This dataset contains ITS metabarcoding data describing fungal communities associated with germinating seeds and early developmental stages of Pyroleae species and Monotropa hypopitys in Sweden. The data were generated using high-throughput sequencing of the ITS2 region to characterize ectomycorrhizal fungal diversity and its relationship to plant development and ecological conditions.DescriptionThe dataset originates from a field-based seed sowing experiment designed to investigate fungal associations during early ontogeny of mycoheterotrophic and partially mycoheterotrophic plants (Johansson et al. 2017). Seed bags were deployed across multiple forest sites and retrieved over multiple years to assess germination, seedling development, and associated fungal communities. DNA was extracted from germinated seedlings and analyzed using ITS metabarcoding of the ITS2 region. The resulting dataset includes operational taxonomic units (OTUs), taxonomic assignments, and sequence read abundances, providing a detailed characterization of fungal diversity associated with early plant life stages.PurposeThe purpose of this dataset is to document the diversity and composition of fungal communities associated with early developmental stages of selected plant species and to support research on plant-fungal interactions, mycoheterotrophy, and forest ecosystem processes, building on the findings presented in Johansson et al. 2017, Mol Ecol, 26: 2591-2604. https://doi.org/10.1111/mec.14050
This dataset was published via the SBDI ASV portal.
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was conducted on the island of Öland, Sweden, across multiple forest sites including coniferous and mixed forests.","boundingBox":{"minLatitude":56.438,"maxLatitude":57.353,"minLongitude":16.387,"maxLongitude":17.093,"globalCoverage":false}}],"temporalCoverages":[],"keywordCollections":[{"thesaurus":"GBIF Dataset Type Vocabulary: http://rs.gbif.org/vocabulary/gbif/dataset_type_2015-07-10.xml","keywords":["Monotropa hypopitys","metabarcoding","Sweden","Pyroleae","dust seeds","ITS","mycoheterotrophy","Occurrence","ectomycorrhizal fungi","seedling development","fungal communities"]}],"samplingDescription":{"studyExtent":"The study was conducted on the island of Öland, Sweden, across multiple forest sites representing different habitat types, including old-growth coniferous forests dominated by Pinus sylvestris and mixed coniferous–deciduous forests. The sites were selected to represent suitable habitats for the target plant species and to allow comparison between locations with and without established adult individuals of the studied species.","sampling":"Seeds of five plant species (Chimaphila umbellata, Moneses uniflora, Monotropa hypopitys, Pyrola chlorantha, and Pyrola rotundifolia) were collected from mature individuals at each study site. Seeds were placed in mesh seed bags and buried in experimental plots in the field. At each site, seed bags were deployed both in plots containing adult plants (occupied plots) and in control plots without adult individuals (unoccupied plots), allowing comparison of germination and fungal associations under different ecological conditions.\n\nSeed bags were retrieved annually over a three-year period following sowing. Upon retrieval, germination status and developmental stage of seedlings were recorded. Seedlings were categorized into developmental stages (germinated, elongated, and branched), and samples of germinated seedlings were collected for molecular analysis of associated fungal communities.","qualityControl":"Sequence data were subjected to multiple quality control steps to ensure reliability. Raw reads were filtered to remove low-quality sequences, chimeric sequences, and singletons. Only sequences passing quality thresholds were retained for further analysis. Operational taxonomic units (OTUs) were clustered at a 97 percent sequence similarity threshold. Taxonomic assignments were performed using reference databases, and assignments were accepted based on sequence similarity criteria. Negative controlsitem-0 were included during laboratory procedures to detect contamination, and non-target sequences were excluded from analyses where appropriate (Johansson et al. 2017).\nRe-annotation against UNITE database took place before publication of this dataset (2026-03-30).","methodSteps":["DNA was extracted from germinated seedlings using a soil DNA extraction protocol. The internal transcribed spacer (ITS) region was amplified using PCR with primers targeting fungal ITS regions. Amplicons were normalized, pooled, and sequenced using 454 pyrosequencing technology.\n\nSequence data were processed using bioinformatics pipelines that included demultiplexing, trimming, and clustering into OTUs. Representative sequences for each OTU were compared against reference databases (including UNITE and INSDC) for taxonomic identification. OTUs were assigned to taxonomic levels based on sequence similarity thresholds, and fungal taxa of interest, particularly ectomycorrhizal groups, were identified for further ecological analysis."]},"countryCoverage":[],"collections":[],"dataDescriptions":[],"dataLanguage":"eng","purpose":"The purpose of this dataset is to characterize the diversity and composition of fungal communities associated with germinating seeds and early seedling development of selected plant species. The dataset supports analyses of host specificity, ontogenetic shifts in fungal associations, and the ecological processes underlying mycoheterotrophy. It also contributes DNA-derived biodiversity data to support broader research on forest ecosystems, species interactions, and biodiversity patterns.
","introduction":"This dataset documents fungal communities associated with early developmental stages of mycoheterotrophic and partially mycoheterotrophic plants in boreal forest ecosystems in Sweden. Using ITS metabarcoding, the dataset captures DNA-derived evidence of fungal taxa associated with germinating seeds and seedlings of Pyroleae species and Monotropa hypopitys. The study provides insight into plant–fungal interactions during critical early life stages and contributes to understanding the ecological role of ectomycorrhizal fungi in plant establishment, as described in Johansson et al. 2017 (https://doi.org/10.1111/mec.14050).
","gettingStarted":"The dataset is structured as a sampling-event dataset. Each event corresponds to a sampling unit defined by site, time of collection, host plant species, and developmental stage of the seedling. Fungal taxa are reported as DNA-derived observations based on ITS metabarcoding and are associated with sampling events through occurrence and measurement data.
Users should note that the dataset represents inferred presence of taxa based on DNA sequences rather than direct observations of organisms. Sequence read counts provide a proxy for relative abundance but should be interpreted with caution. For detailed methodological background and ecological interpretation, users are encouraged to consult Johansson et al. 2017.The dataset is based on DNA metabarcoding and therefore reflects detected DNA rather than confirmed active interactions. Taxonomic resolution depends on reference database completeness, and some OTUs may only be assigned to higher taxonomic levels. Sequence read abundance should not be interpreted as a direct measure of organism abundance.
","pubDate":"2026-03-30T00:00:00.000+00:00","maintenanceUpdateFrequency":"NOT_PLANNED","maintenanceDescription":"","license":"http://creativecommons.org/licenses/by/4.0/legalcode","dwca":{"coreType":"http://rs.tdwg.org/dwc/terms/Occurrence","extensions":["http://rs.iobis.org/obis/terms/ExtendedMeasurementOrFact","http://rs.gbif.org/terms/1.0/DNADerivedData"],"modified":"2026-03-30T14:03:21.001+00:00"},"category":["eDNA"],"approximateCounts":{"occurrenceCount":9922}}