{"type": "FeatureCollection", "features": [{"id": "10.1038/ismej.2009.136", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:17Z", "type": "Journal Article", "created": "2009-12-24", "title": "Biogeography Of Soil Archaea And Bacteria Along A Steep Precipitation Gradient", "description": "Abstract                <p>For centuries, biodiversity has spellbound biologists focusing mainly on macroorganism's diversity and almost neglecting the geographic mediated dynamics of microbial communities. We surveyed the diversity of soil bacteria and archaea along a steep precipitation gradient ranging from the Negev Desert in the south of Israel (&amp;lt;100\uffe2\uff80\uff89mm annual rain) to the Mediterranean forests in the north (&amp;gt;900\uffe2\uff80\uff89mm annual rain). Soil samples were retrieved from triplicate plots at five long-term ecological research stations, collected from two types of patches: plant interspaces and underneath the predominant perennial at each site. The molecular fingerprint of each soil sample was taken using terminal restriction length polymorphism of the 16S rRNA gene to evaluate the bacterial and archaeal community composition and diversity within and across sites. The difference in community compositions was not statistically significant within sites (P=0.33 and 0.77 for bacteria and archaea, respectively), but it differed profoundly by ecosystem type. These differences could largely be explained by the precipitation gradient combined with the vegetation cover: the archaeal and bacterial operational taxonomic units were unique to each climatic region, that is, arid, semiarid and Mediterranean (P=0.0001, for both domains), as well as patch type (P=0.009 and 0.02 for bacteria and archaea, respectively). Our results suggest that unlike macroorganisms that are more diverse in the Mediterranean ecosystems compared with the desert sites, archaeal and bacterial diversities are not constrained by precipitation. However, the community composition is unique to the climate and vegetation cover that delineates each ecosystem.</p>", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Geography", "Biodiversity", "15. Life on land", "Archaea", "DNA Fingerprinting", "DNA", " Ribosomal", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Cluster Analysis", "Israel", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2009.136"}, {"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.2009.136", "name": "item", "description": "10.1038/ismej.2009.136", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2009.136"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-12-24T00:00:00Z"}}, {"id": "10.1038/ismej.2010.3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:17Z", "type": "Journal Article", "created": "2010-02-04", "title": "Shifts In Microbial Community Structure Along An Ecological Gradient Of Hypersaline Soils And Sediments", "description": "Abstract<p>Studies of hypersaline ecosystems often yield novel organisms and contribute to our understanding of extreme environments. Soils and sediments from La Sal del Rey, a previously uncharacterized, hypersaline lake located in southern Texas, USA, were surveyed to characterize the structure and diversity of their microbial communities. Samples were collected along a transect that spanned vegetated uplands, exposed lakebed sediments, and water-logged locations, capturing a wide range of environments and physical and chemical gradients. Community quantitative PCR (qPCR) was used in combination with tag-encoded pyrosequencing, 16S rRNA gene cloning, and Sanger sequencing to characterize the lake's soil and sediment microbial communities. Further, we used multivariate statistics to identify the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa, and sharing significant correlations with site water content, phosphorus and total organic carbon concentrations, and pH. Some individual populations, especially of Archaea, also correlated with sodium concentration and electrical conductivity salinity. Across the transect, Bacteria were numerically dominant relative to Archaea, and among them, three phyla\uffe2\uff80\uff94the Proteobacteria, Bacteroidetes, and Firmicutes\uffe2\uff80\uff94accounted for the majority of taxa detected. Although these taxa were detected with similar abundances to those described in other hypersaline ecosystems, the greater depth of sequencing achieved here resulted in the detection of taxa not described previously in hypersaline sediments. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems.</p>", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Geologic Sediments", "Salinity", "0303 health sciences", "Bacteria", "Genes", " rRNA", "Sequence Analysis", " DNA", "15. Life on land", "Archaea", "Polymerase Chain Reaction", "Texas", "6. Clean water", "Soil", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Water Microbiology", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2010.3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2010.3", "name": "item", "description": "10.1038/ismej.2010.3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2010.3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-02-04T00:00:00Z"}}, {"id": "10.1038/ismej.2016.169", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:17Z", "type": "Journal Article", "created": "2017-01-03", "title": "The Pseudomonas putida T6SS is a plant warden against phytopathogens", "description": "Abstract                <p>Bacterial type VI secretion systems (T6SSs) are molecular weapons designed to deliver toxic effectors into prey cells. These nanomachines have an important role in inter-bacterial competition and provide advantages to T6SS active strains in polymicrobial environments. Here we analyze the genome of the biocontrol agent Pseudomonas putida KT2440 and identify three T6SS gene clusters (K1-, K2- and K3-T6SS). Besides, 10 T6SS effector\uffe2\uff80\uff93immunity pairs were found, including putative nucleases and pore-forming colicins. We show that the K1-T6SS is a potent antibacterial device, which secretes a toxic Rhs-type effector Tke2. Remarkably, P. putida eradicates a broad range of bacteria in a K1-T6SS-dependent manner, including resilient phytopathogens, which demonstrates that the T6SS is instrumental to empower P. putida to fight against competitors. Furthermore, we observed a drastically reduced necrosis on the leaves of Nicotiana benthamiana during co-infection with P. putida and Xanthomonas campestris. Such protection is dependent on the activity of the P. putida T6SS. Many routes have been explored to develop biocontrol agents capable of manipulating the microbial composition of the rhizosphere and phyllosphere. Here we unveil a novel mechanism for plant biocontrol, which needs to be considered for the selection of plant wardens whose mission is to prevent phytopathogen infections.</p>", "keywords": ["PROTEIN SECRETION", "Nicotiana", "0301 basic medicine", "570", "INTESTINAL INFLAMMATION", "05 Environmental Sciences", "VIBRIO-CHOLERAE", "Environmental Sciences & Ecology", "VI SECRETION SYSTEM", "Xanthomonas campestris", "Microbiology", "03 medical and health sciences", "Bacterial Proteins", "10 Technology", "Plant Diseases", "0303 health sciences", "Science & Technology", "Ecology", "Pseudomonas putida", "ROOT MICROBIOME", "Gene Expression Regulation", " Bacterial", "06 Biological Sciences", "Type VI Secretion Systems", "GENOMIC ANALYSIS", "Biological Control Agents", "ESCHERICHIA-COLI", "EFFECTORS", "IMMUNITY PROTEINS", "Original Article", "HOST-RANGE", "Life Sciences & Biomedicine"]}, "links": [{"href": "http://www.nature.com/articles/ismej2016169.pdf"}, {"href": "https://doi.org/10.1038/ismej.2016.169"}, {"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.2016.169", "name": "item", "description": "10.1038/ismej.2016.169", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2016.169"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-03T00:00:00Z"}}, {"id": "10.1038/s41396-022-01225-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:20Z", "type": "Journal Article", "created": "2022-03-30", "title": "Cross-biome antibiotic resistance decays after millions of years of soil development", "description": "Abstract                <p>Soils harbor the most diverse naturally evolved antibiotic resistance genes (ARGs) on Earth, with implications for human health and ecosystem functioning. How ARGs evolve as soils develop over centuries, to millennia (i.e., pedogenesis), remains poorly understood, which introduces uncertainty in predictions of the dynamics of ARGs under changing environmental conditions. Here we investigated changes in the soil resistome by analyzing 16 globally distributed soil chronosequences, from centuries to millennia, spanning a wide range of ecosystem types and substrate age ranges. We show that ARG abundance and diversity decline only after millions of years of soil development as observed in very old chronosequences. Moreover, our data show increases in soil organic carbon content and microbial biomass as soil develops that were negatively correlated with the abundance and diversity of soil ARGs. This work reveals natural dynamics of soil ARGs during pedogenesis and suggests that such ecological patterns are predictable, which together advances our understanding of the environmental drivers of ARGs in terrestrial environments.