Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500\uffc2\uffa0bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large\uffe2\uff80\uff90scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungs\uffc3\uffa4ngen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic\uffe2\uff80\uff90dry part that has a species rich grass\uffe2\uff80\uff90dominated plant community including a high frequency of F.\uffc2\uffa0meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%\uffe2\uff80\uff9340% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.
", "keywords": ["580", "species hypothesis", "Ekologi", "0301 basic medicine", "0303 health sciences", "Ecology", "rDNA", "Biological Systematics", "15. Life on land", "03 medical and health sciences", "14. Life underwater", "ITS", "Research Articles", "clustering"]}, "links": [{"href": "https://pub.epsilon.slu.se/27699/1/eshghi-sahraei-s-et-al-220505.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.8676"}, {"href": "https://doi.org/10.1002/ece3.8676"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology%20and%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ece3.8676", "name": "item", "description": "10.1002/ece3.8676", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ece3.8676"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-01T00:00:00Z"}}, {"id": "10.1002/ajb2.1625", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:11Z", "type": "Journal Article", "created": "2021-03-19", "title": "Phylogeography of a gypsum endemic plant across its entire distribution range in the western Mediterranean", "description": "PREMISEGypsum soils in the Mediterranean Basin house large numbers of edaphic specialists that are adapted to stressful environments. The evolutionary history and standing genetic variation of these taxa have been influenced by the geological and paleoclimatic complexity of this area and the long\uffe2\uff80\uff90standing effect of human activities. However, little is known about the origin of Mediterranean gypsophiles and the factors affecting their genetic diversity and population structure.
METHODSUsing phylogenetic and phylogeographic approaches based on microsatellites and sequence data from nuclear and chloroplast regions, we evaluated the divergence time, genetic diversity, and population structure of 27 different populations of the widespread Iberian gypsophile Lepidium subulatum throughout its entire geographic range.
RESULTSLepidium subulatum diverged from its nearest relatives ~3 million years ago, and ITS and psbA/matK trees supported the monophyly of the species. These results suggest that both geological and climatic changes in the region around the Plio\uffe2\uff80\uff90Pleistocene promoted its origin, compared to other evolutionary processes. We found high genetic diversity in both nuclear and chloroplast markers, but a greater population structure in the chloroplast data. These results suggest that while seed dispersal is limited, pollen flow may be favored by the presence of numerous habitat patches that enhance the movement of pollinators.
CONCLUSIONSDespite being an edaphic endemic, L. subulatum possesses high genetic diversity probably related to its relatively old age and high population sizes across its range. Our study highlights the value of using different markers to fully understand the phylogeographic history of plant species.Meiofauna (all invertebrates smaller than 1\uffe2\uff80\uff89mm) are not only sensitive to environmental changes but also contribute significantly to nutrient cycling and energy transfer to higher trophic levels. Despite their importance, meiofauna distribution and ecology in the Siberian seas remain understudied. Here, we employ sediment environmental DNA metabarcoding to characterize meiofauna diversity across the unexplored Siberian seas. We show that meiofauna community structure is primarily driven by river discharge and coastal erosion, which are heavily influenced by climate change, rather than geographical distinctions between the seas. We observed higher meiofauna diversity in nearshore areas where river plumes promoted colonizer nematode communities that are resilient to disturbances. Yet, their dominance may lead to decreased ecosystem stability in the future. This study provides a valuable baseline for meiofauna diversity in remote Siberian seas undergoing rapid environmental change, which will be useful for assessing the future direction and pace of benthic ecological trajectories.Responses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long\uffe2\uff80\uff90term field experiment which divides conventional and organic agriculture into component pest\uffe2\uff80\uff90control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles, microbial and nematode counts, and denaturing gradient gel electrophoresis (DGGE) to characterise soil microbial communities in plots used for onion (Allium cepa L.) cultivation.
RESULTSMicrobial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest\uffe2\uff80\uff90control treatment plots.
CONCLUSIONOrganic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation. \uffc2\uffa9 2013 Society of Chemical Industry
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Microbial diversity", "Nematoda", "Soil", "03 medical and health sciences", "Onions", "Animals", "DNA", " Fungal", "Ecosystem", "Soil Microbiology", "2. Zero hunger", "Organic Agriculture", "0303 health sciences", "Bacteria", "Denaturing Gradient Gel Electrophoresis", "0402 animal and dairy science", "Fungi", "Denaturing gradient gel electrophoresis", "Agriculture", "Biolog Eco-plates", "04 agricultural and veterinary sciences", "15. Life on land", "Community level physiological profile", "Organic agriculture", "0405 other agricultural sciences"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.6206"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.6206", "name": "item", "description": "10.1002/jsfa.6206", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.6206"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-06-07T00:00:00Z"}}, {"id": "10.1007/s00248-011-9897-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:34Z", "type": "Journal Article", "created": "2011-06-29", "title": "Impacts Of Organic And Inorganic Fertilizers On Nitrification In A Cold Climate Soil Are Linked To The Bacterial Ammonia Oxidizer Community", "description": "The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38\u00b0C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification.", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "China", "Bacteria", "04 agricultural and veterinary sciences", "15. Life on land", "Cold Climate", "Archaea", "Nitrification", "6. Clean water", "Genes", " Archaeal", "Soil", "DNA", " Archaeal", "Ammonia", "Genes", " Bacterial", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidoreductases", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-011-9897-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-011-9897-5", "name": "item", "description": "10.1007/s00248-011-9897-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-011-9897-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-29T00:00:00Z"}}, {"id": "10.1007/s00248-008-9467-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:34Z", "type": "Journal Article", "created": "2008-11-21", "title": "Molecular And Functional Assessment Of Bacterial Community Convergence In Metal-Amended Soils", "description": "Species diversity and the structure of microbial communities in soils are thought to be a function of the cumulative selective pressures within the local environment. Shifts in microbial community structure, as a result of metal stress, may have lasting negative effects on soil ecosystem dynamics if critical microbial community functions are compromised. Three soils in the vicinity of a copper smelter, previously contaminated with background, low and high levels of aerially deposited metals, were amended with metal-salts to determine the potential for metal contamination to shape the structural and functional diversity of microbial communities in soils. We hypothesized that the microbial communities native to the three soils would initially be unique to each site, but would converge on a microbial community with similar structure and function, as a result of metal stress. Initially, the three different sites supported microbial communities with unique structural and functional diversity, and the nonimpacted site supported inherently higher levels of microbial activity and biomass, relative to the metal-contaminated sites. Amendment of the soils with metal-salts resulted in a decrease in microbial activity and biomass, as well as shifts in microbial community structure and function at each site. Soil microbial communities from each site were also observed to be sensitive to changes in soil pH as a result of metal-salt amendment; however, the magnitude of these pH-associated effects varied between soils. Microbial communities from each site did not converge on a structurally or functionally similar community following metal-salt amendment, indicating that other factors may be equally important in shaping microbial communities in soils. Among these factors, soil physiochemical parameters like organic matter and soil pH, which can both influence the bioavailability and toxicity of metals in soils, may be critical.