Approximately one\uffe2\uff80\uff90third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA\uffe2\uff80\uff90Stable Isotope Probing (DNA\uffe2\uff80\uff90SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia. Representative isolates, capable of growth on isoprene as sole carbon and energy source, were obtained from marine and estuarine locations, and isoprene\uffe2\uff80\uff90degrading strains of Gordonia and Mycobacterium were characterised physiologically and their genomes were sequenced. Genes predicted to be required for isoprene metabolism, including four\uffe2\uff80\uff90component isoprene monooxygenases (IsoMO), were identified and compared with previously characterised examples. Transcriptional and activity assays of strains growing on isoprene or alternative carbon sources showed that growth on isoprene is an inducible trait requiring a specific IsoMO. This study is the first to identify active isoprene degraders in estuarine and marine environments using DNA\uffe2\uff80\uff90SIP and to characterise marine isoprene\uffe2\uff80\uff90degrading bacteria at the physiological and molecular level.
", "keywords": ["0301 basic medicine", "570", "Volatile Organic Compounds", "0303 health sciences", "550", "Base Sequence", "610", "QR Microbiology", "Sequence Analysis", " DNA", "Environment", "6. Clean water", "Mixed Function Oxygenases", "Mycobacterium", "03 medical and health sciences", "Hemiterpenes", "13. Climate action", "Pentanes", "Butadienes", "Rhodococcus", "14. Life underwater", "Gordonia Bacterium", "Research Articles", "Genome", " Bacterial", "GE Environmental Sciences"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/63998/4/Published_manuscript.pdf"}, {"href": "http://onlinelibrary.wiley.com/wol1/doi/10.1111/1462-2920.13842/fullpdf"}, {"href": "https://doi.org/10.1111/1462-2920.13842"}, {"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": "10.1111/1462-2920.13842", "name": "item", "description": "10.1111/1462-2920.13842", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13842"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-07-21T00:00:00Z"}}, {"id": "10.1016/j.syapm.2012.10.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:17:07Z", "type": "Journal Article", "created": "2013-01-18", "title": "Shifts In Soil Bacterial Community After Eight Years Of Land-Use Change", "description": "The interaction between plants, soil and microorganisms is considered to be the major driver of ecosystem functions and any modification of plant cover and/or soil properties might affect the microbial structure, which, in turn, will influence ecological processes. Assuming that soil properties are the major drivers of soil bacterial diversity and structure within the same soil type, it can be postulated whether plant cover causes significant shifts in soil bacterial community composition. To address this question, this study used 16S rRNA pyrosequencing to detect differences in diversity, composition and/or relative abundance of bacterial taxa from an area covered by pristine forest, as well as eight-year-old grassland surrounded by the same forest. It was shown that a total of 69% of the operational taxonomic units (OTUs) were shared between environments. Overall, forest and grassland samples presented the same diversity and the clustering analysis did not show the occurrence of very distinctive bacterial communities between environments. However, 11 OTUs were detected in statistically significant higher abundance in the forest samples but in lower abundance in the grassland samples, whereas 12 OTUs occurred in statistically significant higher abundance in the grassland samples but in lower abundance in the forest samples. The results suggested the prevalence of a resilient core microbial community that did not suffer any change related to land use, soil type or edaphic conditions. The results illustrated that the history of land use might influence present-day community structure.", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Plants", "15. Life on land", "Biota", "DNA", " Ribosomal", "Trees", "13. Climate action", "RNA", " Ribosomal", " 16S", "Cluster Analysis", "0401 agriculture", " forestry", " and fisheries", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.syapm.2012.10.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Systematic%20and%20Applied%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.syapm.2012.10.007", "name": "item", "description": "10.1016/j.syapm.2012.10.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.syapm.2012.10.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-03-01T00:00:00Z"}}, {"id": "10.1016/j.syapm.2020.126149", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:17:07Z", "type": "Journal Article", "created": "2020-09-30", "title": "Genetic diversity and phylogeny of indigenous rhizobia nodulating faba bean (Vicia faba L.) in Greece", "description": "The genetic diversity and phylogeny of fast-growing rhizobia isolated from root nodules of Vicia faba grown in different geographical regions of Greece were assessed. Although Rhizobium leguminosarum sv. viciae is the most common symbiont of Vicia spp. in European soils, there is no available information on native rhizobia nodulating faba bean in Greece. Seventy bacterial strains were isolated and grouped into sixteen distinct profiles based on BOX-PCR fingerprinting. The phylogenetic affiliation was further defined by sequence analysis of the rrs and multilocus sequence analysis (MLSA) of three housekeeping genes (recA, atpD and gyrB). Fifty-eight isolates were