</p", "keywords": ["2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "550", "Drug Resistance", " Microbial", "15. Life on land", "Carbon", "6. Clean water", "Anti-Bacterial Agents", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "13. Climate action", "XXXXXX - Unknown", "Humans", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/s41396-022-01225-8"}, {"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/s41396-022-01225-8", "name": "item", "description": "10.1038/s41396-022-01225-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41396-022-01225-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-30T00:00:00Z"}}, {"id": "10.1094/mpmi-03-24-0024-r", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:13Z", "type": "Journal Article", "created": "2024-06-21", "title": "Rhizobial Secretion of Truncated Exopolysaccharides Severely Impairs the Mesorhizobium-Lotus Symbiosis", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p> The symbiosis between Mesorhizobium japonicum R7A and Lotus japonicus Gifu is an important model system for investigating the role of bacterial exopolysaccharides (EPS) in plant-microbe interactions. Previously, we showed that R7A exoB mutants that are affected at an early stage of EPS synthesis and in lipopolysaccharide (LPS) synthesis induce effective nodules on L. japonicus Gifu after a delay, whereas exoU mutants affected in the biosynthesis of the EPS side chain induce small uninfected nodule primordia and are impaired in infection. The presence of a halo around the exoU mutant when grown on Calcofluor-containing media suggested the mutant secreted a truncated version of R7A EPS. A nonpolar \u0394 exoA mutant defective in the addition of the first glucose residue to the EPS backbone was also severely impaired symbiotically. Here, we used a suppressor screen to show that the severe symbiotic phenotype of the exoU mutant was due to the secretion of an acetylated pentasaccharide, as both monomers and oligomers, by the same Wzx/Wzy system that transports wild-type exopolysaccharide. We also present evidence that the \u0394 exoA mutant secretes an oligosaccharide by the same transport system, contributing to its symbiotic phenotype. In contrast, \u0394 exoYF and polar exoA and exoL mutants have a similar phenotype to exoB mutants, forming effective nodules after a delay. These studies provide substantial evidence that secreted incompatible EPS is perceived by the plant, leading to abrogation of the infection process. </p><p> [Formula: see text] Copyright \u00a9 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license . </p></article>", "keywords": ["0301 basic medicine", "0303 health sciences", "exo mutants", "exopolysaccharide secretion", "Polysaccharides", " Bacterial", "Botany", "Mesorhizobium", "Microbiology", "QR1-502", "03 medical and health sciences", "Bacterial Proteins", "QK1-989", "Mutation", "Mesorhizobium-Lotus symbiosis", "Lotus", "truncated exopolysaccharide", "Symbiosis", "Root Nodules", " Plant"]}, "links": [{"href": "https://doi.org/10.1094/mpmi-03-24-0024-r"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecular%20Plant-Microbe%20Interactions%C2%AE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1094/mpmi-03-24-0024-r", "name": "item", "description": "10.1094/mpmi-03-24-0024-r", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1094/mpmi-03-24-0024-r"}, {"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/s41559-017-0259-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:23Z", "type": "Journal Article", "created": "2017-08-06", "title": "Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities", "description": "The legacy impacts of past climates on the current distribution of soil microbial communities are largely unknown. Here, we use data from more than 1,000 sites from five separate global and regional datasets to identify the importance of palaeoclimatic conditions (Last Glacial Maximum and mid-Holocene) in shaping the current structure of soil bacterial communities in natural and agricultural soils. We show that palaeoclimate explains more of the variation in the richness and composition of bacterial communities than current climate. Moreover, palaeoclimate accounts for a unique fraction of this variation that cannot be predicted from geographical location, current climate, soil properties or plant diversity. Climatic legacies (temperature and precipitation anomalies from the present to ~20\u2009kyr ago) probably shape soil bacterial communities both directly and indirectly through shifts in soil properties and plant communities. The ability to predict the distribution of soil bacteria from either palaeoclimate or current climate declines greatly in agricultural soils, highlighting the fact that anthropogenic activities have a strong influence on soil bacterial diversity. We illustrate how climatic legacies can help to explain the current distribution of soil bacteria in natural ecosystems and advocate that climatic legacies should be considered when predicting microbial responses to climate change.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Climate Change", "Microbiota", "Agriculture", "910", "15. Life on land", "soil microbial ecology", "climatic changes", "03 medical and health sciences", "13. Climate action", "XXXXXX - Unknown", "soils", "Soil Microbiology", "palaeoclimatology", "Paleoclimate explains a unique proportion of the global variation in soil bacterial communities"]}, "links": [{"href": "https://www.nature.com/articles/s41559-017-0259-7.pdf"}, {"href": "https://doi.org/10.1038/s41559-017-0259-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Ecology%20%26amp%3B%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41559-017-0259-7", "name": "item", "description": "10.1038/s41559-017-0259-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41559-017-0259-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-08-07T00:00:00Z"}}, {"id": "10.1038/s41598-022-23728-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:27Z", "type": "Journal Article", "created": "2022-11-10", "title": "DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation", "description": "Abstract<p>Polychlorinated biphenyl (PCB)-contaminated soils represent a major treat for ecosystems health. Plant biostimulation of autochthonous microbial PCB degraders is a way to restore polluted sites where traditional remediation techniques are not sustainable, though its success requires the understanding of site-specific plant\uffe2\uff80\uff93microbe interactions. In an historical PCB contaminated soil, we applied DNA stable isotope probing (SIP) using 13C-labeled 4-chlorobiphenyl (4-CB) and 16S rRNA MiSeq amplicon sequencing to determine how the structure of total and PCB-degrading bacterial populations were affected by different treatments: biostimulation with Phalaris arundinacea subjected (PhalRed) or not (Phal) to a redox cycle and the non-planted controls (Bulk and BulkRed). Phal soils hosted the most diverse community and plant biostimulation induced an enrichment of Actinobacteria. Mineralization of 4-CB in SIP microcosms varied between 10% in Bulk and 39% in PhalRed soil. The most abundant taxa deriving carbon from PCB were Betaproteobacteria and Actinobacteria. Comamonadaceae was the family most represented in Phal soils, Rhodocyclaceae and Nocardiaceae in non-planted soils. Planted soils subjected to redox cycle enriched PCB degraders affiliated to Pseudonocardiaceae, Micromonosporaceae and Nocardioidaceae. Overall, we demonstrated different responses of soil bacterial taxa to specific rhizoremediation treatments and we provided new insights into the populations active in PCB biodegradation.</p", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Science", "Q", "R", "DNA", "Plants", "15. Life on land", "Polychlorinated Biphenyls", "Article", "Soil", "03 medical and health sciences", "Biodegradation", " Environmental", "Isotopes", "13. Climate action", "RNA", " Ribosomal", " 16S", "Actinomycetales", "Medicine", "Soil Pollutants", "Soil Microbiology", "Ecosystem"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/945469/2/Vergani%20et%20al.