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "0303 health sciences", "Bacteria", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Soil", "03 medical and health sciences", "13. Climate action", "Metals", " Heavy", "Soil Pollutants", "Biomass", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-008-9467-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-008-9467-7", "name": "item", "description": "10.1007/s00248-008-9467-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-008-9467-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-11-22T00:00:00Z"}}, {"id": "10.1007/s00248-010-9727-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:34Z", "type": "Journal Article", "created": "2010-08-03", "title": "Soil Microbial Abundance And Diversity Along A Low Precipitation Gradient", "description": "The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while \u223c2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (\u223c9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem.", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "0301 basic medicine", "Salinity", "0303 health sciences", "Bacteria", "Mediterranean Region", "Climate", "Rain", "Water", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Soil", "03 medical and health sciences", "Phospholipids", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-010-9727-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-010-9727-1", "name": "item", "description": "10.1007/s00248-010-9727-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-010-9727-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-08-01T00:00:00Z"}}, {"id": "10.1007/s00248-013-0322-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:34Z", "type": "Journal Article", "created": "2013-11-25", "title": "Pyrosequencing Reveals Contrasting Soil Bacterial Diversity And Community Structure Of Two Main Winter Wheat Cropping Systems In China", "description": "Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems.", "keywords": ["Crops", " Agricultural", "DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "China", "0303 health sciences", "Agriculture", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "Zea mays", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Microbiology", "Triticum"]}, "links": [{"href": "https://doi.org/10.1007/s00248-013-0322-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-013-0322-0", "name": "item", "description": "10.1007/s00248-013-0322-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-013-0322-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-26T00:00:00Z"}}, {"id": "10.1007/s00253-011-3535-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:34Z", "type": "Journal Article", "created": "2011-08-17", "title": "Methanotrophic Community Structure And Activity Under Warming And Grazing Of Alpine Meadow On The Tibetan Plateau", "description": "Knowledge about methanotrophs and their activities is important to understand the microbial mediation of the greenhouse gas CH(4) under climate change and human activities in terrestrial ecosystems. The effects of simulated warming and sheep grazing on methanotrophic abundance, community composition, and activity were studied in an alpine meadow soil on the Tibetan Plateau. There was high abundance of methanotrophs (1.2-3.4\u2009\u00d7\u200910(8) pmoA gene copies per gram of dry weight soil) assessed by real-time PCR, and warming significantly increased the abundance regardless of grazing. A total of 64 methanotrophic operational taxonomic units (OTUs) were obtained from 1,439 clone sequences, of these OTUs; 63 OTUs (98.4%) belonged to type I methanotrophs, and only one OTU was Methylocystis of type II methanotrophs. The methanotroph community composition and diversity were not apparently affected by the treatments. Warming and grazing significantly enhanced the potential CH(4) oxidation activity. There were significantly negative correlations between methanotrophic abundance and soil moisture and between methanotrophic abundance and NH(4)-N content. The study suggests that type I methanotrophs, as the dominance, may play a key role in CH(4) oxidation, and the alpine meadow has great potential to consume more CH(4) under future warmer and grazing conditions on the Tibetan Plateau.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Sheep", "Bacteria", "Molecular Sequence Data", "Temperature", "Sequence Analysis", " DNA", "15. Life on land", "Real-Time Polymerase Chain Reaction", "Tibet", "Biota", "Soil", "03 medical and health sciences", "Ammonia", "13. Climate action", "Animals", "Methane", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00253-011-3535-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-011-3535-5", "name": "item", "description": "10.1007/s00253-011-3535-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-011-3535-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-08-17T00:00:00Z"}}, {"id": "10.1007/s00253-016-7736-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:34Z", "type": "Journal Article", "created": "2016-07-27", "title": "Structure Of Bacterial Communities In Soil Following Cover Crop And Organic Fertilizer Incorporation", "description": "Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane\u00ae (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.", "keywords": ["Crops", " Agricultural", "DNA", " Bacterial", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "High-Throughput Nucleotide Sequencing", "Sequence Analysis", " DNA", "15. Life on land", "Biota", "DNA", " Ribosomal", "03 medical and health sciences", "13. Climate action", "RNA", " Ribosomal", " 16S", "Fertilizers", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00253-016-7736-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-016-7736-9", "name": "item", "description": "10.1007/s00253-016-7736-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-016-7736-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-07-27T00:00:00Z"}}, {"id": "10.1007/s00442-012-2471-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:44Z", "type": "Journal Article", "created": "2012-10-03", "title": "Ectomycorrhizal Fungal Succession Coincides With Shifts In Organic Nitrogen Availability And Canopy Closure In Post-Wildfire Jack Pine Forests", "description": "Successional changes in belowground ectomycorrhizal fungal (EMF) communities have been observed with increasing forest stand age; however, mechanisms behind this change remain unclear. It has been hypothesized that declines of inorganic nitrogen (N) and increases of organic N influence changes in EMF taxa over forest development. In a post-wildfire chronosequence of six jack pine (Pinus banksiana) stands ranging in age from 5 to 56 years, we investigated EMF community composition and compared shifts in taxa with detailed soluble inorganic and organic N data. Taxa were identified by internal transcribed spacer rDNA sequencing, and changes in community composition evaluated with non-metric multi-dimensional scaling (NMDS). Dissimilarities in the community data were tested for correlations with N variables. We observed a successional shift along NMDS axis 1 from such taxa as Suillus brevipes and Thelephora terrestris in sites age 5 and 11 to species of Cortinarius and Russula, among others, in the four older sites. This change was positively correlated with soluble organic N (SON) (r(2) = 0.902, P = 0.033) and free amino-acid N (r(2) = 0.945, P = 0.021), but not inorganic N. Overall, our results show a successional shift of EMF communities occurring between stand initiation and canopy closure without a change in species of the dominant plant-host, and associated with SON and free amino-acid N in soil. It is uncertain whether EMF taxa are responding to these organic N forms directly, affecting their availability, or are ultimately responding to changes in other site variables, such as belowground productivity.", "keywords": ["0106 biological sciences", "Mycorrhizae", "DNA", " Ribosomal Spacer", "Population Dynamics", "0401 agriculture", " forestry", " and fisheries", "Biodiversity", "04 agricultural and veterinary sciences", "Nitrogen Cycle", "15. Life on land", "Pinus", "01 natural sciences", "Fires"]}, "links": [{"href": "https://doi.org/10.1007/s00442-012-2471-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-012-2471-0", "name": "item", "description": "10.1007/s00442-012-2471-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-012-2471-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-04T00:00:00Z"}}, {"id": "10.1007/s00572-015-0655-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:46Z", "type": "Journal Article", "created": "2015-07-25", "title": "The Ectomycorrhizal Community Of Conifer Stands On Peat Soils 12 Years After Fertilization With Wood Ash", "description": "We studied long-term effects of fertilization with wood ash on biomass, vitality and mycorrhizal colonization of fine roots in three conifer forest stands growing in Vacciniosa turf. mel. (V), Myrtillosa turf. mel. (M) and Myrtillosa turf. mel./Caricoso-phragmitosa (MC) forest types on peat soils. Fertilization trials amounting 5 kg/m(2) of wood ash were established 12 years prior to this study. A total of 63 soil samples with roots were collected and analysed. Ectomycorrhizal (ECM) fungi in roots were identified by morphotyping and sequencing of the fungal internal transcribed spacer (ITS) region. In all forest types, fine root biomass was higher in fertilized plots than in control plots. In M forest type, proportion of living fine roots was greater in fertilized plots than in control plots, while in V and MC, the result was opposite. Fifty ECM species were identified, of which eight were common to both fertilized and control plots. Species richness and Shannon diversity index were generally higher in fertilized plots than in control plots. The most common species in fertilized plots were Amphinema byssoides (17.8%) and Tuber cf. anniae (12.2%), while in control plots, it was Tylospora asterophora (18.5%) and Lactarius tabidus (20.3%). Our results showed that forest fertilization with wood ash has long-lasting effect on diversity and composition of ECM fungal communities.", "keywords": ["0106 biological sciences", "570", "forest fertilization", "m\u00e4nty", "Molecular Sequence Data", "organic soils", "fine roots", "Plant Roots", "01 natural sciences", "630", "mets\u00e4nlannoitus", "Mycorrhizae", "ectomycorrhizae", "DNA", " Ribosomal Spacer", "Muut aihealueet", "DNA", " Fungal", "2. Zero hunger", "Picea abies", "Pinus