Anthropogenic pressures on tropical forests are rapidly intensifying, but our understanding of their implications for biological diversity is still very limited, especially with regard to soil biota, and in particular soil bacterial communities. Here we evaluated bacterial community composition and diversity across a gradient of land use intensity in the eastern Amazon from undisturbed primary forest, through primary forests varyingly disturbed by fire, regenerating secondary forest, pasture, and mechanized agriculture. Soil bacteria were assessed by paired\uffe2\uff80\uff90end Illumina sequencing of 16S rRNA gene fragments (V4 region). The resulting sequences were clustered into operational taxonomic units (OTU) at a 97% similarity threshold. Land use intensification increased the observed bacterial diversity (both OTU richness and community heterogeneity across space) and this effect was strongly associated with changes in soil pH. Moreover, land use intensification and subsequent changes in soil fertility, especially pH, altered the bacterial community composition, with pastures and areas of mechanized agriculture displaying the most contrasting communities in relation to undisturbed primary forest. Together, these results indicate that tropical forest conversion impacts soil bacteria not through loss of diversity, as previously thought, but mainly by imposing marked shifts on bacterial community composition, with unknown yet potentially important implications for ecological functions and services performed by these communities.
", "keywords": ["Rios de composi\u00e7\u00e3o de comunidade bacteriana", "2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "550", "Bacteria", "Biodiversidade subterr\u00e2nea", "Agriculture", "Biodiversity", "Forests", "15. Life on land", "Below\u2010ground biodiversity", "High\u2010throughput sequencing", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Sequenciamento de alto rendimento", "Rivers of bacterial community composition", "Soil Microbiology"]}, "links": [{"href": "https://eprints.lancs.ac.uk/id/eprint/82660/1/de_Carvalho_et_al_2016_raw_pdf.pdf"}, {"href": "https://doi.org/10.1002/ecy.1513"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/ecy.1513", "name": "item", "description": "10.1002/ecy.1513", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/ecy.1513"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-09-09T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2021.126527", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:54Z", "type": "Journal Article", "created": "2021-06-29", "title": "Reduction of antibiotic resistance determinants in urban wastewater by ozone: Emphasis on the impact of wastewater matrix towards the inactivation kinetics, toxicity and bacterial regrowth", "description": "This study investigated the impact of bench-scale ozonation on the inactivation of total cultivable and antibiotic-resistant bacteria (faecal coliforms, Escherichia coli, Pseudomonas aeruginosa, Enterococcus spp., and total heterotrophs), and the reduction of gene markers (16S rRNA and intl1) and antibiotic resistance genes (qacE\u03941, sul1, aadA1 and dfrA1) indigenously present in wastewater effluents treated by membrane bioreactor (MBR) or conventional activated sludge (CAS). The Chick-Watson model-predicted ozone exposure (CT) requirements, showed that higher CT values were needed for CAS- than MBR-treated effluents to achieve a 3-log reduction of each microbial group, i.e., ~30 and 10 gO3 min gDOC-1 respectively. Ozonation was efficient in inactivating the examined antibiotic-resistant bacteria, and no bacterial regrowth was observed after 72\u00a0h. The genes abundance decreased significantly by ozone, but an increase in their abundance was detected 72\u00a0h after storage of the treated samples. A very low removal of DOC was achieved and at the same time phyto- and eco-toxicity increased after the ozonation treatment in both wastewater matrices. The gene abundance, regrowth and toxicity results of this study may be of high environmental significance for comprehensive evaluation of ozone and may guide future studies in assessing these parameters for other oxidants/disinfectants.", "keywords": ["Bacteria", "0211 other engineering and technologies", "Drug Resistance", " Microbial", "02 engineering and technology", "Wastewater", "Waste Disposal", " Fluid", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Disinfection", "Kinetics", "Ozone", "Genes", "13. Climate action", "Ozonation", "Phytotoxicity", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Ecotoxicity", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2021.126527"}, {"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.2021.126527", "name": "item", "description": "10.1016/j.jhazmat.2021.126527", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2021.126527"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-01T00:00:00Z"}}, {"id": "10.1016/j.envint.2020.106190", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:18Z", "type": "Journal Article", "created": "2020-10-26", "title": "Treated wastewater irrigation promotes the spread of antibiotic resistance into subsoil pore-water", "description": "In the present study, we investigated the impact of treated wastewater (TWW) irrigation on the prevalence of antibiotic resistance genes (ARGs) in subsoil pore-water, a so-far under-appreciated matrix. We hypothesized that TWW irrigation increases ARG prevalence in subsoil pore-water. This hypothesis was tested using a multiphase approach, which consisted of sampling percolated subsoil pore-water from lysimeter-wells of a real-scale TWW-irrigated field, operated for commercial farming practices, and controlled, laboratory microcosms irrigated with freshwater or TWW. We monitored the abundance of six selected ARGs (sul1, blaOXA-58, tetM, qnrS, blaCTX-M-32 and blaTEM), the intI1 gene associated with mobile genetic elements and an indicator for anthropogenic pollution and bacterial abundance (16S rRNA gene) by qPCR. The bacterial load of subsoil pore water was independent of both, irrigation intensity in the field study and irrigation water type in the microcosms. Among the tested genes in the field study, sul1 and intI1 exhibited constantly higher relative abundances. Their abundance was further positively correlated with increasing irrigation intensity. Controlled microcosm experiments verified the observed field study results: the relative abundance of several genes, including sul1 and intI1, increased significantly when irrigating with TWW compared to freshwater irrigation. Overall, TWW irrigation promoted the spread of ARGs and intI1 in the subsoil pore-water, while the bacterial load was maintained. The combined results from the real-scale agricultural field and the controlled lab microcosms indicate that the dissemination of ARGs in various subsurface environments needs to be taken into account during TWW irrigation scenarios.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Agricultural Irrigation", "Antibiotic resistance", "Water", "Subsoil pore-water", "Drug Resistance", " Microbial", "Wastewater", "Wastewater reuse", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Environmental sciences", "qPCR", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "ARGs", "GE1-350", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envint.2020.106190"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environment%20International", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envint.2020.106190", "name": "item", "description": "10.1016/j.envint.2020.106190", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envint.2020.106190"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-01T00:00:00Z"}}, {"id": "10.1007/s00248-007-9276-4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:14:30Z", "type": "Journal Article", "created": "2007-07-17", "title": "Comparison Of Soil Bacterial Communities Under Diverse Agricultural Land Management And Crop Production Practices", "description": "The composition and structure of bacterial communities were examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Five land management programs were initiated in July 2000: conventional, organic, continuous removal of vegetation (disk fallow), undisturbed (weed fallow), and bahiagrass pasture (Paspalum notatum var Argentine). Similar levels in the diversity of bacterial 16S rDNA amplicons were detected in soil samples collected from organically and conventionally managed plots 3 and 4 years after initiation of land management programs, whereas significantly lower levels of diversity were observed in samples collected from bahiagrass pasture. Differences in diversity were attributed to effects on how the relative abundance of individual amplicons were distributed (evenness) and not on the total numbers of bacterial 16S rDNA amplicons detected (richness). Similar levels of diversity were detected among all land management programs in soil samples collected after successive years of tomato (Lycopersicon esculentum) cultivation. A different trend was observed after a multivariate examination of the similarities in genetic composition among soil bacterial communities. After 3 years of land management, similarities in genetic composition of soil bacterial communities were observed in plots where disturbance was minimized (bahiagrass and weed fallow). The genetic compositions in plots managed organically were similar to each other and distinct from bacterial communities in other land management programs. After successive years of tomato cultivation and damage from two major hurricanes, only the composition of soil bacterial communities within organically managed plots continued to maintain a high degree of similarity to each other and remain distinct from other bacterial communities. This study reveals the effects of agricultural land management practices on soil bacterial community composition and diversity in a large-scale, long-term replicated study where the effect of soil type on community attributes was removed.", "keywords": ["Crops", " Agricultural", "DNA", " Bacterial", "2. Zero hunger", "Analysis of Variance", "Conservation of Natural Resources", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "DNA", " Ribosomal", "Polymerase Chain Reaction", "Solanum