The article highlights the available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries while addressing the challenges in NP research and advocating for systematic, collaborative research in Antarctica.
The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H 2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.
IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota , and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment\uffe2\uff80\uff94including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.
", "keywords": ["570", "Bacteria", "Fungi", "Antarctic Regions", "Chloroflexi", "15. Life on land", "Survival strategies", "Cold Temperature", "Extremophiles", "13. Climate action", "Antarctica", "Endolithic communities", "Metagenomics", "14. Life underwater", "Sugars", "Settore BIO/19 - MICROBIOLOGIA GENERALE"]}, "links": [{"href": "https://doi.org/10.1128/aem.02264-23"}, {"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.02264-23", "name": "item", "description": "10.1128/aem.02264-23", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02264-23"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-19T00:00:00Z"}}, {"id": "10.1007/s00122-021-03815-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:33Z", "type": "Journal Article", "created": "2021-03-25", "title": "Genomic prediction models trained with historical records enable populating the German ex situ genebank bio-digital resource center of barley (Hordeum\u00a0sp.) with information on resistances to soilborne barley mosaic viruses", "description": "Abstract Key messageGenomic prediction with special weight of major genes is a valuable tool to populate bio-digital resource centers.
AbstractPhenotypic information of crop genetic resources is a prerequisite for an informed selection that aims to broaden the genetic base of the elite breeding pools. We investigated the potential of genomic prediction based on historical screening data of plant responses against the Barley yellow mosaic viruses for populating the bio-digital resource center of barley. Our study includes dense marker data for 3838 accessions of winter barley, and historical screening data of 1751 accessions for Barley yellow mosaic virus (BaYMV) and of 1771 accessions for Barley mild mosaic virus (BaMMV). Linear mixed models were fitted by considering combinations for the effects of genotypes, years, and locations. The best linear unbiased estimations displayed a broad spectrum of plant responses against BaYMV and BaMMV. Prediction abilities, computed as correlations between predictions and observed phenotypes of accessions, were low for the marker-assisted selection approach amounting to 0.42. In contrast, prediction abilities of genomic best linear unbiased predictions were high, with values of 0.62 for BaYMV and 0.64 for BaMMV. Prediction abilities of genomic prediction were improved by up to\uffe2\uff80\uff89~\uffe2\uff80\uff895% using W-BLUP, in which more weight is given to markers with significant major effects found by association mapping. Our results outline the utility of historical screening data and W-BLUP model to predict the performance of the non-phenotyped individuals in genebank collections. The presented strategy can be considered as part of the different approaches used in genebank genomics to valorize genetic resources for their usage in disease resistance breeding and research.
", "keywords": ["Genetic Markers", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Genotype", "Chromosome Mapping", "Genetic Variation", "Hordeum", "Genomics", "Potyviridae", "Linkage Disequilibrium", "Plant Breeding", "03 medical and health sciences", "Phenotype", "Databases", " Genetic", "Original Article", "Genetic Association Studies", "Disease Resistance", "Plant Diseases"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00122-021-03815-0.pdf"}, {"href": "https://doi.org/10.1007/s00122-021-03815-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Theoretical%20and%20Applied%20Genetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00122-021-03815-0", "name": "item", "description": "10.1007/s00122-021-03815-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00122-021-03815-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-25T00:00:00Z"}}, {"id": "10.1007/s00253-019-09689-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:35Z", "type": "Journal Article", "created": "2019-02-20", "title": "Distribution of Oenococcus oeni populations in natural habitats", "description": "Oenococcus oeni is the lactic acid bacteria species most commonly encountered in wine, where it develops after the alcoholic fermentation and achieves the malolactic fermentation that is needed to improve the quality of most wines. O. oeni is abundant in the oenological environment as well as in apple cider and kombucha, whereas it is a minor species in the natural environment. Numerous studies have shown that there is a great diversity of strains in each wine region and in each product or type of wine. Recently, genomic studies have shed new light on the species diversity, population structure, and environmental distribution. They revealed that O. oeni has unique genomic features that have contributed to its fast evolution and adaptation to the enological environment. They have also unveiled the phylogenetic diversity and genomic properties of strains that develop in different regions or different products. This review explores the distribution of O. oeni and the diversity of strains in natural habitats.", "keywords": ["0106 biological sciences", "0301 basic medicine", "570", "Evolution", "[SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering", "590", "Wine", "01 natural sciences", "Domestication", "Evolution", " Molecular", "03 medical and health sciences", "[SDV.IDA]Life Sciences [q-bio]/Food engineering", "MD Multidisciplinary", "[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering", "Ecosystem", "Oenococcus", "Phylogeny", "0303 health sciences", "Malolactic fermentation", "Genetic Variation", "Genomics", "[SDV.IDA] Life Sciences [q-bio]/Food engineering", "Mini-Review", "Fermentation", "Oenococcus oeni", "Biotechnology"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s00253-019-09689-z.pdf"}, {"href": "https://doi.org/10.1007/s00253-019-09689-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-019-09689-z", "name": "item", "description": "10.1007/s00253-019-09689-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-019-09689-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-20T00:00:00Z"}}, {"id": "10.1007/s00253-020-10811-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:35Z", "type": "Journal Article", "created": "2020-08-13", "title": "Industrial biotechnology of Pseudomonas putida: advances and prospects", "description": "AbstractPseudomonas putidais a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications ofP. putidaas a cell factory.
Key points\uffe2\uff80\uffa2 Pseudomonas putida advances to a global industrial cell factory.
\uffe2\uff80\uffa2 Novel tools enable system-wide understanding and streamlined genomic engineering.