affiliated with recently described genospecies gsF-2, represented by R. laguerreae FB206T, whereas six isolates were closely related to gsB and two isolates might belong to gsA. Two isolates assigned to R. hidalgonense and another two non-nodulating strains could not be assigned to any validly defined species and possibly belong to a new rhizobial lineage. Interestingly, R. laguerreae strains were commonly found at all sampling sites, suggesting that they could be the main symbionts of faba beans in Greek soils. According to the phylogenies of two symbiosis-related genes (nodC and nifH), all nodulating isolates belonged to symbiovar (sv.) viciae harboring four distinct nodC gene haplotypes and they were grouped into two clades together with strains assigned to R. laguerreae and genospecies of R. leguminosarum isolated from other countries and continents. This is the first report that R. hidalgonense strains belong to sv. viciae. No correlation was observed between the nodC haplotypes, geographic origin and chromosomal background of the isolates in the study.", "keywords": ["MLSA", "DNA", " Bacterial", "0301 basic medicine", "0303 health sciences", "Genes", " Essential", "Greece", "Viciae", "Sequence Analysis", " DNA", "DNA Fingerprinting", "Vicia faba", "03 medical and health sciences", "Symbiovar", "Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "Root Nodules", " Plant", "Symbiosis", "Phylogeny", "Soil Microbiology", "Multilocus Sequence Typing", "Rhizobium"]}, "links": [{"href": "https://doi.org/10.1016/j.syapm.2020.126149"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Systematic%20and%20Applied%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.syapm.2020.126149", "name": "item", "description": "10.1016/j.syapm.2020.126149", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.syapm.2020.126149"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-01T00:00:00Z"}}, {"id": "10.1038/s41467-019-14197-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:17:32Z", "type": "Journal Article", "created": "2020-01-24", "title": "High-quality genome sequence of white lupin provides insight into soil exploration and seed quality", "description": "AbstractWhite lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n\uffe2\uff80\uff89=\uffe2\uff80\uff8950, 451\uffe2\uff80\uff89Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.
", "keywords": ["Repetitive Sequences", " Nucleic Acid/genetics", "0301 basic medicine", "[SDV]Life Sciences [q-bio]", "Plant Roots/genetics", "Gene Dosage", "Plant Science", "Crop", "Alkaloids/chemistry", "Plant Roots", "Gene", "Repetitive Sequences", "630", "Agricultural and Biological Sciences", "Domestication", "Soil", "Models", "Symbiotic Nitrogen Fixation in Legumes", "Gene Duplication", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_3224", "Plant Proteins/metabolism", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Genome", "Q", "http://aims.fao.org/aos/agrovoc/c_27583", "Life Sciences", "Transcriptome/genetics", "http://aims.fao.org/aos/agrovoc/c_92382", "Polymorphism", " Single Nucleotide/genetics", "Lupinus", "[SDV] Life Sciences [q-bio]", "Protein Crop", "Seeds", "http://aims.fao.org/aos/agrovoc/c_5956", "White (mutation)", "Single Nucleotide/genetics", "Sequence Analysis", "Genome", " Plant", "expression des g\u00e8nes", "http://aims.fao.org/aos/agrovoc/c_4464", "Synteny/genetics", "Evolution", "Lupin Seeds", "Science", "Centromere", "Lupinus/genetics", "Polymorphism", " Single Nucleotide", "Article", "g\u00e9nomique", "Evolution", " Molecular", "Evolution and Nutritional Properties of Lupin Seeds", "physiologie v\u00e9g\u00e9tale", "03 medical and health sciences", "Alkaloids", "Genetic", "Nucleic Acid/genetics", "Seeds/physiology", "Centromere/genetics", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Polymorphism", "Biology", "Ecology", " Evolution", " Behavior and Systematics", "Repetitive Sequences", " Nucleic Acid", "Sequence assembly", "http://aims.fao.org/aos/agrovoc/c_25189", "Ecotype", "Models", " Genetic", "g\u00e9nome", "Botany", "Molecular", "Genetic Variation", "Molecular Sequence Annotation", "Plant", "DNA", "Sequence Analysis", " DNA", "s\u00e9quence nucl\u00e9otidique", "15. Life on land", "http://aims.fao.org/aos/agrovoc/c_27527", "Agronomy", "Plant Leaves", "Evolution and Ecology of Endophyte-Grass Symbiosis", "Lupinus albus", "FOS: Biological sciences", "Genomic Structural Variation", "Plant Leaves/metabolism", "Gene expression", "Transcriptome", "am\u00e9lioration des plantes"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-14197-9.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-14197-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-14197-9", "name": "item", "description": "10.1038/s41467-019-14197-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-14197-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-24T00:00:00Z"}}, {"id": "10.1038/ismej.2010.3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:17:29Z", "type": "Journal Article", "created": "2010-02-04", "title": "Shifts In Microbial Community Structure Along An Ecological Gradient Of Hypersaline Soils And Sediments", "description": "AbstractStudies of hypersaline ecosystems often yield novel organisms and contribute to our understanding of extreme environments. Soils and sediments from La Sal del Rey, a previously uncharacterized, hypersaline lake located in southern Texas, USA, were surveyed to characterize the structure and diversity of their microbial communities. Samples were collected along a transect that spanned vegetated