%20SIP_2022.pdf"}, {"href": "https://doi.org/10.1038/s41598-022-23728-2"}, {"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/s41598-022-23728-2", "name": "item", "description": "10.1038/s41598-022-23728-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-022-23728-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-10T00:00:00Z"}}, {"id": "10.1038/s41598-023-49194-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:27Z", "type": "Journal Article", "created": "2023-12-13", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "description": "Abstract<p>Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.</p", "keywords": ["0301 basic medicine", "Bacillus", "Gene", "Agricultural and Biological Sciences", "https://purl.org/becyt/ford/1.6", "Phylogeny", "GC-content", "2. Zero hunger", "0303 health sciences", "Genome", "Acinetobacter", "soil bacteria", "Q", "Probiotics and Prebiotics", "R", "Life Sciences", "Anti-Bacterial Agents", "3. Good health", "Ribosomal RNA", "Medicine", "Microbial genetics", "metagenomics assembly", "Biotechnology", "Bacteriocin", "Science", ".", "Synteny", "Microbiology", "Article", "Applied microbiology", "Lipopeptides", "03 medical and health sciences", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "https://purl.org/becyt/ford/1", "Molecular Biology", "Biology", "genetic engineering", "Bacteria", "Secondary metabolites", "In silico", "bacterial genomes", "Whole genome sequencing", "FOS: Biological sciences", "Microbial Enzymes and Biotechnological Applications", "Antibacterial activity", "Genome", " Bacterial", "Food Science", "Phylogenetic tree"]}, "links": [{"href": "https://www.nature.com/articles/s41598-023-49194-y.pdf"}, {"href": "https://doi.org/10.1038/s41598-023-49194-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-023-49194-y", "name": "item", "description": "10.1038/s41598-023-49194-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-023-49194-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-13T00:00:00Z"}}, {"id": "10.1038/s41598-025-00173-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:27Z", "type": "Journal Article", "created": "2025-05-08", "title": "Enhanced understanding of nitrogen fixing bacteria through DNA extraction with polyvinylidene fluoride membrane", "description": "Abstract           <p>The 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%).</p", "keywords": ["DNA", " Bacterial", "Nitrogen-Fixing Bacteria", "nifH", "Science", "Q", "R", "Article", "Nitrogen-fixing bacteria", "PVDF membrane", "Fluorocarbon Polymers", "Bacterial diversity", "Nitrogen Fixation", "Rhizosphere", "Medicine", "Polyvinyls", "Metagenomics", "Triticum", "Soil Microbiology"], "contacts": [{"organization": "Agnieszka Kalwasi\u0144ska, Igor Kr\u00f3likiewicz, Sushma Rani Tirkey, Attila Szab\u00f3, Sweta Binod Kumar,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1038/s41598-025-00173-5"}, {"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/s41598-025-00173-5", "name": "item", "description": "10.1038/s41598-025-00173-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-025-00173-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-05-08T00:00:00Z"}}, {"id": "10.1038/srep03829", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:29Z", "type": "Journal Article", "created": "2014-01-23", "title": "Rapid Recovery Of Soil Bacterial Communities After Wildfire In A Chinese Boreal Forest", "description": "Abstract<p>Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20\uffe2\uff80\uff93100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P &lt; 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties.</p>", "keywords": ["DNA", " Bacterial", "China", "Bacteria", "Nitrogen", "Biodiversity", "04 agricultural and veterinary sciences", "15. Life on land", "Article", "Carbon", "Fires", "13. Climate action", "RNA", " Ribosomal", " 16S", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep03829"}, {"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/srep03829", "name": "item", "description": "10.1038/srep03829", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep03829"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-01-23T00:00:00Z"}}, {"id": "10.1038/srep28981", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:29Z", "type": "Journal Article", "created": "2016-06-30", "title": "Quantitative And Compositional Responses Of Ammonia-Oxidizing Archaea And Bacteria To Long-Term Field Fertilization", "description": "Abstract<p>Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM) and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.</p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Biota", "Article", "6. Clean water", "Genes", " Archaeal", "03 medical and health sciences", "Ammonia", "Genes", " Bacterial", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep28981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep28981", "name": "item", "description": "10.1038/srep28981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep28981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-30T00:00:00Z"}}, {"id": "10.1186/s40793-020-00364-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:28Z", "type": "Journal Article", "created": "2020-05-01", "title": "Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato", "description": "<title>Abstract</title>         <p>Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (<italic>Solanum lycopersicum</italic> LA4024, <italic>S. habrochaites</italic> LA1777) by targeting bacterial 16S rRNA gene fragments.Results Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (10<sup>8</sup>- 10<sup>9</sup> 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, <italic>Alphaproteobacteria</italic> (23.6%) were significantly increased, whereas <italic>Bacilli</italic> (8.6%) were decreased in trichomes. The bacterial family <italic>Sphingomonadacea</italic> (8.4%) was identified as the most prominent, trichome-specific taxa; <italic>Burkholderiaceae</italic> and <italic>Actinobacteria</italic> showed similar pattern. Moreover, <italic>Sphingomonas</italic> was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including <italic>Hymenobacteraceae</italic> and <italic>Alicyclobacillaceae</italic> were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed.Conclusion Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.</p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "Plant microhabitat", "0303 health sciences", "Plant microbiome", "Trichomes", "15. Life on land", "Microbiology", "Bacterial communities", "QR1-502", "Environmental sciences", "03 medical and health sciences", "Solanum lycopersicum", "Solanum habrochaites", "plant microbiome", " bacterial communities", " plant-microbe interactions", " Solanum habrochaites", " Solanum lycopersicum", " plant microhabitat", " phyllosphere", " trichomes", "GE1-350", "Phyllosphere", "Plant-microbe interactions", "Research Article"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-020-00364-9.pdf"}, {"href": "https://doi.org/10.1186/s40793-020-00364-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-020-00364-9", "name": "item", "description": "10.1186/s40793-020-00364-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-020-00364-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-01T00:00:00Z"}}, {"id": "10.1093/femsec/fiae152", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:07Z", "type": "Journal Article", "created": "2024-11-19", "title": "A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum", "description": "Abstract                <p>Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations. The decrease from 10 to 0.1\uffc2\uffa0\uffc2\uffb5M oxygen (3.6 to 0.036 pO2% present atmospheric level, respectively) caused the upregulation of the transcription of genes involved in signal transduction mechanisms, energy production and conversion and secondary metabolites biosynthesis, transport, and catabolism based on clusters of orthologous group categories. Contrary to established observations for aerobic metabolism, key genes in oxidative stress response were significantly upregulated at lower oxygen concentrations, presumably due to an NADH/NAD+ redox ratio imbalance as the cells transitioned into nanoxia. Furthermore, A. capsulatum adapted to nanoxia by inducing a respiro-fermentative metabolism and rerouting fluxes of its central carbon and energy pathways to adapt to high NADH/NAD+ redox ratios. Our results reveal physiological features and metabolic capabilities that allowed A. capsulatum to adapt to oxygen-limited conditions, which could expand into other environmentally relevant soil strains.