sylvestris", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Biota", "hienojuuret", "kuusi", "Tracheophyta", "eloper\u00e4iset maat", "0401 agriculture", " forestry", " and fisheries", "ektomykorritsa"]}, "links": [{"href": "https://doi.org/10.1007/s00572-015-0655-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Mycorrhiza", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00572-015-0655-2", "name": "item", "description": "10.1007/s00572-015-0655-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00572-015-0655-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-07-26T00:00:00Z"}}, {"id": "10.1007/s11104-021-05261-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:14Z", "type": "Journal Article", "created": "2022-01-30", "title": "Tracing hotspots of soil erosion in high mountain environments: how forensic science based on plant eDNA can lead the way. An opinion", "description": "High mountain environments are among the most fragile on Earth. Due to anthropogenic disturbances and the exposure to extreme weather events, the rates of soil erosion have recently been accelerating, resulting in ecological degradation and geological hazards. Ecological restoration of mountains and an improved understanding of nature-based solutions to mitigate land degradation is therefore of utmost urgency. Identifying hotspots of soil erosion is a first step towards improving mitigation strategies. A promising methodology to identify erosion hotspots is sediment source fingerprinting, that differentiates the properties of soil from different sources, using signatures such as elemental geochemistry or radionuclides. However, in areas with complex lithologies or shallow and poorly developed soils, geochemical fingerprints allow only a rough distinction between erosion hotspots. In this opinion paper, we explore the relevance of environmental DNA (eDNA) that originates from plant litter and fixes onto fine soil particles, as a targeted sediment fingerprinting method sensitive to vegetation that could potentially allow the identification of erosion hotspots and their relative importance from sedimentary deposits. Pioneering studies indicate that eDNA allows not only the detection of specific vegetation communities, but also the identification of individual plant species. Supported by the increasing availability and quality of vegetation maps and eDNA reference libraries, we argue that sediment source fingerprinting using eDNA from plant litter, will evolve into a valuable method to identify hotspots of soil erosion and allow stakeholders to prioritize areas where ecological restoration is necessary in high mountain environments.", "keywords": ["Soil and water bioengineering", "Vegetation", "[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", "550", "Sediment source fingerprinting", "Phylogenetics and taxonomy", "[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics", "15. Life on land", "Alpine", "01 natural sciences", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "Landslide", "Erosion", "13. Climate action", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "environment/Ecosystems", "sedDNA", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s11104-021-05261-9.pdf"}, {"href": "https://doi.org/10.1007/s11104-021-05261-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-021-05261-9", "name": "item", "description": "10.1007/s11104-021-05261-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-021-05261-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-30T00:00:00Z"}}, {"id": "10.1007/s12275-012-2409-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:23Z", "type": "Journal Article", "created": "2012-11-03", "title": "Characterization Of The Bacterial And Archaeal Communities In Rice Field Soils Subjected To Long-Term Fertilization Practices", "description": "The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Molecular Sequence Data", "Agriculture", "Oryza", "15. Life on land", "Archaea", "6. Clean water", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Seasons", "Fertilizers", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s12275-012-2409-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s12275-012-2409-6", "name": "item", "description": "10.1007/s12275-012-2409-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s12275-012-2409-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-01T00:00:00Z"}}, {"id": "10.1016/j.agrformet.2020.108031", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:41Z", "type": "Journal Article", "created": "2020-05-29", "title": "Inter-individual variability in spring phenology of temperate deciduous trees depends on species, tree size and previous year autumn phenology", "description": "We explored the inter-individual variability in bud-burst and its potential drivers, in homogeneous mature stands of temperate deciduous trees. Phenological observations of leaves and wood formation were performed weekly from summer 2017 to summer 2018 for pedunculate oak, European beech and silver birch in Belgium. The variability of bud-burst was correlated to previous' year autumn phenology (i.e. the onset of leaf senescence and the cessation of wood formation) and tree size but with important differences among species. In fact, variability of bud-burst was primarily related to onset of leaf senescence, cessation of wood formation and tree height for oak, beech and birch, respectively. The inter-individual variability of onset of leaf senescence was not related to the tree characteristics considered and was much larger than the inter-individual variability in bud-burst. Multi-species multivariate models could explain up to 66% of the bud-burst variability. These findings represent an important advance in our fundamental understanding and modelling of phenology and tree functioning of deciduous tree species.", "keywords": ["Agriculture and Food Sciences", "0106 biological sciences", "Atmospheric Science", "polno olistanje", "Broadleaved forest", "Silver birch", "Edellauvskog", "coloration", "01 natural sciences", "fenologija", "navadna bukev", "Pedunculate oak", "FAGUS-SYLVATICA", "PHLOEM", "Global and Planetary Change", "LEAF PHENOLOGY", "CLIMATE-CHANGE", "VDP::\u00d8kologi: 488", "Physics", "Forestry", "VDP::Ecology: 488", "04 agricultural and veterinary sciences", "dob", "navadna breza", "Chemistry", "Phenology", "info:eu-repo/classification/udc/630*811", "rumenenje listov", "XYLEM", "MODELS", "Article", "leaf unfolding", "Fenologi", "Coloration", "nastanek lesa", "Biology", "Wood formation", "kambij", "Leaf unfolding", "RADIAL GROWTH", "15. Life on land", "listavci", "European beech", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "SENESCENCE", "13. Climate action", "wood formation", "0401 agriculture", " forestry", " and fisheries", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "Agronomy and Crop Science"]}, "links": [{"href": "https://doi.org/10.1016/j.agrformet.2020.108031"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agricultural%20and%20Forest%20Meteorology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.agrformet.2020.108031", "name": "item", "description": "10.1016/j.agrformet.2020.108031", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.agrformet.2020.108031"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2014.06.094", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:00Z", "type": "Journal Article", "created": "2014-08-13", "title": "Influence of tetracycline on the microbial community composition and activity of nitrifying biofilms", "description": "The present work aims to evaluate the bacterial composition and activity (carbon and nitrogen removal) of nitrifying biofilms exposed to 50 \u03bcg L(-1) of tetracycline. The tetracycline removal efficiency and the occurrence of tetracycline resistance (tet) genes were also studied. Two sequencing batch biofilm reactors (SBBRs) fed with synthetic wastewater were operated without (SBBR1) and with (SBBR2) the antibiotic. Both SBBRs showed similar organic matter biodegradation and nitrification activity. Tetracycline removal was about 28% and biodegradation was probably the principal removal mechanism of the antibiotic. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of the bacterial community showed shifts leading to not only the fading of some ribotypes, but also the emergence of new ones in the biofilm with tetracycline. The study of the tet genes showed that tet(S) was only detected in the biofilm with tetracycline, suggesting a relationship between its occurrence and the presence of the antibiotic.", "keywords": ["Science & Technology", "Polymers", "Microbiota", "Molecular Sequence Data", "Tetracycline Resistance", "0211 other engineering and technologies", "Resistance genes", "Sequence Analysis", " DNA", "02 engineering and technology", "Tetracycline", "Nitrification", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Tetracycline removal", "Nitrifying biofilms", "Bacterial Proteins", "Antibiotics", "Biofilms", "11. Sustainability", "Bacterial community", "Adsorption", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2014.06.094"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2014.06.094", "name": "item", "description": "10.1016/j.chemosphere.2014.06.094", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2014.06.094"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-12-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2024.143131", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:00Z", "type": "Journal Article", "created": "2024-08-19", "title": "Photoaging of polystyrene-based microplastics amplifies inflammatory response in macrophages", "description": "The continuous release of municipal and industrial products into the environment poses a growing concern for public health. Among environmental pollutants, polystyrene (PS) stands out as a primary constituent of environmental plastic waste, given its widespread use and high production rates owing to its durability and user-friendly properties. The