{"type": "FeatureCollection", "features": [{"id": "10.1007%2fs00374-010-0497-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:14:06Z", "type": "Journal Article", "created": "2010-09-03", "title": "Crop Residues And Fertilizer Nitrogen Influence Residue Decomposition And Nitrous Oxide Emission From A Vertisol", "description": "Crop residues with high C/N ratio immobilize N released during decomposition in soil, thus reducing N losses through leaching, denitrification, and nitrous oxide (N2O) emission. A laboratory incubation experiment was conducted for 84\u00a0days under controlled conditions (24\u00b0C and moisture content 55% of water-holding capacity) to study the influence of sugarcane, maize, sorghum, cotton and lucerne residues, and mineral N addition, on N mineralization\u2013immobilization and N2O emission. Residues were added at the rate of 3\u00a0t C ha\u22121 to soil with, and without, 150\u00a0kg urea N\u00a0ha\u22121. The addition of sugarcane, maize, and sorghum residues without N fertilizer resulted in a significant immobilization of soil N. Amended soil had significantly (P\u2009<\u20090.05) lower NO 3 \u2212 \u2013N, which reached minimum values of 2.8\u00a0mg\u00a0N kg\u22121 for sugarcane (at day\u00a028), 10.3\u00a0mg\u00a0N kg\u22121 for maize (day\u00a07), and 5.9\u00a0mg\u00a0N kg\u22121 for sorghum (day\u00a07), compared to 22.7\u00a0mg\u00a0N kg\u22121 for the unamended soil (day\u00a07). During 84\u00a0days of incubation, the total mineral N in the residues\u2009+\u2009N treatments were decreased by 45\u00a0mg\u00a0N kg\u22121 in sugarcane, 34\u00a0mg\u00a0kg\u22121 in maize, 29\u00a0mg\u00a0kg\u22121 in sorghum, and 16\u00a0mg\u00a0kg\u22121 in cotton amended soil compared to soil\u2009+\u2009N fertilizer, although soil NO 3 \u2212 \u2013N increased by 7\u00a0mg\u00a0kg\u22121 in lucerne amended soil. The addition of residues also significantly increased amended soil microbial biomass C and N. Maximum emissions of N2O from crop residue amended soils occurred in the first 4\u20135\u00a0days of incubation. Overall, after 84\u00a0days of incubation, the cumulative N2O emission was 25% lower with cotton\u2009+\u2009N fertilizer, compared to soil\u2009+\u2009N fertilizer. The cumulative N2O emission was significantly and positively correlated with NO 3 \u2212 \u2013N (r\u2009=\u20090.92, P\u2009<\u20090.01) and total mineral N (r\u2009=\u20090.93, P\u2009<\u20090.01) after 84\u00a0days of incubation, and had a weak but significant positive correlation with cumulative CO2 in the first 3 and 5\u00a0days of incubation (r\u2009=\u20090.59, P\u2009<\u20090.05).", "keywords": ["2. Zero hunger", "Crop residues", "Nitrous oxide", "571", "2404 Microbiology", "Vertisol", "04 agricultural and veterinary sciences", "15. Life on land", "630", "6. Clean water", "Mineral N", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "1102 Agronomy and Crop Science", "1111 Soil Science", "Fertilizer N"], "contacts": [{"organization": "Muhammad, W, Vaughan, SM, Dalal, RC, Menzies, NW,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007%2fs00374-010-0497-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007%2fs00374-010-0497-1", "name": "item", "description": "10.1007%2fs00374-010-0497-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007%2fs00374-010-0497-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-09-04T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2011.11.017", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:45Z", "type": "Journal Article", "created": "2011-12-11", "title": "Calcium Affects The Competitiveness Of Acid-Sensitive And Acid-Tolerant Strains Of Bradyrhizobium Japonicum In Nodulating And Fixing Nitrogen With Two Soybean Cultivars In Acid Soil", "description": "Abstract A glasshouse experiment studied the role of calcium and pH on competitiveness of acid-sensitive and acid-tolerant Bradyrhizobium japonicum strains with similar N2-fixation effectiveness in nodulating two soybean (Glycine max L. Merr) cultivars selected for tolerance of aluminium (PI416937) or for manganese (Manta). Liming provides calcium (Ca) as well as increasing soil pH. Thus the effect of Ca and pH of soil are difficult to separate. We examined the effects of Ca per se by comparing the response to gypsum and lime amendment on the competitiveness of acid-tolerant and acid-sensitive strains in nodulating soybean in an acid soil. Acid soil was treated with either CaSO4 or CaCO3 and incubated for 2 weeks before sowing soybean seed. Two acid-sensitive and two acid-tolerant B.