lycopersicum", "RNA", " Ribosomal", " 16S", "0401 agriculture", " forestry", " and fisheries", "Cloning", " Molecular", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-007-9276-4"}, {"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/s00248-007-9276-4", "name": "item", "description": "10.1007/s00248-007-9276-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-007-9276-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-07-07T00:00:00Z"}}, {"id": "10.1007/s00248-013-0322-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:14:30Z", "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/s00253-016-7736-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:14:30Z", "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": {"license": "Closed Access", "updated": "2026-04-13T16:14:41Z", "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": "2026-04-13T16:14:42Z", "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/s11274-011-0809-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:17Z", "type": "Journal Article", "created": "2011-06-15", "title": "Soil Bacterial Community Composition And Diversity Respond To Cultivation In Karst Ecosystems", "description": "Soil microorganisms play vital roles in recovering and maintaining the health of ecosystems, particularly in fragile Karst ecosystems that are easily degraded after cultivation. We investigated the composition and diversity of soil bacterial communities, based on RFLP and 16S rDNA sequencing, in a cropland, a naturally revegetated land with former cultivation disturbance and a primeval forest in the subtropical Karst of southwest China. Our results illustrated that Proteobacteria accounted for 44.8% of the 600 tested clones, making it the most dominant phylum observed. This phylum was followed by Acidobacteria and Planctomycetes for the three Karst soils analyzed. Compared with the primeval forest soil, the proportions of Proteobacteria were decreased by 30.2 and 37.9%, while Acidobacteria increased by 93.9 and 87.9%, and the Shannon-Wiener diversity indices and the physicochemical parameters declined in the cropland and the revegetated land, respectively. Among the three soils, the proportion of dominant bacterial phyla and the diversity indices in the revegetated land were similar to the cropland, implying the bacterial community in the cropland was relatively stable, and the after-effects of cultivation were difficult to eliminate. However, similar distributions of the four Proteobacteria subphyla were observed between the revegetated land and the primeval forest soil. Furthermore, the proportion of Rhizobiales belonging to \u03b1-Proteobacteria was sharply decreased with cultivation compared to the primeval forest soil, while a small cluster of Rhizobiales recurred with vegetation recovery. These results indicated that although the subphyla of the dominant bacterial phylum had some positive responses to 20\u00a0years of vegetation recovery, it is a slow process. Our results suggest that priority should be given to conserve the primeval forest and inoculation of functional microorganisms on the basis of vegetation recovery may be more effective for the restoration of Karst ecosystems after cultivation.", "keywords": ["2. Zero hunger", "0301 basic medicine", "China", "0303 health sciences", "Bacteria", "Agriculture", "Biodiversity", "15. Life on land", "Trees", "RNA", " Bacterial", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Metagenome", "Ecosystem", "Phylogeny", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"], "contacts": [{"organization": "Xiangbi Chen, Ya-wei Wei, Wenxue Wei, Jinshui Wu, Yirong Su, Xunyang He,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s11274-011-0809-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/World%20Journal%20of%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11274-011-0809-0", "name": "item", "description": "10.1007/s11274-011-0809-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11274-011-0809-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-15T00:00:00Z"}}, {"id": "10.1007/s12275-012-2409-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:24Z", "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": "10.1007/s12275-014-4129-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:15:24Z", "type": "Journal Article", "created": "2014-12-02", "title": "Effect Of Long-Term Different Fertilization On Bacterial Community Structures And Diversity In Citrus Orchard Soil Of Volcanic Ash", "description": "This study was conducted to assess bacterial species richness, diversity and community distribution according to different fertilization regimes for 16 years in citrus orchard soil of volcanic ash. Soil samples were collected and analyzed from Compost (cattle manure, 2,000 kg/10a), 1/2 NPK+compost (14-20-14+2,000 kg/10a), NPK+compost (28-40-28+2,000 kg/10a), NPK (28-40-28 kg/10a), 3 NPK (84-120-84 kg/10a), and Control (no fertilization) plot which have been managed in the same manners with compost and different amount of chemical fertilization. The range of pyrosequencing reads and OTUs were 4,687-7,330 and 1,790-3,695, respectively. Species richness estimates such as Ace, Chao1, and Shannon index were higher in 1/2 NPK+compost than other treatments, which were 15,202, 9,112, 7.7, respectively. Dominant bacterial groups at level of phylum were Proteobacteria, Acidobacteria, and Actinobacteria. Those were occupied at 70.9% in 1/2 NPK+compost. Dominant bacterial groups at level of genus were Pseudolabrys, Bradyrhizobium, and Acidobacteria. Those were distributed at 14.4% of a total of bacteria in Compost. Soil pH displayed significantly closely related to bacterial species richness estimates such as Ace, Chao1 (p<0.05) and Shannon index (p<0.01). However, it showed the negative correlation with exchangeable aluminum contents (p<0.05). In conclusion, diversity of bacterial community in citrus orchard soil was affected by fertilization management, soil pH changes and characteristics of volcanic ash.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Citrus", "0303 health sciences", "Bacteria", "Agriculture", "Biodiversity", "Volcanic Eruptions", "15. Life on land", "Acidobacteria", "Actinobacteria", "Manure", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Proteobacteria", "Animals", "Cattle", "14. Life underwater", "Fertilizers", "Soil Microbiology", "Alphaproteobacteria"]}, "links": [{"href": "https://doi.org/10.1007/s12275-014-4129-6"}, {"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/s12275-014-4129-6", "name": "item", "description": "10.1007/s12275-014-4129-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s12275-014-4129-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-11-29T00:00:00Z"}}, {"id": "10.1016/j.envres.2019.108608", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:21Z", "type": "Journal Article", "created": "2019-07-26", "title": "Antibiotic resistance gene distribution in agricultural fields and crops. A soil-to-food analysis", "description": "Despite the social concern about the generalization of antibiotic resistance hotspots worldwide, very little is known about the contribution of different potential sources to the global risk. Here we present a quantitative analysis of the distribution of Antibiotic Resistance Genes (ARGs) in soil, rhizospheric soil, roots, leaves and beans in tomato, lettuce and broad beans crops (165 samples in total), grown in nine commercial plots distributed in four geographical zones in the vicinity of Barcelona (North East Spain). We also analyzed five soil samples from a nearby forest, with no record of agricultural activities. DNA samples were analyzed for their content in the ARGs sul1, tetM, qnrS1, blaCTX-M-32, blaOXA-58, mecA, and blaTEM, plus the integron intI1, using qPCR methods. In addition, soil microbiomes from the different plots were analyzed by amplicon-targeted 16S rRNA gene sequencing. Our data show a decreasing gradient of ARG loads from soil to fruits and beans, the latter showing only from 0.1 to 0.01% of the abundance values in soil. The type of crop was the main determinant for both ARG distribution and microbiome composition among the different plots, with minor contributions of geographic location and irrigation water source. We propose that soil amendment and/or fertilization, more than irrigation water, are the main drivers of ARG loads on the edible parts of the crop, and that they should therefore be specifically controlled.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Microbiomes", "Agriculture", "Drug Resistance", " Microbial", "Irrigation water", "15. Life on land", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "qPCR", "Soil", "03 medical and health sciences", "Antibiotic resistance genes", "Genes", " Bacterial", "Spain", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Endophytes", "Food Analysis", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envres.2019.108608"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envres.2019.108608", "name": "item", "description": "10.1016/j.envres.2019.108608", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envres.2019.108608"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-01T00:00:00Z"}}, {"id": "10.1016/j.foodres.2022.112162", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:26Z", "type": "Journal Article", "created": "2022-11-19", "title": "High pressure processing at the early stages of ripening enhances the safety and quality of dry fermented sausages elaborated with or without starter culture", "description": "To study the quality of chorizo de Le\u00f3n dry fermented sausages (DFS), high pressure processing (HPP) applied at the early stages of ripening and the use of a functional starter culture were evaluated as additional safety measures. Furthermore, the ability to control the populations of artificially inoculated Listeria monocytogenes and Salmonella Typhimurium was investigated and the evolution of microbial communities was assessed by amplicon 16S rRNA metataxonomics. The use of HPP and the starter culture, independently or combined, induced a reduction of Listeria monocytogenes of 1.5, 4.3 and\u00a0>\u00a04.8 log CFU/g respectively, as compared to control. Salmonella Typhimurium counts were under the detection limit (<1 log) in all treated end-product