</p", "keywords": ["0301 basic medicine", "106022 Mikrobiologie", "0303 health sciences", "Acidobacteriota", "NADH imbalances", "microaerobic respiration", "Gene Expression Regulation", " Bacterial", "Adaptation", " Physiological", "oxygen limitation", "Acidobacteria", "Oxygen", "Oxidative Stress", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "Fermentation", "106022 Microbiology", "106026 Ecosystem research", "fermentation", "transcriptome", "Oxidation-Reduction", "Soil Microbiology", "Research Article"]}, "links": [{"href": "https://doi.org/10.1093/femsec/fiae152"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiae152", "name": "item", "description": "10.1093/femsec/fiae152", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiae152"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-11-18T00:00:00Z"}}, {"id": "10.1073/pnas.1812668115", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:19:47Z", "type": "Journal Article", "created": "2018-11-30", "title": "Poplar phyllosphere harbors disparate isoprene-degrading bacteria", "description": "<p>             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.           </p>", "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": "10.1093/femsec/fiaa058", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:07Z", "type": "Journal Article", "created": "2020-03-27", "title": "Persistence of wastewater antibiotic resistant bacteria and their genes in human fecal material", "description": "ABSTRACT<p>Domestic wastewater is a recognized source of antibiotic resistant bacteria and antibiotic resistance genes (ARB&amp;ARGs), whose risk of transmission to humans cannot be ignored. The fitness of wastewater ARB in the complex fecal microbiota of a healthy human was investigated in feces-based microcosm assays (FMAs). FMAs were inoculated with two wastewater isolates, Escherichia coli strain A2FCC14 (MLST ST131) and Enterococcus faecium strain H1EV10 (MLST ST78), harboring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The FMAs, incubated in the presence or absence of oxygen or in the presence or absence of the antibiotics cefotaxime or vancomycin, were monitored based on cultivation, ARGs quantification and bacterial community analysis. The fecal bacterial community was dominated by members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The ARGs harbored by the wastewater isolates could be quantified after one week, in FMAs incubated under both aerobic and anaerobic conditions. These observations were not significantly different in FMAs incubated anaerobically, supplemented with sub-inhibitory concentrations of cefotaxime or vancomycin. The observation that ARGs of wastewater ARB persisted in presence of the human fecal microbiota for at least one week supports the hypothesis of a potential transmission to humans, a topic that deserves further investigation.</p>", "keywords": ["0301 basic medicine", "Microcosm assays", "0303 health sciences", "Bacteria", "Angiotensin-Converting Enzyme Inhibitors", "Wastewater", "Human fecal microbiota", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "Angiotensin Receptor Antagonists", "Feces", "03 medical and health sciences", "Antibiotic resistance genes", "Antibiotic resistant bacteria", "Genes", " Bacterial", "11. Sustainability", "Humans", "Antibiotic resistance transmission", "Microcosm effect", "Multilocus Sequence Typing"]}, "links": [{"href": "http://academic.oup.com/femsec/article-pdf/96/6/fiaa058/33327470/fiaa058.pdf"}, {"href": "https://doi.org/10.1093/femsec/fiaa058"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiaa058", "name": "item", "description": "10.1093/femsec/fiaa058", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiaa058"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-02T00:00:00Z"}}, {"id": "10.1093/femsec/fiab059", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:07Z", "type": "Journal Article", "created": "2021-04-14", "title": "Fungus-bacterium associations are widespread in fungal cultures isolated from a semi-arid natural grassland in Germany", "description": "ABSTRACT                <p>We report on a study that aimed at establishing a large soil\uffe2\uff80\uff93fungal culture collection spanning a wide taxonomic diversity and systematically screening the collection for bacterial associations. Fungal cultures were isolated from soil samples obtained from a natural grassland in eastern Germany and bacterial associations were assessed by PCR-amplification and sequencing of bacterial 16S rRNA. In addition, intraspecies genetic diversities of a subset of the isolated species were estimated by double-digest restriction associated DNA sequencing. A total of 688 fungal cultures, representing at least 106 fungal species from 36 different families, were obtained and even though clonal isolates were identified in almost all fungal species subjected to ddRAD-seq, relatively high genetic diversities could be observed in some of the isolated species. A total of 69% of the fungal isolates in our collection were found to be associated with bacteria and the most commonly identified bacterial genera were Pelomonas, Enterobacter and Burkholderia. Our results indicate that bacterial associations commonly occur in soil fungi, even if antibiotics are being applied during the isolation process, and provide a basis for the use of our culture collection in ecological experiments that want to acknowledge the importance of intraspecies genetic diversity.</p>", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "bepress|Life Sciences|Ecology and Evolutionary Biology|Terrestrial and Aquatic Ecology", "0303 health sciences", "Terrestrial and Aquatic Ecology", "Bacteria", "Ecology and Evolutionary Biology", "Fungi", "Life Sciences", "15. Life on land", "bepress|Life Sciences|Ecology and Evolutionary Biology", "Grassland", "Soil", "03 medical and health sciences", "bepress|Life Sciences", "Germany", "RNA", " Ribosomal", " 16S", "Humans", "Bacteria ; Fungal-bacterial Interaction ; Soil Fungi ; Ddrad Sequencing", "Soil Microbiology"]}, "links": [{"href": "https://academic.oup.com/femsec/article-pdf/97/5/fiab059/37624504/fiab059.pdf"}, {"href": "https://doi.org/10.1093/femsec/fiab059"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiab059", "name": "item", "description": "10.1093/femsec/fiab059", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiab059"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-06T00:00:00Z"}}, {"id": "10.1093/femsec/fiv066", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:07Z", "type": "Journal Article", "created": "2015-06-20", "title": "Effects Of Warming And Drought On Potential N2o Emissions And Denitrifying Bacteria Abundance In Grasslands With Different Land-Use", "description": "Increased warming in spring and prolonged summer drought may alter soil microbial denitrification. We measured potential denitrification activity and denitrifier marker gene abundances (nirK, nirS, nosZ) in grasslands soils in three geographic regions characterized by site-specific land-use indices (LUI) after warming in spring, at an intermediate sampling and after summer drought. Potential denitrification was significantly increased by warming, but did not persist over the intermediate sampling. At the intermediate sampling, the relevance of grassland land-use intensity was reflected by increased potential N2O production at sites with higher LUI. Abundances of total bacteria did not respond to experimental warming or drought treatments, displaying resilience to minor and short-term effects of climate change. In contrast, nirS- and nirK-type denitrifiers were more influenced by drought in combination with LUI and pH, while the nosZ abundance responded to the summer drought manipulation. Land-use was a strong driver for potential denitrification as grasslands with higher LUI also had greater potentials for N2O emissions. We conclude that both warming and drought affected the denitrifying communities and the potential denitrification in grassland soils. However, these effects are overruled by regional and site-specific differences in soil chemical and physical properties which are also related to grassland land-use intensity.", "keywords": ["0301 basic medicine", "570", "UFSP13-8 Global Change and Biodiversity", "Climate Change", "Microbial Consortia", "580 Plants (Botany)", "Nitric Oxide", "142-005 142-005", "Soil", "03 medical and health sciences", "potential N2O emissions", "RNA", " Ribosomal", " 16S", "2402 Applied Microbiology and Biotechnology", "use index", "Soil Microbiology", "2. Zero hunger", "Biodiversity Exploratories", "denitrification", "Bacteria", "2404 Microbiology", "04 agricultural and veterinary sciences", "15. Life on land", "Grassland", "6. Clean water", "Droughts", "land", "climate change", "Genes", " Bacterial", "13. Climate action", "8. Economic growth", "Denitrification", "0401 agriculture", " forestry", " and fisheries", "grassland", "microbial community", "2303 Ecology"]}, "links": [{"href": "https://doi.org/10.1093/femsec/fiv066"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiv066", "name": "item", "description": "10.1093/femsec/fiv066", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiv066"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-06-19T00:00:00Z"}}, {"id": "10.1099/mic.0.000931", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:16Z", "type": "Journal Article", "created": "2020-05-22", "title": "Microbial metabolism of isoprene: a much-neglected climate-active gas", "description": "<p>The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.