\u00a0japonicum strains were mixed with each other (one acid-sensitive plus one acid-tolerant) and were inoculated onto soybean seeds at the rate of 106cfu\u00a0seed\u22121. Soil pH, as amended by lime addition, had more effect on nodulation than Ca addition in the form of gypsum. The response was affected by cultivar and strain in a complicated fashion with a marked strain\u00a0\u00d7\u00a0cultivar interaction. One acid-tolerant strain formed most nodules with both cultivars in the unamended soil of pH 4.36 in competition with one acid-sensitive strain. The same acid-tolerant strain was not competitive against the second acid-sensitive strain with Manta but was with PI416937. The second acid-tolerant strain was not competitive with either acid-sensitive strain in unamended and gypsum treated soils. It was only competitive with PI416937 in limed soil, a rather surprising result. Inoculation of this soil with no native soybean nodulating strains, increased shoot weight, %N, N uptake. N2-fixation was greatly increased by inoculation and lime addition, and to a lesser extent by gypsum addition for Manta. This experiment indicates that addition of Ca per se as gypsum to an acid soil has little effect on symbiotic performance, but changing pH by liming has a major effect, that both soybean cultivar and B.\u00a0japonicum strain influence the competitiveness of strains in acid soil and that acid-tolerance does not necessarily increase a strain's competitiveness.", "keywords": ["0301 basic medicine", "2. Zero hunger", "2404 Microbiology", "Acid-sensitive", "04 agricultural and veterinary sciences", "15. Life on land", "630", "6. Clean water", "03 medical and health sciences", "Acid-tolerant", "0401 agriculture", " forestry", " and fisheries", "Bradyrhizobium", "Soybean", "1111 Soil Science"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2011.11.017"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2011.11.017", "name": "item", "description": "10.1016/j.soilbio.2011.11.017", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2011.11.017"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-03-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2012.10.013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:46Z", "type": "Journal Article", "created": "2012-11-02", "title": "Inorganic And Organic Carbon Dynamics In A Limed Acid Soil Are Mediated By Plants", "description": "Abstract Lime is commonly used to overcome soil acidification in agricultural production systems; however, its impact on inorganic and organic soil carbon dynamics remains largely unknown. In a column experiment, we monitored rhizosphere effects on lime dissolution, CO2 effluxes, and the concentrations of dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) in leachate from an acidic Kandosol. The experiment consisted of four treatments viz: soil only (control), soil\u00a0+\u00a0lime, soil\u00a0+\u00a0wheat, and soil\u00a0+\u00a0lime\u00a0+\u00a0wheat. We measured CO2-C effluxes at 7, 43 and 98 days after planting (DAP) and leachate was collected at 56 and 101 DAP. The soil CO2-C efflux rate increased significantly with lime addition at 7 and 43 DAP compared to control. At 43 DAP, the largest increase in CO2-C effluxes was observed in the lime\u00a0+\u00a0wheat treatment. However, at 98 DAP similar CO2-C effluxes were observed from wheat and lime\u00a0+\u00a0wheat treatments, suggesting that most of the lime was dissolved in the lime\u00a0+\u00a0wheat treatment. Both DOC and DIC concentrations in the leachate increased significantly with lime and wheat only treatments (cf. control). In contrast to DOC, there was an increase in the DIC concentration in the soil leachate from lime\u00a0+\u00a0wheat treatment columns at 101 DAP (significant wheat\u00a0\u00d7\u00a0lime interaction), thus, accentuating the pronounced role of wheat roots. We conclude that plant mediated dissolution of lime increased the concentration of DIC in the soil leachate, while both liming and presence of plants enhanced DOC leaching.", "keywords": ["2. Zero hunger", "Dissolved inorganic carbon", "Carbon effluxes", "Rhizosphere", "2404 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Liming", "04 agricultural and veterinary sciences", "15. Life on land", "1111 Soil Science", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2012.10.013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2012.10.013", "name": "item", "description": "10.1016/j.soilbio.2012.10.013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2012.10.013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-02-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2013.11.013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:47Z", "type": "Journal Article", "created": "2013-12-03", "title": "Ryegrass-Derived