detection of polystyrene microparticles (PS-MPs) in various living organisms has been well-documented, posing a serious threat due to their potential passage into the human ecosystem. In this manuscript, we aimed to study the toxicological effects of low concentrations of pristine and photoaged PS-MPs in a murine macrophage cell line. To this purpose, PS-MPs were photoaged by indoor exposure to visible light to simulate environmental weathering due to solar irradiation (PS-MPs3h). Physical characterization revealed that the irradiation treatment results in particle degradation and the possible release of nanoparticles. Monocultures of the RAW264.7\u00a0cell line were then exposed to PS-MPs and PS-MPs3h at concentrations comparable to experimental measurements from biological samples, to assess cytotoxicity, intracellular oxidative stress, primary genotoxicity, and inflammatory effects. Significant toxicity-related outcomes were observed in cells treated with both pristine PS-MPs and PS-MPs3h even at low concentrations (0,10\u00a0\u03bcg/ml and 1\u00a0\u03bcg/ml). PS-MPs3h exhibited greater adverse effects compared to PS-MPs, including reduced cell viability, increased ROS production, elevated DNA damage, and upregulation of IL-6 and NOS2 gene expression. Therefore, we can conclude that changes induced by environmental aging in the physicochemical composition of PS microplastics play a crucial role in the adverse health outcomes associated with microplastic exposure.", "keywords": ["Inflammation", "Mice", "Oxidative Stress", "RAW 264.7 Cells", "microplastics", " polystyrene", " macrophages", "Cell Survival", "Microplastics", "Macrophages", "Polystyrenes", "Animals", "Environmental Pollutants", "Reactive Oxygen Species", "DNA Damage"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/493702/1/Aloi%20et%20al%20Chemospere%202024.pdf"}, {"href": "https://doi.org/10.1016/j.chemosphere.2024.143131"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2024.143131", "name": "item", "description": "10.1016/j.chemosphere.2024.143131", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2024.143131"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "10.1016/j.copbio.2018.11.014", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:01Z", "type": "Journal Article", "created": "2018-12-11", "title": "Multi-omics and potential applications in wine production", "description": "The wine microbiome - that is the microbial communities associated with the fermentation of must, is one of the most important factors in transforming grapes to wine, including flavour and aroma. Recent developments in high throughput sequencing and other 'omics methodologies are rapidly changing the level and complexity of information that we are able to extract from the wine microbiome. This will significantly enhance not only our understanding of which microbes are present at the various stages of the grapevine growth and winemaking process, but also improve our understanding of the complex interactions between microbes, the substrate and environment, ultimately shaping wine production. In this perspective we describe the role and future potential of such techniques in wine production, and highlight the potential challenges that will be simultaneously faced.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "03 medical and health sciences", "13. Climate action", "Microbiota", "DNA Barcoding", " Taxonomic", "Wine", "Genomics"]}, "links": [{"href": "https://doi.org/10.1016/j.copbio.2018.11.014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Opinion%20in%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.copbio.2018.11.014", "name": "item", "description": "10.1016/j.copbio.2018.11.014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.copbio.2018.11.014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-01T00:00:00Z"}}, {"id": "10.1016/j.csbj.2022.08.002", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:02Z", "type": "Journal Article", "created": "2022-08-08", "title": "Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA", "description": "ADP-ribosylation is an ancient, highly conserved, and reversible covalent modification critical for a variety of endogenous processes in both prokaryotes and eukaryotes. ADP-ribosylation targets proteins, nucleic acids, and small molecules (including antibiotics). ADP-ribosylation signalling involves enzymes that add ADP-ribose to the target molecule, the (ADP-ribosyl)transferases; and those that remove it, the (ADP-ribosyl)hydrolases. Recently, the toxin/antitoxin pair DarT/DarG composed of a DNA ADP-ribosylating toxin, DarT, and (ADP-ribosyl)hydrolase antitoxin, DarG, was described. DarT modifies thymidine in single-stranded DNA in a sequence-specific manner while DarG reverses this modification, thereby rescuing cells from DarT toxicity. We studied the DarG homologue SCO6735 which is highly conserved in all Streptomyces species and known to be associated with antibiotic production in the bacterium S. coelicolor. SCO6735 shares a high structural similarity with the bacterial DarG and human TARG1. Like DarG and TARG1, SCO6735 can also readily reverse thymidine-linked ADP-ribosylation catalysed by DarT in vitro and in cells. SCO6735 active site analysis including molecular dynamic simulations of its complex with ADP-ribosylated thymidine suggests a novel catalytic mechanism of DNA-(ADP-ribose) hydrolysis. Moreover, a comparison of SCO6735 structure with ALC1-like homologues revealed an evolutionarily conserved feature characteristic for this subclass of macrodomain hydrolases.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "ADP-ribosylation", " DNA ADP-ribosylation", " Macrodomain", " Streptomyces", " SCO6735", "SCO6735", "540", "Streptomyces", "DNA ADP-ribosylation", "03 medical and health sciences", "TP248.13-248.65", "ADP-ribosylation", "Macrodomain", "Biotechnology", "Research Article"]}, "links": [{"href": "https://doi.org/10.1016/j.csbj.2022.08.002"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Computational%20and%20Structural%20Biotechnology%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.csbj.2022.08.002", "name": "item", "description": "10.1016/j.csbj.2022.08.002", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.csbj.2022.08.002"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10.1111/mec.16716", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:23Z", "type": "Journal Article", "created": "2022-10-05", "title": "Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest", "description": "AbstractSoils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall) and the distribution of those already described is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies of mitochondrial genes, and other artefacts lead to taxonomic inflation, which compromise the reliability of biodiversity inventories. Here, we explore the potential of a bioinformatic approach to jointly \uffe2\uff80\uff9cdenoise\uffe2\uff80\uff9d and filter nonauthentic mitochondrial sequences from metabarcode reads to obtain reliable soil beetle inventories and address open questions in soil biodiversity research, such as the scale of dispersal constraints in different soil layers. We sampled cloud forest arthropod communities from 49 sites in the Anaga peninsula of Tenerife (Canary Islands). We performed whole organism community DNA (wocDNA) metabarcoding, and built a local reference database with COI barcode sequences of 310 species of Coleoptera for filtering reads and the identification of metabarcoded species. This resulted in reliable haplotype data after considerably reducing nuclear mitochondrial copies and other artefacts. Comparing our results with previous beetle inventories, we found: (i) new species records, potentially representing undescribed species; (ii) new distribution records, and (iii) validated phylogeographic structure when compared with traditional sequencing approaches. Analyses also revealed evidence for higher dispersal constraint within deeper soil beetle communities, compared to those closer to the surface. The combined power of barcoding and metabarcoding contribute to mitigate the important shortfalls associated with soil arthropod diversity data, and thus address unresolved questions for this vast biodiversity fraction.Cessation of xylem formation or wood growth (CWG) and onset of foliar senescence (OFS) are key autumn phenological events in temperate deciduous trees. Their timing is fundamental for the development and survival of trees, ecosystem nutrient cycling and the seasonal exchange of matter and energy between the biosphere and atmosphere, and affects the impact and feedback of forests to global change. A large-scale experimental effort and improved observational methods have allowed us to compare the timing of CWG and OFS for different deciduous tree species in Western Europe, particularly in silver birch, a pioneer species, and European beech, a late-succession species, at stands of different latitudes, of different levels of site fertility, for 2 years with contrasting meteorological and drought conditions, i.e., the low moderately dry 2017 and the extremely dry 2018. Specifically, we tested whether foliar senescence started before, after or concurrently with CWG. Onset of foliar senescence and CWG occurred generally between late September and early November, with larger differences across species and sites for OFS. Foliar senescence started concurrently with CWG in most cases, except for the drier 2018 and, for beech, at the coldest site, where OFS occurred significantly later than CWG. The behavior of beech in Spain, the southern edge of its European distribution, was unclear, with no CWG, but very low wood growth at the time of OFS. Our study suggests that OFS is generally triggered by the same drivers of CWG or when wood growth decreases in late summer, indicating an overarching mechanism of sink limitation as a possible regulator of the timing of foliar senescence.
