sciences", "550", "Bacteria", "Review", "Plants", "15. Life on land", "03 medical and health sciences", "Biodegradation", " Environmental", "Hemiterpenes", "Genes", " Bacterial", "13. Climate action", "8. Economic growth", "Butadienes", "Seawater", "Metabolic Networks and Pathways", "Soil Microbiology"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/75324/1/Published_Version.pdf"}, {"href": "https://repository.essex.ac.uk/29368/1/Microbial%20metabolism%20of%20isoprene%20a%20much-neglected%20climate-active%20gas.pdf"}, {"href": "https://doi.org/10.1099/mic.0.000931"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1099/mic.0.000931", "name": "item", "description": "10.1099/mic.0.000931", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1099/mic.0.000931"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-07-01T00:00:00Z"}}, {"id": "10.1101/2021.03.18.435447", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:20:17Z", "type": "Journal Article", "created": "2021-03-19", "title": "Predicting tomato field-yield using continuous monitoring of young tomato water status", "description": "Abstract

To address the challenge of predicting tomato yields in the field, we used whole-plant functional phenotyping to evaluate water relations under well-irrigated and drought conditions. The genotypes tested are known to exhibit variability in their yields in wet and dry fields. The examined lines included two lines with recessive mutations that affect carotenoid biosynthesis, zetaz2083and tangerinet3406, both isogenic to the processing tomato variety M82. The two mutant lines were reciprocally grafted onto M82, and multiple physiological characteristics were measured continuously, before, during and after drought treatment in the greenhouse. A comparative analysis of greenhouse and field yields showed that the whole-canopy stomatal conductance (gsc) in the morning and cumulative transpiration (CT) were strongly correlated with field measurements of total yield (TY:r2= 0.9 and 0.77, respectively) and plant vegetative weight (PW:r2= 0.6 and 0.94, respectively). Furthermore, the minimum CT during drought and the rate of recovery when irrigation was resumed were both found to predict resilience.

", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "Dehydration", "Genotype", "Genetic Variation", "15. Life on land", "Genes", " Plant", "Adaptation", " Physiological", "6. Clean water", "Droughts", "03 medical and health sciences", "Phenotype", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Mutation", "Plant Physiological Phenomena", "Forecasting"]}, "links": [{"href": "https://doi.org/10.1101/2021.03.18.435447"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2021.03.18.435447", "name": "item", "description": "10.1101/2021.03.18.435447", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2021.03.18.435447"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-19T00:00:00Z"}}, {"id": "10.1101/2024.05.03.592357", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:18Z", "type": "Journal Article", "created": "2025-06-27", "title": "The evolutionary history and functional specialization of microRNA genes in Arabidopsis halleri and A. lyrata", "description": "Abstract

MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in plant genomes. While some miRNA genes are deeply conserved, the majority appear to be species-specific, raising the question of how they emerge and integrate into cellular regulatory networks. To address this question, we first performed a detailed annotation of miRNA genes in the closely related Arabidopsis halleri and A. lyrata, then evaluated their phylogenetic conservation across 87 plant species. We then characterized the process by which newly emerged miRNA genes progressively acquire the properties of \uffe2\uff80\uff9ccanonical\uffe2\uff80\uff9d miRNA genes, in terms of size and stability of the hairpin precursor, loading of their cleavage products into Argonaute proteins, and potential to regulate downstream target genes. Analysis of nucleotide polymorphism distribution along the hairpin sequence (stem, mature miRNA, terminal loop) revealed that the selective constraints on recently emerged miRNA genes were initially weak, gradually increasing toward evolutionarily conserved miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary progression toward canonical miRNAs by which a small fraction of de novo formed miRNA genes eventually integrate into \uffe2\uff80\uff9ccore\uffe2\uff80\uff9d biological processes.Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen\uffe2\uff80\uff90rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO\uffe2\uff80\uff901, oxidizing ammonia to hydroxylamine and ending in the production of N2 gas. Genome analysis revealed that strain HO\uffe2\uff80\uff901 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO\uffe2\uff80\uff901 denitrified nitrite (not nitrate) to N2 and N2O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N2 production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO\uffe2\uff80\uff901 and enabled E. coli accumulated hydroxylamine. Sub\uffe2\uff80\uff90cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to 15N2 from (15NH4)2SO4. Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO\uffe2\uff80\uff901 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N2.

", "keywords": ["Alcaligenes ammonioxydans sp. nov.", "0301 basic medicine", "106014 Genomics", "Nitrogen", "HYDROXYLAMINE OXIDASE", "direct ammonia oxidation (Dirammox)", "OXIDATION", "REDUCTASE", "Water Purification", "THIOSPHAERA-PANTOTROPHA", "PYRUVIC-OXIME", "03 medical and health sciences", "heterotrophic nitrifier", "Ammonia", "106014 Genomik", "Escherichia coli", "Alcaligenes", "wastewater", "Nitrites", "106022 Mikrobiologie", "HETEROTROPHIC NITRIFICATION", "0303 health sciences", "PURIFICATION", "Sewage", "AEROBIC DENITRIFICATION", "Nitrification", "Aerobiosis", "6. Clean water", "NITROGEN", "FAECALIS", "Denitrification", "106022 Microbiology", "Oxidation-Reduction"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15751"}, {"href": "https://doi.org/10.1111/1462-2920.15751"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.15751", "name": "item", "description": "10.1111/1462-2920.15751", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.15751"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-28T00:00:00Z"}}, {"id": "10.1111/1574-6941.12009", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:20:28Z", "type": "Journal Article", "created": "2012-09-13", "title": "Chronic N-Amended Soils Exhibit An Altered Bacterial Community Structure In Harvard Forest, Ma, Usa", "description": "At the Harvard Forest, Petersham, MA, the impact of 20 years of annual ammonium nitrate application to the mixed hardwood stand on soil bacterial communities was studied using 16S rRNA genes pyrosequencing. Amplification of 16S rRNA genes was done using DNA extracted from 30 soil samples (three treatments \u00d7 two horizons \u00d7 five subplots) collected from untreated (control), low N-amended (50 kg ha(-1) year(-1)) and high N-amended (150 kg ha(-1) year(-1)) plots. A total of 1.3 million sequences were processed using qiime. Although Acidobacteria represented the most abundant phylum based on the number of sequences, Proteobacteria were the most diverse in terms of operational taxonomic units (OTUs). UniFrac analyses revealed that the bacterial communities differed significantly among soil horizons and treatments. Microsite variability among the five subplots was also evident. Nonmetric multidimensional scaling ordination of normalized OTU data followed by permutational manova further confirmed these observations. Richness indicators and indicator species analyses revealed higher bacterial diversity associated with N amendment. Differences in bacterial diversity and community composition associated with the N treatments were also observed at lower phylogenetic levels. Only 28-35% of the 6 936 total OTUs identified were common to three treatments, while the rest were specific to one treatment or common to two.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Environmental Microbiology and Microbial Ecology", "Nitrates", "Bacteria", "Genes", " rRNA", "Biodiversity", "15. Life on land", "Trees", "Scientific Contribution Number 2470", "Soil", "03 medical and health sciences", "Massachusetts", "RNA", " Ribosomal", " 16S", "Fertilizers", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/1574-6941.12009"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1574-6941.12009", "name": "item", "description": "10.1111/1574-6941.12009", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1574-6941.12009"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-11T00:00:00Z"}}, {"id": "10.1111/gcb.13737", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:20:36Z", "type": "Journal Article", "created": "2017-05-02", "title": "Higher yields and lower methane emissions with new rice cultivars", "description": "Abstract

Breeding high\uffe2\uff80\uff90yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH4) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high\uffe2\uff80\uff90yielding rice cultivars actually reduce CH4 emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH4 emissions in a soil with a high carbon (C) content. Compared to a low\uffe2\uff80\uff90yielding cultivar, a high\uffe2\uff80\uff90yielding cultivar significantly increased root porosity and the abundance of methane\uffe2\uff80\uff90consuming microorganisms, suggesting that the larger and more porous root systems of high\uffe2\uff80\uff90yielding cultivars facilitated CH4 oxidation by promoting O2 transport to soils. Our results were further supported by a meta\uffe2\uff80\uff90analysis, showing that high\uffe2\uff80\uff90yielding rice cultivars strongly decrease CH4 emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH4 emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high\uffe2\uff80\uff90yielding cultivars can substantially mitigate paddy CH4 emission in China and other rice growing regions.