samples. Both additional measures reduced the activity of undesirable microbiota, such as Serratia and Brochothrix, during the production of DFS. Moreover, the starter culture highly influencedthe taxonomic profile of samples.No adverse sensory effects were observed, and panelists showed preference for HPP treated DFS. In conclusion, this new approach of applying HPP at the early stages of ripening of DFS in combination with the use of a defined starter culture improved the safety and quality of the meat product.", "keywords": ["Salmonella typhimurium", "2. Zero hunger", "Tecnolog\u00eda de los alimentos", "Ripening", "Microbial communities", "04 agricultural and veterinary sciences", "Preservation", "Meat Products", "High Hydrostatic Pressure", "0404 agricultural biotechnology", "RNA", " Ribosomal", " 16S", "Fermentation", "Lactic acid bacteria", "Fermented meat", "0405 other agricultural sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.foodres.2022.112162"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Food%20Research%20International", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foodres.2022.112162", "name": "item", "description": "10.1016/j.foodres.2022.112162", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foodres.2022.112162"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-01T00:00:00Z"}}, {"id": "10.1016/j.ijfoodmicro.2021.109504", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:45Z", "type": "Journal Article", "created": "2021-12-21", "title": "Development of a rapid qPCR method to quantify lactic acid bacteria in cold-smoked salmon", "description": "Quantification of lactic acid bacteria (LAB) is essential to control quality of seafood products like cold-smoked salmon (CSS). In the present study, we report the design and optimization of a dual-labelled TaqMan \u2122 probe targeting the V7 region of 16S rRNA gene for the detection of LAB in CSS. This quantitative PCR (qPCR) assays is useful for the simultaneous detection of the ten LAB genera communally encountered in CSS as Aerococcus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Macrococcus, Streptococcus, Vagococcus and Weissella. The specificity of this method was demonstrated against 14 genera (44 isolates, 35 species) of Gram-positive bacteria and 19 genera of Gram-negative (40 isolates, 34 species). Calibration of the method was performed in CSS matrix using a mix of equimolar cultured solution of five LAB. Quantification with the qPCR method range from 3.5 to 8.5 Log CFU/g in CSS matrix, covering 5 orders of magnitude. On these artificially contaminated CSS slices, PCR method results correlated successfully (R2\u00a0=\u00a00.9945) with the conventional enumeration on Elliker medium. In addition, the new method was successful on commercial CSS from five different origins with a quantification range from 3.7 Log CFU/g to 8.0 Log CFU/g. This one-step quantitative methodology is proposed as a rapid and complementary tool of the cultural methods to investigate the LAB microbiota and biodiversity of CSS.", "keywords": ["LAB", "0301 basic medicine", "0303 health sciences", "Colony Count", " Microbial", "Real-Time Polymerase Chain Reaction", "Lactobacillus", "03 medical and health sciences", "Seafood", "TaqMan TM probe", "Lactobacillales", "Salmon", "RNA", " Ribosomal", " 16S", "Food Microbiology", "Animals", "Real-time PCR"]}, "links": [{"href": "https://doi.org/10.1016/j.ijfoodmicro.2021.109504"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Food%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ijfoodmicro.2021.109504", "name": "item", "description": "10.1016/j.ijfoodmicro.2021.109504", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ijfoodmicro.2021.109504"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2020.123676", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:53Z", "type": "Journal Article", "created": "2020-08-14", "title": "Simultaneous adsorption and biodegradation of trichloroethylene occurs in a biochar packed column treating contaminated landfill leachate", "description": "Trichloroethylene (TCE) is a human carcinogen that is commonly found in landfill leachate as a result of anthropogenic activities. Contaminated leachate plumes may be intercepted prior to reaching groundwater and treated in situ using permeable reactive barriers (PRB). This study used a packed column system containing herbal pomace and spruce biochar, previously shown to have TCE adsorptive capabilities, to investigate the feasibility of using pyrolysed waste as a fill material in a PRB. Influent containing raw or autoclaved landfill leachate was used to investigate the potential for environmental micro-organisms to establish a TCE-dechlorinating biofilm on the biochar, in order to prolong the operational life span of the system. TCE removal \u2265 99.7 was observed by both spruce and herbal pomace based biochars. No dichloroethylene (DCE) isomers were present in the column effluents, but cis-1,2 DCE was adsorbed to the biochar treating raw landfill leachate, indicating that dechlorination was occurring biologically in these columns. Known microbial species that are individually capable of complete dechlorination of TCE to ethene were not detected by 16S rRNA gene sequencing, but several species capable of partial TCE dechlorination (Desulfitobacterium spp., Sulfurospirillium spp. and Desulfuromonas spp) were present in the biofilms of the columns treating raw landfill leachate. These data demonstrate that biochar from waste material may be capable of supporting a dechlorinating biofilm to promote bioremediation of TCE.", "keywords": ["Permeable Reactive Barrier", "Waste reuse", "01 natural sciences", "6. Clean water", "Trichloroethylene", "12. Responsible consumption", "3. Good health", "Biochar", "Biodegradation", " Environmental", "13. Climate action", "Charcoal", "RNA", " Ribosomal", " 16S", "Humans", "Adsorption", "Water Pollutants", " Chemical", "Bioremediation", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2020.123676"}, {"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.2020.123676", "name": "item", "description": "10.1016/j.jhazmat.2020.123676", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2020.123676"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2021.127155", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:54Z", "type": "Journal Article", "created": "2021-09-09", "title": "Elevated levels of antibiotic resistance in groundwater during treated wastewater irrigation associated with infiltration and accumulation of antibiotic residues", "description": "Treated wastewater irrigation (TWW) releases antibiotics and antibiotic resistance genes (ARGs) into the environment and might thus promote the dissemination of antibiotic resistance in groundwater (GW). We hypothesized that TWW irrigation increases ARG abundance in GW through two potential mechanisms: the contamination of GW with resistant bacteria and the accumulation of antibiotics in GW. To test this, the GW below a real-scale TWW-irrigated field was sampled for six months. Sampling took place before, during and after high-intensity TWW irrigation. Samples were analysed with 16S rRNA amplicon sequencing, qPCR of six ARGs and the class 1 integron-integrase gene intI1, while liquid chromatography tandem mass spectrometry was performed to detect antibiotic and pharmaceutical residues. Absolute abundance of 16S rRNA in GW decreased rather than increased during long-term irrigation. Also, the relative abundance of TWW-related bacteria did not increase in GW during long-term irrigation. In contrast, long-term TWW irrigation increased the relative abundance of sul1 and intI1 in the GW microbiome. Furthermore, GW contained elevated concentrations of sulfonamide antibiotics, especially sulfamethoxazole, to which sul1 confers resistance. Total sulfonamide concentrations in GW correlated with sul1 relative abundance. Consequently, TWW irrigation promoted sul1 and intI1 dissemination in the GW microbiome, most likely due to the accumulation of drug residues.", "keywords": ["Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "Drug Resistance", " Microbial", "Wastewater", "Groundwater", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2021.127155"}, {"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.2021.127155", "name": "item", "description": "10.1016/j.jhazmat.2021.127155", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2021.127155"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-01T00:00:00Z"}}, {"id": "10.1016/j.mib.2019.08.004", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:16:57Z", "type": "Journal Article", "created": "2019-10-22", "title": "The mycobiota: fungi take their place between plants and bacteria", "description": "Eukaryotes host numerous intracellular and associated microbes in their microbiota. Fungi, the so-called Mycobiota, are important members of both human and plant microbiota. Moreover, members of the plant mycobiota host their own microbiota on their surfaces and inside their hyphae. The microbiota of the mycobiota includes mycorrhizal helper bacteria (for mycorrhizal fungi) and fungal endobacteria, which are critical for the fungal host and, as such, likely affect the plant. This review discusses the contribution that these often-overlooked members make to the composition and performance of the plant microbiota.