", "keywords": ["0106 biological sciences", "listna senescenca", "nastajanje lesa", "cambium", "info:eu-repo/classification/udc/630*18:630*8", "autumn phenology", " xylem formation", " foliar senescence", " cambium", " chlorophyll", " radial growth", " wood", " decidiuous trees", " common aspen", " common beech", " pedunculate oak", " silver birch", "01 natural sciences", "jesenska fenologija", " nastajanje lesa", " listna senescenca", " kambij", " klorofil", " debelinska rast", " les", " listavci", " trepetlika", " navadna bukev", " dob", " navadna breza", "trepetlika", "Trees", "navadna bukev", "klorofil", "les", "chlorophyll", "pedunculate oak", "Biology", "info:eu-repo/classification/udc/630*1", "Ecosystem", "xylem formation", "kambij", "silver birch", "Temperature", "sink limitation", "04 agricultural and veterinary sciences", "dob", "navadna breza", "15. Life on land", "debelinska rast", "common beech", "listavci", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "Europe", "Plant Leaves", "radial growth", "jesenska fenologija", "common aspen", "Spain", "13. Climate action", "foliar senescence", "wood growth", "0401 agriculture", " forestry", " and fisheries", "Seasons", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "autumn phenology", "decidiuous trees", "wood"]}, "links": [{"href": "https://doi.org/10.1093/treephys/tpaa058"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Tree%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/treephys/tpaa058", "name": "item", "description": "10.1093/treephys/tpaa058", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/treephys/tpaa058"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-27T00:00:00Z"}}, {"id": "10.1016/j.jbiotec.2023.07.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:41Z", "type": "Journal Article", "created": "2023-07-25", "title": "Fast and reliable method to estimate global DNA methylation in plants and fungi with high-pressure liquid chromatography (HPLC)-ultraviolet detection and even more sensitive one with HPLC-mass spectrometry", "description": "DNA (Deoxyribonucleic acid) methylation is one of the epigenetic modifications of DNA, acting as a bridge between genotype and phenotype. Thus, disruption of DNA methylation pattern has tremendous consequences for organism development. Current methods to determine DNA methylation suffer from methodological drawbacks like high requirement of DNA and poor reproducibility of chromatograms. Here we provide a fast and reliable method using high-pressure liquid chromatography (HPLC)-ultraviolet (UV) detector and even more sensitive one with HPLC- mass spectrometry (MS) and we test this method with various plant and fungal DNA isolates. We optimized the preparation of the DNA degradation step to decrease background noise, we improved separation conditions to provide reliable and reproducible chromatograms and conditions to measure nucleotides in HPLC-MS. We showed that global DNA methylation level can be accurately and reproducibly measured with as little as 0.2\u00a0\u00b5M for HPLC-UV and 0.02\u00a0\u00b5M for HPLC-MS of methylated cytosine.", "keywords": ["Chromatography", "Plant DNA", "DNA methylation", "ta1183", "ta1182", "Fungi", "610", "Reproducibility of Results", "DNA Methylation", "Mass Spectrometry", "Fungal DNA", "chromatography", "DNA", " Fungal", "ta116", "Chromatography", " High Pressure Liquid"]}, "links": [{"href": "https://doi.org/10.1016/j.jbiotec.2023.07.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jbiotec.2023.07.008", "name": "item", "description": "10.1016/j.jbiotec.2023.07.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jbiotec.2023.07.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-09-01T00:00:00Z"}}, {"id": "10.1016/j.jflm.2018.03.016", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:44Z", "type": "Journal Article", "created": "2018-03-28", "title": "Poisoning histories in the Italian renaissance: The case of Pico Della Mirandola and Angelo Poliziano", "description": "Giovanni Pico della Mirandola and Angelo Poliziano were two of the most important humanists of the Italian Renaissance. They died suddenly in 1494 and their deaths have been for centuries a subject of debate. The exhumation of their remains offered the opportunity to study the cause of their death through a multidisciplinary research project. Anthropological analyses, together with documentary evidences, radiocarbon dating and ancient DNA analysis supported the identification of the remains attributed to Pico. Macroscopic examination did not reveal paleopathological lesions or signs related to syphilis. Heavy metals analysis, carried out on bones and mummified tissues, showed that in Pico's remains there were potentially lethal levels of arsenic, supporting the philosopher's poisoning theory reported by documentary sources. The arsenic concentrations obtained from analysis of Poliziano's remains, are probably more related to an As chronic exposure or diagenetic processes rather than poisoning.", "keywords": ["Male", "Microscopy", "Spectrum Analysis", "Environmental Exposure", "Mummies", "06 humanities and the arts", "Bone and Bones", "Arsenic", "Forensic Toxicology", "03 medical and health sciences", "0302 clinical medicine", "Italy", "Arsenic Poisoning", "Microscopy", " Electron", " Scanning", "Humans", "0601 history and archaeology", "Carbon Radioisotopes", "Ancient DNA; Angelo Poliziano; Arsenic poisoning; Girolamo benivieni; Pico della Mirandola; Radiocarbon dating", "DNA", " Ancient", "History", " 15th Century"]}, "links": [{"href": "https://doi.org/10.1016/j.jflm.2018.03.016"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Forensic%20and%20Legal%20Medicine", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jflm.2018.03.016", "name": "item", "description": "10.1016/j.jflm.2018.03.016", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jflm.2018.03.016"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-05-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2010.11.073", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:44Z", "type": "Journal Article", "created": "2010-11-26", "title": "Genotoxic Endpoints In The Earthworms Sub-Lethal Assay To Evaluate Natural Soils Contaminated By Metals And Radionuclides", "description": "Eisenia andrei was exposed, for 56 days, to a contaminated soil from an abandoned uranium mine and to the natural reference soil LUFA 2.2. The organisms were sampled after 0, 1, 2, 7, 14 and 56 days of exposure, to assess metals bioaccumulation, coelomocytes DNA integrity and cytotoxicity. Radionuclides bioaccumulation and growth were also determined at 0 h, 14 and 56 days of exposure. Results have shown the bioaccumulation of metals and radionuclides, as well as, growth reduction, DNA damages and cytotoxicity in earthworms exposed to contaminated soil. The usefulness of the comet assay and flow cytometry, to evaluate the toxicity of contaminants such as metals and radionuclides in earthworms are herein reported. We also demonstrated that DNA strand breakage and immune cells frequency are important endpoints to be employed in the earthworm reproduction assay, for the evaluation of soil geno and cytotoxicity, as part of the risk assessment of contaminated areas. This is the first study that integrates DNA damage and cytotoxicity evaluation, growth and bioaccumulation of metals and radionuclides in a sub lethal assay, for earthworms exposed to soil contaminated with metals and radionuclides.", "keywords": ["Eisenia andrei", "Cytotoxicity", "DNA damages", "Flow Cytometry", "01 natural sciences", "3. Good health", "Metals", "Animals", "Soil Pollutants", "Oligochaeta", "Radionuclides", "DNA Damage", "Mutagens", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2010.11.073"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2010.11.073", "name": "item", "description": "10.1016/j.jhazmat.2010.11.073", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2010.11.073"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-02-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2024.134885", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:45Z", "type": "Journal Article", "created": "2024-06-12", "title": "Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes", "description": "Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.", "keywords": ["Bacteria", "Antibiotic resistance", "Microbiota", "Water Pollution", "Metagenome assembled genomes", "Drug Resistance", " Microbial", "Horizontal gene transfer", "Wastewater", "extracellular DNA; antibiotic resistance; metagenome assembled genomes; transformation; horizontal gene transfer", "Transformation", "Anti-Bacterial Agents", "Lakes", "Extracellular DNA", "Genes", " Bacterial", "Drug Resistance", " Bacterial", "Water Microbiology", "Plasmids"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/1115155/2/Sivalingam%20et%20al%202024.pdf"}, {"href": "https://doi.org/10.1016/j.jhazmat.2024.134885"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2024.134885", "name": "item", "description": "10.1016/j.jhazmat.2024.134885", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2024.134885"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2006.08.033", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:54Z", "type": "Journal Article", "created": "2006-10-05", "title": "Changes In Lead Availability Affect Bacterial Community Structure But Not Basal Respiration In A Microcosm Study With Forest Soils", "description": "This study investigates the effects of Pb during time on the bacterial communities of forest soils using water-extractable Pb concentrations in the soil solution as predictors of Pb bioavailability. In a microcosm experiment we applied increasing concentrations of Pb(NO(3))(2) solutions (0.5, 2, 8, 32 mM) to 5 forest soils of pH<5 and to a calcareous soil of pH>6.5. Sampling of the microcosms was performed after 3, 30 and 90 days of incubation. Community analysis included basal respiration rates and changes in the structure of the bacterial communities through T-RFLP fingerprinting. We also