", "keywords": ["roots", "2. Zero hunger", "China", "Agriculture", "Oryza", "methanogenesis", "04 agricultural and veterinary sciences", "15. Life on land", "630", "Carbon", "meta-analysis", "Greenhouse Gases", "Soil", "13. Climate action", "methanotrophy", "0401 agriculture", " forestry", " and fisheries", "Biomass", "soil carbon", "Methane"]}, "links": [{"href": "https://doi.org/10.1111/gcb.13737"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/gcb.13737", "name": "item", "description": "10.1111/gcb.13737", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.13737"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-06-01T00:00:00Z"}}, {"id": "10.1111/ele.13648", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-06-26T16:20:34Z", "type": "Journal Article", "created": "2020-11-30", "title": "Soil element coupling is driven by ecological context and atomic mass", "description": "Abstract

The biogeochemical cycling of multiple soil elements is fundamental for life on Earth. Here, we conducted a global field survey across 16 chronosequences from contrasting biomes with soil ages ranging from centuries to millions of years. For this, we collected and analysed 435 topsoil samples (0\uffe2\uff80\uff9310\uffc2\uffa0cm) from 87 locations. We showed that high levels of topsoil element coupling, defined as the average correlation among nineteen soil elements, are maintained over geological timescales globally. Cross\uffe2\uff80\uff90biome changes in plant biodiversity, soil microbial structure, weathering, soil pH and texture, and mineral\uffe2\uff80\uff90free unprotected organic matter content largely controlled multi\uffe2\uff80\uff90element coupling. Moreover, elements with heavier atomic mass were naturally more decoupled and unpredictable in space than those with lighter mass. Only the coupling of carbon, nitrogen and phosphorus, which are essential to life on Earth, deviated from this predictable pattern, suggesting that this anomaly may be an undeniable fingerprint of life in terrestrial soils.p1Plants transitioned from an aquatic to a terrestrial lifestyle during their evolution. On land, fluctuations on water availability in the environment became one of the major problems they encountered. The appearance of morpho-physiological adaptations to cope with and tolerate water loss from the cells was undeniably useful to survive on dry land. Some of these adaptations, such as carbon concentrating mechanisms (CCMs), desiccation tolerance (DT) and root impermeabilization, appeared in multiple plant lineages. Despite being crucial for evolution on land, it has been unclear how these adaptations convergently evolved in the various plant lineages. Recent advances on whole genome and transcriptome sequencing are revealing that co-option of genes and gene regulatory networks (GRNs) is a common feature underlying the convergent evolution of these adaptations. In this review we address how the study of CCMs and DT have provided insight into convergent evolution of GRNs underlying plant adaptation to dry environments, and how these insights could be applied to currently emerging understanding of evolution of root impermeabilization through different barrier cell types. We discuss examples of co-option, conservation, and innovation of genes and GRNs at the cell, tissue and organ levels revealed by recent phylogenomic (comparative genomic) and comparative transcriptomic studies.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Physiology", "desiccation tolerance", "exodermis", "Adaptation", " Biological", "Reviews", "Plant Science", "comparative genomics", "Plants", "15. Life on land", "Genes", " Plant", "Biological Evolution", "03 medical and health sciences", "apoplastic barriers", "Gene Regulatory Networks", "Desert Climate"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14143"}, {"href": "https://doi.org/10.1111/pce.14143"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%2C%20Cell%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/pce.14143", "name": "item", "description": "10.1111/pce.14143", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/pce.14143"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-17T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2006.00235.x", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:21:00Z", "type": "Journal Article", "created": "2006-11-21", "title": "The Effects Of Stubble Retention And Nitrogen Application On Soil Microbial Community Structure And Functional Gene Abundance Under Irrigated Maize", "description": "The effects of agronomic management practices on the soil microbial community were investigated in a maize production system in New South Wales, Australia. The site has been intensively studied to measure the impact of stubble management and N-fertilizer application on greenhouse gas emissions (CO(2) and N(2)O), N-cycling, pathology, soil structure and yield. As all of these endpoints can be regulated by microbial processes, the microbiology of the system was examined. Soil samples were taken after a winter fallow period and the diversity of the bacterial and fungal communities was measured using PCR-denaturing gradient gel electrophoresis. Stubble and N shifted the structure of bacterial and fungal communities with the primary driver being stubble addition on the fungal community structure (P<0.05 for all effects). Changes in C, N (total and NO(3)), K and Na, were correlated (P<0.05) with variation in the microbial community structure. Quantitative PCR showed that nifH (nitrogen fixation) and napA (denitrification) gene abundance increased upon stubble retention, whereas amoA gene numbers were increased by N addition. These results showed that the management of both stubble and N have significant and long-term impacts on the size and structure of the soil microbial community at phylogenetic and functional levels.", "keywords": ["Electrophoresis", "0301 basic medicine", "Nitrogen", "Genes", " Fungal", "Polymerase Chain Reaction", "Zea mays", "630", "Soil", "03 medical and health sciences", "Nitrogen Fixation", "Cluster Analysis", "Electrophoresis", " Gel", " Two-Dimensional", "Fertilizers", "Soil Microbiology", "2. Zero hunger", "Gel", "0303 health sciences", "Bacteria", "Bacterial", "Australia", "Fungi", "Agriculture", "15. Life on land", "6. Clean water", "Fungal", "Genes", "Genes", " Bacterial", "13. Climate action", "Two-Dimensional"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2006.00235.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2006.00235.x", "name": "item", "description": "10.1111/j.1574-6941.2006.00235.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2006.00235.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-03-01T00:00:00Z"}}, {"id": "10.1111/nph.15582", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:21:05Z", "type": "Journal Article", "created": "2018-11-05", "title": "Methane emissions from tree stems: a new frontier in the global carbon cycle", "description": "Summary

Tree stems from wetland, floodplain and upland forests can produce and emit methane (CH4). Tree CH4 stem emissions have high spatial and temporal variability, but there is no consensus on the biophysical mechanisms that drive stem CH4 production and emissions. Here, we summarize up to 30 opportunities and challenges for stem CH4 emissions research, which, when addressed, will improve estimates of the magnitudes, patterns and drivers of CH4 emissions and trace their potential origin. We identified the need: (1) for both long\uffe2\uff80\uff90term, high\uffe2\uff80\uff90frequency measurements of stem CH4 emissions to understand the fine\uffe2\uff80\uff90scale processes, alongside rapid large\uffe2\uff80\uff90scale measurements designed to understand the variability across individuals, species and ecosystems; (2) to identify microorganisms and biogeochemical pathways associated with CH4 production; and (3) to develop a mechanistic model including passive and active transport of CH4 from the soil\uffe2\uff80\uff93tree\uffe2\uff80\uff93atmosphere continuum. Addressing these challenges will help to constrain the magnitudes and patterns of CH4 emissions, and allow for the integration of pathways and mechanisms of CH4 production and emissions into process\uffe2\uff80\uff90based models. These advances will facilitate the upscaling of stem CH4 emissions to the ecosystem level and quantify the role of stem CH4 emissions for the local to global CH4 budget.