uplands, exposed lakebed sediments, and water-logged locations, capturing a wide range of environments and physical and chemical gradients. Community quantitative PCR (qPCR) was used in combination with tag-encoded pyrosequencing, 16S rRNA gene cloning, and Sanger sequencing to characterize the lake's soil and sediment microbial communities. Further, we used multivariate statistics to identify the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa, and sharing significant correlations with site water content, phosphorus and total organic carbon concentrations, and pH. Some individual populations, especially of Archaea, also correlated with sodium concentration and electrical conductivity salinity. Across the transect, Bacteria were numerically dominant relative to Archaea, and among them, three phyla\uffe2\uff80\uff94the Proteobacteria, Bacteroidetes, and Firmicutes\uffe2\uff80\uff94accounted for the majority of taxa detected. Although these taxa were detected with similar abundances to those described in other hypersaline ecosystems, the greater depth of sequencing achieved here resulted in the detection of taxa not described previously in hypersaline sediments. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Geologic Sediments", "Salinity", "0303 health sciences", "Bacteria", "Genes", " rRNA", "Sequence Analysis", " DNA", "15. Life on land", "Archaea", "Polymerase Chain Reaction", "Texas", "6. Clean water", "Soil", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Water Microbiology", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2010.3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2010.3", "name": "item", "description": "10.1038/ismej.2010.3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2010.3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-02-04T00:00:00Z"}}, {"id": "10.1038/srep28981", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:17:38Z", "type": "Journal Article", "created": "2016-06-30", "title": "Quantitative And Compositional Responses Of Ammonia-Oxidizing Archaea And Bacteria To Long-Term Field Fertilization", "description": "AbstractArchaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM) and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Biota", "Article", "6. Clean water", "Genes", " Archaeal", "03 medical and health sciences", "Ammonia", "Genes", " Bacterial", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep28981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep28981", "name": "item", "description": "10.1038/srep28981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep28981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-30T00:00:00Z"}}, {"id": "10.1111/1574-6941.12018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:21Z", "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": "10.1128/aem.01355-07", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-24T16:18:52Z", "type": "Journal Article", "created": "2007-11-17", "title": "Effects Of Wildfire And Harvest Disturbances On Forest Soil Bacterial Communities", "description": "ABSTRACTWildfires 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.
", "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": "10.1111/j.1462-2920.2008.01735.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:39Z", "type": "Journal Article", "created": "2008-09-01", "title": "The Effects Of Chronic Nitrogen Fertilization On Alpine Tundra Soil Microbial Communities: Implications For Carbon And Nitrogen Cycling", "description": "SummaryMany studies have shown that changes in nitrogen (N) availability affect primary productivity in a variety of terrestrial systems, but less is known about the effects of the changing N cycle on soil organic matter (SOM) decomposition. We used a variety of techniques to examine the effects of chronic N amendments on SOM chemistry and microbial community structure and function in an alpine tundra soil. We collected surface soil (0\uffe2\uff80\uff935\uffe2\uff80\uff83cm) samples from five control and five long\uffe2\uff80\uff90term N\uffe2\uff80\uff90amended plots established and maintained at the Niwot Ridge Long\uffe2\uff80\uff90term Ecological Research (LTER) site. Samples were bulked by treatment and all analyses were conducted on composite samples. The fungal community shifted in response to N amendments, with a decrease in the relative abundance of basidiomycetes. Bacterial community composition also shifted in the fertilized soil, with increases in the relative abundance of sequences related to the Bacteroidetes and Gemmatimonadetes, and decreases in the relative abundance of the Verrucomicrobia. We did not uncover any bacterial sequences that were closely related to known nitrifiers in either soil, but sequences related to archaeal nitrifiers were found in control soils. The ratio of fungi to bacteria did not change in the N\uffe2\uff80\uff90amended soils, but the ratio of archaea to bacteria dropped from 20% to less than 1% in the N\uffe2\uff80\uff90amended plots. Comparisons of aliphatic and aromatic carbon compounds, two broad categories of soil carbon compounds, revealed no between treatment differences. However, G\uffe2\uff80\uff90lignins were found in higher relative abundance in the fertilized soils, while proteins were detected in lower relative abundance. Finally, the activities of two soil enzymes involved in N cycling changed in response to chronic N amendments. These results suggest that chronic N fertilization induces significant shifts in soil carbon dynamics that correspond to shifts in microbial community structure and function.