investigated functional stability in terms of resistance, expressed as the effects on basal respiration after 3 days of incubation, and of resilience, expressed as the recovery of bacterial community structure and of respiration rates after 90 days of incubation. Water-extractable Pb increased with time in most of the soils, in parallel with an increase of water-extractable dissolved organic carbon (DOC). The increased concentrations slightly affected bacterial community structure, although OTU (operational taxonomic unit) richness was not significantly reduced with Pb concentrations in any of the soils. The highest Pb treatment (32 mM) caused significant effects on basal respiration in some of the acidic soils, but no clear trend was observed in relation to increased Pb bioavailability with time. Resistance to Pb additions was evident in five of the six soils, but only two showed resilience after 90 days. This is the first study showing the effects of time on Pb bioavailability in soils and on the resulting reactions of the soil microbial communities.", "keywords": ["DNA", " Bacterial", "Nitrates", "04 agricultural and veterinary sciences", "15. Life on land", "Models", " Biological", "6. Clean water", "Trees", "Oxygen", "RNA", " Bacterial", "Soil", "Lead", "RNA", " Ribosomal", " 16S", "Soil Pollutants", "0401 agriculture", " forestry", " and fisheries", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2006.08.033"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2006.08.033", "name": "item", "description": "10.1016/j.scitotenv.2006.08.033", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2006.08.033"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-12-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2009.08.045", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:55Z", "type": "Journal Article", "created": "2009-09-23", "title": "Application Of Temporal Temperature Gradient Gel Electrophoresis For Characterisation Of Fungal Endophyte Communities Of Salix Caprea L. In A Heavy Metal Polluted Soil", "description": "Fungal endophytes can affect the heavy metal uptake of their host plants and increase the tolerance of their host plants to heavy metal stress. Therefore, in the present study, a wide-range screening of the fungal endophyte communities was conducted to determine the fungal distribution and diversity on S. caprea roots on a metal polluted site. Fungal communities were screened using amplification with the 5.8S-ITS2-28S part of the rDNA operon, with the resulting amplicons analysed by temporal temperature gradient gel electrophoresis (TTGE) and sequencing. This technique is reproducible and shows good coverage of ascomycete and basidiomycete taxa, as 68% and 32% of all of the sequences, respectively. No clear shift in fungal ITS-TTGE profiles from S. caprea roots was seen along the secondary succession stages. Ascomycetes dominated the more polluted plots, while there was a greater diversity of basidiomycetes in the less polluted and control plots, suggesting greater tolerance of ascomycetes in comparison with basidiomycete fungi. The high diversity of DSEs was confirmed at the highly metal-enriched locations, with species belonging to the genera Phialophora, Phialocephala and Leptodontidium. Furthermore, the DSE colonisation of S. caprea roots and the frequency of the sequences showing affinity towards DSE genus Phialophora, showed good correspondence with soil Pb, Cd and plant-available P concentrations, possibly indicating that DSEs improve metal tolerance of willows to high heavy metal contamination.", "keywords": ["Electrophoresis", " Agar Gel", "0301 basic medicine", "dark septate endophytes", "Fungi", "Temperature", "mycorrhiza", "Salix", "04 agricultural and veterinary sciences", "info:eu-repo/classification/udc/581", "15. Life on land", "heavy metal pollution", "community fingerprinting", "Soil", "03 medical and health sciences", "13. Climate action", "Metals", " Heavy", "Soil Pollutants", "0401 agriculture", " forestry", " and fisheries", "DNA", " Fungal", "Phylogeny", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2009.08.045"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2009.08.045", "name": "item", "description": "10.1016/j.scitotenv.2009.08.045", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2009.08.045"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-12-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2021.108357", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:14Z", "type": "Journal Article", "created": "2021-07-10", "title": "A critical perspective on interpreting amplicon sequencing data in soil ecological research", "description": "Abstract Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation, and availability to improve the rigor of future studies.", "keywords": ["2. Zero hunger", "0301 basic medicine", "Soil microbial diversity", "0303 health sciences", "Soil metabarcoding", "DIVERSITY", "Ecology; Soil microbes; Amplicon sequencing", "Compositional data", "SCALE SPATIAL HETEROGENEITY", "15. Life on land", "BIOMASS", "03 medical and health sciences", "106026 \u00d6kosystemforschung", "Soil complexity", "CARBON-USE EFFICIENCY", "BACTERIA", "DNA EXTRACTION", "MICROORGANISMS", "MICROBIAL COMMUNITIES", "106026 Ecosystem research", "RIBOSOMAL-RNA", "Amplicon sequencing", "Soil microorganisms", "GENERATION"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2021.108357"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2021.108357", "name": "item", "description": "10.1016/j.soilbio.2021.108357", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2021.108357"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-01T00:00:00Z"}}, {"id": "10.1016/j.still.2005.08.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:18Z", "type": "Journal Article", "created": "2005-09-09", "title": "Soil Aggregation And Bacterial Community Structure As Affected By Tillage And Cover Cropping In The Brazilian Cerrados", "description": "Microbial-based indicators of soil quality are believed to be more dynamic than those based on physical and chemical properties. Recent developments in molecular biology based techniques have led to rapid and reliable tools to characterize microbial community structures. We determined the effects of conventional and no-tillage in cropping systems with and without cover crops on bacterial community structure, total organic carbon (TOC) and soil aggregation. Tillage and rotation did not affect TOC from bulk soil. However, TOC was greater in the largest aggregate size class (7.98-19 mm), and had greater mean-weight diameter under no-tillage than under conventional tillage in the 0-5 cm soil layer. Soil bacterial community structure, based on denaturing gradient gel electrophoresis of polymerase chain reaction amplified DNA (PCR/DGGE) using two different genes as biomarkers, 16S rRNA and rpoB genes, indicated different populations in response to cultivation, tillage and depth, but not due to cover cropping. Soil bacterial community structure and meanweight diameter of soil aggregates indicated alterations in soil conditions due to tillage system. (c) 2005 Elsevier B.V. All rights reserved.
", "keywords": ["2. Zero hunger", "GENES", "Cerrados", "16S RIBOSOMAL-RNA", "no-tillage", "04 agricultural and veterinary sciences", "15. Life on land", "DGGE profiling", "SUSTAINABILITY", "PCR", "16S rDNA", "GRADIENT GEL-ELECTROPHORESIS", "MANAGEMENT", "0401 agriculture", " forestry", " and fisheries", "NO-TILLAGE", "HETEROGENEITY", "DGGE", "soil structure", "rpoB", "MICROBIAL DIVERSITY"]}, "links": [{"href": "https://doi.org/10.1016/j.still.2005.08.001"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20and%20Tillage%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.still.2005.08.001", "name": "item", "description": "10.1016/j.still.2005.08.001", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.still.2005.08.001"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-11-01T00:00:00Z"}}, {"id": "10.1016/j.syapm.2020.126149", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:28Z", "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": "10.1016/j.syapm.2012.10.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:28Z", "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.watres.2019.114916", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:30Z", "type": "Journal Article", "created": "2019-07-25", "title": "Removal of extracellular free DNA and antibiotic resistance genes from water and wastewater by membranes ranging from microfiltration to reverse osmosis", "description": "The final publication is available via https://doi.org/10.1016/j.watres.2019.114916.", "keywords": ["Osmosis", "0211 other engineering and technologies", "membrane filtration", "Wastewater treatment", "02 engineering and technology", "water reuse", "Wastewater", "01 natural sciences", "Water Purification", "12. Responsible consumption", "Water reuse", "antibiotic resistance genes", "free extracellular DNA", "Antibiotic resistance genes", "11. Sustainability", "Humans", "Drinking water treatment", "0105 earth and related environmental sciences", "Water", "Drug Resistance", " Microbial", "DNA", "drinking water treatment", "6. Clean water", "Anti-Bacterial Agents", "wastewater treatment", "Genes", " Bacterial", "Free extracellular DNA", "Membrane filtration"]}, "links": [{"href": "https://doi.org/10.1016/j.watres.2019.114916"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.watres.2019.114916", "name": "item", "description": "10.1016/j.watres.2019.114916", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.watres.2019.114916"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-01T00:00:00Z"}}, {"id": "10.1038/srep03829", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:03Z", "type": "Journal Article", "created": "2014-01-23", "title": "Rapid Recovery Of Soil Bacterial Communities After Wildfire In A Chinese Boreal Forest", "description": "AbstractFires 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 < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties.