\uffe2\uff80\uffa2 Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
", "keywords": ["0301 basic medicine", "ddc:500", "0303 health sciences", "Pseudomonas putida", "EDEMP cycle", "PHA", "Systems Biology", "500", "Genomics", "Mini-Review", "Bioeconomy", "Bacterial chassis", "Lignin", "03 medical and health sciences", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "Microbial cell factory", "13. Climate action", "Biocatalysis", "Synthetic Biology", "KT2440", "Metabolic engineering", "Biotransformation", "Synthetic biology", "Biotechnology"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00253-020-10811-9.pdf"}, {"href": "https://doi.org/10.1007/s00253-020-10811-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-020-10811-9", "name": "item", "description": "10.1007/s00253-020-10811-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-020-10811-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-13T00:00:00Z"}}, {"id": "10.1007/s00253-021-11565-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:35Z", "type": "Journal Article", "created": "2021-09-14", "title": "Submerged macrophytes recruit unique microbial communities and drive functional zonation in an aquatic system", "description": "Aquatic and wetland systems are widely used for landscapes and water regeneration. Microbiomes and submerged macrophytes (hydrophytes) play essential roles in conversions of organic and inorganic compounds in those ecosystems. The systems were extensively investigated for microbial diversities and compositions. However, little is known about how hydrophytes recruited diverse microbiota and affected functional zonation in aquatic systems. To address this issue, epiphytic leaf and root, sediment, and surrounding water samples were collected from the dragon-shape aquatic system in Beijing Olympic Park. Metagenomic DNAs were extracted and subjected to sequencing. Results showed that epiphytic leaf and root microbiomes and metabolic marker genes were remarkably different from that of surrounding environment. Twenty indicator bacterial genera for epiphytic microbiomes were identified and 50 metabolic marker genes were applied to evaluate the function of epiphytic leaf and root, water, and sediment microbiomes. Co-occurrence analysis revealed highly modularized pattern of metabolic marker genes and indicator bacterial genera related to metabolic functions. These results suggested that hydrophytes shaped microbiomes and drove functional zonation in aquatic systems. KEY POINTS: \u2022 Microbiomes of hydrophytes and their surrounding environments were investigated. \u2022 Twenty indicator bacterial genera highly specific to epiphytic biofilms were identified. \u2022 Epiphytes recruited unique microbiomes and drove functional zonation in aquatic systems.", "keywords": ["0106 biological sciences", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Beijing", "Microbiota", "Metagenomics", "15. Life on land", "01 natural sciences", "6. Clean water"], "contacts": [{"organization": "Hai-Zhen Zhu, Min-Zhi Jiang, Min-Zhi Jiang, Shuang-Jiang Liu, Shuang-Jiang Liu, Cheng-Ying Jiang, Nan Zhou,", "roles": ["creator"]}]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00253-021-11565-8.pdf"}, {"href": "https://doi.org/10.1007/s00253-021-11565-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-021-11565-8", "name": "item", "description": "10.1007/s00253-021-11565-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-021-11565-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-14T00:00:00Z"}}, {"id": "10.1007/s10123-021-00215-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:50Z", "type": "Journal Article", "created": "2021-10-23", "title": "Novel methods of microbiome analysis in the food industry", "description": "The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies.", "keywords": ["2. Zero hunger", "0301 basic medicine", "Food metagenome", "0303 health sciences", "Food microbiome", "3309 Tecnolog\u00eda de Los Alimentos", "Tecnolog\u00eda de los alimentos", "Metataxonomics", "Microbiota", "3309.90 Microbiolog\u00eda de Alimentos", "Drug Resistance", " Microbial", "Resistome", "03 medical and health sciences", "Food Industry", "Metagenome", "Metagenomics"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s10123-021-00215-8.pdf"}, {"href": "https://doi.org/10.1007/s10123-021-00215-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10123-021-00215-8", "name": "item", "description": "10.1007/s10123-021-00215-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10123-021-00215-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-23T00:00:00Z"}}, {"id": "10.1016/j.cub.2020.09.063", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:02Z", "type": "Journal Article", "created": "2020-10-15", "title": "Newly explored\u00a0Faecalibacterium\u00a0diversity is connected to age, lifestyle, geography, and disease.", "description": "Faecalibacterium is prevalent in the human gut and a promising microbe for the development of next-generation probiotics (NGPs) or biotherapeutics. Analyzing reference Faecalibacterium genomes and almost 3,000 Faecalibacterium-like metagenome-assembled genomes (MAGs) reconstructed from 7,907 human and 203 non-human primate gut metagenomes, we identified the presence of 22 different Faecalibacterium-like species-level genome bins (SGBs), some further divided in different strains according to the subject geographical origin. Twelve SGBs are globally spread in the human gut and show different genomic potential in the utilization of complex polysaccharides, suggesting that higher SGB diversity may be related with increased utilization of plant-based foods. Moreover, up to 11 different species may co-occur in the same subject, with lower diversity in Western populations, as well as intestinal inflammatory states and obesity. The newly explored Faecalibacterium diversity will be able to support the choice of strains suitable as NGPs, guided by the consideration of the differences existing in their functional potential.", "keywords": ["Adult", "0301 basic medicine", "pangenome", "Adolescent", "gut microbiome", "Datasets as Topic", "General Biochemistry", " Genetics and Molecular Biology", "Innovation action", "Feces", "03 medical and health sciences", "Animals", "Humans", "biotherapeutics", "European Commission", "Child", "Life Style", "Faecalibacterium", "Aged", "Aurora Universities Network", "Horizon 2020", "0303 health sciences", "EC", "Geography", "Faecalibacterium prausnitzii", "H2020", "Age Factors", "Infant", "Middle Aged", "Gastrointestinal Microbiome", "Faecalibacterium prausnitzii", " gut microbiome", " strain diversity", " pangenome", " novel probiotics", " biotherapeutics", "Child", " Preschool", "novel probiotics", "Dysbiosis", "Macaca", "Metagenome", "strain diversity", "Metagenomics", "General Agricultural and Biological Sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/819607/1/PIIS0960982220314330.pdf"}, {"href": "https://doi.org/10.1016/j.cub.2020.09.063"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.cub.2020.09.063", "name": "item", "description": "10.1016/j.cub.2020.09.063", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.cub.2020.09.063"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-01T00:00:00Z"}}, {"id": "10.1007/s13225-024-00533-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:24Z", "type": "Journal Article", "created": "2024-02-26", "title": "Class-wide genomic tendency throughout specific extremes in black fungi", "description": "Open AccessPeer reviewed", "keywords": ["570", "Black Fungi", "Plant Biology", "Mycology & Parasitology", "Evolutionary biology", "Microbiology", "Genetics", "Black fungi \u00b7 Stress resistance \u00b7 Comparative genomics \u00b7 Extreme environments", "14. Life underwater", "Plant biology", "2. Zero hunger", "Evolutionary Biology", "Black fungi", "Comparative genomics", "Human Genome", "500", "Extreme environments", "Biological Sciences", "15. Life on land", "3. Good health", "Health Disparities", "13. Climate action", "8. Economic growth", "Stress resistance", "Settore BIO/19 - MICROBIOLOGIA GENERALE", "Biotechnology"]}, "links": [{"href": "https://iris.unitn.it/bitstream/11572/450837/1/FUDI_Coleine%20et%20al%20v2..pdf"}, {"href": "https://iris.unitn.it/bitstream/11572/450837/3/s13225-024-00533-y.pdf"}, {"href": "https://escholarship.org/content/qt86f967px/qt86f967px.pdf"}, {"href": "https://doi.org/10.1007/s13225-024-00533-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Fungal%20Diversity", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s13225-024-00533-y", "name": "item", "description": "10.1007/s13225-024-00533-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s13225-024-00533-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-26T00:00:00Z"}}, {"id": "10.1016/j.cofs.2020.11.012", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:00Z", "type": "Journal Article", "created": "2020-12-09", "title": "Environmental microbiome mapping as a strategy to improve quality and safety in the food industry", "description": "In food industries, an environmentally-adapted microbiome can colonize the surfaces of equipment and tools and be transferred to the food product or intermediates of production. These complex microbial consortia may include microbial spoilers, pathogens, as well as beneficial microbes. Advances in sequencing technologies and metagenomics provide the opportunity to map the environmental microbiome in food industries at an unprecedented