", "keywords": ["0301 basic medicine", "570", "upland forests", "methane emissions", "temporal variability", "Methanogenesis", "wetland forests", "Spatial variability", "Models", " Biological", "01 natural sciences", "Carbon Cycle", "Trees", "Tree stems", "03 medical and health sciences", "Wetland forests", "tree stems", "0105 earth and related environmental sciences", "Methane emissions", "CH transport", "Plant Stems", "Upland forests", "Temporal variability", "Water", "CH4 transport", "methanogenesis", "15. Life on land", "13. Climate action", "spatial variability", "Methane"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15582"}, {"href": "https://doi.org/10.1111/nph.15582"}, {"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.15582", "name": "item", "description": "10.1111/nph.15582", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.15582"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-18T00:00:00Z"}}, {"id": "10.1128/aem.00033-11", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:21:13Z", "type": "Journal Article", "created": "2011-04-23", "title": "Association Of Earthworm-Denitrifier Interactions With Increased Emission Of Nitrous Oxide From Soil Mesocosms Amended With Crop Residue", "description": "ABSTRACT

Earthworm activity is known to increase emissions of nitrous oxide (N 2 O) from arable soils. Earthworm gut, casts, and burrows have exhibited higher denitrification activities than the bulk soil, implicating priming of denitrifying organisms as a possible mechanism for this effect. Furthermore, the earthworm feeding strategy may drive N 2 O emissions, as it determines access to fresh organic matter for denitrification. Here, we determined whether interactions between earthworm feeding strategy and the soil denitrifier community can predict N 2 O emissions from the soil. We set up a 90-day mesocosm experiment in which 15 N-labeled maize ( Zea mays L.) was either mixed in or applied on top of the soil in the presence or absence of the epigeic earthworm Lumbricus rubellus and/or the endogeic earthworm Aporrectodea caliginosa . We measured N 2 O fluxes and tested the bulk soil for denitrification enzyme activity and the abundance of 16S rRNA and denitrifier genes nirS and nosZ through real-time quantitative PCR. Compared to the control, L. rubellus increased denitrification enzyme activity and N 2 O emissions on days 21 and 90 (day 21, P = 0.034 and P = 0.002, respectively; day 90, P = 0.001 and P = 0.007, respectively), as well as cumulative N 2 O emissions (76%; P = 0.014). A. caliginosa activity led to a transient increase of N 2 O emissions on days 8 to 18 of the experiment. Abundance of nosZ was significantly increased (100%) on day 90 in the treatment mixture containing L. rubellus alone. We conclude that L. rubellus increased cumulative N 2 O emissions by affecting denitrifier community activity via incorporation of fresh residue into the soil and supplying a steady, labile carbon source.

", "keywords": ["2. Zero hunger", "agricultural soil", "Bacteria", "nosz genes", "carbon", "Nitrous Oxide", "n2o emission", "n2o-producing microorganisms", "04 agricultural and veterinary sciences", "15. Life on land", "pcr data", "microbial activity", "Animal Feed", "Zea mays", "lumbricus-rubellus", "Soil", "Denitrification", "Animals", "0401 agriculture", " forestry", " and fisheries", "community composition", "Oligochaeta", "organic-matter"]}, "links": [{"href": "https://doi.org/10.1128/aem.00033-11"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.00033-11", "name": "item", "description": "10.1128/aem.00033-11", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.00033-11"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-15T00:00:00Z"}}, {"id": "10.1128/aem.02218-17", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:13Z", "type": "Journal Article", "created": "2017-11-27", "title": "Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog", "description": "ABSTRACT

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA -based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities.

IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects.

", "keywords": ["0301 basic medicine", "570", "oxidation", "hiili", "ta1172", "Euryarchaeota", "630", "Mining", "Soil", "03 medical and health sciences", "Sphagnum", "Bacterial Proteins", "Nitrogen Fixation", "Sphagnopsida", "14. Life underwater", "ennallistaminen", "turvemaat", "Ecosystem", "Phylogeny", "Soil Microbiology", "0303 health sciences", "nifH", "methane", "Microbiota", "ta1182", "land use", "methanogenesis", "15. Life on land", "Carbon", "kasvihuonekaasup\u00e4\u00e4st\u00f6t", "nitrogen fixation", "13. Climate action", "international", "Wetlands", "Oxygenases", "ta1181", "Methane", "Oxidation-Reduction"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.02218-17"}, {"href": "https://doi.org/10.1128/aem.02218-17"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.02218-17", "name": "item", "description": "10.1128/aem.02218-17", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02218-17"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-01T00:00:00Z"}}, {"id": "10.1128/aem.03393-12", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:21:14Z", "type": "Journal Article", "created": "2012-12-16", "title": "Functional Gene Differences In Soil Microbial Communities From Conventional, Low-Input, And Organic Farmlands", "description": "ABSTRACT

Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO 3 \uffe2\uff88\uff92 , NH 4 + , available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO 3 \uffe2\uff88\uff92 concentration and denitrification genes, NH 4 + concentration and ammonification genes, and N 2 O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.

", "keywords": ["2. Zero hunger", "Michigan", "Nitrogen", "Agriculture", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Microarray Analysis", "Biota", "Carbon", "Soil", "Genes", " Bacterial", "Metagenome", "0401 agriculture", " forestry", " and fisheries", "Metabolic Networks and Pathways", "Soil Microbiology", "Sulfur"]}, "links": [{"href": "https://doi.org/10.1128/aem.03393-12"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.03393-12", "name": "item", "description": "10.1128/aem.03393-12", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.03393-12"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-02-15T00:00:00Z"}}, {"id": "10.1186/s40168-020-00941-7", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:21:27Z", "type": "Journal Article", "created": "2020-11-19", "title": "Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms", "description": "Abstract Background

The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms.

Results

Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms.

Conclusions

Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production.

", "keywords": ["0301 basic medicine", "Farms", "Sanidad animal", "Swine", "Antimicrobial resistance", "Microbial ecology", "Sustainable farming", "Cerdos", "Feces", "03 medical and health sciences", "Anti-Infective Agents", "Environmental Microbiology", "Animals", "Mobilome", "Antiinfecciosos", "One health", "2. Zero hunger", "Excrementos", "0303 health sciences", "Research", "QR100-130", "Drug Resistance", " Microbial", "15. Life on land", "Farm environment", "6. Clean water", "Genes", " Bacterial", "Animals", " Domestic", "2401.05 desarrollo Animal", "Metagenome", "Veterinaria"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40168-020-00941-7.pdf"}, {"href": "https://doi.org/10.1186/s40168-020-00941-7"}, {"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/s40168-020-00941-7", "name": "item", "description": "10.1186/s40168-020-00941-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-020-00941-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-19T00:00:00Z"}}, {"id": "10.1186/s40168-021-01131-9", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:21:27Z", "type": "Journal Article", "created": "2021-10-14", "title": "Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity", "description": "AbstractBackground

The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.

Results

We identified a relatively restricted principal microbiota dominated byPseudomonasduring the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g.,Acinetobacter,Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and \uffce\uffb2-dispersion of ARGs, which were predominantly assigned toAcinetobacterand associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum \uffce\uffb2-lactamase-producingEnterobacteriaceaeand vancomycin-resistantEnterococcaceaewas observed when cutting activities started. ARGs associated with resistance to \uffce\uffb2-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.

Conclusions

The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Food Handling", "Swine", "Tecnolog\u00eda de los alimentos", "Research", "QR100-130", "610", "Food processing environments", "Antimicrobial resistance", "Gen\u00e9tica", "630", "Anti-Bacterial Agents", "Microbial ecology", "Red Meat", "03 medical and health sciences", "Genes", " Bacterial", "Pork Meat", "Animals", "Metagenomics"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40168-021-01131-9.pdf"}, {"href": "https://doi.org/10.1186/s40168-021-01131-9"}, {"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/s40168-021-01131-9", "name": "item", "description": "10.1186/s40168-021-01131-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-021-01131-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-14T00:00:00Z"}}, {"id": "10.1186/s40168-022-01405-w", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:21:27Z", "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": "10.3390/su17031093", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:39Z", "type": "Journal Article", "created": "2025-01-29", "title": "Microbial Bioindicators for Monitoring the Impact of Emerging Contaminants on Soil Health in the European Framework", "description": "

Antibiotic resistance (AR) is recognized by the World Health Organization as a major threat to human health, and recent studies highlight the role of microplastics (MPs) in its spread. MPs in the environment may act as vectors for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Bacterial communities on the plastisphere, the surface of MPs, are influenced by plastic properties, allowing ARB to colonize and form biofilms. These biofilms facilitate the transfer of ARGs within microbial communities. This study analyzed data from the LUCAS soil dataset (885 soil samples across EU countries) using the Emu tool to characterize microbial communities at the genus/species level. Functional annotation via PICRUSt2, supported by a custom tool for Emu output formatting, revealed significant correlations between the genera Solirubrobacter, Bradyrhizobium, Nocardioides, and Bacillus with pathways linked to microplastic degradation and antibiotic resistance. These genera were consistently present in various soil types (woodland, grassland, and cropland), suggesting their potential as bioindicators of soil health in relation to MP pollution. The findings underscore MPs as hotspots for ARB and ARGs, offering new insights into the identification of bioindicators for monitoring soil health and the ecological impacts related to MP contamination.

