{"type": "FeatureCollection", "facets": {"type": {"type": "terms", "property": "type", "buckets": [{"value": "Journal Article", "count": 60}, {"value": "Dataset", "count": 3}, {"value": "Report", "count": 1}]}, "soil_chemical_properties": {"type": "terms", "property": "soil_chemical_properties", "buckets": [{"value": "carbon", "count": 5}, {"value": "ammonia", "count": 3}, {"value": "soil organic carbon", "count": 2}]}, "soil_biological_properties": {"type": "terms", "property": "soil_biological_properties", "buckets": [{"value": "microbiome", "count": 64}, {"value": "soil animal diversity", "count": 2}, {"value": "microbial biomass", "count": 1}, {"value": "plants", "count": 1}, {"value": "soil organisms", "count": 1}]}, "soil_physical_properties": {"type": "terms", "property": "soil_physical_properties", "buckets": [{"value": "water", "count": 2}]}, "soil_classification": {"type": "terms", "property": "soil_classification", "buckets": []}, "soil_functions": {"type": "terms", "property": "soil_functions", "buckets": []}, "soil_threats": {"type": "terms", "property": "soil_threats", "buckets": [{"value": "contamination", "count": 1}, {"value": "soil pollution", "count": 1}]}, "soil_processes": {"type": "terms", "property": "soil_processes", "buckets": [{"value": "sedimentation", "count": 1}]}, "soil_management": {"type": "terms", "property": "soil_management", "buckets": [{"value": "cultivation", "count": 1}]}, "ecosystem_services": {"type": "terms", "property": "ecosystem_services", "buckets": []}}, "features": [{"id": "2946862318", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-04T16:26:27Z", "type": "Journal Article", "created": "2019-06-03", "title": "Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes", "description": "

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe\u2013plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant\u2013growth\u2013promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

", "keywords": ["0301 basic medicine", "570", "plant\u2013growth\u2013promotion (PGP)", "metagenomically-assembled-genomes (MAGs)", "Article", "03 medical and health sciences", "carbon dioxide fixation", "Ammonia", "metagenomic binning", "Germany", "soil microbiome", "Proteobacteria", "Humans", "biocontrol", "secondary metabolite synthesis", "suppressive soil", "Phylogeny", "Soil Microbiology", "soil microbiome; suppressive soil; biocontrol; plant\u2013growth\u2013promotion (PGP); metagenomic binning; metagenomically-assembled-genomes (MAGs); secondary metabolite synthesis; carbon dioxide fixation; carbohydrate-active enzymes; differentially abundant features (DAFs)", "2. Zero hunger", "Bacteria", "Bacteroidetes", "Agriculture", "differentially abundant features (DAFs)", "15. Life on land", "Archaea", "Actinobacteria", "13. Climate action", "carbohydrate-active enzymes", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://doi.org/2946862318"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2946862318", "name": "item", "description": "2946862318", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2946862318"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-03T00:00:00Z"}}, {"id": "3132814372", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-04T16:26:44Z", "type": "Journal Article", "created": "2021-02-25", "title": "Mycobiome Composition and Diversity under the Long-Term Application of Spent Mushroom Substrate and Chicken Manure", "description": "