", "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": "10.1371/journal.pone.0076447", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:50Z", "type": "Journal Article", "created": "2013-09-26", "title": "The Arbuscular Mycorrhizal Fungal Community Response To Warming And Grazing Differs Between Soil And Roots On The Qinghai-Tibetan Plateau", "description": "Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most plant species in terrestrial ecosystems, and are affected by environmental variations. To reveal the impact of disturbance on an AM fungal community under future global warming, we examined the abundance and community composition of AM fungi in both soil and mixed roots in an alpine meadow on the Qinghai-Tibetan Plateau, China. Warming and grazing had no significant effect on AM root colonization, spore density and extraradical hyphal density. A total of 65 operational taxonomic units (OTUs) of AM fungi were identified from soil and roots using molecular techniques. AM fungal OTU richness was higher in soil (54 OTUs) than in roots (34 OTUs), and some AM fungi that differed between soil and roots, showed significantly biased occurrence to warming or grazing. Warming and grazing did not significantly affect AM fungal OTU richness in soil, but warming with grazing significantly increased AM fungal OTU richness in roots compared to the grazing-only treatment. Non-metric multidimensional scaling analysis showed that the AM fungal community composition was significantly different between soil and roots, and was significantly affected by grazing in roots, whereas in soil it was significantly affected by warming and plant species richness. The results suggest that the AM fungal community responds differently to warming and grazing in soil compared with roots. This study provides insights into the role of AM fungi under global environmental change scenarios in alpine meadows of the Qinghai-Tibetan Plateau.", "keywords": ["0106 biological sciences", "Hot Temperature", "Science", "Molecular Sequence Data", "Population Dynamics", "Global Warming", "Plant Roots", "Polymerase Chain Reaction", "01 natural sciences", "Species Specificity", "Mycorrhizae", "Herbivory", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Analysis of Variance", "Base Sequence", "Models", " Genetic", "Altitude", "Q", "R", "Bayes Theorem", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Spores", " Fungal", "15. Life on land", "Biota", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Polymorphism", " Restriction Fragment Length", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0076447"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0076447", "name": "item", "description": "10.1371/journal.pone.0076447", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0076447"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-09-26T00:00:00Z"}}, {"id": "10.1038/s41598-025-00173-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:02Z", "type": "Journal Article", "created": "2025-05-08", "title": "Enhanced understanding of nitrogen fixing bacteria through DNA extraction with polyvinylidene fluoride membrane", "description": "AbstractThe rhizobiota, particularly nitrogen-fixing bacteria, play a crucial role in plant functioning by providing essential nutrients and defense against pathogens. This study investigated the diversity of nitrogen-fixing bacteria in a relatively understudied habitat: technosoils developed from industrial soda production. To analyze the bacterial diversity in the rhizosphere soils of wheat (Triticum aestivum L.) and aster (Tripolium pannonicum Jacq.), regions of the nifH gene were amplified and sequenced from the resident bacterial communities. A polyvinylidene fluoride (PVDF) membrane was employed for metagenomic DNA extraction, enhancing the detection of nitrogen-fixing bacteria. Prior to standard DNA extraction, an enrichment step was conducted in nitrogen-free JMV medium at 26\uffc2\uffa0\uffc2\uffb0C for 24\uffc2\uffa0h, with a modification that replaced soil with the PVDF membrane. This approach enabled a more comprehensive analysis of the rhizosphere bacterial community, revealing that unique amplicon sequence variants (ASVs) in aster and wheat membrane samples accounted for a notable proportion of all ASVs in the dataset (8.5% and 23%, respectively) that were not captured using the standard method. Additionally, our findings demonstrated higher alpha diversity of nitrogen-fixing bacteria in the wheat rhizosphere compared to the aster rhizosphere. In wheat, the dominant genus was Insolitispirillum (38.80%), followed by unclassified genera within Gammaproteobacteria (9.76%) and Rhodospirillaceae (4.74%). In contrast, the aster rhizosphere was predominantly occupied by Azotobacter (95.69%).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 (<100\uffe2\uff80\uff89mm annual rain) to the Mediterranean forests in the north (>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.
", "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.2007.89", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:53Z", "type": "Journal Article", "created": "2007-10-25", "title": "The Effect Of Experimental Warming On The Root-Associated Fungal Community Of Salix Arctica", "description": "AbstractThe effect of experimental warming on the root-associated fungal community of arctic willow (Salix arctica) was studied in three distinct habitats at a tundra site in the Canadian High Arctic. Plots were passively warmed for 5\uffe2\uff80\uff937 years using open-top chambers and compared to control plots at ambient temperature. Fungal communities were assessed using terminal restriction fragment length polymorphisms. We found the following: (1) the root-associated fungal community in these high arctic tundra habitats is highly diverse; (2) site and soil characteristics are the most important drivers of community structure and (3) warming increased the density of different genotypes on individual root sections but has not (yet) affected the composition, richness or evenness of the community. The change in genotype density in the warmed plots was associated with an increase in PCR amplification efficiency, suggesting that increased C allocation belowground is increasing the overall biomass of the fungal community.
", "keywords": ["0106 biological sciences", "0301 basic medicine", "Canada", "Fungi", "Salix", "15. Life on land", "Plant Roots", "01 natural sciences", "Heating", "03 medical and health sciences", "Cluster Analysis", "DNA", " Fungal", "Ecosystem", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"], "contacts": [{"organization": "Gregory H. R. Henry, Keith N. Egger, Kei E. Fujimura,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1038/ismej.2007.89"}, {"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.2007.89", "name": "item", "description": "10.1038/ismej.2007.89", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2007.89"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-10-25T00:00:00Z"}}, {"id": "10.1038/ismej.2010.3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:53Z", "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/nature02051", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:54Z", "type": "Journal Article", "created": "2003-10-29", "title": "Motor Neuron Columnar Fate Imposed By Sequential Phases Of Hox-C Activity", "description": "The organization of neurons into columns is a prominent feature of central nervous system structure and function. In many regions of the central nervous system the grouping of neurons into columns links cell-body position to axonal trajectory, thus contributing to the establishment of topographic neural maps. This link is prominent in the developing spinal cord, where columnar sets of motor neurons innervate distinct targets in the periphery. We show here that sequential phases of Hox-c protein expression and activity control the columnar differentiation of spinal motor neurons. Hox expression in neural progenitors is established by graded fibroblast growth factor signalling and translated into a distinct motor neuron Hox pattern. Motor neuron columnar fate then emerges through cell autonomous repressor and activator functions of Hox proteins. Hox proteins also direct the expression of genes that establish motor topographic projections, thus implicating Hox proteins as critical determinants of spinal motor neuron identity and organization.", "keywords": ["Homeodomain Proteins", "Motor Neurons", "0301 basic medicine", "0303 health sciences", "Fibroblast Growth Factor 8", "Stem Cells", "Gene Expression Regulation", " Developmental", "Mitosis", "Cell Differentiation", "Chick Embryo", "Neoplasm Proteins", "3. Good health", "DNA-Binding Proteins", "Fibroblast Growth Factors", "Mice", "03 medical and health sciences", "Spinal Cord", "Animals", "RNA", " Messenger", "Body Patterning", "Signal Transduction"], "contacts": [{"organization": "Thomas M. Jessell, Jeh-Ping Liu, Jeremy S. Dasen,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1038/nature02051"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/nature02051", "name": "item", "description": "10.1038/nature02051", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/nature02051"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-10-01T00:00:00Z"}}, {"id": "10.1038/s41467-019-10373-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:56Z", "type": "Journal Article", "created": "2019-05-30", "title": "A few Ascomycota taxa dominate soil fungal communities worldwide", "description": "AbstractDespite having key functions in terrestrial ecosystems, information on the dominant soil fungi and their ecological preferences at the global scale is lacking. To fill this knowledge gap, we surveyed 235 soils from across the globe. Our findings indicate that 83 phylotypes (<0.1% of the retrieved fungi), mostly belonging to wind dispersed, generalist Ascomycota, dominate soils globally. We identify patterns and ecological drivers of dominant soil fungal taxa occurrence, and present a map of their distribution in soils worldwide. Whole-genome comparisons with less dominant, generalist fungi point at a significantly higher number of genes related to stress-tolerance and resource uptake in the dominant fungi, suggesting that they might be better in colonising a wide range of environments. Our findings constitute a major advance in our understanding of the ecology of fungi, and have implications for the development of strategies to preserve them and the ecosystem functions they provide.White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n\uffe2\uff80\uff89=\uffe2\uff80\uff8950, 451\uffe2\uff80\uff89Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.