</p>", "keywords": ["0301 basic medicine", "0303 health sciences", "550", "Bacteria", "Review", "Plants", "15. Life on land", "03 medical and health sciences", "Biodegradation", " Environmental", "Hemiterpenes", "Genes", " Bacterial", "13. Climate action", "8. Economic growth", "Butadienes", "Seawater", "Metabolic Networks and Pathways", "Soil Microbiology"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/75324/1/Published_Version.pdf"}, {"href": "https://repository.essex.ac.uk/29368/1/Microbial%20metabolism%20of%20isoprene%20a%20much-neglected%20climate-active%20gas.pdf"}, {"href": "https://doi.org/10.1099/mic.0.000931"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1099/mic.0.000931", "name": "item", "description": "10.1099/mic.0.000931", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1099/mic.0.000931"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-07-01T00:00:00Z"}}, {"id": "10.1101/117887", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:16Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics", "description": "Abstract<p>Environmental 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.</p", "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/10.1101/117887"}, {"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": "10.1101/117887", "name": "item", "description": "10.1101/117887", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/117887"}, {"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": "10.1111/1462-2920.15018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:27Z", "type": "Journal Article", "created": "2020-04-14", "title": "Subsistence and complexity of antimicrobial resistance on a community\u2010wide level", "description": "Summary<p>There are a multitude of resistance strategies that microbes can apply to avoid inhibition by antimicrobials. One of these strategies is the enzymatic modification of the antibiotic, in a process generally termed inactivation. Furthermore, some microorganisms may not be limited to the mere inactivation of the antimicrobial compounds. They can continue by further enzymatic degradation of the compounds' carbon backbone, taking nutritional and energetic advantage of the former antibiotic. This driving force to harness an additional food source in a complex environment adds another level of complexity to the reasonably well\uffe2\uff80\uff90understood process of antibiotic resistance proliferation on a single cell level: It brings bioprotection into play at the level of microbial community. Despite the possible implications of a resistant community in a host and a lurking antibiotic failure, knowledge of degradation pathways of antibiotics and their connections is scarce. Currently, it is limited to only a few families of antibiotics (e.g. \uffce\uffb2\uffe2\uff80\uff90lactams and sulfonamides). In this article, we discuss the fluctuating nature of the relationship between antibiotic resistance and the biodegradation of antibiotics. This distinction mainly depends on the genetic background of the microbe, as general resistance genes can be recruited to function in a biodegradation pathway.</p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "Opinion", "Sulfonamides", "0303 health sciences", "03 medical and health sciences", "Biodegradation", " Environmental", "Bacteria", "Drug Resistance", " Bacterial", "Humans", "beta-Lactams", "Anti-Bacterial Agents"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15018"}, {"href": "https://doi.org/10.1111/1462-2920.15018"}, {"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": "10.1111/1462-2920.15018", "name": "item", "description": "10.1111/1462-2920.15018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.15018"}, {"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": "10.1111/1574-6941.12009", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:28Z", "type": "Journal Article", "created": "2012-09-13", "title": "Chronic N-Amended Soils Exhibit An Altered Bacterial Community Structure In Harvard Forest, Ma, Usa", "description": "At the Harvard Forest, Petersham, MA, the impact of 20 years of annual ammonium nitrate application to the mixed hardwood stand on soil bacterial communities was studied using 16S rRNA genes pyrosequencing. Amplification of 16S rRNA genes was done using DNA extracted from 30 soil samples (three treatments \u00d7 two horizons \u00d7 five subplots) collected from untreated (control), low N-amended (50 kg ha(-1) year(-1)) and high N-amended (150 kg ha(-1) year(-1)) plots. A total of 1.3 million sequences were processed using qiime. Although Acidobacteria represented the most abundant phylum based on the number of sequences, Proteobacteria were the most diverse in terms of operational taxonomic units (OTUs). UniFrac analyses revealed that the bacterial communities differed significantly among soil horizons and treatments. Microsite variability among the five subplots was also evident. Nonmetric multidimensional scaling ordination of normalized OTU data followed by permutational manova further confirmed these observations. Richness indicators and indicator species analyses revealed higher bacterial diversity associated with N amendment. Differences in bacterial diversity and community composition associated with the N treatments were also observed at lower phylogenetic levels. Only 28-35% of the 6 936 total OTUs identified were common to three treatments, while the rest were specific to one treatment or common to two.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Environmental Microbiology and Microbial Ecology", "Nitrates", "Bacteria", "Genes", " rRNA", "Biodiversity", "15. Life on land", "Trees", "Scientific Contribution Number 2470", "Soil", "03 medical and health sciences", "Massachusetts", "RNA", " Ribosomal", " 16S", "Fertilizers", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/1574-6941.12009"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1574-6941.12009", "name": "item", "description": "10.1111/1574-6941.12009", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1574-6941.12009"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-11T00:00:00Z"}}, {"id": "10.1111/1574-6941.12018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:20:28Z", "type": "Journal Article", "created": "2012-09-26", "title": "Acidobacterial Community Responses To Agricultural Management Of Soybean In Amazon Forest Soils", "description": "This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1-8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Glycine max", "Agriculture", "Sequence Analysis", " DNA", "15. Life on land", "Acidobacteria", "Trees", "Soil", "03 medical and health sciences", "international", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Brazil", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/1574-6941.12018"}, {"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": "10.1111/1574-6941.12018", "name": "item", "description": "10.1111/1574-6941.12018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1574-6941.12018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-19T00:00:00Z"}}, {"id": "10.1111/1751-7915.13383", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-26T16:20:28Z", "type": "Journal Article", "created": "2019-03-13", "title": "Physical decoupling of XylS/ Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida", "description": "Summary<p>Most of the gene expression systems available for Gram\uffe2\uff80\uff90negative bacteria are afflicted by relatively high levels of basal (i.e. leaky) expression of the target gene(s). This occurrence affects the system dynamics, ultimately reducing the output and productivity of engineered pathways and synthetic circuits. In order to circumvent this problem, we have designed a novel expression system based on the well\uffe2\uff80\uff90known XylS/Pm transcriptional regulator/promoter pair from the soil bacterium Pseudomonas putida mt\uffe2\uff80\uff902, in which the key functional elements are physically decoupled. By integrating the xylS gene into the chromosome of the platform strain KT2440, while placing the Pm promoter into a set of standard plasmid vectors, the inducibility of the system (i.e. the output difference between the induced and uninduced state) improved up to 170\uffe2\uff80\uff90fold. We further combined this modular system with an extra layer of post\uffe2\uff80\uff90translational control by means of conditional proteolysis. In this setup, the target gene is tagged with a synthetic motif dictating protein degradation. When the system features were characterized using the monomeric superfolder GFP as a model protein, the basal levels of fluorescence were brought down to zero (i.e. below the limit of detection). In all, these novel expression systems constitute an alternative tool to altogether suppress leaky gene expression, and they can be easily adapted to other vector formats and plugged\uffe2\uff80\uff90in into different Gram\uffe2\uff80\uff90negative bacterial species at the user's will.