Waste exogenous organic matter, including spent mushroom substrate (SMS) and chicken manure (CM), can be used as the basis of a soil-improving cropping system in sustainable agriculture. However, there is\u2014as yet\u2014a lack of information about important quality indicators such as the fungal community relative abundance, structure and biodiversity in soils treated with these additives. In this study, the responses of the soil fungal community composition and mycobiome diversity to SMS and CM application compared to the control soil were evaluated using a combination of the following molecular approaches: quantitative polymerase chain reactions, denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism, and next-generation sequencing. The most abundant phylum for both treatments was Ascomycota, followed by Basidiomycota. The application of SMS and CM increased the abundance of fungi, including Tremellomycetes and Pezizomycetes for the SMS additive, while the Mortierellomycetes, Pezizomycetes, and Leotiomycetes levels increased after CM addition. SMS and CM beneficially reduced the relative abundance of several operational taxonomic units (OTUs) which are potential crop pathogens. The results provide a novel insight into the fungal community associated with organic additives, which should be beneficial in the task of managing the soil mycobiome as well as crop protection and productivity.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "soil fungal diversity", "S", "phytopathogens", "microbiome", "Agriculture", "15. Life on land", "exogenous organic additives", "6. Clean water", "fungal fingerprinting", "03 medical and health sciences", "mycobiota"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/11/3/410/pdf"}, {"href": "https://www.mdpi.com/2073-4395/11/3/410/pdf"}, {"href": "https://doi.org/3132814372"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3132814372", "name": "item", "description": "3132814372", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3132814372"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-24T00:00:00Z"}}, {"id": "3116316209", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-04T16:26:43Z", "type": "Journal Article", "created": "2020-12-29", "title": "Linking microbial functional gene abundance and soil extracellular enzyme activity: Implications for soil carbon dynamics", "description": "Emerging evidence indicates that enzyme-catalyzed transformation and degradation of soil organic matter at the ecosystem scale is more likely driven by microbial functional gene abundance, rather than short term induction/repression responses. In this paper, we are trying to highlight the potential links between microbial functional gene abundance and soil extracellular enzyme activity. Those links will likely offer a new path for optimizing the model performance of microbial-mediated soil C dynamics from microbial functional gene perspectives.", "keywords": ["Soil", "Nitrogen", "01 natural sciences", "Carbon", "Ecosystem", "Soil Microbiology", "Mycobiome", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/3116316209"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3116316209", "name": "item", "description": "3116316209", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3116316209"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-17T00:00:00Z"}}, {"id": "3136853395", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-04T16:26:44Z", "type": "Journal Article", "created": "2021-03-15", "title": "Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil", "description": "