", "keywords": ["2. Zero hunger", "Bacteria", "Nitrogen", "Molecular Sequence Data", "Fungi", "Biodiversity", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Carbon", "6. Clean water", "Soil", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Organic Chemicals", "Fertilizers", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/j.1462-2920.2008.01735.x"}, {"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/j.1462-2920.2008.01735.x", "name": "item", "description": "10.1111/j.1462-2920.2008.01735.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1462-2920.2008.01735.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-09-30T00:00:00Z"}}, {"id": "10.1371/journal.pone.0076447", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:19:08Z", "type": "Journal Article", "created": "2013-09-26", "title": "The Arbuscular Mycorrhizal Fungal Community Response To Warming And Grazing Differs Between Soil And Roots On The Qinghai-Tibetan Plateau", "description": "Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most plant species in terrestrial ecosystems, and are affected by environmental variations. To reveal the impact of disturbance on an AM fungal community under future global warming, we examined the abundance and community composition of AM fungi in both soil and mixed roots in an alpine meadow on the Qinghai-Tibetan Plateau, China. Warming and grazing had no significant effect on AM root colonization, spore density and extraradical hyphal density. A total of 65 operational taxonomic units (OTUs) of AM fungi were identified from soil and roots using molecular techniques. AM fungal OTU richness was higher in soil (54 OTUs) than in roots (34 OTUs), and some AM fungi that differed between soil and roots, showed significantly biased occurrence to warming or grazing. Warming and grazing did not significantly affect AM fungal OTU richness in soil, but warming with grazing significantly increased AM fungal OTU richness in roots compared to the grazing-only treatment. Non-metric multidimensional scaling analysis showed that the AM fungal community composition was significantly different between soil and roots, and was significantly affected by grazing in roots, whereas in soil it was significantly affected by warming and plant species richness. The results suggest that the AM fungal community responds differently to warming and grazing in soil compared with roots. This study provides insights into the role of AM fungi under global environmental change scenarios in alpine meadows of the Qinghai-Tibetan Plateau.", "keywords": ["0106 biological sciences", "Hot Temperature", "Science", "Molecular Sequence Data", "Population Dynamics", "Global Warming", "Plant Roots", "Polymerase Chain Reaction", "01 natural sciences", "Species Specificity", "Mycorrhizae", "Herbivory", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Analysis of Variance", "Base Sequence", "Models", " Genetic", "Altitude", "Q", "R", "Bayes Theorem", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Spores", " Fungal", "15. Life on land", "Biota", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Polymorphism", " Restriction Fragment Length", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0076447"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0076447", "name": "item", "description": "10.1371/journal.pone.0076447", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0076447"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-09-26T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2007.00394.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:43Z", "type": "Journal Article", "created": "2007-10-19", "title": "Quantitation And Diversity Analysis Of Ruminal Methanogenic Populations In Response To The Antimethanogenic Compound Bromochloromethane", "description": "Methyl coenzyme-M reductase A (mcrA) clone libraries were generated from microbial DNA extracted from the rumen of cattle fed a roughage diet with and without supplementation of the antimethanogenic compound bromochloromethane. Bromochloromethane reduced total methane emissions by c. 30%, with a resultant increase in propionate and branched chain fatty acids. The mcrA clone libraries revealed that Methanobrevibacter spp. were the dominant species identified. A decrease in the incidence of Methanobrevibacter spp. from the clone library generated from bromochloromethane treatment was observed. In addition, a more diverse methanogenic population with representatives from Methanococcales, Methanomicrobiales and Methanosacinales orders was observed for the bromochloromethane library. Sequence data generated from these libraries aided in the design of an mcrA-targeted quantitative PCR (qPCR) assay. The reduction in methane production by bromochloromethane was associated with an average decrease of 34% in the number of methanogenic Archaea when monitored with this qPCR assay. Dissociation curve analysis of mcrA amplicons