depth, highlighting the importance of the resident microbial communities in influencing food quality and safety, as well as the main factors shaping its composition and activities. However, specific technical issues must be considered. Although microbiome mapping in the food industry has the potential to revolutionize food safety and quality management systems, its application as routine practice is still challenging and technical issues limit the exploitation of the powerful information that can be obtained by the application of such state-of-the-art approaches.", "keywords": ["Aurora Universities Network", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "EC", "food industry", "H2020", "food quality", "Applied Microbiology and Biotechnology", "Horizon 2020 Framework Programme", "Innovation action", "food safety", "03 medical and health sciences", "contamination", "13. Climate action", "Metagenomics", "European Commission", "Knowmad Institut", "environmental microbiome", "Food Science"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/828326/1/COFS%2c2021_EnvMapping.pdf"}, {"href": "https://doi.org/10.1016/j.cofs.2020.11.012"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Opinion%20in%20Food%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.cofs.2020.11.012", "name": "item", "description": "10.1016/j.cofs.2020.11.012", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.cofs.2020.11.012"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-01T00:00:00Z"}}, {"id": "10.1016/j.copbio.2018.11.014", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:01Z", "type": "Journal Article", "created": "2018-12-11", "title": "Multi-omics and potential applications in wine production", "description": "The wine microbiome - that is the microbial communities associated with the fermentation of must, is one of the most important factors in transforming grapes to wine, including flavour and aroma. Recent developments in high throughput sequencing and other 'omics methodologies are rapidly changing the level and complexity of information that we are able to extract from the wine microbiome. This will significantly enhance not only our understanding of which microbes are present at the various stages of the grapevine growth and winemaking process, but also improve our understanding of the complex interactions between microbes, the substrate and environment, ultimately shaping wine production. In this perspective we describe the role and future potential of such techniques in wine production, and highlight the potential challenges that will be simultaneously faced.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "03 medical and health sciences", "13. Climate action", "Microbiota", "DNA Barcoding", " Taxonomic", "Wine", "Genomics"]}, "links": [{"href": "https://doi.org/10.1016/j.copbio.2018.11.014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Opinion%20in%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.copbio.2018.11.014", "name": "item", "description": "10.1016/j.copbio.2018.11.014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.copbio.2018.11.014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2023.121325", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:15Z", "type": "Journal Article", "created": "2023-02-22", "title": "Extracellular DNA includes an important fraction of high-risk antibiotic resistance genes in treated wastewaters", "description": "Wastewater treatment plants are among the main hotspots for the release of antibiotic resistance genes (ARGs) into the environment. ARGs in treated wastewater can be found in the intracellular DNA (iDNA) and in the extracellular DNA (eDNA). In this study, we investigated the fate and the distribution (either in eDNA or in iDNA) of ARGs in the treated wastewaters pre and post-disinfection by shotgun metagenomics. The richness of the intracellular resistome was found to be higher than the extracellular one. However, the latter included different high risk ARGs. About 11% of the recovered metagenome assembled genomes (MAGs) from the extracted DNA was positive for at least one ARG and, among them, several were positive for more ARGs. The high-risk ARG bacA was the most frequently detected gene among the MAGs. The disinfection demonstrated to be an important driver of the composition of the antibiotic resistomes. Our results demonstrated that eDNA represents an important fraction of the overall ARGs, including a number of high-risk ARGs, which reach the environment with treated wastewater effluents. The studied disinfections only marginally affect the whole antibiotic resistome but cause important shifts from intracellular to extracellular DNA, potentially threating human health.", "keywords": ["0301 basic medicine", "0303 health sciences", "Drug Resistance", " Microbial", "DNA", "Wastewater", "Antimicrobial resistance", "6. Clean water", "MAG", "Anti-Bacterial Agents", "Disinfection", "03 medical and health sciences", "13. Climate action", "Extracellular DNA", "Genes", " Bacterial", "Humans", "Metagenomics"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2023.121325"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envpol.2023.121325", "name": "item", "description": "10.1016/j.envpol.2023.121325", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2023.121325"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-01T00:00:00Z"}}, {"id": "10.1016/j.foodres.2022.112202", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:20Z", "type": "Journal Article", "created": "2022-11-19", "title": "Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities", "description": "Daily consumption of fresh vegetables is highly recommended by international health organizations, because of their high content of nutrients. However, fresh vegetables might harbour several pathogenic microorganisms or contribute to spread antibiotic resistance, thus representing a hazard for consumers. In addition, little is known about the transmission routes of the residential microbiome from the food handling environment to vegetables. Therefore, we collected environmental and food samples from three manufactures producing fresh vegetables to estimate the relevance of the built environment microbiome on that of the finished products. Our results show that food contact surfaces sampled after routine cleaning and disinfection procedures host a highly diverse microbiome, including pathogens such as the enterotoxigenic Bacillus cereus sensu stricto. In addition, we provide evidence of the presence of a wide range of antibiotic resistance and virulence genes on food contact surfaces associated with multiple taxa, thus supporting the hypothesis that selection of resistant and pathogenic taxa might occur on sanitized surfaces. This study also highlights the potential of microbiome mapping routinely applied in food industries monitoring programs to ensure food safety.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Food industry", "Virulence", "3309 Tecnolog\u00eda de Los Alimentos", "Antimicrobials", "Biolog\u00eda", "Tecnolog\u00eda de los alimentos", "Biofilm", "Microbiota", "Drug Resistance", " Microbial", "Anti-Bacterial Agents", "03 medical and health sciences", "Bacillus cereus", "Vegetables", "Antimicrobials; Bacillus cereus; Biofilm; Food industry; Metagenomics", "Metagenomics", "2414 Microbiolog\u00eda"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/903001/1/1-s2.0-S0963996922012601-main.pdf"}, {"href": "https://doi.org/10.1016/j.foodres.2022.112202"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Food%20Research%20International", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foodres.2022.112202", "name": "item", "description": "10.1016/j.foodres.2022.112202", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foodres.2022.112202"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-01T00:00:00Z"}}, {"id": "10.1016/j.geoderma.2015.04.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:33Z", "type": "Journal Article", "created": "2015-04-18", "title": "Will Changes In Climate And Land Use Affect Soil Organic Matter Composition? Evidence From An Ecotonal Climosequence", "description": "Abstract As the largest actively cycling pool of terrestrial C, the response of soil organic matter (SOM) to climate change may greatly affect global C cycling and climate change feedbacks. Despite the influence of SOM chemistry\u2014here defined as soil organic C (SOC) and soil organic N (SON) functional groups and compounds\u2014on decomposition, uncertainty exists regarding the response of SOM chemistry to climate change and associated land use shifts. Here, we adopt a climosequence approach, using latitude along a uniform glacial till deposit at the grassland\u2013forest ecotone in central Canada as a surrogate for the effects of climate change on SOM chemistry. Additionally, we evaluate differences in SOM chemistry from paired native grassland, native trembling aspen ( Populus tremuloides ) forest, and arable soil profiles to investigate the effects of likely climate-induced land use alterations. The combination of C and N K -edge X-ray absorption near edge structure (XANES) with pyrolysis-field ionization mass spectrometry (Py-FIMS) techniques was used to examine SOM chemistry at atomic and molecular scales, respectively. These techniques revealed only modest differences in surface SOM chemistry related to land use and latitude. Greater variation was apparent in the vertical stratification of SOM constituents from soil depth profiles. These findings indicate that pedon-scale processes have greater control over SOM chemistry than do processes operating on landscape (e.g. land use) and regional (e.g. climate) scales. Additionally they imply that SOM chemistry is largely unresponsive to climatic change on the magnitude of the mean annual temperature (MAT) gradient under study (~\u00a00.7\u00a0\u00b0C), despite its location at the grassland\u2013forest boundary highlighting its sensitivity, and is similarly unresponsive to associated land use shifts.", "keywords": ["Vegetation", "Ecology and Evolutionary Biology", "Plant Sciences", "Agriculture", "Genetics and Genomics", "04 agricultural and veterinary sciences", "15. Life on land", "Soil quality", "13. Climate action", "Land use", "Climate change", "0401 agriculture", " forestry", " and fisheries", "Organic nitrogen", "Forest Sciences", "Organic carbon"], "contacts": [{"organization": "Purton, Kendra, Pennock, Dan, Leinweber, Peter, Walley, Fran,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.geoderma.2015.04.