The soil microbiome consists of a vast variety of microorganisms which contribute to essential ecosystem services including nutrient recycling, protecting soil structure, and pathogen suppression. Recalcitrant organic compounds present in soils contaminated with fuel oil can lead to a decrease in functional redundancy within soil microbiomes. Ecopiling is a passive bioremediation technique involving biostimulation of indigenous hydrocarbon degraders, bioaugmentation through inoculation with known petroleum-degrading consortia, and phytoremediation. The current study investigates the assemblage of soil microbial communities and pollutant-degrading potential in soil undergoing the Ecopiling process, through the amplicon marker gene and metagenomics analysis of the contaminated soil. The analysis of key community members including bacteria, fungi, and nematodes revealed a surprisingly diverse microbial community composition within the contaminated soil. The soil bacterial community was found to be dominated by Alphaproteobacteria (60\uffe2\uff80\uff9370%) with the most abundant genera such as Lysobacter, Dietzia, Pseudomonas, and Extensimonas. The fungal community consisted mainly of Ascomycota (50\uffe2\uff80\uff9370% relative abundance). Soil sequencing data allowed the identification of key enzymes involved in the biodegradation of hydrocarbons, providing a novel window into the function of individual bacterial groups in the Ecopile. Although the genus Lysobacter was identified as the most abundant bacterial genus (11\uffe2\uff80\uff9346%) in all of the contaminated soil samples, the metagenomic data were unable to confirm a role for this group in petrochemical degradation. Conversely, genera with relatively low abundance such as Dietzia (0.4\uffe2\uff80\uff939.0%), Pusillimonas (0.7\uffe2\uff80\uff932.3%), and Bradyrhizobium (0.8\uffe2\uff80\uff931.8%) did possess genes involved in aliphatic or aromatic compound degradation.Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.Conventional methods of agricultural pest control and crop fertilisation are contributing to a crisis of biodiversity loss, biogeochemical cycle dysregulation, and ecosystem collapse. Thus, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome may contribute to this goal as microbes can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. We applied 16S rRNA gene & fungal 18S rRNA gene (ITS2 region) amplicon sequencing to profile the diversity of the bacterial, archaeal & fungal communities associated with the roots of UK elite spring bread wheat varietyTriticum aestivum var.Paragon in different soils and developmental stages. This revealed that community composition shifted significantly for all three groups across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these wereStreptomycetaceaeandBurkholderiaceae.Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. To understand which microbes are using wheat root exudates in the rhizosphere, root exudates were labelled in a13CO2DNA stable isotope probing experiment. This shows that bacterial taxa within theBurkholderiaceaefamily among other core enriched taxa, such asPseudomonadaceae,were able to use root exudates butStreptomycetaceaewere not. Overall, this work provides a better understanding of the wheat microbiome, including the endosphere community. Understanding crop microbiome formation will contribute to ecologically responsible methods for yield improvement and biocontrol in the future.The climate\uffe2\uff80\uff90driven encroachment of shrubs into the Arctic is accompanied by shifts in soil fungal communities that could contribute to a net release of carbon from tundra soils. At the same time, arctic grazers are known to prevent the establishment of deciduous shrubs and, under certain conditions, promote the dominance of evergreen shrubs. As these different vegetation types associate with contrasting fungal communities, the belowground consequences of climate change could vary among grazing regimes. Yet, at present, the impact of grazing on soil fungal communities and their links to soil carbon have remained speculative. Here we tested how soil fungal community composition, diversity and function depend on tree vicinity and long\uffe2\uff80\uff90term reindeer grazing regime and assessed how the fungal communities relate to organic soil carbon stocks in an alpine treeline ecotone in Northern Scandinavia. We determined soil carbon stocks and characterized soil fungal communities directly underneath and >3\uffc2\uffa0m away from mountain birches (Betula pubescens ssp. czerepanovii) in two adjacent 55\uffe2\uff80\uff90year\uffe2\uff80\uff90old grazing regimes with or without summer grazing by reindeer (Rangifer tarandus). We show that the area exposed to year\uffe2\uff80\uff90round grazing dominated by evergreen dwarf shrubs had higher soil C:N ratio, higher fungal abundance and lower fungal diversity compared with the area with only winter grazing and higher abundance of mountain birch. Although soil carbon stocks did not differ between the grazing regimes, stocks were positively associated with root\uffe2\uff80\uff90associated ascomycetes, typical to the year\uffe2\uff80\uff90round grazing regime, and negatively associated with free\uffe2\uff80\uff90living saprotrophs, typical to the winter grazing regime. These findings suggest that when grazers promote dominance of evergreen dwarf shrubs, they induce shifts in soil fungal communities that increase soil carbon sequestration in the long term. Thus, to predict climate\uffe2\uff80\uff90driven changes in soil carbon, grazer\uffe2\uff80\uff90induced shifts in vegetation and soil fungal communities need to be accounted for.Microplastics affect soil functions depending on drought conditions. However, how their combined effect influences soil fungi and their linkages with ecosystem functions is still unknown. To address this, we used rhizosphere soil from a previous experiment in which we employed microplastic fibres addition and drought in a factorial design, and evaluated their effects on soil fungal communities. Microplastics decreased soil fungal richness under well\uffe2\uff80\uff90watered conditions, likely linked to microplastics leaching toxic substances into the soil, and microplastic effects on root fineness. Under drought, by contrast, microplastics increased pathogen and total fungal richness, likely related to microplastic positive effects on soil properties, such as water holding capacity, porosity or aggregation. Soil fungal richness was the attribute most affected by microplastics and drought. Microplastics altered the relationships between soil fungi and ecosystem functions to the point that many of them flipped from positive to negative or disappeared. The combined effect of microplastics and drought on fungal richness mitigated their individual negative effect (antagonism), suggesting that changes in soil water conditions may alter the action mode of microplastics in soil. Microplastic leaching of harmful substances can be mitigated under drought, while the improvement of soil properties by microplastics may alleviate such drought conditions.Disruption of the microbial community in the respiratory tract due to infections, like influenza, could impact transmission of bacterial pathogens. Using samples from a household study, we determined whether metagenomic-type analyses of the microbiome provide the resolution necessary to track transmission of airway bacteria. Microbiome studies have shown that the microbial community across various body sites tends to be more similar between individuals who cohabit in the same household than between individuals from different households. We tested whether there was increased sharing of bacteria from the airways within households with influenza infections as compared to control households with no influenza.

Results

We obtained 221 respiratory samples that were collected from 54 individuals at 4 to 5 time points across 10 households, with and without influenza infection, in Managua, Nicaragua. From these samples, we generated metagenomic (whole genome shotgun sequencing) datasets to profile microbial taxonomy. Overall, specific bacteria and phages were differentially abundant between influenza positive households and control (no influenza infection) households, with bacteria like Rothia, and phages like Staphylococcus P68virus that were significantly enriched in the influenza-positive households. We identified CRISPR spacers detected in the metagenomic sequence reads and used these to track bacteria transmission within and across households. We observed a clear sharing of bacterial commensals and pathobionts, such as Rothia, Neisseria, and Prevotella, within and between households. However, due to the relatively small number of households in our study, we could not determine if there was a correlation between increased bacterial transmission and influenza infection.