showed a clear difference in melting temperatures for Methanobrevibacter spp. (80-82 degrees C) and all other methanongens (84-86 degrees C). A decrease in the intensity of the Methanobrevibacter spp. specific peak and an increase for the other peak in the bromochloromethane-treated animals corresponded with the changes within the clone libraries.", "keywords": ["Male", "0301 basic medicine", "Rumen", "Bromochloromethane", "Methanogens", "Molecular Sequence Data", "Euryarchaeota", "Methanobrevibacter", "Polymerase Chain Reaction", "630", "03 medical and health sciences", "2402 Applied Microbiology and Biotechnology", "Animals", "Methyl coenzyme-M reductase", "Phylogeny", "Gene Library", "2. Zero hunger", "0303 health sciences", "Hydrocarbons", " Halogenated", "2404 Microbiology", "Sequence Analysis", " DNA", "mcrA", "qPCR", "DNA", " Archaeal", "Cattle", "Oxidoreductases", "2303 Ecology", "Methane"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2007.00394.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.1574-6941.2007.00394.x", "name": "item", "description": "10.1111/j.1574-6941.2007.00394.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-12-01T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2011.01192.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:43Z", "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": "10.1111/mec.13010", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:46Z", "type": "Journal Article", "created": "2014-11-20", "title": "Long-Term Balanced Fertilization Increases The Soil Microbial Functional Diversity In A Phosphorus-Limited Paddy Soil", "description": "AbstractThe influence of long\uffe2\uff80\uff90term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22\uffe2\uff80\uff90year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array\uffe2\uff80\uff90based analysis revealed that long\uffe2\uff80\uff90term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer\uffe2\uff80\uff90induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P\uffe2\uff80\uff90limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions.
", "keywords": ["2. Zero hunger", "Bacteria", "Nitrogen", "Oryza", "Phosphorus", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Nitrogen Cycle", "15. Life on land", "6. Clean water", "Carbon Cycle", "Soil", "13. Climate action", "RNA", " Ribosomal", " 16S", "Potassium", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Fertilizers", "Ecosystem", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/mec.13010"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecular%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/mec.13010", "name": "item", "description": "10.1111/mec.13010", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/mec.13010"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-12-31T00:00:00Z"}}, {"id": "10.1128/aem.01126-09", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:52Z", "type": "Journal Article", "created": "2009-08-22", "title": "Afforestation Alters The Composition Of Functional Genes In Soil And Biogeochemical Processes In South American Grasslands", "description": "ABSTRACTSoil microbes are highly diverse and control most soil biogeochemical reactions. We examined how microbial functional genes and biogeochemical pools responded to the altered chemical inputs accompanying land use change. We examined paired native grasslands and adjacentEucalyptusplantations (previously grassland) in Uruguay, a region that lacked forests before European settlement. Along with measurements of soil carbon, nitrogen, and bacterial diversity, we analyzed functional genes using the GeoChip 2.0 microarray, which simultaneously quantified several thousand genes involved in soil carbon and nitrogen cycling. Plantations and grassland differed significantly in functional gene profiles, bacterial diversity, and biogeochemical pool sizes. Most grassland profiles were similar, but plantation profiles generally differed from those of grasslands due to differences in functional gene abundance across diverse taxa. Eucalypts decreased ammonification and N fixation functional genes by 11% and 7.9% (P< 0.01), which correlated with decreased microbial biomass N and more NH4+in plantation soils. Chitinase abundance decreased 7.8% in plantations compared to levels in grassland (P= 0.017), and C polymer-degrading genes decreased by 1.5% overall (P< 0.05), which likely contributed to 54% (P< 0.05) more C in undecomposed extractable soil pools and 27% less microbial C (P< 0.01) in plantation soils. In general, afforestation altered the abundance of many microbial functional genes, corresponding with changes in soil biogeochemistry, in part through altered abundance of overall functional gene types rather than simply through changes in specific taxa. Such changes in microbial functional genes correspond with altered C and N storage and have implications for long-term productivity in these soils.