", "keywords": ["microplastics; antibiotic resistance genes; soil microbiome; LUCAS soil"], "contacts": [{"organization": "Andrea Visca, Luciana Di Gregorio, Manuela Costanzo, Elisa Clagnan, Lorenzo Nolfi, Roberta Bernini, Alberto Orgiazzi, Arwyn Jones, Francesco Vitali, Stefano Mocali, Annamaria Bevivino,", "roles": ["creator"]}]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/1142151/2/sustainability-17-01093.pdf"}, {"href": "https://www.mdpi.com/2071-1050/17/3/1093/pdf"}, {"href": "https://doi.org/10.3390/su17031093"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sustainability", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/su17031093", "name": "item", "description": "10.3390/su17031093", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/su17031093"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-01-29T00:00:00Z"}}, {"id": "10.3389/fpls.2021.698640", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:23:14Z", "type": "Journal Article", "created": "2021-08-06", "title": "High-Resolution X-Ray Computed Tomography: A New Workflow for the Analysis of Xylogenesis and Intra-Seasonal Wood Biomass Production", "description": "

Understanding tree growth and carbon sequestration are of crucial interest to forecast the feedback of forests to climate change. To have a global understanding of the wood formation, it is necessary to develop new methodologies for xylogenesis measurements, valid across diverse wood structures and applicable to both angiosperms and gymnosperms. In this study, the authors present a new workflow to study xylogenesis using high-resolution X-ray computed tomography (HRXCT), which is generic and offers high potential for automatization. The HXRCT-based approach was benchmarked with the current classical approach (microtomy) on three tree species with contrasted wood anatomy (Pinus nigra, Fagus sylvatica, and Quercus robur). HRXCT proved to estimate the relevant xylogenesis parameters (timing, duration, and growth rates) across species with high accuracy. HRXCT showed to be an efficient avenue to investigate tree xylogenesis for a wide range of wood anatomies, structures, and species. HRXCT also showed its potential to provide quantification of intra-annual dynamics of biomass production through high-resolution 3D mapping of wood biomass within the forming growth ring.

", "keywords": ["0106 biological sciences", "[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", "XYLEM", "tree growth", "secondary growth phenology", "Plant Science", "01 natural sciences", "7. Clean energy", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics", "SB1-1110", "Tree growth", "Secondary growth phenology", "microtomy", "PHENOLOGY", "[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "FAGUS-SYLVATICA", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "Biology", "TREE", "Xylogenesis", "580", "xylogenesis", "high-resolution X-ray computed tomography", "Biology and Life Sciences", "Plant culture", "Phylogenetics and taxonomy", "Microtomy", "[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics", "15. Life on land", "BEECH", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "13. Climate action", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "PLANT STRUCTURE", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "environment/Ecosystems", "Engineering sciences. Technology"]}, "links": [{"href": "https://doi.org/10.3389/fpls.2021.698640"}, {"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.2021.698640", "name": "item", "description": "10.3389/fpls.2021.698640", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2021.698640"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-06T00:00:00Z"}}, {"id": "10.1371%2fjournal.pone.0044697", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:35Z", "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": "10.15167/2421-4248/jpmh2019.60.3s1", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:21:50Z", "type": "Journal Article", "title": "I cambiamenti climatici e la coltivazione del pomodoro: la valutazione dell\u2019impatto ambientale nel progetto TOMRES", "description": "Atti del 52\u00b0 Congresso Nazionale Societ\u00e0 Italiana di Igiene, Medicina Preventiva e Sanit\u00e0 Pubblica (SItI) Perugia 16-19 ottobre 2019", "keywords": ["03 medical and health sciences", "0302 clinical medicine", "/", "WAT_CHALLENGE; acque reflue; saggi biologici; cancerogenesi; mutagensi", "promozione della salute", " salutogenesi", "0305 other medical science", "Mycobacterium chimaera", " Heater Cooler Units (HCU)", "3. Good health"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/477031/1/8.2_2019_Sieroprevalenza%20HAV_Siti%20Perugia%2016_19%20Ott_2019.pdf"}, {"href": "https://iris.unimore.it/bitstream/11380/1188860/1/MV_196_SITI-Perugia_metodologia-risk-assessment_2019.pdf"}, {"href": "https://iris.unito.it/bitstream/2318/1803227/1/Atti_SItI.pdf"}, {"href": "https://doi.org/10.15167/2421-4248/jpmh2019.60.3s1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20preventive%20Medicine%20and%20Hygiene", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.15167/2421-4248/jpmh2019.60.3s1", "name": "item", "description": "10.15167/2421-4248/jpmh2019.60.3s1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.15167/2421-4248/jpmh2019.60.3s1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-01T00:00:00Z"}}, {"id": "10.15482/usda.adc/1518485", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-06-26T16:21:57Z", "type": "Dataset", "title": "Data from: Genome sequence of the chestnut blight fungus Cryphonectria parasitica EP155: A fundamental resource for an archetypical invasive plant pathogen", "description": "The ascomycete fungus Cryphonectria parasitica is the causal agent of chestnut blight disease. This deadly fungal pathogen was introduced into North America from Asia before the turn of the 20th century, quickly spreading throughout the natural range of the American chestnut tree. In the course of a single generation, chestnut blight destroyed billions of American chestnut trees in forests across North America, driving it almost to extinction. The genome assembly for C. parasitica EP155 (v. 2.0, available at https://mycocosm.jgi.doe.gov/Crypa2/Crypa2.info.html) contains 26 main genome scaffolds totaling 43.9 Mb, and was sequenced at the U.S. Department of Energy Joint Genome Institute. The information and documents contained within this Ag Data Commons dataset provide supplementary data about the EP155 genome assembly, including scaffold summaries, genetic maps, mitochondrial DNA, P450s, secondary metabolite clusters, vegetative incompatibility genes, and transposable elements. These data are freely available for research purposes.", "keywords": ["15. Life on land", "chestnut blight", "Cryphonectria parasitica", "vegetative incompatibility", "transposons", "P450", "secondary metabolite", "mitochondria", "fungi", "Forest & Plant Health", "american chestnut", "genome assembly", "transposable elements", "genetic maps", "NP303", "Cryphonectria parasitica", "fungi", "invasive species", "plant pathogens", "Asia", "Castanea dentata", "trees", "forests", "extinction", "genome assembly", "United States", "silver", "data collection", "mitochondrial DNA", "secondary metabolites", "genes", "transposons", "phylogeny", "cytochrome P-450", "enzymes", "nuclear genome", "mitochondria"]}, "links": [{"href": "https://doi.org/10.15482/usda.adc/1518485"}, {"rel": "self", "type": "application/geo+json", "title": "10.15482/usda.adc/1518485", "name": "item", "description": "10.15482/usda.adc/1518485", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.15482/usda.adc/1518485"}, {"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": "10.1631/jzus.b1200013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:22:03Z", "type": "Journal Article", "created": "2012-10-03", "title": "Abundance And Composition Of Ammonia-Oxidizing Bacteria And Archaea In Different Types Of Soil In The Yangtze River Estuary", "description": "Tidal flats are soil resources of great significance. Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process. The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR). The different abundances of AOB and AOA were negatively correlated with the salinity. The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene. Among AOB, nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process, i.e., tidal flats, while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process, farm land and wild land. The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate. As for AOA, there was no obvious correlation with the changes in the physicochemical properties of the soil. This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "China", "Conservation of Natural Resources", "Archaeal Proteins", "Molecular Sequence Data", "Genes", " Archaeal", "03 medical and health sciences", "Bacterial Proteins", "Rivers", "Ammonia", "14. Life underwater", "Phylogeny", "0303 health sciences", "Bacteria", "Biodiversity", "Nitrogen Cycle", "15. Life on land", "Archaea", "Nitrification", "6. Clean water", "DNA", " Archaeal", "Genes", " Bacterial", "13. Climate action", "Estuaries", "Oxidoreductases", "Oxidation-Reduction"]}, "links": [{"href": "https://doi.org/10.1631/jzus.b1200013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Zhejiang%20University%20SCIENCE%20B", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1631/jzus.b1200013", "name": "item", "description": "10.1631/jzus.b1200013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1631/jzus.b1200013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-01T00:00:00Z"}}, {"id": "10.3389/fmicb.2022.813480", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:12Z", "type": "Journal Article", "created": "2022-03-01", "title": "Metatranscriptomic analyses unravel dynamic changes in the microbial and metabolic transcriptional profiles in artisanal Austrian hard-cheeses during ripening", "description": "