Conclusion

We observed that airway microbial composition differences across households were associated with what appeared to be different susceptibility to influenza infection. We also demonstrate that CRISPR spacers from the whole microbial community can be used as markers to study bacterial transmission between individuals. Although additional evidence is needed to study transmission of specific bacterial strains, we observed sharing of respiratory commensals and pathobionts within and across households.

", "keywords": ["Bacteria", "Research", "Microbiota", "QR100-130", "3. Good health", "Microbial ecology", "Influenza", " Human", "Humans", "Metagenome", "Clustered Regularly Interspaced Short Palindromic Repeats", "Metagenomics", "Microbiome", "Influenza virus", "Micrococcaceae"]}, "links": [{"href": "https://doi.org/PMC10276449"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC10276449", "name": "item", "description": "PMC10276449", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC10276449"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-17T00:00:00Z"}}, {"id": "PMC8215762", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-04T16:29:04Z", "type": "Journal Article", "created": "2021-02-10", "title": "Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome", "description": "Abstract

Conventional methods of agricultural pest control and crop fertilisation are contributing to a crisis of biodiversity loss, biogeochemical cycle dysregulation, and ecosystem collapse. Thus, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome may contribute to this goal as microbes can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. We applied 16S rRNA gene & fungal 18S rRNA gene (ITS2 region) amplicon sequencing to profile the diversity of the bacterial, archaeal & fungal communities associated with the roots of UK elite spring bread wheat varietyTriticum aestivum var.Paragon in different soils and developmental stages. This revealed that community composition shifted significantly for all three groups across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these wereStreptomycetaceaeandBurkholderiaceae.Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. To understand which microbes are using wheat root exudates in the rhizosphere, root exudates were labelled in a13CO2DNA stable isotope probing experiment. This shows that bacterial taxa within theBurkholderiaceaefamily among other core enriched taxa, such asPseudomonadaceae,were able to use root exudates butStreptomycetaceaewere not. Overall, this work provides a better understanding of the wheat microbiome, including the endosphere community. Understanding crop microbiome formation will contribute to ecologically responsible methods for yield improvement and biocontrol in the future. 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"}}, {"id": "PMC6627896", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-04T16:29:01Z", "type": "Journal Article", "created": "2019-06-03", "title": "Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes", "description": "

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe\u2013plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant\u2013growth\u2013promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

", "keywords": ["0301 basic medicine", "570", "plant\u2013growth\u2013promotion (PGP)", "metagenomically-assembled-genomes (MAGs)", "Article", "03 medical and health sciences", "carbon dioxide fixation", "Ammonia", "metagenomic binning", "Germany", "soil microbiome", "Proteobacteria", "Humans", "biocontrol", "secondary metabolite synthesis", "suppressive soil", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "Bacteria", "Bacteroidetes", "Agriculture", "differentially abundant features (DAFs)", "15. Life on land", "Archaea", "Actinobacteria", "13. Climate action", "carbohydrate-active enzymes", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://doi.org/PMC6627896"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC6627896", "name": "item", "description": "PMC6627896", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC6627896"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-03T00:00:00Z"}}, {"id": "PMC8215787", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-04T16:29:04Z", "type": "Journal Article", "created": "2021-06-07", "title": "Dynamics of Soil Bacterial and Fungal Communities During the Secondary Succession Following Swidden Agriculture IN Lowland Forests", "description": "

Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate effects of soil ages (spanning at least 60 years) after disturbance, geographic distance (from 0.1 to 10 km) and edaphic property gradients (soil pH, conductivity, C, N, P, Ca, Mg, and K), on soil bacterial and fungal communities along a chronosequence of sites representing the spontaneous succession following swidden agriculture in lowland forests in Papua New Guinea. During succession, bacterial communities (OTU level) as well as its abundant (OTU with relative abundance > 0.5%) and rare (<0.05%) subcommunities, showed less variation but more stage-dependent patterns than those of fungi. Fungal community dynamics were significantly associated only with geographic distance, whereas bacterial community dynamics were significantly associated with edaphic factors and geographic distance. During succession, more OTUs were consistently abundant (n = 12) or rare (n = 653) for bacteria than fungi (abundant = 6, rare = 5), indicating bacteria were more tolerant than fungi to environmental gradients. Rare taxa showed higher successional dynamics than abundant taxa, and rare bacteria (mainly from Actinobacteria, Proteobacteria, Acidobacteria, and Verrucomicrobia) largely accounted for bacterial community development and niche differentiation during succession.