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Geoderma", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.geoderma.2015.04.007", "name": "item", "description": "10.1016/j.geoderma.2015.04.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.geoderma.2015.04.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-09-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2024.170290", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:00Z", "type": "Journal Article", "created": "2024-01-19", "title": "Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability", "description": "Survival and growth strategies of Antarctic endolithic microbes residing in Earth's driest and coldest desert remain virtually unknown. From 109 endolithic microbiomes, 4539 metagenome-assembled genomes were generated, 49.3\u00a0% of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability.", "keywords": ["570", "Bacteria", "Microbiota", "Habitability", "500", "Antarctic Regions", "Astronomical Sciences", "15. Life on land", "Extremophiles", "13. Climate action", "Physical Sciences", "Antarctica", "Metagenome", "Metagenomics", "14. Life underwater", "Adaptation", "MAGs", "Settore BIO/19 - MICROBIOLOGIA GENERALE", "Environmental Sciences"]}, "links": [{"href": "https://openpub.fmach.it/bitstream/10449/83880/5/2024%20STE%20Albanese.pdf"}, {"href": "https://doi.org/10.1016/j.scitotenv.2024.170290"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2024.170290", "name": "item", "description": "10.1016/j.scitotenv.2024.170290", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.170290"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-03-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2023.168050", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:00Z", "type": "Journal Article", "created": "2023-10-28", "title": "Geology and elevation shape bacterial assembly in Antarctic endolithic communities", "description": "Ice free areas of continental Antarctica are among the coldest and driest environments on Earth, and yet, they support surprisingly diverse and highly adapted microbial communities. Endolithic growth is one of the key adaptations to such extreme environments and often represents the dominant life-form. Despite growing scientific interest, little is known of the mechanisms that influence the assembly of endolithic microbiomes across these harsh environments. Here, we used metagenomics to examine the diversity and assembly of endolithic bacterial communities across Antarctica within different rock types and over a large elevation range. While granite supported richer and more heterogeneous communities than sandstone, elevation had no apparent effect on taxonomic richness, regardless of rock type. Conversely, elevation was clearly associated with turnover in community composition, with the deterministic process of variable selection driving microbial assembly along the elevation gradient. The turnover associated with elevation was modulated by geology, whereby for a given elevation difference, turnover was consistently larger between communities inhabiting different rock types. Overall, selection imposed by elevation and geology appeared stronger than turnover related to other spatially-structured environmental drivers. Our findings indicate that at the cold-arid limit of life on Earth, geology and elevation are key determinants of endolithic bacterial heterogeneity. This also suggests that warming temperatures may threaten the persistence of such extreme-adapted organisms.", "keywords": ["570", "Endolithic microbiome", "Shotgun metagenomics", "550", "Community assembly", "Settore BIO/07 - ECOLOGIA", "Altitude", "Granite", "Antarctica", "Sandstone"]}, "links": [{"href": "https://openpub.fmach.it/bitstream/10449/83878/1/2024%20STE%20Larsen.pdf"}, {"href": "https://doi.org/10.1016/j.scitotenv.2023.168050"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2023.168050", "name": "item", "description": "10.1016/j.scitotenv.2023.168050", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2023.168050"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "10.1016/j.xgen.2024.100639", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:31Z", "type": "Journal Article", "created": "2024-08-30", "title": "ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers", "description": "The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.", "keywords": ["330", "Bioinformatics", "Genome", " Human", "610", "Genomics", "Medical Oncology", "Somatic variant calling", "Polymorphism", " Single Nucleotide", "Article", "Benchmarking", "Oncology", "INDEL Mutation", "\u00c0rees tem\u00e0tiques de la UPC::Inform\u00e0tica::Aplicacions de la inform\u00e0tica::Bioinform\u00e0tica", "Neoplasms", "Cancer genomics", "Humans", "Benchmarking data", "Precision Medicine", "Software"]}, "links": [{"href": "https://doi.org/10.1016/j.xgen.2024.100639"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Cell%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.xgen.2024.100639", "name": "item", "description": "10.1016/j.xgen.2024.100639", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.xgen.2024.100639"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-09-01T00:00:00Z"}}, {"id": "10.1038/s41438-020-00353-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:56Z", "type": "Journal Article", "created": "2020-09-01", "title": "ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean \u2018da serbo\u2019 type long shelf-life germplasm", "description": "AbstractDouble digest restriction-site associated sequencing (ddRAD-seq) is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm collections. Using this methodology, we investigated the genomic diversity of a panel of 288 diverse tomato (Solanum lycopersicumL.) accessions enriched in \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 (called \uffe2\uff80\uff98de penjar\uffe2\uff80\uff99 in Spain) long shelf life (LSL) materials (152 accessions) mostly originating from Italy and Spain. The rest of the materials originate from different countries and include landraces for fresh consumption, elite cultivars, heirlooms, and breeding lines. Apart from their LSL trait, \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 landraces are of remarkable interest for their resilience. We identified 32,799 high-quality SNPs, which were used for model ancestry population structure and non-parametric hierarchical clustering. Six genetic subgroups were revealed, clearly separating most \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 landraces, but also the Spanish germplasm, suggesting a subdivision of the population based on type and geographical provenance. Linkage disequilibrium (LD) in the collection decayed very rapidly within <5\uffe2\uff80\uff89kb. We then investigated SNPs showing contrasted minor frequency allele (MAF) in \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 materials, resulting in the identification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such asCTR1andJAR1. Finally, a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits. Our findings suggest the presence of a genetic footprint of the \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 germplasm selected in the Mediterranean basin. Moreover, we provide novel insights on LSL \uffe2\uff80\uff98da serbo\uffe2\uff80\uff99 germplasm as a promising source of alleles for tolerance to stresses.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "GENETICA", "0303 health sciences", "03 medical and health sciences", "Genetic markers", "Genomics", "Plant breeding", "Article", "02.