Vorarlberger Bergk\uffc3\uffa4se (VB) is an artisanal Austrian washed-rind hard cheese produced from alpine cows\uffe2\uff80\uff99 raw milk without the addition of ripening cultures. Ripening time is a key factor in VB, as it strongly influences the microbial communities present in the cheeses and the organoleptic properties of the product. In this study, the microbial and metabolic transcriptional profiles in VB rinds at different ripening times were investigated. VB products before (30\uffe2\uff80\uff89days of ripening) and after (90\uffe2\uff80\uff89days of ripening) selling were selected, RNA was extracted and subjected to shotgun metatranscriptomic sequencing. The analysis revealed some of the previously described abundant bacterial taxa of Brevibacterium, Corynebacterium, Halomonas, Psychrobacter, and Staphylococcus to be highly active in VB rinds. Additionally, the investigation of most important metabolic pathways in cheese ripening clearly showed differences in the gene transcription profiles and the active microbiota between the two ripening points investigated. At 30\uffe2\uff80\uff89days of ripening, metabolic events related with the degradation of residual lactose, lactate, citrate, proteolysis, and lipolysis were significantly more transcribed and mainly associated with Staphylococcus. On the other hand, genes involved in the degradation of smaller compounds derived from previous metabolism (i.e., metabolism of free amino acids and fatty acids) were significantly more expressed in VB rinds with 90 of ripening, and mainly associated with Brevibacterium and Corynebacterium. These latter metabolic activities are responsible of the generation of compounds, such as methanethiol and 2,3-butanediol, that are very important for the flavor and aroma characteristics of cheeses. This study shows the dynamic changes in the gene transcriptional profiles associated with energy substrates metabolism and the generation of organoleptic compounds during VB ripening and uncovers bacterial taxa as key drivers of the ripening process. These taxa might be the target for future studies toward an accelerated cheese ripening and the enhancement of its organoleptic properties.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "791", "metatranscriptomics", "organoleptic compounds", "cheese ripening", "DegreeDisciplines::Life Sciences::Animal Sciences", "microbial dynamics", "Microbiology", "QR1-502", "differential gene transcription", "03 medical and health sciences", "metabolic pathways", "Bacteria; Identification; Quality; Communities; Microflora; Alignment; Pathways; Products; Genes; Acid", "DegreeDisciplines::Life Sciences::Food Science::Food Microbiology"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2022.813480"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2022.813480", "name": "item", "description": "10.3389/fmicb.2022.813480", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2022.813480"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-01T00:00:00Z"}}, {"id": "10.20350/digitalcsic/13978", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:22:17Z", "type": "Report", "title": "Gu\u00eda c\u00e1lculo de erosi\u00f3n en ladera con QGIS", "description": "Open AccessDesde finales de 2019, la colaboraci\u00f3n de la DOP de Estepa, el Instituto de Agricultura Sostenible del CSIC (IAS-CSIC) y el Dpto. de Agronom\u00eda de la Universidad de C\u00f3rdoba , ha permitido crear una herramienta para identificar a nivel de parcela la degradaci\u00f3n de suelo por erosi\u00f3n h\u00eddrica . Esta herramienta se ha desarrollado bajo los principios de la utilizaci\u00f3n de software libre (en concreto el sistema de informaci\u00f3n geogr\u00e1fica QGIS) y de informaci\u00f3n de uso abierto. En la guia adjunta se explica c\u00f3mo se ha obtenido dicho mapa para el control de la erosi\u00f3n en el territorio olivarero de la Denominaci\u00f3n de Origen de Estepa.", "keywords": ["Erosi\u00f3n", "Imagenes de sat\u00e9lite", "15. Life on land", "QGIS"], "contacts": [{"organization": "S\u00e1nchez Montero, Ana, G\u00f3mez Calero, Jos\u00e9 Alfonso, Guzm\u00e1n, Gema,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.20350/digitalcsic/13978"}, {"rel": "self", "type": "application/geo+json", "title": "10.20350/digitalcsic/13978", "name": "item", "description": "10.20350/digitalcsic/13978", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.20350/digitalcsic/13978"}, {"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": "10.3168/jds.2010-3281", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:06Z", "type": "Journal Article", "created": "2010-11-21", "title": "Nitrate And Sulfate: Effective Alternative Hydrogen Sinks For Mitigation Of Ruminal Methane Production In Sheep", "description": "Twenty male crossbred Texel lambs were used in a 2 \u00d7 2 factorial design experiment to assess the effect of dietary addition of nitrate (2.6% of dry matter) and sulfate (2.6% of dry matter) on enteric methane emissions, rumen volatile fatty acid concentrations, rumen microbial composition, and the occurrence of methemoglobinemia. Lambs were gradually introduced to nitrate and sulfate in a corn silage-based diet over a period of 4 wk, and methane production was subsequently determined in respiration chambers. Diets were given at 95% of the lowest ad libitum intake observed within one block in the week before methane yield was measured to ensure equal feed intake of animals between treatments. All diets were formulated to be isonitrogenous. Methane production decreased with both supplements (nitrate: -32%, sulfate: -16%, and nitrate+sulfate: -47% relative to control). The decrease in methane production due to nitrate feeding was most pronounced in the period immediately after feeding, whereas the decrease in methane yield due to sulfate feeding was observed during the entire day. Methane-suppressing effects of nitrate and sulfate were independent and additive. The highest methemoglobin value observed in the blood of the nitrate-fed animals was 7% of hemoglobin. When nitrate was fed in combination with sulfate, methemoglobin remained below the detection limit of 2% of hemoglobin. Dietary nitrate decreased heat production (-7%), whereas supplementation with sulfate increased heat production (+3%). Feeding nitrate or sulfate had no effects on volatile fatty acid concentrations in rumen fluid samples taken 24h after feeding, except for the molar proportion of branched-chain volatile fatty acids, which was higher when sulfate was fed and lower when nitrate was fed, but not different when both products were included in the diet. The total number of rumen bacteria increased as a result of sulfate inclusion in the diet. The number of methanogens was reduced when nitrate was fed. Enhanced levels of sulfate in the diet increased the number of sulfate-reducing bacteria. The number of protozoa was not affected by nitrate or sulfate addition. Supplementation of a diet with nitrate and sulfate is an effective means for mitigating enteric methane emissions from sheep.", "keywords": ["Male", "Rumen", "reduction", "in-vitro", "nitrogen", "Random Allocation", "fumaric-acid", "Animals", "Intestinal Mucosa", "real-time pcr", "2. Zero hunger", "rumen", "Nitrates", "Sheep", "Sulfates", "emissions", "0402 animal and dairy science", "methanogenesis", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Fatty Acids", " Volatile", "Diet", "Agricultural Land Management", "cattle", "Dietary Supplements", "Fermentation", "Animal Nutritional Physiological Phenomena", "feed-intake", "Methemoglobinemia", "Methane"]}, "links": [{"href": "https://doi.org/10.3168/jds.2010-3281"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Dairy%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3168/jds.2010-3281", "name": "item", "description": "10.3168/jds.2010-3281", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3168/jds.2010-3281"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-12-01T00:00:00Z"}}, {"id": "10.3168/jds.2010-3635", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:06Z", "type": "Journal Article", "created": "2011-02-20", "title": "Effects Of A Combination Of Feed Additives On Methane Production, Diet Digestibility, And Animal Performance In Lactating Dairy Cows", "description": "Two experiments were conducted to assess the effects of a mixture of dietary additives on enteric methane production, rumen fermentation, diet digestibility, energy balance, and animal performance in lactating dairy cows. Identical diets were fed in both experiments. The mixture of feed additives investigated contained lauric acid, myristic acid, linseed oil, and calcium fumarate. These additives were included at 0.4, 1.2, 1.5, and 0.7% of dietary dry matter, respectively (treatment ADD). Experimental fat sources were exchanged for a rumen inert source of fat in the control diet (treatment CON) to maintain isolipidic rations. Cows (experiment 1, n=20; experiment 2, n=12) were fed restricted amounts of feed to avoid confounding effects of dry matter intake on methane production. In experiment 1, methane production and energy balance were studied using open-circuit indirect calorimetry. In experiment 2, 10 rumen-fistulated animals were used to measure rumen fermentation characteristics. In both experiments animal performance was monitored. The inclusion of dietary additives decreased methane emissions (g/d) by 10%. Milk yield and milk fat content tended to be lower for ADD in experiment 1. In experiment 2, milk production was not affected by ADD, but milk fat content was lower. Fat- and protein-corrected milk was lower for ADD in both experiments. Milk urea nitrogen content was lowered by ADD in experiment 1 and tended to be lower in experiment 2. Apparent total tract digestibility of fat, but not that of starch or neutral detergent fiber, was higher for ADD. Energy retention did not differ between treatments. The decrease in methane production (g/d) was not evident when methane emission was expressed per kilogram of milk produced. Feeding ADD resulted in increases of C12:0 and C14:0 and the intermediates of linseed oil biohydrogenation in milk in both experiments. In experiment 2, ADD-fed cows tended to have a decreased number of protozoa in rumen fluid when compared with that in control cows. Total volatile fatty acid concentrations were lower for ADD, whereas molar proportions of propionate increased at the expense of acetate and butyrate.", "keywords": ["chain fatty-acids", "Linseed Oil", "Rumen", "extruded linseed", "Myristic Acid", "0403 veterinary science", "crude linseed", "Fumarates", "fumaric-acid", "ruminal methanogenesis", "Animals", "Lactation", "myristic acid", "beef-cattle", "coconut oil", "2. Zero hunger", "0402 animal and dairy science", "Lauric Acids", "04 agricultural and veterinary sciences", "linseed oil", "Animal Feed", "Diet", "Fermentation", "Cattle", "Digestion", "Female", "Food Additives", "detergent fiber", "Energy Metabolism", "Methane"]}, "links": [{"href": "https://doi.org/10.3168/jds.2010-3635"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Dairy%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3168/jds.2010-3635", "name": "item", "description": "10.3168/jds.2010-3635", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3168/jds.2010-3635"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-03-01T00:00:00Z"}}, {"id": "10.22541/au.162389526.68400631/v1", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:22:51Z", "type": "Journal Article", "created": "2021-06-17", "title": "Convergent evolution of gene regulatory networks underlying plant adaptations to dry environments", "description": "