Pyrogenic Organic Matter Changes Organic Carbon And Nitrogen Mineralization In A Temperate Forest Soil", "description": "Abstract Pyrogenic organic matter (PyOM) is considered as a technique to improve soil fertility and store carbon (C) in soil. However, little is known regarding soil organic C and nitrogen (N) mineralization in PyOM-amended soils. To investigate the relationship between the C and N mineralization rates and the possible consequences in terms of C storage and N availability, we incubated ryegrass-derived PyOM (pyrolyzed at 450\u00a0\u00b0C) enriched in 13 C (4.33 atom %) in a forest Cambisol for 158 days with and without mineral N addition. We determined PyOM and native soil organic C mineralization, NH 4 + and NO 3 \u2212 contents in the soil, gross N mineralization, phenol-oxidase and protease activities, and microbial biomass throughout the incubation experiment and the incorporation of PyOM in microbial biomass at the end of the experiment (158 days). We determined that 4.3% of the initial PyOM-C was mineralized after 158 days. Moreover, PyOM induced a strongly positive priming effect within the first 18 days; a negative priming effect was observed from Days 18 to 158. The initial increase in organic matter mineralization corresponded to a higher gross N mineralization and NH 4 + content in the PyOM-treated soil than in the untreated soil. Ammonium was rapidly transformed into nitrate and stored in this form until the end of the experiment. We conclude that the presence of PyOM affected the mineralization pattern of native soil organic matter mineralization and increased mineral N content, while N addition did not influence PyOM or soil organic matter mineralization.", "keywords": ["2. Zero hunger", "10122 Institute of Geography", "UFSP13-8 Global Change and Biodiversity", "2404 Microbiology", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "910 Geography & travel", "15. Life on land", "1111 Soil Science", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2013.11.013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2013.11.013", "name": "item", "description": "10.1016/j.soilbio.2013.11.013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2013.11.013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-02-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2015.06.022", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:16:48Z", "type": "Journal Article", "created": "2015-07-05", "title": "Precipitation Modifies The Effects Of Warming And Nitrogen Addition On Soil Microbial Communities In Northern Chinese Grasslands", "description": "Terrestrial ecosystems experience simultaneous shifts in multiple drivers of global change, which can interactively affect various resources. The concept that different resources co-limit plant productivity has been well studied. However, co-limitation of soil microbial communities by multiple resources has not been as thoroughly investigated. Specifically, it is not clearly understood how microbial communities respond to shifts in multiple interacting resources such as water, temperature, and nitrogen (N), in the context of global change. To test the effects of these various resources on soil microorganisms, we established a field experiment with temperature and N manipulation in three grasslands of northern China, where there is a decrease in precipitation from east to west across the region. We found that microbial responses to temperature depended upon seasonal water regimes in these temperate steppes. When there was sufficient water present, warming had positive effects on soil microorganisms, suggesting an interaction between water and increases in temperature enhanced local microbial communities. When drought or alternating wet\u2013dry stress occurred, warming had detrimental effects on soil microbial communities. Our results also provide clear evidence for serial co-limitation of microorganisms by water and N at the functional group and community levels, where water is a primary limiting factor and N addition positively affects soil microorganisms only when water is sufficient. We predict that future microbial responses to changes in temperature and N availability could be seasonal or exist only in non-drought years, and will strongly rely on future precipitation regimes.", "keywords": ["2. Zero hunger", "10127 Institute of Evolutionary Biology and Environmental Studies", "13. Climate action", "2404 Microbiology", "570 Life sciences; biology", "590 Animals (Zoology)", "Soil Science", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "Microbiology", "1111 Soil Science", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2015.06.022"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2015.06.022", "name": "item", "description": "10.1016/j.soilbio.2015.06.022", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2015.06.022"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-10-01T00:00:00Z"}}, {"id": "10.1093/femsec/fiv066", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:18:12Z", "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": "10.1111/j.1574-6941.2007.00394.