- Poner fin al hambre", " conseguir la seguridad alimentaria y una mejor nutrici\u00f3n", " y promover la agricultura sostenible"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/451962/1/41438_2020_article_353.pdf"}, {"href": "https://www.nature.com/articles/s41438-020-00353-6.pdf"}, {"href": "https://doi.org/10.1038/s41438-020-00353-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Horticulture%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41438-020-00353-6", "name": "item", "description": "10.1038/s41438-020-00353-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41438-020-00353-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-01T00:00:00Z"}}, {"id": "10.1038/s41598-025-00173-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:02Z", "type": "Journal Article", "created": "2025-05-08", "title": "Enhanced understanding of nitrogen fixing bacteria through DNA extraction with polyvinylidene fluoride membrane", "description": "AbstractThe rhizobiota, particularly nitrogen-fixing bacteria, play a crucial role in plant functioning by providing essential nutrients and defense against pathogens. This study investigated the diversity of nitrogen-fixing bacteria in a relatively understudied habitat: technosoils developed from industrial soda production. To analyze the bacterial diversity in the rhizosphere soils of wheat (Triticum aestivum L.) and aster (Tripolium pannonicum Jacq.), regions of the nifH gene were amplified and sequenced from the resident bacterial communities. A polyvinylidene fluoride (PVDF) membrane was employed for metagenomic DNA extraction, enhancing the detection of nitrogen-fixing bacteria. Prior to standard DNA extraction, an enrichment step was conducted in nitrogen-free JMV medium at 26\uffc2\uffa0\uffc2\uffb0C for 24\uffc2\uffa0h, with a modification that replaced soil with the PVDF membrane. This approach enabled a more comprehensive analysis of the rhizosphere bacterial community, revealing that unique amplicon sequence variants (ASVs) in aster and wheat membrane samples accounted for a notable proportion of all ASVs in the dataset (8.5% and 23%, respectively) that were not captured using the standard method. Additionally, our findings demonstrated higher alpha diversity of nitrogen-fixing bacteria in the wheat rhizosphere compared to the aster rhizosphere. In wheat, the dominant genus was Insolitispirillum (38.80%), followed by unclassified genera within Gammaproteobacteria (9.76%) and Rhodospirillaceae (4.74%). In contrast, the aster rhizosphere was predominantly occupied by Azotobacter (95.69%).Soil organic matter (SOM) stocks contain nearly three times as much carbon (C) as the atmosphere and changes in soil C stocks may have a major impact on future atmospheric carbon dioxide concentrations and climate. Over the past two decades, much research has been devoted to examining the influence of warming on SOM decomposition in topsoil. Most SOM, however, is old and stored in subsoil. The fate of subsoil SOM under future warming remains highly uncertain. Here, by combining a long-term field warming experiment and a meta-analysis study, we showed that warming significantly increased SOM decomposition in subsoil. We also showed that a decade of warming promoted decomposition of subsoil SOM with turnover times of decades to millennia in a tall grass prairie and this effect was largely associated with shifts in the functional gene structure of microbial communities. By coupling stable isotope probing with metagenomics, we found that microbial communities in warmed soils possessed a higher relative abundance of key functional genes involved in the degradation of organic materials with varying recalcitrance than those in control soils. These findings suggest warming may considerably alter the stability of the vast pool of old SOM in subsoil, contributing to the long-term positive feedback between the C cycle and climate.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "Technology", "0303 health sciences", "Hot Temperature", "Ecology", "Bacteria", "Climate Change", "Biological Sciences", "15. Life on land", "Microbiology", "630", "Carbon", "Climate Action", "Environmental sciences", "Biological sciences", "Soil", "03 medical and health sciences", "13. Climate action", "Original Article", "Metagenomics", "Environmental Sciences", "Soil Microbiology"]}, "links": [{"href": "https://escholarship.org/content/qt8mp28182/qt8mp28182.pdf"}, {"href": "https://doi.org/10.1038/ismej.2017.48"}, {"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.2017.48", "name": "item", "description": "10.1038/ismej.2017.48", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2017.48"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-04-21T00:00:00Z"}}, {"id": "10.1038/nature02053", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:54Z", "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/s41538-021-00087-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:58Z", "type": "Journal Article", "created": "2020-09-12", "title": "Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples.", "description": "AbstractFood processing environments can harbor microorganisms responsible for food spoilage or foodborne disease. Efficient and accurate identification of microorganisms throughout the food chain can allow the identification of sources of contamination and the timely implementation of control measures. Currently, microbial monitoring of the food chain relies heavily on culture-based techniques. These assays are determined on the microbes expected to be present in the environment, and thus do not cater for unexpected contaminants. Many culture-based assays are also unable to distinguish between undesirable taxa and closely related harmless species. Furthermore, even when multiple culture-based approaches are used in parallel, it is still not possible to comprehensively characterize the entire microbiology of a food-chain sample.
High throughput DNA sequencing represents a potential means through which microbial monitoring of the food chain can be enhanced. While sequencing platforms, such as the Illumina MiSeq, NextSeq and NovaSeq, are most typically found in research or commercial sequencing laboratories, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. In this study, having initially assessed the ability of rapid MinION-based sequencing to discriminate between different microbes within a simple mock metagenomic mixture of related food spoilage, spore-forming microorganisms. Subsequently, we proceeded to compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility.
Overall, ONT MinION sequencing provided accurate classification to species level, which was comparable to Illumina-derived outputs. However, while the MinION-based approach provided a means of easy library preparations and portability, the high concentrations of DNA needed to run the rapid sequencing protocols was a limiting factor, requiring the random amplification of template DNA in order to generate sufficient material for analysis.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "03 medical and health sciences", "Nutrition. Foods and food supply", "13. Climate action", "0206 medical engineering", "TX341-641", "Metagenomics", "02 engineering and technology", "Food microbiology", "TP368-456", "Food processing and manufacture", "Article"]}, "links": [{"href": "https://www.nature.com/articles/s41538-021-00087-2.pdf"}, {"href": "https://doi.org/10.1038/s41538-021-00087-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/npj%20Science%20of%20Food", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41538-021-00087-2", "name": "item", "description": "10.1038/s41538-021-00087-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41538-021-00087-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-11T00:00:00Z"}}, {"id": "10.1038/s41586-023-05791-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:00Z", "type": "Journal Article", "created": "2023-03-08", "title": "The giant diploid faba genome unlocks variation in a global protein crop", "description": "AbstractIncreasing 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.The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.
", "keywords": ["0301 basic medicine", "Evolutionary Biology", "0303 health sciences", "Genome", "Fungi", "Computational Biology", "Eukaryota", "Genomics", "Article", "Workflow", "Evolutionsbiologi", "03 medical and health sciences", "13. Climate action", "Algorithms"]}, "links": [{"href": "https://www.nature.com/articles/s41598-020-58025-3.pdf"}, {"href": "https://doi.org/10.1038/s41598-020-58025-3"}, {"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/s41598-020-58025-3", "name": "item", "description": "10.1038/s41598-020-58025-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-020-58025-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-28T00:00:00Z"}}, {"id": "10.1038/s41598-023-49194-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:02Z", "type": "Journal Article", "created": "2023-12-13", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "description": "AbstractBacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.A hot topic in recent decades, the application of organic amendments to arid-degraded soils has been shown to benefit microbially-mediated processes. However, despite the importance of soils for global sustainability, a gap has not been addressed yet in soil science: is there any connection between ecosystem-community processes, cellular functionality and microbial lifestyles (i.e. oligotrophy-copiotrophy) in restored soils? Together with classical ecosystem indicators (fatty-acids, extracellular-enzyme activities, basal respiration), state-of-the-art metaproteomics was applied to fill this gap in a model-restoration experiment initiated 10-years ago by the addition of sewage-sludge and compost. Organic amendment strongly impacted ecosystem processes. Furthermore, the type of material used induced differences in the cellular functionalities through variations in the percentages of proteins involved in translation, transcription, energy production and C-fixation. We conclude that the long-term impact of organic restoration goes beyond ecosystem processes and affects cellular functionalities and phyla-lifestyles coupled with differences in microbial-community structures.