</p>", "keywords": ["0301 basic medicine", "0303 health sciences", "Pseudomonas putida", "Gene Expression", "Gene Expression Regulation", " Bacterial", "03 medical and health sciences", "Bacterial Proteins", "Proteolysis", "Trans-Activators", "Brief Reports", "Promoter Regions", " Genetic", "TP248.13-248.65", "Biotechnology", "Plasmids"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.13383"}, {"href": "https://doi.org/10.1111/1751-7915.13383"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1751-7915.13383", "name": "item", "description": "10.1111/1751-7915.13383", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1751-7915.13383"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-12T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2006.00235.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:00Z", "type": "Journal Article", "created": "2006-11-21", "title": "The Effects Of Stubble Retention And Nitrogen Application On Soil Microbial Community Structure And Functional Gene Abundance Under Irrigated Maize", "description": "The effects of agronomic management practices on the soil microbial community were investigated in a maize production system in New South Wales, Australia. The site has been intensively studied to measure the impact of stubble management and N-fertilizer application on greenhouse gas emissions (CO(2) and N(2)O), N-cycling, pathology, soil structure and yield. As all of these endpoints can be regulated by microbial processes, the microbiology of the system was examined. Soil samples were taken after a winter fallow period and the diversity of the bacterial and fungal communities was measured using PCR-denaturing gradient gel electrophoresis. Stubble and N shifted the structure of bacterial and fungal communities with the primary driver being stubble addition on the fungal community structure (P<0.05 for all effects). Changes in C, N (total and NO(3)), K and Na, were correlated (P<0.05) with variation in the microbial community structure. Quantitative PCR showed that nifH (nitrogen fixation) and napA (denitrification) gene abundance increased upon stubble retention, whereas amoA gene numbers were increased by N addition. These results showed that the management of both stubble and N have significant and long-term impacts on the size and structure of the soil microbial community at phylogenetic and functional levels.", "keywords": ["Electrophoresis", "0301 basic medicine", "Nitrogen", "Genes", " Fungal", "Polymerase Chain Reaction", "Zea mays", "630", "Soil", "03 medical and health sciences", "Nitrogen Fixation", "Cluster Analysis", "Electrophoresis", " Gel", " Two-Dimensional", "Fertilizers", "Soil Microbiology", "2. Zero hunger", "Gel", "0303 health sciences", "Bacteria", "Bacterial", "Australia", "Fungi", "Agriculture", "15. Life on land", "6. Clean water", "Fungal", "Genes", "Genes", " Bacterial", "13. Climate action", "Two-Dimensional"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2006.00235.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2006.00235.x", "name": "item", "description": "10.1111/j.1574-6941.2006.00235.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2006.00235.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-03-01T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2011.01192.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:00Z", "type": "Journal Article", "created": "2011-09-01", "title": "Soil Characteristics More Strongly Influence Soil Bacterial Communities Than Land-Use Type", "description": "To gain insight into the factors driving the structure of bacterial communities in soil, we applied real-time PCR, PCR-denaturing gradient gel electrophoreses, and phylogenetic microarray approaches targeting the 16S rRNA gene across a range of different land usages in the Netherlands. We observed that the main differences in the bacterial communities were not related to land-use type, but rather to soil factors. An exception was the bacterial community of pine forest soils (PFS), which was clearly different from all other sites. PFS had lowest bacterial abundance, lowest numbers of operational taxonomic units (OTUs), lowest soil pH, and highest C : N ratios. C : N ratio strongly influenced bacterial community structure and was the main factor separating PFS from other fields. For the sites other than PFS, phosphate was the most important factor explaining the differences in bacterial communities across fields. Firmicutes were the most dominant group in almost all fields, except in PFS and deciduous forest soils (DFS). In PFS, Alphaproteobacteria was most represented, while in DFS, Firmicutes and Gammaproteobacteria were both highly represented. Interestingly, Bacillii and Clostridium OTUs correlated with pH and phosphate, which might explain their high abundance across many of the Dutch soils. Numerous bacterial groups were highly correlated with specific soil factors, suggesting that they might be useful as indicators of soil status.", "keywords": ["land use change", "DNA", " Bacterial", "0301 basic medicine", "RNA 16S", "polymerase chain reaction", "soil nitrogen", "DNA sequence", "soil microorganism", "electrokinesis", "chemistry", "phylogeny", "Real-Time Polymerase Chain Reaction", "soil", "Soil", "03 medical and health sciences", "NIOO", "RNA", " Ribosomal", " 16S", "genetics", "soil carbon", "Phylogeny", "Soil Microbiology", "phosphate", "biodiversity", "Alphaproteobacteria", "Netherlands", "growth", " development and aging", "2. Zero hunger", "abundance", "0303 health sciences", "real time", "Bacteria", "pH", "Denaturing Gradient Gel Electrophoresis", "microbiology", "denaturing gradient gel electrophoresis", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "bacterium", "bacterial DNA", "phylogenetics", "classification", "real time polymerase chain reaction", "microbial community", "Gammaproteobacteria"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2011.01192.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2011.01192.x", "name": "item", "description": "10.1111/j.1574-6941.2011.01192.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2011.01192.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-09-19T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:14Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACT                                     <p>               Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s               V               = 0.857, and Theil\uffe2\uff80\uff99s               U               = 0.316). For species-level community profiling, we found strong correlations (               r                                s                              &gt; 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average               r                                s                              = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.             </p>                            IMPORTANCE               <p>A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.</p>", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/10.1128/msystems.00859-24"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00859-24", "name": "item", "description": "10.1128/msystems.00859-24", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00859-24"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "10.1128/aem.00527-11", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:13Z", "type": "Journal Article", "created": "2011-09-17", "title": "Microbial Communities Show Parallels At Sites With Distinct Litter And Soil Characteristics", "description": "ABSTRACT<p>Plant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated byermresistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.