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Bacteria", "Host Microbial Interactions", "RNA", " Ribosomal", " 16S", "Fungi", "Microbial Interactions", "Plants", "Bacterial Physiological Phenomena", "Symbiosis", "Phylogeny", "Mycobiome"], "contacts": [{"organization": "Bonfante P., Venice F., Lanfranco L.,", "roles": ["creator"]}]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1728500/7/Bonfante%2c%20Venice%20and%20Lanfranco_Current%20Opinion%20Author%20final%20version.pdf"}, {"href": "https://doi.org/10.1016/j.mib.2019.08.004"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Current%20Opinion%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.mib.2019.08.004", "name": "item", "description": "10.1016/j.mib.2019.08.004", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.mib.2019.08.004"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2006.08.033", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:03Z", "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.2012.11.052", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:04Z", "type": "Journal Article", "created": "2012-12-07", "title": "Characterization Of Soil Bacterial Community Structure And Physicochemical Properties In Created And Natural Wetlands", "description": "We used multi-tag pyrosequencing of 16S ribosomal DNA to characterize bacterial communities of wetland soils collected from created and natural wetlands located in the Virginia piedmont. Soils were also evaluated for their physicochemical properties [i.e., percent moisture, pH, soil organic matter (SOM), total organic carbon (TOC), total nitrogen (TN), and C:N ratio]. Soil moisture varied from 15% up to 55% among the wetlands. Soil pH ranged between 4.2 and 5.8, showing the typical characteristic of acidic soils in the Piedmont region. Soil organic matter contents ranged from 3% up to 6%. Soil bacterial community structures and their differences between the wetlands were distinguished by pyrosequencing. Soil bacterial communities in the created wetlands were less dissimilar to each other than to those of either natural wetland, with little difference in diversity (Shannon's H') between created and natural wetlands, except one natural wetland consistently showing a lower H'. The greatest difference of bacterial community structure was observed between the two natural wetlands (R=0.937, p<0.05), suggesting these two natural wetlands were actually quite different reflecting differences in their soil physicochemistry. The major phylogenic groups of all soils included Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatinomadetes, Nitrospira, and Proteobacteria with Proteobacteria being the majority of the community composition. Acidobacteria group was more abundant in natural wetlands than in created wetlands. We found a significant association between bacterial community structures and physicochemical properties of soils such as C:N ratio (\u03c1=0.43, p<0.01) and pH (\u03c1=0.39, p<0.01). The outcomes of the study show that the development of ecological functions, mostly mediated by microbial communities, is connected with the development of soil properties in created wetlands. Soil properties should be carefully monitored to examine the progress of functional wetland mitigation.", "keywords": ["Principal Component Analysis", "Bacteria", "RNA", " Ribosomal", " 16S", "Wetlands", "15. Life on land", "Polymerase Chain Reaction", "01 natural sciences", "Soil Microbiology", "6. Clean water", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2012.11.052"}, {"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.2012.11.052", "name": "item", "description": "10.1016/j.scitotenv.2012.11.052", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2012.11.052"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-01-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2016.05.073", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:06Z", "type": "Journal Article", "created": "2016-06-09", "title": "Associations Between Soil Bacterial Community Structure And Nutrient Cycling Functions In Long-Term Organic Farm Soils Following Cover Crop And Organic Fertilizer Amendment", "description": "Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(\u00ae) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-\u03b2-d-glucosaminidase and \u03b2-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were better explained using both soil physicochemical test values and bacterial community structure data than using soil tests alone. Pursuing a better understanding of bacterial community composition and how it is affected by farming practices is a promising avenue for increasing our ability to predict the impact of management practices on important soil functions.", "keywords": ["Crops", " Agricultural", "2. Zero hunger", "Environmental Engineering", "Farms", "Bacteria", "Microbiota", "Agriculture", "04 agricultural and veterinary sciences", "15. Life on land", "Pollution", "6. Clean water", "RNA", " Bacterial", "Soil", "13. Climate action", "RNA", " Ribosomal", " 16S", "Environmental Chemistry", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Waste Management and Disposal", "Soil Microbiology", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2016.05.073"}, {"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.2016.05.073", "name": "item", "description": "10.1016/j.scitotenv.2016.05.073", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2016.05.073"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-10-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2019.135733", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:08Z", "type": "Journal Article", "created": "2019-11-26", "title": "International tempo-spatial study of antibiotic resistance genes across the Rhine river using newly developed multiplex qPCR assays", "description": "The aim of this study was to capture and explain changes in antibiotic resistance gene (ARG) presence and concentration internationally across the Rhine river. Intl1 concentrations and national antibiotic usage were investigated as proxies to predict anthropogenic ARG pollution. Newly-developed multiplex qPCR assays were employed to investigate ARG profiles across 8 locations (L1-L8) in three countries (Switzerland, Germany, the Netherlands) and to detect potential regional causes for variation. Two of these locations were further monitored, over the duration of one month. A total of 13 ARGs, Intl1 and 16S rRNA were quantified. ARG presence and concentrations initially increased from L1(Diepoldsau) to L3(Darmstadt). A continuous increase could not be observed at subsequent locations, with the large river volume likely being a major contributing factor for stability. ARG presence and concentrations fluctuated widely across different locations. L2(Basel) and L3 were the two most polluted locations, coinciding with these locations being well-developed pharmaceutical production locations. We draw attention to the characteristic, clearly distinct ARG profiles, with gene presence being consistent and gene concentrations varying significantly less over time than across different locations. Five genes were Rhine-typical (ermB, ermF, Intl1, sul1 and tetM). Intl1 and sul1 were the genes with highest and second-highest concentration, respectively. Aph(III)a and blaOXA were permanently introduced downstream of L1, indicating no source of these genes prior to L1. We highlight that correlations between Intl1 and ARG concentrations (R2\u00a0=\u00a00.72) were driven by correlations to sul1 and disappeared when excluding sul1 from the analysis (R2\u00a0=\u00a00.05). Intl1 therefore seems to be a good proxy for sul1 concentrations but not necessarily for overall (anthropogenic) ARG pollution. Aminoglycoside usage per country correlated with concentrations of aph(III)a and several unrelated antibiotic resistance genes (blaOXA,ermB, ermF and tetM). This correlation can be explained by co-resistance caused by mobile genetic elements (MGEs), such as Tn1545.", "keywords": ["0301 basic medicine", "03 medical and health sciences", "Rivers", "Genes", " Bacterial", "13. Climate action", "Germany", "RNA", " Ribosomal", " 16S", "Drug Resistance", " Microbial", "01 natural sciences", "Switzerland", "Anti-Bacterial Agents", "Netherlands", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2019.135733"}, {"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.2019.135733", "name": "item", "description": "10.1016/j.scitotenv.2019.135733", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2019.135733"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}, {"id": "10.1016/j.still.2005.08.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:29Z", "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": "2026-04-13T16:17:40Z", "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": "2026-04-13T16:17:40Z", "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.2021.116818", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:43Z", "type": "Journal Article", "created": "2021-01-08", "title": "Antibiotic resistance gene load and irrigation intensity determine the impact of wastewater irrigation on antimicrobial resistance in the soil microbiome", "description": "Treated wastewater (TWW) irrigation is a useful counter-measure against the depletion of freshwater (FW) resources. However, TWW contains several contaminants of emerging concern, such as antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). Thus, TWW irrigation might promote the spread of antimicrobial resistance in soil environments. In the present work, we hypothesized that the ARG load and irrigation intensity define the effect of TWW irrigation on ARG spread dynamics in soil. This hypothesis was tested using a multiphase approach: a) comparing soil from a full-scale, commercially operated, TWW irrigated field with non-irrigated soil, b) long-term sampling of the TWW irrigated field over one year with different irrigation intensities and intercepted by irrigation breaks and c) laboratory-scale soil microcosms irrigated with TWW compared to FW. Six ARGs, the integrase gene intI1 and the 16S rRNA were quantified using qPCR. In addition, effects of TWW irrigation on bacterial community composition of microcosm-samples were analysed with 16S rRNA amplicon sequencing. The genes sul1, qnrS, blaOXA-58, tet(M) and intI1 were significantly more abundant in the TWW irrigated field soil, whereas blaCTX--M-32 and blaTEM, the least abundant genes in the TWW irrigation, showed higher abundance in the non-irrigated soil. The relative abundance of sul1, qnrS, blaOXA-58, tet(M) and intI1 correlated with TWW irrigation intensity and decreased during irrigation breaks. Despite the decrease, the levels of these genes remained consistently higher than the non-irrigated soil indicating persistence upon their introduction into the soil. Microcosm experiments verified observations from the field study: TWW irrigation promoted the spread of ARGs and intI1 into soil at far elevated levels compared to FW irrigation. However, the impact of TWW irrigation on 16S rRNA absolute abundance and the soil microbial community composition was negligible. In conclusion, the impact of TWW irrigation depends mainly on the introduced ARG load and the irrigation intensity.