", "keywords": ["Proteomics", "2. Zero hunger", "0301 basic medicine", "1000 Multidisciplinary", "Sewage", "610 Medicine & health", "10071 Functional Genomics Center Zurich", "04 agricultural and veterinary sciences", "15. Life on land", "Article", "6. Clean water", "Enzymes", "Environmental sciences", "Soil", "03 medical and health sciences", "Soil microbiology", "13. Climate action", "11. Sustainability", "570 Life sciences; biology", "0401 agriculture", " forestry", " and fisheries", "Soil microbiology; Environmental sciences", "Ecosystem", "Environmental Restoration and Remediation", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep15550"}, {"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/srep15550", "name": "item", "description": "10.1038/srep15550", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep15550"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-10-27T00:00:00Z"}}, {"id": "10.1039/d0mt00043d", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:05Z", "type": "Journal Article", "created": "2020-05-20", "title": "Biomolecular approaches to understanding metal tolerance and hyperaccumulation in plants", "description": "AbstractTrace metal elements are essential for plant growth but become toxic at high concentrations, while some non-essential elements, such as Cd and As, show toxicity even in traces. Thus, metal homeostasis is tightly regulated in plants. Plant species colonising metalliferous soils have evolved mechanisms to hypertolerate metals and, in rare cases, can hyperaccumulate them in excess amounts in their shoots. The molecular mechanisms of metal hypertolerance and hyperaccumulation are likely derived from alterations in the basic mechanisms involved in general metal homeostasis. Genes involved in metal transport, synthesis of metal chelators and oxidative stress responses are constitutively and highly expressed in metal hypertolerant and hyperaccumulator species. Plant specialized metabolites and cell wall components have been proposed as major players in these mechanisms. In addition, the high intra-specific natural variation of metal hypertolerance and hyperaccumulation suggests that various molecular mechanisms might be involved in the evolution of these traits. To date, the potential of wild plant populations as systems to study metal tolerance and hyperaccumulation has not been fully exploited. The advent of next-generation sequencing (NGS) has enabled the study of non-model species, providing an opportunity to study natural populations and new tolerant and/or hyperaccumulating species, and will provide new insights into metal tolerance and hyperaccumulation. In this review we highlight background knowledge about metal tolerance and hyperaccumulation in plants and the current state-of-the-art techniques to study and identify the underlying mechanisms of metal hypertolerance and hyperaccumulation. We also outline for the reader the importance of the multidisciplinarity of this research field and how the integration of multiomic approaches will benefit facing the future scientific challenges. The article highlights the available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries while addressing the challenges in NP research and advocating for systematic, collaborative research in Antarctica.
It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species,Arabidopsis halleriandArabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in severalA. hallerigenes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.
This article is part of the theme issue \uffe2\uff80\uff98Convergent evolution in the genomics era: new insights and directions\uffe2\uff80\uff99. The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus Rhodococcus proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably Variovorax , a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from Variovorax in a heterologous host. A Variovorax strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "QH301 Biology", "Biological Sciences", "15. Life on land", "Mixed Function Oxygenases", "Comamonadaceae", "03 medical and health sciences", "Biodegradation", " Environmental", "Hemiterpenes", "Populus", "13. Climate action", "Butadienes", "Rhodococcus", "Metagenomics", "Genome", " Bacterial", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/69197/1/Published_manuscript.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.1812668115"}, {"href": "https://repository.essex.ac.uk/23631/1/1812668115.full.pdf"}, {"href": "https://doi.org/10.1073/pnas.1812668115"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.1812668115", "name": "item", "description": "10.1073/pnas.1812668115", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.1812668115"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-29T00:00:00Z"}}, {"id": "10.1080/1040841x.2022.2132850", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:31Z", "type": "Journal Article", "created": "2022-10-26", "title": "Bioinformatic approaches for studying the microbiome of fermented food", "description": "High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.", "keywords": ["2. Zero hunger", "0301 basic medicine", "metatranscriptomics", "Microbiota", "0206 medical engineering", "high-throughput sequencing", "Computational Biology", "High-Throughput Nucleotide Sequencing", "bioinformatics", "02 engineering and technology", "fermented foods", "03 medical and health sciences", "Metagenome", "Metagenomics", "Fermented Foods"]}, "links": [{"href": "https://www.tandfonline.com/doi/pdf/10.1080/1040841X.2022.2132850"}, {"href": "https://doi.org/10.1080/1040841x.2022.2132850"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Critical%20Reviews%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1080/1040841x.2022.2132850", "name": "item", "description": "10.1080/1040841x.2022.2132850", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1080/1040841x.2022.2132850"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-10-26T00:00:00Z"}}, {"id": "10.1093/bioinformatics/btac037", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:37Z", "type": "Journal Article", "created": "2022-01-26", "title": "GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis", "description": "Abstract MotivationAnalysis 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.
ResultsWe 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 implementationGenomeTornadoPlot 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": "10.1101/117887", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:46Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics", "description": "AbstractEnvironmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.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": "10.1111/1574-6941.12384", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:54Z", "type": "Journal Article", "created": "2014-07-21", "title": "Impact Of Long-Term N, P, K, And Npk Fertilization On The Composition And Potential Functions Of The Bacterial Community In Grassland Soil", "description": "Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem.", "keywords": ["0301 basic medicine", "sandy loam", "Nitrogen", "verrucomicrobia", "microbial communities", "nitrogen", "diversity", "Phosphates", "Soil", "03 medical and health sciences", "Fertilizers", "Soil Microbiology", "2. Zero hunger", "metagenomics", "0303 health sciences", "Bacteria", "national", "15. Life on land", "Grassland", "13. Climate action", "genome size", "ammonia-oxidizing bacteria", "Potassium", "Metagenomics", "ecosystems", "management"]}, "links": [{"href": "https://doi.org/10.1111/1574-6941.12384"}, {"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": "10.1111/1574-6941.12384", "name": "item", "description": "10.1111/1574-6941.12384", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1574-6941.12384"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-08-21T00:00:00Z"}}, {"id": "10.1111/nph.17365", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:25Z", "type": "Journal Article", "created": "2021-03-29", "title": "New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing", "description": "SummaryMethane (CH4) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH4 cycle. Recent studies have focused on quantifying tree stems as sources of CH4 and understanding abiotic CH4 emissions in plant canopies, with the role of microbial in situ CH4 formation receiving less attention. Moreover, despite initial reports revealing CH4 consumption, studies have not adequately evaluated the potential of microbial CH4 oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH4 exchange of plants, and particularly in boreal trees. We detected CH4\uffe2\uff80\uff90producing methanogens and novel monooxygenases, potentially involved in CH4 consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH4 emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH4 exchange. Our findings, together with the emerging diversity of novel CH4\uffe2\uff80\uff90producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH4 exchange.