</p>", "keywords": ["DNA", " Bacterial", "Nitrogen", "Molecular Sequence Data", "Colony Count", " Microbial", "104004 Chemical biology", "Soil", "Cluster Analysis", "Organic Chemicals", "Chromatography", " High Pressure Liquid", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Bacteria", "Fungi", "Biodiversity", "Methyltransferases", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Plants", "15. Life on land", "Bacterial Load", "Carbon", "104004 Chemische Biologie", "0401 agriculture", " forestry", " and fisheries", "Polymorphism", " Restriction Fragment Length"]}, "links": [{"href": "https://doi.org/10.1128/aem.00527-11"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.00527-11", "name": "item", "description": "10.1128/aem.00527-11", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.00527-11"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-11-01T00:00:00Z"}}, {"id": "10.1128/mBio.00799-17", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:14Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics", "description": "Abstract<p>Environmental 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.</p>", "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/aem.01355-07", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:13Z", "type": "Journal Article", "created": "2007-11-17", "title": "Effects Of Wildfire And Harvest Disturbances On Forest Soil Bacterial Communities", "description": "ABSTRACT           <p>             Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH             4             +             and NO             3             \uffe2\uff88\uff92             due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments.             Gamma             - and             Alphaproteobacteria             were highly characteristic of the unburned treatments, while             Betaproteobacteria             and members of             Bacillus             were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.           </p>", "keywords": ["DNA", " Bacterial", "Electrophoresis", "0301 basic medicine", "0303 health sciences", "Bacteria", "Molecular Sequence Data", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "Nucleic Acid Denaturation", "DNA", " Ribosomal", "Fires", "6. Clean water", "Alberta", "Trees", "03 medical and health sciences", "13. Climate action", "DNA", " Ribosomal Spacer", "Biomass", "Soil Microbiology"], "contacts": [{"organization": "B.E. Kishchuk, William W. Mohn, Nancy R. Smith,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1128/aem.01355-07"}, {"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.01355-07", "name": "item", "description": "10.1128/aem.01355-07", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01355-07"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-01-01T00:00:00Z"}}, {"id": "10.1128/aem.02209-19", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:13Z", "type": "Journal Article", "created": "2019-12-04", "title": "Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous \u201cMost-Wanted\u201d Core Bacterial Taxon from Municipal Wastewater Treatment Plants", "description": "<p>             The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon             C. huifangae             was cultivated and characterized. This study revealed that             C. huifangae             functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.           </p>", "keywords": ["0301 basic medicine", "activated sludge microbiome", "DATABASE", "DIVERSITY", "nitrogen and phosphorus removal", "GENOME ANNOTATION", "POLYPHOSPHATE-ACCUMULATING ORGANISMS", "12. Responsible consumption", "ACTIVATED-SLUDGE", "03 medical and health sciences", "SEARCH", "RNA", " Ribosomal", " 16S", "11. Sustainability", "microbial network", "Phylogeny", "WWTP", "0303 health sciences", "IDENTIFICATION", "Sewage", "Microbiota", "Betaproteobacteria", "core taxa", "15. Life on land", "6. Clean water", "COMMUNITY", "RNA", " Bacterial", "Casimicrobium huifangae", "13. Climate action", "Earth and Environmental Sciences", "BIOLOGICAL PHOSPHORUS REMOVAL", "municipal wastewater treatment plant", "CARBON SOURCE"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.02209-19"}, {"href": "https://doi.org/10.1128/aem.02209-19"}, {"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.02209-19", "name": "item", "description": "10.1128/aem.02209-19", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02209-19"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-03T00:00:00Z"}}, {"id": "10.1128/aem.02541-13", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:14Z", "type": "Journal Article", "created": "2013-09-21", "title": "Impact Of Logging And Forest Conversion To Oil Palm Plantations On Soil Bacterial Communities In Borneo", "description": "ABSTRACT           <p>Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale \uffce\uffb1-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true \uffce\uffb2-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of \uffce\uffb2-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall \uffce\uffb3-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.</p>", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Tropical Climate", "0303 health sciences", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "15. Life on land", "Biota", "DNA", " Ribosomal", "333", "Trees", "03 medical and health sciences", "Borneo", "13. Climate action", "RNA", " Ribosomal", " 16S", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1128/aem.02541-13"}, {"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.02541-13", "name": "item", "description": "10.1128/aem.02541-13", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02541-13"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-12-01T00:00:00Z"}}, {"id": "10.1128/aem.03393-12", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:14Z", "type": "Journal Article", "created": "2012-12-16", "title": "Functional Gene Differences In Soil Microbial Communities From Conventional, Low-Input, And Organic Farmlands", "description": "ABSTRACT           <p>             Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO             3             \uffe2\uff88\uff92             , NH             4             +             , available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO             3             \uffe2\uff88\uff92             concentration and denitrification genes, NH             4             +             concentration and ammonification genes, and N             2             O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.           </p>", "keywords": ["2. Zero hunger", "Michigan", "Nitrogen", "Agriculture", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Microarray Analysis", "Biota", "Carbon", "Soil", "Genes", " Bacterial", "Metagenome", "0401 agriculture", " forestry", " and fisheries", "Metabolic Networks and Pathways", "Soil Microbiology", "Sulfur"]}, "links": [{"href": "https://doi.org/10.1128/aem.03393-12"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.03393-12", "name": "item", "description": "10.1128/aem.03393-12", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.03393-12"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-02-15T00:00:00Z"}}, {"id": "10.3390/genes13050850", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:23:24Z", "type": "Journal Article", "created": "2022-05-11", "title": "Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community\u2019s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 \u00b0C + 50% water holding capacity (WHC)); increased air temperature (15\u201325 \u00b0C or 20\u201330 \u00b0C + 50% WHC); flood (20 \u00b0C + 75% WHC); drought (20 \u00b0C + 25% WHC); and ultraviolet radiation (UV) (20 \u00b0C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community\u2019s physiological profile and the bacterial community\u2019s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20\u201330 \u00b0C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome\u2013invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.