", "keywords": ["Repetitive Sequences", " Nucleic Acid/genetics", "0301 basic medicine", "[SDV]Life Sciences [q-bio]", "Plant Roots/genetics", "Gene Dosage", "Plant Science", "Crop", "Alkaloids/chemistry", "Plant Roots", "Gene", "Repetitive Sequences", "630", "Agricultural and Biological Sciences", "Domestication", "Soil", "Models", "Symbiotic Nitrogen Fixation in Legumes", "Gene Duplication", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_3224", "Plant Proteins/metabolism", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Genome", "Q", "http://aims.fao.org/aos/agrovoc/c_27583", "Life Sciences", "Transcriptome/genetics", "http://aims.fao.org/aos/agrovoc/c_92382", "Polymorphism", " Single Nucleotide/genetics", "Lupinus", "[SDV] Life Sciences [q-bio]", "Protein Crop", "Seeds", "http://aims.fao.org/aos/agrovoc/c_5956", "White (mutation)", "Single Nucleotide/genetics", "Sequence Analysis", "Genome", " Plant", "expression des g\u00e8nes", "http://aims.fao.org/aos/agrovoc/c_4464", "Synteny/genetics", "Evolution", "Lupin Seeds", "Science", "Centromere", "Lupinus/genetics", "Polymorphism", " Single Nucleotide", "Article", "g\u00e9nomique", "Evolution", " Molecular", "Evolution and Nutritional Properties of Lupin Seeds", "physiologie v\u00e9g\u00e9tale", "03 medical and health sciences", "Alkaloids", "Genetic", "Nucleic Acid/genetics", "Seeds/physiology", "Centromere/genetics", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Polymorphism", "Biology", "Ecology", " Evolution", " Behavior and Systematics", "Repetitive Sequences", " Nucleic Acid", "Sequence assembly", "http://aims.fao.org/aos/agrovoc/c_25189", "Ecotype", "Models", " Genetic", "g\u00e9nome", "Botany", "Molecular", "Genetic Variation", "Molecular Sequence Annotation", "Plant", "DNA", "Sequence Analysis", " DNA", "s\u00e9quence nucl\u00e9otidique", "15. Life on land", "http://aims.fao.org/aos/agrovoc/c_27527", "Agronomy", "Plant Leaves", "Evolution and Ecology of Endophyte-Grass Symbiosis", "Lupinus albus", "FOS: Biological sciences", "Genomic Structural Variation", "Plant Leaves/metabolism", "Gene expression", "Transcriptome", "am\u00e9lioration des plantes"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-14197-9.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-14197-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-14197-9", "name": "item", "description": "10.1038/s41467-019-14197-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-14197-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-24T00:00:00Z"}}, {"id": "10.1038/s41586-023-05791-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:00Z", "type": "Journal Article", "created": "2023-03-08", "title": "The giant diploid faba genome unlocks variation in a global protein crop", "description": "AbstractIncreasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia fabaL.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13\uffe2\uff80\uff89Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the\uffc2\uffa0improvement of sustainable protein production across the\uffc2\uffa0Mediterranean, subtropical and northern temperate agroecological zones.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.Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM) and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Biota", "Article", "6. Clean water", "Genes", " Archaeal", "03 medical and health sciences", "Ammonia", "Genes", " Bacterial", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep28981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep28981", "name": "item", "description": "10.1038/srep28981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep28981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-30T00:00:00Z"}}, {"id": "10.1093/jambio/lxac048", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:39Z", "type": "Journal Article", "created": "2023-03-17", "title": "Two species-specific TaqMan-based quantitative polymerase chain reaction assays for the detection in soil ofPaenibacillus polymyxainocula", "description": "AbstractAimsThe increasingly widespread use of beneficial microbial inocula in agriculture gives rise to two primary needs: i) the assessment of the environmental risk, i.e. their impact on local soil microbiome and soil properties; ii) being able to track them and monitor their persistence and fate to both optimize their formulation and application method. In previous years, PCR-based methods have detected bacterial or fungal bioinoculant at the species or strain level. However, the selective detection, quantification, and monitoring of target microbial species in a complex ecosystem such as soil require that the tests possess high specificity and sensitivity.
Methods and resultsThe work proposes a quantitative real-time PCR detection method using TaqMan chemistry, showing high specificity and sensitivity for the Paenibacillus polymyxa K16 strain. The primer and probe sets were designed using the polymyxin gene cluster targeting pmxC and pmxE sequences. Validation tests showed that these assays allowed a discriminant and specific detection of P. polymyxa K16 in soil.
ConclusionThe TaqMan-assay developed could thus ensure the necessary level of discrimination required by commercial and regulatory purposes to detect and monitor the bioinoculant in soil. The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus Rhodococcus proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably Variovorax , a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from Variovorax in a heterologous host. A Variovorax strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "QH301 Biology", "Biological Sciences", "15. Life on land", "Mixed Function Oxygenases", "Comamonadaceae", "03 medical and health sciences", "Biodegradation", " Environmental", "Hemiterpenes", "Populus", "13. Climate action", "Butadienes", "Rhodococcus", "Metagenomics", "Genome", " Bacterial", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/69197/1/Published_manuscript.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.1812668115"}, {"href": "https://repository.essex.ac.uk/23631/1/1812668115.full.pdf"}, {"href": "https://doi.org/10.1073/pnas.1812668115"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.1812668115", "name": "item", "description": "10.1073/pnas.1812668115", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.1812668115"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-29T00:00:00Z"}}, {"id": "10.1109/lcomm.2018.2868666", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:51Z", "type": "Journal Article", "created": "2018-09-05", "title": "Asymptotically Optimal Codes Correcting Fixed-Length Duplication Errors in DNA Storage Systems", "description": "Open AccessTo appear in IEEE Communications Letters", "keywords": ["FOS: Computer and information sciences", "Discrete Mathematics (cs.DM)", "bounds on codes", "DNA storage", "Computer Science - Information Theory", "Information Theory (cs.IT)", "synchronization error", "repetition error", "sticky insertion", "0102 computer and information sciences", "02 engineering and technology", "01 natural sciences", "tandem duplication", "0202 electrical engineering", " electronic engineering", " information engineering", "94B20", " 94B25", " 94B50", " 94B65", " 68P20", " 68P30", " 68R05", "Computer Science - Discrete Mathematics"]}, "links": [{"href": "https://doi.org/10.1109/lcomm.2018.2868666"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/IEEE%20Communications%20Letters", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1109/lcomm.2018.2868666", "name": "item", "description": "10.1109/lcomm.2018.2868666", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1109/lcomm.2018.2868666"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-01T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=DNA&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=DNA&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=DNA&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=DNA&offset=50", "hreflang": "en-US"}], "numberMatched": 171, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-04-05T04:12:28.895424Z"}