", "keywords": ["Nitrogen", "Argentina", "Sequence Homology", "soil science", "Microbiology", "333", "Trees", "Soil", "afforestation", "Cluster Analysis", "Biology", "Soil Microbiology", "Oligonucleotide Array Sequence Analysis", "2. Zero hunger", "Environmental Microbiology and Microbial Ecology", "Bacteria", "Chitinases", "Biodiversity", "DNA", "Gene Pool", "04 agricultural and veterinary sciences", "South America", "15. Life on land", "Microarray Analysis", "Carbon", "Uruguay", "0401 agriculture", " forestry", " and fisheries", "Eucalyptus plantation"]}, "links": [{"href": "https://doi.org/10.1128/aem.01126-09"}, {"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.01126-09", "name": "item", "description": "10.1128/aem.01126-09", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01126-09"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-10-01T00:00:00Z"}}, {"id": "10.1128/aem.00527-11", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:52Z", "type": "Journal Article", "created": "2011-09-17", "title": "Microbial Communities Show Parallels At Sites With Distinct Litter And Soil Characteristics", "description": "ABSTRACTPlant 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.
", "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/aem.01536-06", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:52Z", "type": "Journal Article", "created": "2006-11-14", "title": "Community Structure Of Ammonia-Oxidizing Bacteria Under Long-Term Application Of Mineral Fertilizer And Organic Manure In A Sandy Loam Soil", "description": "ABSTRACTThe effects of mineral fertilizer (NPK) and organic manure on the community structure of soil ammonia-oxidizing bacteria (AOB) was investigated in a long-term (16-year) fertilizer experiment. The experiment included seven treatments: organic manure, half organic manure N plus half fertilizer N, fertilizer NPK, fertilizer NP, fertilizer NK, fertilizer PK, and the control (without fertilization). N fertilization greatly increased soil nitrification potential, and mineral N fertilizer had a greater impact than organic manure, while N deficiency treatment (PK) had no significant effect. AOB community structure was analyzed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of the amoA gene, which encodes the \uffce\uffb1 subunit of ammonia monooxygenase. DGGE profiles showed that the AOB community was more diverse in N-fertilized treatments than in the PK-fertilized treatment or the control, while one dominant band observed in the control could not be detected in any of the fertilized treatments. Phylogenetic analysis showed that the DGGE bands derived from N-fertilized treatments belonged to Nitrosospira cluster 3, indicating that N fertilization resulted in the dominance of Nitrosospira cluster 3 in soil. These results demonstrate that long-term application of N fertilizers could result in increased soil nitrification potential and the AOB community shifts in soil. Our results also showed the different effects of mineral fertilizer N versus organic manure N; the effects of P and K on the soil AOB community; and the importance of balanced fertilization with N, P, and K in promoting nitrification functions in arable soils.
", "keywords": ["2. Zero hunger", "Minerals", "Bacteria", "Nitrogen", "Molecular Sequence Data", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "6. Clean water", "Manure", "Ammonia", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidoreductases", "Ecosystem", "Gammaproteobacteria", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1128/aem.01536-06"}, {"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.01536-06", "name": "item", "description": "10.1128/aem.01536-06", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01536-06"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-01-15T00:00:00Z"}}, {"id": "10.1128/aem.02453-08", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:52Z", "type": "Journal Article", "created": "2009-02-07", "title": "A Vaccine Against Rumen Methanogens Can Alter The Composition Of Archaeal Populations", "description": "ABSTRACTThe objectives of this study were to formulate a vaccine based upon the different species/strains of methanogens present in sheep intended to be immunized and to determine if a targeted vaccine could be used to decrease the methane output of the sheep. Two 16S rRNA gene libraries were used to survey the methanogenic archaea in sheep prior to vaccination, and methanogens representing five phylotypes were found to account for >52% of the different species/strains of methanogens detected. A vaccine based on a mixture of these five methanogens was then formulated, and 32 sheep were vaccinated on days 0, 28, and 103 with either a control or the anti-methanogen vaccine. Enzyme-linked immunosorbent assay analysis revealed that each vaccination with the anti-methanogen formulation resulted in higher specific immunoglobulin G titers in plasma, saliva, and rumen fluid. Methane output levels corrected for dry-matter intake for the control and treatment groups were not significantly different, and real-time PCR data also indicated that methanogen numbers were not significantly different for the two groups after the second vaccination. However, clone library data indicated that methanogen diversity was significantly greater in sheep receiving the anti-methanogen vaccine and that the vaccine may have altered the composition of the methanogen population. A correlation between 16S rRNA gene sequence relatedness and cross-reactivity for the methanogens ( R 2 = 0.90) also exists, which suggests that a highly specific vaccine can be made to target specific strains of methanogens and that a more broad-spectrum approach is needed for success in the rumen. Our data also suggest that methanogens take longer than 4 weeks to adapt to dietary changes and call into question the validity of experimental results based upon a 2- to 4-week acclimatization period normally observed for bacteria.