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Agricultural Irrigation", "Microbiota", "Angiotensin-Converting Enzyme Inhibitors", "Wastewater", "15. Life on land", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Angiotensin Receptor Antagonists", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "Drug Resistance", " Bacterial", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.watres.2021.116818"}, {"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.2021.116818", "name": "item", "description": "10.1016/j.watres.2021.116818", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.watres.2021.116818"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-01T00:00:00Z"}}, {"id": "10.1021/acs.est.0c01565", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:49Z", "type": "Journal Article", "created": "2020-05-15", "title": "Changes in Antibiotic Resistance Gene Levels in Soil after Irrigation with Treated Wastewater: A Comparison between Heterogeneous Photocatalysis and Chlorination", "description": "Wastewater (WW) reuse is expected to be increasingly indispensable in future water management to mitigate water scarcity. However, this increases the risk of antibiotic resistance (AR) dissemination via irrigation. Herein, a conventional (chlorination) and an advanced oxidation process (heterogeneous photocatalysis (HPC)) were used to disinfect urban WW to the same target of Escherichia coli <10 CFU/100 mL and used to irrigate lettuce plants (Lactuca sativa) set up in four groups, each receiving one of four water types, secondary WW (positive control), fresh water (negative control), chlorinated WW, and HPC WW. Four genes were monitored in water and soil, 16S rRNA as an indicator of total bacterial load, intI1 as a gene commonly associated with anthropogenic activity and AR, and two AR genes blaOXA-10 and qnrS. Irrigation with secondary WW resulted in higher dry soil levels of intI1 (from 1.4 \u00d7 104 copies/g before irrigation to 3.3 \u00d7 105 copies/g after). HPC-treated wastewater showed higher copy numbers of intI1 in the irrigated soil than chlorination, but the opposite was true for blaOXA-10. The results indicate that the current treatment is insufficient to prevent dissemination of AR markers and that HPC does not offer a clear advantage over chlorination.", "keywords": ["Agricultural Irrigation", "Halogenation", "0211 other engineering and technologies", "Drug Resistance", " Microbial", "02 engineering and technology", "Wastewater", "Waste Disposal", " Fluid", "01 natural sciences", "6. Clean water", "3. Good health", "Soil", "antibiotic resistance; wastewater reuse; photocatalysis; wastewater irrigation", "RNA", " Ribosomal", " 16S", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.iris.unisa.it/bitstream/11386/4749040/1/es-2020-01565f.R1_Proof_hi.pdf"}, {"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.0c01565"}, {"href": "https://doi.org/10.1021/acs.est.0c01565"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.0c01565", "name": "item", "description": "10.1021/acs.est.0c01565", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.0c01565"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-15T00:00:00Z"}}, {"id": "10.1093/femsec/fiv066", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:57Z", "type": "Journal Article", "created": "2015-06-20", "title": "Effects Of Warming And Drought On Potential N2o Emissions And Denitrifying Bacteria Abundance In Grasslands With Different Land-Use", "description": "Increased warming in spring and prolonged summer drought may alter soil microbial denitrification. We measured potential denitrification activity and denitrifier marker gene abundances (nirK, nirS, nosZ) in grasslands soils in three geographic regions characterized by site-specific land-use indices (LUI) after warming in spring, at an intermediate sampling and after summer drought. Potential denitrification was significantly increased by warming, but did not persist over the intermediate sampling. At the intermediate sampling, the relevance of grassland land-use intensity was reflected by increased potential N2O production at sites with higher LUI. Abundances of total bacteria did not respond to experimental warming or drought treatments, displaying resilience to minor and short-term effects of climate change. In contrast, nirS- and nirK-type denitrifiers were more influenced by drought in combination with LUI and pH, while the nosZ abundance responded to the summer drought manipulation. Land-use was a strong driver for potential denitrification as grasslands with higher LUI also had greater potentials for N2O emissions. We conclude that both warming and drought affected the denitrifying communities and the potential denitrification in grassland soils. However, these effects are overruled by regional and site-specific differences in soil chemical and physical properties which are also related to grassland land-use intensity.", "keywords": ["0301 basic medicine", "570", "UFSP13-8 Global Change and Biodiversity", "Climate Change", "Microbial Consortia", "580 Plants (Botany)", "Nitric Oxide", "142-005 142-005", "Soil", "03 medical and health sciences", "potential N2O emissions", "RNA", " Ribosomal", " 16S", "2402 Applied Microbiology and Biotechnology", "use index", "Soil Microbiology", "2. Zero hunger", "Biodiversity Exploratories", "denitrification", "Bacteria", "2404 Microbiology", "04 agricultural and veterinary sciences", "15. Life on land", "Grassland", "6. Clean water", "Droughts", "land", "climate change", "Genes", " Bacterial", "13. Climate action", "8. Economic growth", "Denitrification", "0401 agriculture", " forestry", " and fisheries", "grassland", "microbial community", "2303 Ecology"]}, "links": [{"href": "https://doi.org/10.1093/femsec/fiv066"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiv066", "name": "item", "description": "10.1093/femsec/fiv066", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiv066"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-06-19T00:00:00Z"}}, {"id": "10.1021/acs.est.9b07562", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:17:50Z", "type": "Journal Article", "created": "2020-02-24", "title": "Silver Nanoparticles Alter Soil Microbial Community Compositions and Metabolite Profiles in Unplanted and Cucumber-Planted Soils", "description": "The rapid development of nanotechnology makes the environmental impact assessment a necessity to ensure the sustainable use of engineered nanomaterials. Here, silver nanoparticles (AgNPs) at 100 mg/kg were added to soils in the absence or presence of cucumber (Cucumis sativa) plants for 60 days. The response of the soil microbial community and associated soil metabolites was investigated by 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics, respectively. The results show that AgNP exposure significantly increased the soil pH in both unplanted and cucumber-planted soils. The soil bacterial community structure was altered upon Ag exposure in both soils. Several functionally significant bacterial groups, which are associated with carbon, nitrogen, and phosphorus cycling, were compromised by AgNPs in both unplanted and cucumber-planted soils. Generally, plants played a limited role in mediating the impact of AgNPs on the bacterial community. Soil metabolomic analysis showed that AgNPs altered the metabolite profile in both unplanted and cucumber-planted soils. The significantly changed metabolites are involved in sugar and amino acid-related metabolic pathways, indicating the perturbation of C and N metabolism, which is consistent with the bacterial community structure results. In addition, several fatty acids were significantly decreased upon exposure to AgNPs in both unplanted and cucumber-planted soils, suggesting the possible oxidative stress imposed on microbial cell membranes. These results provide valuable information for understanding the biological and biochemical impact of AgNP exposure on both plant species and on soil microbial communities; such understanding is needed to understand the risk posed by these materials in the environment.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Silver", "Microbiota", "Metal Nanoparticles", "15. Life on land", "6. Clean water", "Soil", "03 medical and health sciences", "13. Climate action", "RNA", " Ribosomal", " 16S", "Cucumis sativus", "Soil Microbiology"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.9b07562"}, {"href": "https://doi.org/10.1021/acs.est.9b07562"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.9b07562", "name": "item", "description": "10.1021/acs.est.9b07562", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.9b07562"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-24T00:00:00Z"}}, {"id": "10.1038/ismej.2009.136", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:08Z", "type": "Journal Article", "created": "2009-12-24", "title": "Biogeography Of Soil Archaea And Bacteria Along A Steep Precipitation Gradient", "description": "AbstractFor 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.2010.3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:08Z", "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/ismej.2011.124", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:08Z", "type": "Journal Article", "created": "2011-09-22", "title": "Shifts In Soil Microorganisms In Response To Warming Are Consistent Across A Range Of Antarctic Environments", "description": "AbstractBecause of severe abiotic limitations, Antarctic soils represent simplified systems, where microorganisms are the principal drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report highly consistent responses in microbial communities across disparate sub-Antarctic and Antarctic environments in response to 3 years of experimental field warming (+0.5 to 2 \uffc2\uffb0C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio, which could result in an increase in soil respiration. Furthermore, shifts toward generalist bacterial communities following warming weakened the linkage between the bacterial taxonomic and functional richness. GeoChip microarray analyses also revealed significant warming effects on functional communities, specifically in the N-cycling microorganisms. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures.