Plants transitioned from an aquatic to a terrestrial lifestyle during their evolution. On land, fluctuations on water availability in the environment became one of the major problems they encountered. The appearance of morpho-physiological adaptations to cope with and tolerate water loss from the cells was undeniably useful to survive on dry land. Some of these adaptations, such as carbon concentrating mechanisms (CCMs), desiccation tolerance (DT) and root impermeabilization, appeared in multiple plant lineages. Despite being crucial for evolution on land, it has been unclear how these adaptations convergently evolved in the various plant lineages. Recent advances on whole genome and transcriptome sequencing are revealing that co-option of genes and gene regulatory networks (GRNs) is a common feature underlying the convergent evolution of these adaptations. In this review we address how the study of CCMs and DT have provided insight into convergent evolution of GRNs underlying plant adaptation to dry environments, and how these insights could be applied to currently emerging understanding of evolution of root impermeabilization through different barrier cell types. We discuss examples of co-option, conservation, and innovation of genes and GRNs at the cell, tissue and organ levels revealed by recent phylogenomic (comparative genomic) and comparative transcriptomic studies.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Physiology", "desiccation tolerance", "exodermis", "Adaptation", " Biological", "Reviews", "Plant Science", "comparative genomics", "Plants", "15. Life on land", "Genes", " Plant", "Biological Evolution", "03 medical and health sciences", "apoplastic barriers", "Gene Regulatory Networks", "Desert Climate"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14143"}, {"href": "https://doi.org/10.22541/au.162389526.68400631/v1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%2C%20Cell%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.22541/au.162389526.68400631/v1", "name": "item", "description": "10.22541/au.162389526.68400631/v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.22541/au.162389526.68400631/v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-17T00:00:00Z"}}, {"id": "10.2527/jas.2011-4209", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:23:00Z", "type": "Journal Article", "created": "2012-01-28", "title": "Dietary Nitrate Supplementation Reduces Methane Emission In Beef Cattle Fed Sugarcane-Based Diets", "description": "The objective of this study was to determine the effect of dietary nitrate on methane emission and rumen fermentation parameters in Nellore \u00d7 Guzera (Bos indicus) beef cattle fed a sugarcane based diet. The experiment was conducted with 16 steers weighing 283 \u00b1 49 kg (mean \u00b1 SD), 6 rumen cannulated and 10 intact steers, in a cross-over design. The animals were blocked according to BW and presence or absence of rumen cannula and randomly allocated to either the nitrate diet (22 g nitrate/kg DM) or the control diet made isonitrogenous by the addition of urea. The diets consisted of freshly chopped sugarcane and concentrate (60:40 on DM basis), fed as a mixed ration. A 16-d adaptation period was used to allow the rumen microbes to adapt to dietary nitrate. Methane emission was measured using the sulfur hexafluoride tracer technique. Dry matter intake (P = 0.09) tended to be less when nitrate was present in the diet compared with the control, 6.60 and 7.05 kg/d DMI, respectively. The daily methane production was reduced (P < 0.01) by 32% when steers were fed the nitrate diet (85 g/d) compared with the urea diet (125 g/d). Methane emission per kilogram DMI was 27% less (P < 0.01) on the nitrate diet (13.3 g methane/kg DMI) than on the control diet (18.2 g methane/kg DMI). Methane losses as a fraction of gross energy intake (GEI) were less (P < 0.01) on the nitrate diet (4.2% of GEI) than on the control diet (5.9% of GEI). Nitrate mitigated enteric methane production by 87% of the theoretical potential. The rumen fluid ammonia-nitrogen (NH(3)-N()) concentration was significantly greater (P < 0.05) for the nitrate diet. The total concentration of VFA was not affected (P = 0.61) by nitrate in the diet, while the proportion of acetic acid tended to be greater (P = 0.09), propionic acid less (P = 0.06) and acetate/propionate ratio tended to be greater (P = 0.06) for the nitrate diet. Dietary nitrate reduced enteric methane emission in beef cattle fed sugarcane based diet.", "keywords": ["sheep", "Rumen", "Sulfur Hexafluoride", "urea", "mitigation", "Ammonia", "Animals", "Urea", "wall", "nitrite", "2. Zero hunger", "Cross-Over Studies", "Nitrates", "0402 animal and dairy science", "methanogenesis", "04 agricultural and veterinary sciences", "Animal Feed", "Diet", "Saccharum", "livestock", "rumen fermentation", "13. Climate action", "manipulation", "Dietary Supplements", "dairy", "Animal Nutritional Physiological Phenomena", "Cattle", "Methane"]}, "links": [{"href": "https://doi.org/10.2527/jas.2011-4209"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Animal%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2527/jas.2011-4209", "name": "item", "description": "10.2527/jas.2011-4209", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2527/jas.2011-4209"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-07-01T00:00:00Z"}}, {"id": "10.25384/sage.c.4412903.v1", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-06-26T16:23:01Z", "type": "Dataset", "created": "2019-02-23", "title": "The Efficacy of Cognitive Behavioral Therapy to Treat Depression and Anxiety and Improve Quality of Life Among Early-Stage Breast Cancer Patients", "description": "Purpose: Positive results have appeared among nonmetastatic breast cancer patients with the use of cognitive behavioral therapy (CBT). However, earlier stage patient results have been mixed. This novelty of this study was the focus on stage I and II breast cancer patients. The objective of the current study was to conduct a meta-analysis of psychosocial functions in early-stage breast cancer survivors to determine its efficacy. Methods: A search of Cochrane Library, EMBASE, MEDLINE, PsycInfo, and PubMed yielded 3237 abstracts, which were independently evaluated by research pairs. Meta-analysis was conducted on 8 studies that included a total of 1053 patients. Psychosocial functions were categorized according to 3 domains: (1) anxiety, (2) depression, and (3) quality of life. Results: Improvement in anxiety was observed in patients treated with CBT relative to controls without CBT (P = .04). Depression and quality of life improvement was not observed in the CBT group within or after 4 months of treatment (P > .05). Conclusions: The results indicated that observed improvements in anxiety in patients with early-stage breast cancer were moderate. The effectiveness of CBT for the improvement of patient outcomes could not be determined, given the methodological and clinical shortcomings of the included trials.", "keywords": ["111708 Health and Community Services", "FOS: Clinical medicine", "111702 Aged Health Care", "FOS: Health sciences", "110306 Endocrinology", "111299 Oncology and Carcinogenesis not elsewhere classified"], "contacts": [{"organization": "Haoyao Sun, Hualei Huang, Shengjun Ji, Xiaochen Chen, Yongqing Xu, Fenglan Zhu, Jinchang Wu,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.25384/sage.c.4412903.v1"}, {"rel": "self", "type": "application/geo+json", "title": "10.25384/sage.c.4412903.v1", "name": "item", "description": "10.25384/sage.c.4412903.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.25384/sage.c.4412903.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-01T00:00:00Z"}}, {"id": "10.3389/fmicb.2018.01176", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:11Z", "type": "Journal Article", "created": "2018-06-08", "title": "Enhanced Bacterial Fitness Under Residual Fluoroquinolone Concentrations Is Associated With Increased Gene Expression in Wastewater-Derived qnr Plasmid-Harboring Strains", "description": "Plasmids harboring qnr genes confer resistance to low fluoroquinolone concentrations. These genes are of significant clinical, evolutionary and environmental importance, since they are widely distributed in a diverse array of natural and clinical environments. We previously extracted and sequenced a large (\u223c185 Kbp) qnrB-harboring plasmid, and several small (\u223c8 Kbp) qnrS-harboring plasmids, from Klebsiella pneumoniae isolates from municipal wastewater biosolids, and hypothesized that these plasmids provide host bacteria a selective advantage in wastewater treatment plants (WWTPs) that often contain residual concentrations of fluoroquinolones. The objectives of this study were therefore to determine the effect of residual fluoroquinolone concentrations on the growth kinetics of qnr plasmid-harboring bacteria; and on the copy number of qnr plasmids and expression of qnr genes. Electrotransformants harboring either one of the two types of plasmids could grow at ciprofloxacin concentrations exceeding 0.5 \u03bcg ml-1, but growth was significantly decreased at concentrations higher than 0.1 \u03bcg ml-1. In contrast, plasmid-free strains failed to grow even at 0.05 \u03bcg ml-1. No differences were observed in plasmid copy number under the tested ciprofloxacin concentrations, but qnr expression increased incrementally from 0 to 0.4 \u03bcg ml-1, suggesting that the transcription of this gene is regulated by antibiotic concentration. This study reveals that wastewater-derived qnr plasmids confer a selective advantage in the presence of residual fluoroquinolone concentrations and provides a mechanistic explanation for this phenomenon.", "keywords": ["0301 basic medicine", "0303 health sciences", "qnr genes", "Microbiology", "QR1-502", "6. Clean water", "fitness", "3. Good health", "wastewater treatment", "03 medical and health sciences", "qPCR expression analysis", "plasmid", "11. Sustainability", "qnr genes", " wastewater treatment", " plasmid", " qPCR expression analysis", " fitness"], "contacts": [{"organization": "Roberto B. M. Marano, Roberto B. M. Marano, Edouard Jurkevitch, Eddie Cytryn, Ella Kaplan, Ella Kaplan,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2018.01176"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2018.01176", "name": "item", "description": "10.3389/fmicb.2018.01176", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2018.01176"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-08T00:00:00Z"}}, {"id": "10.3390/agronomy12020450", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:18Z", "type": "Journal Article", "created": "2022-02-14", "title": "The Analysis of Partial Sequences of the Flavonone 3 Hydroxylase Gene in Lupinus mutabilis Reveals Differential Expression of Two Paralogues Potentially Related to Seed Coat Colour", "description": "