", "keywords": ["Rumen", "Molecular Sequence Data", "DNA", " Ribosomal", "630", "Antibodies", "Plasma", "RNA", " Ribosomal", " 16S", "2402 Applied Microbiology and Biotechnology", "Animals", "Saliva", "1106 Food Science", "2. Zero hunger", "Vaccines", "Gastric Juice", "Sheep", "0402 animal and dairy science", "Biodiversity", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Archaea", "3. Good health", "DNA", " Archaeal", "Immunoglobulin G", "1305 Biotechnology", "2303 Ecology", "Methane"]}, "links": [{"href": "https://doi.org/10.1128/aem.02453-08"}, {"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.02453-08", "name": "item", "description": "10.1128/aem.02453-08", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02453-08"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-04-01T00:00:00Z"}}, {"id": "10.1128/aem.02541-13", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-24T16:18:52Z", "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": "ABSTRACTTropical 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.
", "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.04040-14", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:52Z", "type": "Journal Article", "created": "2015-01-24", "title": "Fungal Communities Respond To Long-Term Co2 Elevation By Community Reassembly", "description": "ABSTRACTFungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO 2 (eCO 2 ), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON (biodiversity, CO 2 , and N deposition) experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO 2 for 12 years. Long-term eCO 2 did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. The relative abundances of 119 operational taxonomic units (OTU; \uffe2\uff88\uffbc27% of the total captured sequences) were changed significantly. Significantly changed OTU under eCO 2 were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Co-occurrence ecological network analysis indicated that eCO 2 increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO 2 network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO 2 , especially with increased plant biomass and NH 4 + availability. This study provided novel insights into how eCO 2 shapes soil fungal communities in grassland ecosystems.
", "keywords": ["580", "0301 basic medicine", "0303 health sciences", "electric network topology", "Minnesota", "Molecular Sequence Data", "Fungi", "carbon dioxide", "Sequence Analysis", " DNA", "Carbon Dioxide", "15. Life on land", "Biota", "DNA", " Ribosomal", "333", "03 medical and health sciences", "13. Climate action", "XXXXXX - Unknown", "RNA", " Ribosomal", " 28S", "11. Sustainability", "fungi", "ecology", "DNA", " Fungal", "Soil Microbiology", "biodiversity"]}, "links": [{"href": "https://doi.org/10.1128/aem.04040-14"}, {"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.04040-14", "name": "item", "description": "10.1128/aem.04040-14", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.04040-14"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-04-01T00:00:00Z"}}, {"id": "10.1186/s40168-018-0607-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:19:01Z", "type": "Journal Article", "created": "2018-12-07", "title": "Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment", "description": "Approximately 500\u00a0Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the \u03b1-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments.The new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria.This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas.", "keywords": ["0301 basic medicine", "570", "Isoprene", "Climate", "Mixed Function Oxygenases", "Microbial ecology", "Comamonadaceae", "03 medical and health sciences", "Hemiterpenes", "Bacterial Proteins", "Butadienes", "Isoprene monooxygenase", "Rhodococcus", "Gene probes", "14. Life underwater", "Phylogeny", "Soil Microbiology", "DNA Primers", "0303 health sciences", "Bacteria", "Research", "isoA", "QR100-130", "QR Microbiology", "Sequence Analysis", " DNA", "15. Life on land", "Sphingomonadaceae", "Biodegradation", " Environmental", "13. Climate action"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/69294/1/Published_manuscript.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1186/s40168-018-0607-0.pdf"}, {"href": "https://repository.essex.ac.uk/23630/1/s40168-018-0607-0.pdf"}, {"href": "https://doi.org/10.1186/s40168-018-0607-0"}, {"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/s40168-018-0607-0", "name": "item", "description": "10.1186/s40168-018-0607-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-018-0607-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-01T00:00:00Z"}}, {"id": "10.1266/ggs.88.93", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:19:02Z", "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": "10.3390/v11070611", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:20:38Z", "type": "Journal Article", "created": "2019-06-12", "title": "Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum\u2014A Novel Lineage of Lactobacillus Phages Comprising Five New Members", "description": "Lactobacillus plantarum is a bacterium with promising applications to the food industry and agriculture and probiotic properties. So far, bacteriophages of this bacterium have been moderately addressed. We examined the diversity of five new L. plantarum phages via whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. These analyses revealed a high degree of similarity among the five phages, which extended to the vast majority of predicted virion-associated proteins. Based on these, we selected one of the phages as a representative and performed transmission electron microscopy and structural protein sequencing tests. Overall, the results suggested that the five phages belong to the family Myoviridae, they have a long genome of 137.973-141.344 bp, a G/C content of 36,3-36,6% that is quite distinct from their host’s, and, surprisingly, seven to 15 tRNAs. Only an average 41/174 of their predicted genes were assigned a function. The comparative analyses unraveled considerable genetic diversity for the five L. plantarum phages of this study. Hence, the new genus “Semelevirus” was proposed, which comprises exclusively the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp.. The five new Lactobacillus phages have a potential value for the development of more robust starters through, for example, the selection of mutants insensitive to phage infections. The five phages could also form part of phage cocktails, which producers would apply in different stages of L. plantarum fermentations in order to create a range of organoleptic outputs.