", "keywords": ["0301 basic medicine", "Climate Change", "Antarctic Regions", "global warming", "open-top chambers", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "carbon cycle", "nitrogen cycle", "SDG 13 - Climate Action", "SDG 14 - Life Below Water", "14. Life underwater", "Soil Microbiology", "0303 health sciences", "Bacteria", "GeoChip microarrays", "Fungi", "Temperature", "Nitrogen Cycle", "15. Life on land", "Microarray Analysis", "Biota", "13. Climate action", "international", "Antarctica"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2011.124"}, {"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.2011.124", "name": "item", "description": "10.1038/ismej.2011.124", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2011.124"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-09-22T00:00:00Z"}}, {"id": "10.1038/s41467-022-28658-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:12Z", "type": "Journal Article", "created": "2022-02-25", "title": "Different gut microbial communities correlate with efficacy of albendazole-ivermectin against soil-transmitted helminthiases", "description": "AbstractSoil-transmitted helminth infections represent a large burden with over a quarter of the world\uffe2\uff80\uff99s population at risk. Low cure rates are observed with standard of care (albendazole); therefore, a more effective combination therapy (albendazole and ivermectin) is being investigated but showed variable treatment efficacies without evidence of intrinsic parasite resistance. Here, we analyzed the microbiome ofTrichuris trichiuraand hookworm-infected patients and found an association of different enterotypes with treatment efficacy. 80\uffe2\uff80\uff89T. trichiura-infected patients with hookworm co-infections\uffc2\uffa0from Pak-Khan, Laos, received either albendazole (n\uffe2\uff80\uff89=\uffe2\uff80\uff8941) or albendazole and ivermectin combination therapy (n\uffe2\uff80\uff89=\uffe2\uff80\uff8939). Pre-/post-treatment stool samples were collected to monitor treatment efficacy and microbial communities were profiled using 16S rRNA gene sequencing, qPCR, and shotgun sequencing. We identified three bacterial enterotypes and show that pre-treatment enterotype is associated with efficacy of the combination treatment for bothT. trichiura(CRET1\uffe2\uff80\uff89=\uffe2\uff80\uff895.8%; CRET2\uffe2\uff80\uff89=\uffe2\uff80\uff8916.6%; CRET3\uffe2\uff80\uff89=\uffe2\uff80\uff8968.8%) and hookworm (CRET1\uffe2\uff80\uff89=\uffe2\uff80\uff8931.3%; CRET2\uffe2\uff80\uff89=\uffe2\uff80\uff8916.6%; CRET3\uffe2\uff80\uff89=\uffe2\uff80\uff8978.6%). This study shows that pre-treatment enterotype enables predicting treatment outcome of combination therapy forT. trichiuraand hookworm infections.
Trial registration: ClinicalTrials.gov, NCT03527732. Registered 17 May 2018,https://clinicaltrials.gov/ct2/show/NCT03527732.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.Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20\uffe2\uff80\uff93100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P < 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.0200979", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:20:17Z", "type": "Journal Article", "created": "2019-04-11", "title": "Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR", "description": "AbstractSoil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition.
To address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer\uffc2\uffae, marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers between 1.00 and 2.20 m below ground level.
Importantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition.
Finally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier.
These outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Science", "Microbial Consortia", "DIVERSITY", "SOFTWARE", "Real-Time Polymerase Chain Reaction", "BACILLUS-SUBTILIS", "BIOMASS", "03 medical and health sciences", "BIOAUGMENTATION", "DNA", " Bacterial/chemistry", "MICROBIAL COMMUNITIES", "Soil Microbiology", "2. Zero hunger", "0303 health sciences", "16S RIBOSOMAL-RNA", "Q", "R", "PROFILES", "ACIDS", "TRANSFORMATION", "6. Clean water", "Microbial Consortia/genetics", "Enhancer Elements", " Genetic", "13. Climate action", "Medicine", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/365395v1.full.pdf"}, {"href": "https://doi.org/10.1371/journal.pone.0200979"}, {"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.0200979", "name": "item", "description": "10.1371/journal.pone.0200979", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0200979"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-09T00:00:00Z"}}, {"id": "10.1080/15324982.2016.1177749", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-13T16:18:51Z", "type": "Journal Article", "created": "2016-06-17", "title": "Arbuscular Mycorrhizal Fungal Community Of Wheat Under Long-Term Mineral And Organic Amendments In Semi-Arid Mediterranean Turkey", "description": "A minimal amount of information is currently available concerning arbuscular mycorrhizal (AM) fungal associations with crops in semi-arid zones on Leptosols in Turkey. Therefore, using molecular ecological techniques, we studied the effects of different management practices (without fertilization, chemical fertilization, farmyard manure, and plant compost amendments) on AM fungal communities associated with wheat roots. Experiments were conducted in a field established in 1996 in southern Mediterranean Turkey where soil productivity is low owing to unfavorable climatic effects and soil characteristics. We determined 201 partial sequences of AM fungal nuclear ribosomal large subunit genes. The higher AM fungal richness was found in the control treatment without fertilization and plant compost treatments compared with the chemical fertilization and farmyard manure treatments. Clones related to Rhizophagus were found in all treatments and accounted for 37% of the total AM fungal clones, whereas those of Funneliformis were dominant under chemical fertilization. Redundancy analysis based on the frequency of operational taxonomic units revealed that AM fungal communities were divided into three groups, namely, the control treatment, the chemical fertilization treatment, and the organic treatments (farmyard manure and plant compost treatments). Although different organic amendments supported relatively similar AM fungal communities, plant compost induced higher AM fungal richness than farmyard manure fertilization.", "keywords": ["2. Zero hunger", "Leptosol", "southern Mediterranean Turkey", "organic fertilization", "large ribosomal subunits (LSU rDNA)", "Arbuscular mycorrhizal fungi", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "community analysis"]}, "links": [{"href": "https://doi.org/10.1080/15324982.2016.1177749"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Arid%20Land%20Research%20and%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1080/15324982.2016.1177749", "name": "item", "description": "10.1080/15324982.2016.1177749", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1080/15324982.2016.1177749"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-17T00:00:00Z"}}, {"id": "10.1093/femsec/fiab059", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:56Z", "type": "Journal Article", "created": "2021-04-14", "title": "Fungus-bacterium associations are widespread in fungal cultures isolated from a semi-arid natural grassland in Germany", "description": "ABSTRACTWe report on a study that aimed at establishing a large soil\uffe2\uff80\uff93fungal culture collection spanning a wide taxonomic diversity and systematically screening the collection for bacterial associations. Fungal cultures were isolated from soil samples obtained from a natural grassland in eastern Germany and bacterial associations were assessed by PCR-amplification and sequencing of bacterial 16S rRNA. In addition, intraspecies genetic diversities of a subset of the isolated species were estimated by double-digest restriction associated DNA sequencing. A total of 688 fungal cultures, representing at least 106 fungal species from 36 different families, were obtained and even though clonal isolates were identified in almost all fungal species subjected to ddRAD-seq, relatively high genetic diversities could be observed in some of the isolated species. A total of 69% of the fungal isolates in our collection were found to be associated with bacteria and the most commonly identified bacterial genera were Pelomonas, Enterobacter and Burkholderia. Our results indicate that bacterial associations commonly occur in soil fungi, even if antibiotics are being applied during the isolation process, and provide a basis for the use of our culture collection in ecological experiments that want to acknowledge the importance of intraspecies genetic diversity.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "bepress|Life Sciences|Ecology and Evolutionary Biology|Terrestrial and Aquatic Ecology", "0303 health sciences", "Terrestrial and Aquatic Ecology", "Bacteria", "Ecology and Evolutionary Biology", "Fungi", "Life Sciences", "15. Life on land", "bepress|Life Sciences|Ecology and Evolutionary Biology", "Grassland", "Soil", "03 medical and health sciences", "bepress|Life Sciences", "Germany", "RNA", " Ribosomal", " 16S", "Humans", "Bacteria ; Fungal-bacterial Interaction ; Soil Fungi ; Ddrad Sequencing", "Soil Microbiology"]}, "links": [{"href": "https://academic.oup.com/femsec/article-pdf/97/5/fiab059/37624504/fiab059.pdf"}, {"href": "https://doi.org/10.1093/femsec/fiab059"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/femsec/fiab059", "name": "item", "description": "10.1093/femsec/fiab059", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/femsec/fiab059"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-06T00:00:00Z"}}, {"id": "10.1093/ismejo/wrae012", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:18:58Z", "type": "Journal Article", "created": "2024-01-29", "title": "Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth", "description": "AbstractMicroorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth.The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA\uffe2\uff80\uff93DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.