Flavonone 3 hydroxylases (EC 1.14.11.9) are key enzymes in the synthesis of anthocyanins and other flavonoids. Such compounds are involved in seed coat colour and stem pigmentation. Lupinus mutabilis (tarwi) is a legume crop domesticated in the Andean region, valued for the high protein and oil content of its seeds. Tarwi accessions are being selected for cultivation in Europe under defined breeding criteria. Seed coat colour patterns are relevant breeding traits in tarwi, and these are conditioned by anthocyanin content. We identified and isolated part of the tarwi flavonone 3-hydroxylase gene (LmF3h) from two accessions with distinct seed coat colour patterns. Two partial LmF3h paralogues, with predicted 20% amino-acid changes but little predicted tertiary structure alterations, were identified in the coloured seed genotype, while only one was present in the white seed genotype. Upon selection and validation of appropriate reference genes, a RT-qPCR analysis showed that these paralogues have different levels of expression during seed development in both genotypes, although they follow the same expression patterns. DNA and transcription analyses enabled to highlight potential F3H paralogues relatable to seed coat pigmentation in tarwi and, upon biochemical and genetic confirmation, prompt marker-assisted breeding for relevant phenotypic traits associated with flavonoid synthesis.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "F3H", "0303 health sciences", "S", "Agriculture", "Lupinus mutabilis", "03 medical and health sciences", "F3H", "seed coat", "gene expression", "Lupinus mutabilis", "Lupinus mutabilis; F3H; seed coat; gene expression; RT-qPCR reference genes", "RT-qPCR reference genes"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/12/2/450/pdf"}, {"href": "https://doi.org/10.3390/agronomy12020450"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agronomy12020450", "name": "item", "description": "10.3390/agronomy12020450", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agronomy12020450"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-11T00:00:00Z"}}, {"id": "10.3390/biology11040519", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:23:21Z", "type": "Journal Article", "created": "2022-03-30", "title": "Genome characterisation of an isoprene-degrading Alcaligenes sp. isolated from a tropical restored forest", "description": "

Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 \uffc3\uff97 105 ppbv and 7.2 \uffc3\uff97 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism.

", "keywords": ["0301 basic medicine", "0303 health sciences", "550", "QH301-705.5", "Alcaligenes", "15. Life on land", "climate-active gas", "630", "Article", "03 medical and health sciences", "isoprene; climate-active gas; isoprene degradation; genome; Alcaligenes", "isoprene degradation", "Biology (General)", "isoprene", "genome"]}, "links": [{"href": "http://www.mdpi.com/2079-7737/11/4/519/pdf"}, {"href": "https://ueaeprints.uea.ac.uk/id/eprint/84897/1/biology_11_00519.pdf"}, {"href": "https://www.mdpi.com/2079-7737/11/4/519/pdf"}, {"href": "https://repository.essex.ac.uk/33476/1/biology-11-00519.pdf"}, {"href": "https://doi.org/10.3390/biology11040519"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/biology11040519", "name": "item", "description": "10.3390/biology11040519", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/biology11040519"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-28T00:00:00Z"}}, {"id": "10.3390/genes10080601", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:23:24Z", "type": "Journal Article", "created": "2019-08-09", "title": "Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics", "description": "

The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.