", "keywords": ["0301 basic medicine", "Annotation", "comparative genomics", "Genome", " Viral", "Lactobacillus plantarum", "Microbiology", "Article", "Isolation", "diversity", "03 medical and health sciences", "Microscopy", " Electron", " Transmission", "DNA Packaging", "phage", "Bacteriophages", "Phylogeny", "Viral Structural Proteins", "2. Zero hunger", "Diversity", "Base Composition", "0303 health sciences", "Comparative genomics", "new genus", "Genomics", "Sequence Analysis", " DNA", "QR1-502", "virology", "Phylogenetics", "phylogenetics", "Lactobacillus", "annotation", "Myoviridae", "Phage", "New genus", "isolation", "Lactobacillus plantarum"]}, "links": [{"href": "http://www.mdpi.com/1999-4915/11/7/611/pdf"}, {"href": "https://www.mdpi.com/1999-4915/11/7/611/pdf"}, {"href": "https://doi.org/10.3390/v11070611"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Viruses", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/v11070611", "name": "item", "description": "10.3390/v11070611", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/v11070611"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-11T00:00:00Z"}}, {"id": "ff581516-596e-4e89-9f0d-29d506d36aef", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[5.81, 47.26], [5.81, 54.76], [15.77, 54.76], [15.77, 47.26], [5.81, 47.26]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "sequence analysis"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "Apple replant disease (ARD)"}, {"id": "amplicon sequencing"}, {"id": "16S rRNA gene"}, {"id": "ITS"}], "scheme": "Individual"}, {"concepts": [{"id": "Bodennutzung"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "license": "CC BY", "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - ORDIAmur's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2025-09-25", "type": "Dataset", "created": "2025-09-17", "language": "eng", "title": "Raw amplicon sequence data of bacterial and fungal rhizosphere communities of apple plants inoculated with Priestia megaterium B1L5 and grown in ARD or grass soils", "description": "This dataset contains raw amplicon sequencing data of bacterial and fungal rhizosphere communities associated with apple plantlets. Plantlets were grown under controlled conditions in climate chambers using two soil types: grass soil without a history of apple cultivation and apple replant diseased (ARD) soil. Soils were collected at a site in Heidgraben, Germany (x-coordinate 53.699199; y-coordinate 9.683171; WGS 84, Schleswig-Holstein, northern Germany). Treatments included inoculation with vegetative cells or spores of GFP-labelled Priestia megaterium B1L5 as well as uninoculated controls. Rhizosphere samples were collected at two time points, 6 and 33 days post inoculation. For bacterial community profiling, the V4 region of the 16S rRNA gene was amplified, while for fungal community profiling, the internal transcribed spacer (ITS) region was targeted. Raw sequencing reads are deposited in the National Center for Biotechnology Information (NCBI) under BioProject accession number PRJNA700828 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA700828). The 16S rRNA gene reads are available under accession numbers SRX26424303\u2013SRX26424386, and the ITS reads are deposited under accession numbers SRX26437416\u2013SRX26437498 (see Supplemental Material).", "formats": [{"name": "CSV"}], "keywords": ["sequence analysis", "Apple replant disease (ARD)", "amplicon sequencing", "16S rRNA gene", "ITS", "Bodennutzung"], "contacts": [{"name": null, "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Fatma M. 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