</p></article>", "keywords": ["0301 basic medicine", "Soil invertebrates", "Ultraviolet Rays", "drought", "microbial activity", "DNA", " Ribosomal", "Flood", "Article", "Quantitative PCR", "Soil", "03 medical and health sciences", "soil microbiome", "2. Zero hunger", "metagenomics", "increased temperature; drought; flood; UV exposure; microbial activity; bacterial diversity; metagenomics; quantitative PCR; soil microbiome; soil invertebrates", "Soil microbiome", "0303 health sciences", "Drought", "Bacteria", "Microbiota", "bacterial diversity", "Temperature", "Water", "flood", "15. Life on land", "soil invertebrates", "6. Clean water", "UV exposure", "Microbial activity", "Bacterial diversity", "13. Climate action", "quantitative PCR", "Metagenomics", "Increased temperature", "increased temperature"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/13/5/850/pdf"}, {"href": "https://doi.org/10.3390/genes13050850"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes13050850", "name": "item", "description": "10.3390/genes13050850", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes13050850"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-10T00:00:00Z"}}, {"id": "10.1186/s12864-019-5692-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:26Z", "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/s40168-020-00941-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:27Z", "type": "Journal Article", "created": "2020-11-19", "title": "Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms", "description": "Abstract Background <p>The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms.</p>  Results <p>Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms.</p>  Conclusions <p>Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production.</p>", "keywords": ["0301 basic medicine", "Farms", "Sanidad animal", "Swine", "Antimicrobial resistance", "Microbial ecology", "Sustainable farming", "Cerdos", "Feces", "03 medical and health sciences", "Anti-Infective Agents", "Environmental Microbiology", "Animals", "Mobilome", "Antiinfecciosos", "One health", "2. Zero hunger", "Excrementos", "0303 health sciences", "Research", "QR100-130", "Drug Resistance", " Microbial", "15. Life on land", "Farm environment", "6. Clean water", "Genes", " Bacterial", "Animals", " Domestic", "2401.05 desarrollo Animal", "Metagenome", "Veterinaria"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40168-020-00941-7.pdf"}, {"href": "https://doi.org/10.1186/s40168-020-00941-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-020-00941-7", "name": "item", "description": "10.1186/s40168-020-00941-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-020-00941-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-19T00:00:00Z"}}, {"id": "10.1186/s40168-021-01131-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:27Z", "type": "Journal Article", "created": "2021-10-14", "title": "Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity", "description": "AbstractBackground<p>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.</p>Results<p>We identified a relatively restricted principal microbiota dominated byPseudomonasduring the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g.,Acinetobacter,Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and \uffce\uffb2-dispersion of ARGs, which were predominantly assigned toAcinetobacterand associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum \uffce\uffb2-lactamase-producingEnterobacteriaceaeand vancomycin-resistantEnterococcaceaewas observed when cutting activities started. ARGs associated with resistance to \uffce\uffb2-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.</p>Conclusions<p>The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility.</p>", "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": "10.1266/ggs.88.93", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:29Z", "type": "Journal Article", "created": "2015-03-03", "title": "Soil Bacterial Community Structure In Five Tropical Forests In Malaysia And One Temperate Forest In Japan Revealed By Pyrosequencing Analyses Of 16s Rrna Gene Sequence Variation", "description": "Bacterial community structure was investigated in five tropical rainforests in Sarawak, Malaysia and one temperate forest in Kyoto, Japan. A hierarchical sampling approach was employed, in which soil samples were collected from five sampling-sites within each forest. Pyrosequencing was performed to analyze a total of 493,790 16S rRNA amplicons. Despite differences in aboveground conditions, the composition of bacterial groups was similar across all sampling-sites and forests, with Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes and Bacteroidetes accounting for 90% of all Phyla detected. At higher taxonomic levels, the same taxa were predominant, although there was significant heterogeneity in relative abundance of specific taxa across sampling-sites within one forest or across different forests. In all forests, the level of bacterial diversity, estimated using the Chao1 index, was on the order of 1,000, suggesting that tropical rainforests did not necessarily have a large soil bacterial diversity. The average number of reads per species (OTUs) per sampling-site was 8.0, and more than 40-50% of species were singletons, indicating that most bacterial species occurred infrequently and that few bacterial species achieved high predominance. Approximately 30% of species were specific to one sampling-site within a forest, and 40-60% of species were uniquely detected in one of the six forests studied here. Only 0.2% of species were detected in all forests, while on average 32.1% of species were detected in all sampling-sites within a forest. The results suggested that bacterial communities adapted to specific micro- and macro-environments, but macro-environmental diversity made a larger contribution to total bacterial diversity in forest soil.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "0303 health sciences", "Bacteria", "Malaysia", "Genetic Variation", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "Polymerase Chain Reaction", "Trees", "03 medical and health sciences", "Japan", "RNA", " Ribosomal", " 16S", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1266/ggs.88.93"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes%20%26amp%3B%20Genetic%20Systems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1266/ggs.88.93", "name": "item", "description": "10.1266/ggs.88.93", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1266/ggs.88.93"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-01-01T00:00:00Z"}}, {"id": "10.13145/bacdive109630.20190402.4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:33Z", "type": "Dataset", "title": "Streptomyces sp.", "description": "The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.", "keywords": ["Strain-linked information about bacterial and archaeal biodiversity"], "contacts": [{"organization": "Reimer, L.C., Sarda Carbasse, J., Podstawka, A., Overmann, J.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.13145/bacdive109630.20190402.4"}, {"rel": "self", "type": "application/geo+json", "title": "10.13145/bacdive109630.20190402.4", "name": "item", "description": "10.13145/bacdive109630.20190402.4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.13145/bacdive109630.20190402.4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-02T00:00:00Z"}}, {"id": "10.13145/bacdive113332.20170425.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:34Z", "type": "Dataset", "title": "Streptomyces sp.", "description": "The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.", "keywords": ["Strain-linked information about bacterial and archaeal biodiversity"], "contacts": [{"organization": "Reimer, L.C., Vetcininova, A., Soehngen, C., Podstawka, A., Gleim, D., Overmann, J.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.13145/bacdive113332.20170425.1"}, {"rel": "self", "type": "application/geo+json", "title": "10.13145/bacdive113332.20170425.1", "name": "item", "description": "10.13145/bacdive113332.20170425.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.13145/bacdive113332.20170425.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-04-25T00:00:00Z"}}, {"id": "10.13145/bacdive114128.20230509.8.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:34Z", "type": "Dataset", "title": "Streptomyces sp.", "description": "The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.", "keywords": ["Strain-linked information about bacterial and archaeal biodiversity"], "contacts": [{"organization": "Reimer, L.C., Sarda Carbasse, J., Schober, I., Koblitz, J., Podstawka, A., Overmann, J.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.13145/bacdive114128.20230509.8.1"}, {"rel": "self", "type": "application/geo+json", "title": "10.13145/bacdive114128.20230509.8.1", "name": "item", "description": "10.13145/bacdive114128.20230509.8.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.13145/bacdive114128.20230509.8.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-21T00:00:00Z"}}, {"id": "10.13145/bacdive11415.20170425.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-26T16:21:34Z", "type": "Dataset", "title": "Brevibacillus parabrevis (Takagi et al. 1993) Shida et al. 1996", "description": "The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.", "keywords": ["Strain-linked information about bacterial and archaeal biodiversity", "15. 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