", "keywords": ["0301 basic medicine", "330", "ta1172", "metaani", "bakteerit", "Trees", "03 medical and health sciences", "boreal forests", "Ymp\u00e4rist\u00f6tiede", "2. Zero hunger", "0303 health sciences", "Norway", "ta1183", "kasvifysiologia", "puut (kasvit)", "genomiikka", "15. Life on land", "ta4112", "methanogenic archaea", "mets\u00e4t", "plant microbiome", "tree", "methane exchange", "boreaalinen vy\u00f6hyke", "mikrobisto", "13. Climate action", "Environmental Science", "aineiden kierto", "Metagenomics", "methanotrophic bacteria", "arkeonit", "Methane", "captured metagenomics"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.17365"}, {"href": "https://doi.org/10.1111/nph.17365"}, {"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.17365", "name": "item", "description": "10.1111/nph.17365", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.17365"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-05-02T00:00:00Z"}}, {"id": "10.1111/pce.14143", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:26Z", "type": "Journal Article", "created": "2021-06-17", "title": "Convergent evolution of gene regulatory networks underlying plant adaptations to dry environments", "description": "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": "10.1128/aem.01081-21", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:30Z", "type": "Journal Article", "created": "2021-09-01", "title": "Seasonality and geography have a greater influence than the use of chlorine-based cleaning agents on the microbiota of bulk tank raw milk.", "description": "The microbiota of raw milk is affected by many factors that can control or promote the introduction of undesirable microorganisms. Chlorine-based cleaning agents have been commonly used due to their effectiveness in controlling undesirable microorganisms, but they have been associated with the formation of chlorine residues that are detrimental to product quality and may impact consumer health.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Geography", "Microbiota", "Dairy", "Dairying", "03 medical and health sciences", "Milk", "Food Microbiology", "Animals", "Equipment Contamination", "DNA sequencing", "Metagenomics", "Seasons", "Chlorine", "Ireland", "Disinfectants"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.01081-21"}, {"href": "https://doi.org/10.1128/aem.01081-21"}, {"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.01081-21", "name": "item", "description": "10.1128/aem.01081-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01081-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-28T00:00:00Z"}}, {"id": "10.1128/mBio.00799-17", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:31Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics", "description": "AbstractEnvironmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.
", "keywords": ["Q Science", "0301 basic medicine", "330", "Supplementary Data", "ecophysiology", "Ecophysiology", "NE/E006353/1", "Bacterial Physiological Phenomena", "Microbiology", "Soil", "03 medical and health sciences", "Virology", "European Commission", "Ecosystem", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "655240", "metagenomics", "0303 health sciences", "Bacteria", "Natural Environment Research Council (NERC)", "Q", "NE/M017125/1", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Adaptation", " Physiological", "soil microbiology", "QR1-502", "United Kingdom", "3. Good health", "Soil microbiology", "Metagenomics", "Genome", " Bacterial", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/117887v1.full.pdf"}, {"href": "https://journals.asm.org/doi/pdf/10.1128/mBio.00799-17"}, {"href": "https://doi.org/10.1128/mBio.00799-17"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mBio", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/mBio.00799-17", "name": "item", "description": "10.1128/mBio.00799-17", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/mBio.00799-17"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-18T00:00:00Z"}}, {"id": "10.1128/msystems.00226-20", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:31Z", "type": "Journal Article", "created": "2020-04-06", "title": "Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder", "description": "Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from raw milk to the end product. Routine implementation of high-throughput sequencing would elucidate the factors that influence population dynamics. This will enable a manufacturer to adopt control measures specific to each stage of processing and respond in an effective manner, which would ultimately lead to increased food safety and quality.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "metagenomics", "0303 health sciences", "whole-milk silo", "collection tanker", "bulk tank milk", "Microbiology", "QR1-502", "3. Good health", "03 medical and health sciences", "skimmed milk silo", "skimmed milk powder", "microbiota", "dairy", "processing", "16S rRNA gene amplicon sequencing", "Research Article"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSystems.00226-20"}, {"href": "https://doi.org/10.1128/msystems.00226-20"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00226-20", "name": "item", "description": "10.1128/msystems.00226-20", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00226-20"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-28T00:00:00Z"}}, {"id": "10.1128/msystems.00786-20", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:31Z", "type": "Journal Article", "created": "2021-01-11", "title": "Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community", "description": "This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy.
Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by Siphoviridae and other members of the order Caudovirales . The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as Siphoviridae , Padoviridae , and Myoviridae were positive for putative ARGs. Among the detected ARGs, i.e., dfr B6, rpo B mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated.
IMPORTANCEWWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.
", "keywords": ["metagenomics", "bacteriophages", "11. Sustainability", "Bacteriophages", "metagenomic assembled genomes", "antimicrobial resistance", "antimicrobial resistome", "wastewater treatment plants", "Microbiology", "6. Clean water", "QR1-502", "12. Responsible consumption", "Research Article"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/spectrum.01101-23"}, {"href": "https://doi.org/10.1128/spectrum.01101-23"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology%20Spectrum", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/spectrum.01101-23", "name": "item", "description": "10.1128/spectrum.01101-23", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/spectrum.01101-23"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-17T00:00:00Z"}}, {"id": "10.1139/x82-111", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:35Z", "type": "Journal Article", "created": "2008-05-01", "title": "Effects Of Thinning On Biomass Growth In Young Populus-Tremuloides Plots", "description": "Stem, branch, and leaf biomass and leaf-area index (LAI) were estimated for 4 years of growth in plots of thinned and unthinned 7-year-old Populustremuloides Michx. In 1978, transmitted photosynthetically active radiation (PAR) was monitored to estimate percent PAR transmitted. Four years after thinning total aboveground biomass and LAI in the thinned plots exceeded prethinning levels, but were still much less than in the unthinned plots. Leaf biomass and LAI in the unthinned plots increased to 3900\uffe2\uff80\uff82kg ha\uffe2\uff88\uff921 and 5.7, respectively, but were still increasing in the thinned plots. Annual net stem and branch production during the study was relatively constant at about 5300\uffe2\uff80\uff82kg ha\uffe2\uff88\uff921 year\uffe2\uff88\uff921 in the unthinned plots, while net production in the thinned plots was still increasing. Transmitted PAR attenuated rapidly to LAI 3.5, approaching asymptote near LAI 5. Results suggest that, in the short term, thinning of young stands will decrease total aboveground biomass, but net annual biomass accumulation may not be greatly different between thinned and unthinned stands. LAI 3.5 may be an acceptable value for 11-year-old stands but should be permitted to increase to near LAI 5 in older stands.