", "keywords": ["0301 basic medicine", "0303 health sciences", "PCB", "Whole Genome Sequencing", "AlkB Enzymes", "Rhodococcus; biodegradation; PAH; PCB; hydrocarbons; complete genome", "High-Throughput Nucleotide Sequencing", "PAH", "Naphthalenes", "Xylenes", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "biodegradation", "Polychlorinated Biphenyls", "Hydrocarbons", "Complete genome", "03 medical and health sciences", "Biodegradation", " Environmental", "RNA", " Ribosomal", " 16S", "Biodegradation", "Cluster Analysis", "Rhodococcus", "Phylogeny", "Research Article"]}, "links": [{"href": "https://doi.org/10.1099/mgen.0.000363"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1099/mgen.0.000363", "name": "item", "description": "10.1099/mgen.0.000363", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1099/mgen.0.000363"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-01T00:00:00Z"}}, {"id": "10.1111/1462-2920.16268", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:14Z", "type": "Journal Article", "created": "2022-11-03", "title": "Environmental micro\u2010niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas' glacier forefield", "description": "AbstractThe pedogenesis from the mineral substrate released upon glacier melting has been explained with the succession of consortia of pioneer microorganisms, whose structure and functionality are determined by the environmental conditions developing in the moraine. However, the microbiome variability that can be expected in the environmentally heterogeneous niches occurring in a moraine at a given successional stage is poorly investigated. In a 50\uffe2\uff80\uff89m2 area in the forefield of the Lobuche glacier (Himalayas, 5050\uffe2\uff80\uff89m above sea level), we studied six sites of primary colonization presenting different topographical features (orientation, elevation and slope) and harbouring greyish/dark biological soil crusts (BSCs). The spatial vicinity of the sites opposed to their topographical differences, allowed us to examine the effect of environmental conditions independently from the time of deglaciation. The bacterial microbiome diversity and their co\uffe2\uff80\uff90occurrence network, the bacterial metabolisms predicted from 16S rRNA gene high\uffe2\uff80\uff90throughput sequencing, and the microbiome intact polar lipids were investigated in the BSCs and the underlying sediment deep layers (DLs). Different bacterial microbiomes inhabited the BSCs and the DLs, and their composition varied among sites, indicating a niche\uffe2\uff80\uff90specific role of the micro\uffe2\uff80\uff90environmental conditions in the bacterial communities' assembly. In the heterogeneous sediments of glacier moraines, physico\uffe2\uff80\uff90chemical and micro\uffe2\uff80\uff90climatic variations at the site\uffe2\uff80\uff90spatial scale are crucial in shaping the microbiome microvariability and structuring the pioneer bacterial communities during pedogenesis.
", "keywords": ["0301 basic medicine", "Pedogenesis", "0303 health sciences", "Glacier Foreland Succession", "Bacteria", "Biological soil crust", "15. Life on land", "Primary Colonization", "Soil", "03 medical and health sciences", "13. Climate action", "RNA", " Ribosomal", " 16S", "Glacier Moraines", "Cold Deserts", "Pioneer Bacterial Communities", "Ice Cover", "Soil moisture", "Research Articles", "Soil Microbiology"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/949070/2/Rolli%20et%20al%202022%20Environmental%20micro%e2%80%90niche%20filtering%20shapes%20bacterial%20pioneer%20communities.pdf"}, {"href": "https://eprints.ncl.ac.uk/fulltext.aspx?url=302678/40A25368-9064-4886-B8E6-E7942511FA71.pdf&pub_id=302678"}, {"href": "https://doi.org/10.1111/1462-2920.16268"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.16268", "name": "item", "description": "10.1111/1462-2920.16268", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.16268"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-18T00:00:00Z"}}, {"id": "10.1111/1574-6941.12009", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:14Z", "type": "Journal Article", "created": "2012-09-13", "title": "Chronic N-Amended Soils Exhibit An Altered Bacterial Community Structure In Harvard Forest, Ma, Usa", "description": "At the Harvard Forest, Petersham, MA, the impact of 20 years of annual ammonium nitrate application to the mixed hardwood stand on soil bacterial communities was studied using 16S rRNA genes pyrosequencing. Amplification of 16S rRNA genes was done using DNA extracted from 30 soil samples (three treatments \u00d7 two horizons \u00d7 five subplots) collected from untreated (control), low N-amended (50 kg ha(-1) year(-1)) and high N-amended (150 kg ha(-1) year(-1)) plots. A total of 1.3 million sequences were processed using qiime. Although Acidobacteria represented the most abundant phylum based on the number of sequences, Proteobacteria were the most diverse in terms of operational taxonomic units (OTUs). UniFrac analyses revealed that the bacterial communities differed significantly among soil horizons and treatments. Microsite variability among the five subplots was also evident. Nonmetric multidimensional scaling ordination of normalized OTU data followed by permutational manova further confirmed these observations. Richness indicators and indicator species analyses revealed higher bacterial diversity associated with N amendment. Differences in bacterial diversity and community composition associated with the N treatments were also observed at lower phylogenetic levels. Only 28-35% of the 6 936 total OTUs identified were common to three treatments, while the rest were specific to one treatment or common to two.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Environmental Microbiology and Microbial Ecology", "Nitrates", "Bacteria", "Genes", " rRNA", "Biodiversity", "15. Life on land", "Trees", "Scientific Contribution Number 2470", "Soil", "03 medical and health sciences", "Massachusetts", "RNA", " Ribosomal", " 16S", "Fertilizers", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/1574-6941.12009"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1574-6941.12009", "name": "item", "description": "10.1111/1574-6941.12009", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1574-6941.12009"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-11T00:00:00Z"}}, {"id": "10.1111/1574-6941.12018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:14Z", "type": "Journal Article", "created": "2012-09-26", "title": "Acidobacterial Community Responses To Agricultural Management Of Soybean In Amazon Forest Soils", "description": "This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1-8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Glycine max", "Agriculture", "Sequence Analysis", " DNA", "15. Life on land", "Acidobacteria", "Trees", "Soil", "03 medical and health sciences", "international", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Brazil", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/1574-6941.12018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1574-6941.12018", "name": "item", "description": "10.1111/1574-6941.12018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1574-6941.12018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-19T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2011.01192.