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:18:52Z", "type": "Journal Article", "created": "2007-10-19", "title": "Quantitation And Diversity Analysis Of Ruminal Methanogenic Populations In Response To The Antimethanogenic Compound Bromochloromethane", "description": "Methyl coenzyme-M reductase A (mcrA) clone libraries were generated from microbial DNA extracted from the rumen of cattle fed a roughage diet with and without supplementation of the antimethanogenic compound bromochloromethane. Bromochloromethane reduced total methane emissions by c. 30%, with a resultant increase in propionate and branched chain fatty acids. The mcrA clone libraries revealed that Methanobrevibacter spp. were the dominant species identified. A decrease in the incidence of Methanobrevibacter spp. from the clone library generated from bromochloromethane treatment was observed. In addition, a more diverse methanogenic population with representatives from Methanococcales, Methanomicrobiales and Methanosacinales orders was observed for the bromochloromethane library. Sequence data generated from these libraries aided in the design of an mcrA-targeted quantitative PCR (qPCR) assay. The reduction in methane production by bromochloromethane was associated with an average decrease of 34% in the number of methanogenic Archaea when monitored with this qPCR assay. Dissociation curve analysis of mcrA amplicons showed a clear difference in melting temperatures for Methanobrevibacter spp. (80-82 degrees C) and all other methanongens (84-86 degrees C). A decrease in the intensity of the Methanobrevibacter spp. specific peak and an increase for the other peak in the bromochloromethane-treated animals corresponded with the changes within the clone libraries.", "keywords": ["Male", "0301 basic medicine", "Rumen", "Bromochloromethane", "Methanogens", "Molecular Sequence Data", "Euryarchaeota", "Methanobrevibacter", "Polymerase Chain Reaction", "630", "03 medical and health sciences", "2402 Applied Microbiology and Biotechnology", "Animals", "Methyl coenzyme-M reductase", "Phylogeny", "Gene Library", "2. Zero hunger", "0303 health sciences", "Hydrocarbons", " Halogenated", "2404 Microbiology", "Sequence Analysis", " DNA", "mcrA", "qPCR", "DNA", " Archaeal", "Cattle", "Oxidoreductases", "2303 Ecology", "Methane"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2007.00394.x", "name": "item", "description": "10.1111/j.1574-6941.2007.00394.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-12-01T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:19:03Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACT

Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s V = 0.857, and Theil\uffe2\uff80\uff99s U = 0.316). For species-level community profiling, we found strong correlations ( r s > 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.

IMPORTANCE

A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.

", "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": "PMC11494973", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:28:18Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACT

Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s V = 0.857, and Theil\uffe2\uff80\uff99s U = 0.316). For species-level community profiling, we found strong correlations ( r s > 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.

IMPORTANCE

A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.

", "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/PMC11494973"}, {"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": "PMC11494973", "name": "item", "description": "PMC11494973", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11494973"}, {"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"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=2404+Microbiology&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=2404+Microbiology&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=2404+Microbiology&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=2404+Microbiology&offset=9", "hreflang": "en-US"}], "numberMatched": 9, "numberReturned": 9, "distributedFeatures": [], "timeStamp": "2026-07-27T11:05:22.998163Z"}