", "keywords": ["0106 biological sciences", "Ecology and Evolutionary Biology", "Plant Sciences", "0401 agriculture", " forestry", " and fisheries", "Agriculture", "Genetics and Genomics", "04 agricultural and veterinary sciences", "15. Life on land", "Forest Sciences", "01 natural sciences"], "contacts": [{"organization": "Hocker, H. W., Jr.", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1139/x82-111"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Canadian%20Journal%20of%20Forest%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1139/x82-111", "name": "item", "description": "10.1139/x82-111", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1139/x82-111"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1982-12-01T00:00:00Z"}}, {"id": "10.1139/x75-087", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:35Z", "type": "Journal Article", "created": "2008-05-01", "title": "Wildfire Effects On Nutrient Distribution And Leaching In A Coniferous Ecosystem", "description": "Distribution of nutrients after the Entiat fire in north central Washington was examined. This intense fire produced an average ash weight on the soil surface of 2900\uffe2\uff80\uff82kg/ha. The ash layer contained 23\uffe2\uff80\uff82kg/ha N, 314\uffe2\uff80\uff82kg/ha Ca, 54\uffe2\uff80\uff82kg/ha Mg, 70\uffe2\uff80\uff82kg/ha K, and 22\uffe2\uff80\uff82kg/ha Na. Nutrient losses during the fire as a result of combined volatilization and ash convection were 855\uffe2\uff80\uff82kg/ha N, 75\uffe2\uff80\uff82kg/ha Ca, 33\uffe2\uff80\uff82kg/ha Mg, 282\uffe2\uff80\uff82kg/ha K, and 698\uffe2\uff80\uff82kg/ha Na. Nitrogen loss apparently was proportional to fuel dry weight loss.Leaching of the ash layer in the 1st year after burning transferred a trace of N, 149\uffe2\uff80\uff82kg/ha Ca, 50\uffe2\uff80\uff82kg/ha Mg, 92\uffe2\uff80\uff82kg/ha K, and 33\uffe2\uff80\uff82kg/ha Na from the ash layer to the soil. Of the amounts leached from the ash, 134\uffe2\uff80\uff82kg/ha Ca, 48\uffe2\uff80\uff82kg/ha Mg, and 84\uffe2\uff80\uff82kg/ha K were retained in the 0-to 19-cm layer of soil. In the same interval a net loss of 29\uffe2\uff80\uff82kg/ha Na was observed from the 0-to 19-cm layer of soil.Cation leaching from ash layers was primarily related to water percolation through the ash. Equations are given that describe leaching of Ca, Mg, K, and Na from an average ash layer of the Entiat fire.
", "keywords": ["0106 biological sciences", "13. Climate action", "Ecology and Evolutionary Biology", "Plant Sciences", "0401 agriculture", " forestry", " and fisheries", "Agriculture", "Genetics and Genomics", "04 agricultural and veterinary sciences", "15. Life on land", "Forest Sciences", "01 natural sciences"], "contacts": [{"organization": "Grier, Charles C.", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1139/x75-087"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Canadian%20Journal%20of%20Forest%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1139/x75-087", "name": "item", "description": "10.1139/x75-087", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1139/x75-087"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1975-12-01T00:00:00Z"}}, {"id": "10.1186/s12864-019-5692-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:41Z", "type": "Journal Article", "created": "2019-05-02", "title": "Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains", "description": "Oenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethanol-rich environments of wine and cider fermentation, where it performs the crucial role of malolactic fermentation. It has a small genome and has lost the mutS-mutL DNA mismatch repair genes, making it a hypermutable and highly specialized species. Two main lineages of strains, named groups A and B, have been described to date, as well as other subgroups correlated to different types of wines or regions. A third group 'C' has also been hypothesized based on sequence analysis, but it remains controversial. In this study we have elucidated the species population structure by sequencing 14 genomes of new strains isolated from cider and kombucha and performing comparative genomics analyses.Sequence-based phylogenetic trees confirmed a population structure of 4 clades: The previously identified A and B, a third group 'C' consisting of the new cider strains and a small subgroup of wine strains previously attributed to group B, and a fourth group 'D' exclusively represented by kombucha strains. A pair of complete genomes from group C and D were compared to the circularized O. oeni PSU-1 strain reference genome and no genomic rearrangements were found. Phylogenetic trees, K-means clustering and pangenome gene clusters evidenced the existence of smaller, specialized subgroups of strains. Using the pangenome, genomic differences in stress resistance and biosynthetic pathways were found to uniquely distinguish the C and D clades.The obtained results, including the additional cider and kombucha strains, firmly established the O. oeni population structure. Group C does not appear as fully domesticated as group A to wine, but showed several unique patterns which may be due to ongoing specialization to the cider environment. Group D was shown to be the most divergent member of O. oeni to date, appearing as the closest to a pre-domestication state of the species.", "keywords": ["0301 basic medicine", "570", "Wine", "QH426-470", "Pan-genome", "Industrial microbiology", "630", "03 medical and health sciences", "Lactic acid bacteria", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Oenococcus", "Phylogeny", "2. Zero hunger", "0303 health sciences", "Genome", "Whole Genome Sequencing", "Comparative genomics", "Bacterial", "Phylogenomics", "Kombucha Tea", "Biodiversity", "15. Life on land", "Malus", "Oenococcus oeni", "TP248.13-248.65", "Genome", " Bacterial", "Biotechnology", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s12864-019-5692-3.pdf"}, {"href": "https://doi.org/10.1186/s12864-019-5692-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BMC%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s12864-019-5692-3", "name": "item", "description": "10.1186/s12864-019-5692-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s12864-019-5692-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-02T00:00:00Z"}}, {"id": "10.1186/s13568-024-01764-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:41Z", "type": "Journal Article", "created": "2024-09-28", "title": "Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils", "description": "AbstractA bacterial consortium was isolated from a soil in Noblejas (Toledo, Spain) with a long history of mixed hydrocarbons pollution, by enrichment cultivation. Serial cultures of hydrocarbons polluted soil samples were grown in a minimal medium using diesel (1\uffc2\uffa0mL/L) as the sole carbon and energy source. The bacterial composition of the Noblejas Consortium (NC) was determined by sequencing 16S rRNA gene amplicon libraries. The consortium contained around 50 amplicon sequence variants (ASVs) and the major populations belonged to the genera Pseudomonas, Enterobacter, Delftia, Stenotrophomonas, Achromobacter, Acinetobacter, Novosphingobium, Allorhizobium-Neorhizobium-Rhizobium, Ochrobactrum and Luteibacter. All other genera were below 1%. Metagenomic analysis of NC has shown a high abundance of genes encoding enzymes implicated in aliphatic and (poly) aromatic hydrocarbons degradation, and almost all pathways for hydrocarbon degradation are represented. Metagenomic analysis has also allowed the construction of metagenome assembled genomes (MAGs) for the major players of NC. Metatranscriptomic analysis has shown that several of the ASVs are implicated in hydrocarbon degradation, being Pseudomonas, Acinetobacter and Delftia the most active populations.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.
ResultsWe 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.
ConclusionsThe 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": "10.12688/openreseurope.13987.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:43Z", "type": "Journal Article", "created": "2022-09-05", "title": "Chromosome-scale assembly of the yellow mealworm genome", "description": "