", "keywords": ["COMPARATIVE GENOMICS", "0301 basic medicine", "570", "Antifungal Agents", "Plant-growth promotion", "Biolog\u00eda", "comparative genomics", "Phloroglucinol", "PLANT-GROWTH PROMOTION", "Article", "Rhizoctonia", "transcriptomics", "03 medical and health sciences", "https://purl.org/becyt/ford/1.6", "Genome mining", "Hydrogen Cyanide", "Pseudomonas", "genome mining", "RNA SEQUENCING", "TRANSCRIPTOMICS", "biocontrol", "GENOME MINING", "PSEUDOMONASBRASSICACEARUM", "https://purl.org/becyt/ford/1", "Transcriptomics", "0303 health sciences", "Comparative genomics", "Biocontrol", "RNA sequencing", "Pseudomonas brassicacearum", "BIOCONTROL", "Pseudomonas brassicacearum", "Biological Control Agents", "Genes", " Bacterial", "Transcriptome", "plant-growth promotion"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://doi.org/10.3390/genes10080601"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10080601", "name": "item", "description": "10.3390/genes10080601", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10080601"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-09T00:00:00Z"}}, {"id": "10.3390/land12020388", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:23:27Z", "type": "Journal Article", "created": "2023-02-01", "title": "The Soils of Early Farmers and Their Neighbors in the Southern Buh Catchment (Ukraine): Micromorphology and Archaeological Context", "description": "

The problems regarding hunter-gatherer/early farmer interactions are quite an important topic in southeast European archaeology. According to the available data, the two economic subsistence systems have coexisted for some 2000 years during the 6th\uffe2\uff80\uff934th millennia cal BC (Telegin 1985; Lillie et al., 2001). In some areas, hunter-gatherer and early farmer sites are located just a few kilometers apart. The Southern Buh River valley has yielded evidence of Linear Pottery culture, early Trypillia and Trypillia B1 Neolithic settlements as well as hunter-gatherer sites with pottery attributable to the so-called sub-Neolithic or para-Neolithic (Haskevych et al., 2019; Kiosak et al., 2021). Trial-trenches have been opened within some of these sites, which have been radiocarbon-dated from Bern University laboratory (LARA). Soil samples for micromorphological analysis have been collected from these sites to interpret their paleogenetic formation. The soil development is attested since, at least, the beginning of the 5th mill BC, followed by the developed of chernozem soils, which was interrupted by an erosional episode in the end of 5th millennium BC. The available data show that the soils of early farmers arable as are the present day ones. The early farmers were able to exploit relatively heavy soils to cultivate wheat and barley as early as 5250\uffe2\uff80\uff935050 cal BC. In contrast, the sites of ceramic hunter-gatherers were often located on the soils which formed under wet conditions along seasonally flooded riverbanks, which were almost unsuitable for agricultural practices.

", "keywords": ["2. Zero hunger", "S", "radiocarbon dates", "Neolithization of eastern Europe", "Agriculture", "0601 history and archaeology", "06 humanities and the arts", "15. Life on land", "Ukraine", "paleopedogenesis", "Neolithization of eastern Europe; Ukraine; radiocarbon dates; soil micromorphology; paleopedogenesis", "soil micromorphology"]}, "links": [{"href": "http://www.mdpi.com/2073-445X/12/2/388/pdf"}, {"href": "https://iris.unive.it/bitstream/10278/5017342/1/land-12-00388%20%283%29.pdf"}, {"href": "https://www.mdpi.com/2073-445X/12/2/388/pdf"}, {"href": "https://doi.org/10.3390/land12020388"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Land", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/land12020388", "name": "item", "description": "10.3390/land12020388", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/land12020388"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-31T00:00:00Z"}}, {"id": "10.3390/microorganisms8030349", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:23:29Z", "type": "Journal Article", "created": "2020-03-02", "title": "Isoprene Oxidation by the Gram-Negative Model bacterium Variovorax sp. WS11", "description": "

Plant-produced isoprene (2-methyl-1,3-butadiene) represents a significant portion of global volatile organic compound production, equaled only by methane. A metabolic pathway for the degradation of isoprene was first described for the Gram-positive bacterium Rhodococcus sp. AD45, and an alternative model organism has yet to be characterised. Here, we report the characterisation of a novel Gram-negative isoprene-degrading bacterium, Variovorax sp. WS11. Isoprene metabolism in this bacterium involves a plasmid-encoded iso metabolic gene cluster which differs from that found in Rhodococcus sp. AD45 in terms of organisation and regulation. Expression of iso metabolic genes is significantly upregulated by both isoprene and epoxyisoprene. The enzyme responsible for the initial oxidation of isoprene, isoprene monooxygenase, oxidises a wide range of alkene substrates in a manner which is strongly influenced by the presence of alkyl side-chains and differs from other well-characterised soluble diiron monooxygenases according to its response to alkyne inhibitors. This study presents Variovorax sp. WS11 as both a comparative and contrasting model organism for the study of isoprene metabolism in bacteria, aiding our understanding of the conservation of this biochemical pathway across diverse ecological niches.

", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "03 medical and health sciences", "QH301-705.5", "microbiology", "monooxygenase", "Biology (General)", "isoprene", "mutagenesis", "Article", "isoprene-fed fermentor"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/3/349/pdf"}, {"href": "https://ueaeprints.uea.ac.uk/id/eprint/74586/1/Published_Version.pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/3/349/pdf"}, {"href": "https://doi.org/10.3390/microorganisms8030349"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms8030349", "name": "item", "description": "10.3390/microorganisms8030349", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms8030349"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-29T00:00:00Z"}}, {"id": "10.3390/molecules25122723", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:30Z", "type": "Journal Article", "created": "2020-06-16", "title": "Ammonium Recovery and Biogas Upgrading in a Tubular Micro-Pilot Microbial Electrolysis Cell (MEC)", "description": "

Here, a 12-liter tubular microbial electrolysis cell (MEC) was developed as a post treatment unit for simultaneous biogas upgrading and ammonium recovery from the liquid effluent of an anaerobic digestion process. The MEC configuration adopted a cation exchange membrane to separate the inner anodic chamber and the external cathodic chamber, which were filled with graphite granules. The cathodic chamber performed the CO2 removal through the bioelectromethanogenesis reaction and alkalinity generation while the anodic oxidation of a synthetic fermentate partially sustained the energy demand of the process. Three different nitrogen load rates (73, 365, and 2229 mg N/Ld) were applied to the inner anodic chamber to test the performances of the whole process in terms of COD (Chemical Oxygen Demand) removal, CO2 removal, and nitrogen recovery. By maintaining the organic load rate at 2.55 g COD/Ld and the anodic chamber polarization at +0.2 V vs. SHE (Standard Hydrogen Electrode), the increase of the nitrogen load rate promoted the ammonium migration and recovery, i.e., the percentage of current counterbalanced by the ammonium migration increased from 1% to 100% by increasing the nitrogen load rate by 30-fold. The CO2 removal slightly increased during the three periods, and permitted the removal of 65% of the influent CO2, which corresponded to an average removal of 2.2 g CO2/Ld. During the operation with the higher nitrogen load rate, the MEC energy consumption, which was simultaneously used for the different operations, was lower than the selected benchmark technologies, i.e., 0.47 kW/N\uffc2\uffb7m3 for CO2 removal and 0.88 kW\uffc2\uffb7h/kg COD for COD oxidation were consumed by the MEC while the ammonium nitrogen recovery consumed 2.3 kW\uffc2\uffb7h/kg N.

", "keywords": ["Bioelectric Energy Sources", "Nitrogen", "Organic chemistry", "Pilot Projects", "Waste Disposal", " Fluid", "01 natural sciences", "7. Clean energy", "Article", "Electrolysis", "biogas upgrading", " nitrogen recovery", " microbial electrolysis cell", " bioelectromethanogenesis", " digestate", "biogas upgrading", "QD241-441", "Bioreactors", "Ammonium Compounds", "Anaerobiosis", "Cation Exchange Resins", "Electrodes", "0105 earth and related environmental sciences", "Biological Oxygen Demand Analysis", "Electrochemical Techniques", "microbial electrolysis cell", "6. Clean water", "Biodegradation", " Environmental", "13. Climate action", "digestate", "Biofuels", "nitrogen recovery", "bioelectromethanogenesis"]}, "links": [{"href": "http://www.mdpi.com/1420-3049/25/12/2723/pdf"}, {"href": "https://iris.uniroma1.it/bitstream/11573/1415412/1/Cristiani_Ammonium_2020.pdf"}, {"href": "https://www.mdpi.com/1420-3049/25/12/2723/pdf"}, {"href": "https://doi.org/10.3390/molecules25122723"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecules", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/molecules25122723", "name": "item", "description": "10.3390/molecules25122723", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/molecules25122723"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-12T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genes&offset=50&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=Genes&offset=50&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": "prev", "title": "items (prev)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genes&offset=0", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genes&offset=100", "hreflang": "en-US"}], "numberMatched": 161, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-06-26T20:02:39.743939Z"}