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:43Z", "type": "Journal Article", "created": "2011-09-01", "title": "Soil Characteristics More Strongly Influence Soil Bacterial Communities Than Land-Use Type", "description": "To gain insight into the factors driving the structure of bacterial communities in soil, we applied real-time PCR, PCR-denaturing gradient gel electrophoreses, and phylogenetic microarray approaches targeting the 16S rRNA gene across a range of different land usages in the Netherlands. We observed that the main differences in the bacterial communities were not related to land-use type, but rather to soil factors. An exception was the bacterial community of pine forest soils (PFS), which was clearly different from all other sites. PFS had lowest bacterial abundance, lowest numbers of operational taxonomic units (OTUs), lowest soil pH, and highest C : N ratios. C : N ratio strongly influenced bacterial community structure and was the main factor separating PFS from other fields. For the sites other than PFS, phosphate was the most important factor explaining the differences in bacterial communities across fields. Firmicutes were the most dominant group in almost all fields, except in PFS and deciduous forest soils (DFS). In PFS, Alphaproteobacteria was most represented, while in DFS, Firmicutes and Gammaproteobacteria were both highly represented. Interestingly, Bacillii and Clostridium OTUs correlated with pH and phosphate, which might explain their high abundance across many of the Dutch soils. Numerous bacterial groups were highly correlated with specific soil factors, suggesting that they might be useful as indicators of soil status.", "keywords": ["land use change", "DNA", " Bacterial", "0301 basic medicine", "RNA 16S", "polymerase chain reaction", "soil nitrogen", "DNA sequence", "soil microorganism", "electrokinesis", "chemistry", "phylogeny", "Real-Time Polymerase Chain Reaction", "soil", "Soil", "03 medical and health sciences", "NIOO", "RNA", " Ribosomal", " 16S", "genetics", "soil carbon", "Phylogeny", "Soil Microbiology", "phosphate", "biodiversity", "Alphaproteobacteria", "Netherlands", "growth", " development and aging", "2. Zero hunger", "abundance", "0303 health sciences", "real time", "Bacteria", "pH", "Denaturing Gradient Gel Electrophoresis", "microbiology", "denaturing gradient gel electrophoresis", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "bacterium", "bacterial DNA", "phylogenetics", "classification", "real time polymerase chain reaction", "microbial community", "Gammaproteobacteria"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2011.01192.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2011.01192.x", "name": "item", "description": "10.1111/j.1574-6941.2011.01192.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2011.01192.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-09-19T00:00:00Z"}}, {"id": "10.1111/mec.13010", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:47Z", "type": "Journal Article", "created": "2014-11-20", "title": "Long-Term Balanced Fertilization Increases The Soil Microbial Functional Diversity In A Phosphorus-Limited Paddy Soil", "description": "AbstractThe influence of long\uffe2\uff80\uff90term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22\uffe2\uff80\uff90year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array\uffe2\uff80\uff90based analysis revealed that long\uffe2\uff80\uff90term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer\uffe2\uff80\uff90induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P\uffe2\uff80\uff90limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions.
", "keywords": ["2. Zero hunger", "Bacteria", "Nitrogen", "Oryza", "Phosphorus", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Nitrogen Cycle", "15. Life on land", "6. Clean water", "Carbon Cycle", "Soil", "13. Climate action", "RNA", " Ribosomal", " 16S", "Potassium", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Fertilizers", "Ecosystem", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/mec.13010"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecular%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/mec.13010", "name": "item", "description": "10.1111/mec.13010", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/mec.13010"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-12-31T00:00:00Z"}}, {"id": "10.1111/mec.13620", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:47Z", "type": "Journal Article", "created": "2016-03-19", "title": "The Impact Of Tropical Forest Logging And Oil Palm Agriculture On The Soil Microbiome", "description": "AbstractSelective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land\uffe2\uff80\uff90use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once\uffe2\uff80\uff90logged and twice\uffe2\uff80\uff90logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell\uffe2\uff80\uff93cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land\uffe2\uff80\uff90use changes on the interaction of soil microbes.
", "keywords": ["0301 basic medicine", "Conservation of Natural Resources", "0303 health sciences", "Bacteria", "Microbiota", "Agriculture", "Forestry", "Biodiversity", "Arecaceae", "Forests", "15. Life on land", "03 medical and health sciences", "Borneo", "international", "RNA", " Ribosomal", " 16S", "Metagenome", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/mec.13620"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecular%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/mec.13620", "name": "item", "description": "10.1111/mec.13620", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/mec.13620"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-20T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:55Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACTDue to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s V = 0.857, and Theil\uffe2\uff80\uff99s U = 0.316). For species-level community profiling, we found strong correlations ( r s > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average r s = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.
IMPORTANCEA quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.
", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/10.1128/msystems.00859-24"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00859-24", "name": "item", "description": "10.1128/msystems.00859-24", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00859-24"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "10.1128/msphere.00130-21", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:55Z", "type": "Journal Article", "created": "2021-08-11", "title": "Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield", "description": "Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield.
", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "Biological Products", "0303 health sciences", "Bacteria", "Microbiota", "Fungi", "High-Throughput Nucleotide Sequencing", "Agriculture", "Agricultural Inoculants", "15. Life on land", "Microbiology", "QR1-502", "United States", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Soil Microbiology", "Research Article", "Solanum tuberosum"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSphere.00130-21"}, {"href": "https://doi.org/10.1128/msphere.00130-21"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msphere.00130-21", "name": "item", "description": "10.1128/msphere.00130-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msphere.00130-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-25T00:00:00Z"}}, {"id": "10.1128/aem.01355-07", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:54Z", "type": "Journal Article", "created": "2007-11-17", "title": "Effects Of Wildfire And Harvest Disturbances On Forest Soil Bacterial Communities", "description": "ABSTRACTWildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH 4 + and NO 3 \uffe2\uff88\uff92 due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma - and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.
", "keywords": ["DNA", " Bacterial", "Electrophoresis", "0301 basic medicine", "0303 health sciences", "Bacteria", "Molecular Sequence Data", "Biodiversity", "Sequence Analysis", " DNA", "15. Life on land", "Nucleic Acid Denaturation", "DNA", " Ribosomal", "Fires", "6. Clean water", "Alberta", "Trees", "03 medical and health sciences", "13. Climate action", "DNA", " Ribosomal Spacer", "Biomass", "Soil Microbiology"], "contacts": [{"organization": "B.E. Kishchuk, William W. Mohn, Nancy R. Smith,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1128/aem.01355-07"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.01355-07", "name": "item", "description": "10.1128/aem.01355-07", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01355-07"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-01-01T00:00:00Z"}}, {"id": "10.1128/aem.02209-19", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-13T16:19:54Z", "type": "Journal Article", "created": "2019-12-04", "title": "Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous \u201cMost-Wanted\u201d Core Bacterial Taxon from Municipal Wastewater Treatment Plants", "description": "The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.
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