Description
Data Records
The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 9,922 records.
2 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.
This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.
Versions
The table below shows only published versions of the resource that are publicly accessible.
How to cite
Researchers should cite this work as follows:
Johansson V (2026). Fungal ITS2 data from Pyroleae and Monotropa hypopitys germination study. Version 1.1. Stockholm University. Occurrence dataset. https://www.gbif.se/ipt/resource?r=pyrola-its2-2011-2012&v=1.1
Rights
Researchers should respect the following rights statement:
The publisher and rights holder of this work is Stockholm University. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF Registration
This resource has been registered with GBIF, and assigned the following GBIF UUID: d19074ea-f1cf-42ba-9109-e99a5e6a50a5. Stockholm University publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF Sweden.
Keywords
Occurrence; ITS; metabarcoding; fungal communities; ectomycorrhizal fungi; mycoheterotrophy; seedling development; Pyroleae; Monotropa hypopitys; dust seeds; Sweden
Contacts
- Metadata Provider ●
- Originator ●
- Point Of Contact
- GBIF Sweden Node Manager
- Box 50007
- +468-51954036
https://orcid.org/https://orcid.org/0000-0002-3028-9947
- Principal Investigator
- Author
- Author
- Author
Geographic Coverage
Sampling was conducted on the island of Öland, Sweden, across multiple forest sites including coniferous and mixed forests.
| Bounding Coordinates | South West [56.438, 16.387], North East [57.353, 17.093] |
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Taxonomic Coverage
N/A
| Kingdom | Fungi |
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| Phylum | Mortierellomycota, Basidiobolomycota, Entorrhizomycota, Mucoromycota, Ascomycota, Zoopagomycota, Rozellomycota, Basidiomycota, Chytridiomycota |
| Class | Geminibasidiomycetes, Rhizophydiomycetes, Rozellomycota_cls_Incertae_sedis, Tremellomycetes, GS27, Atractiellomycetes, Spizellomycetes, Mortierellomycetes, Microbotryomycetes, Basidiobolomycota_cls_Incertae_sedis, Malasseziomycetes, Pezizomycotina_cls_Incertae_sedis, Dothideomycetes, Candelariomycetes, Eurotiomycetes, Entorrhizomycetes, Umbelopsidomycetes, Exobasidiomycetes, Sordariomycetes, Saccharomycetes, Lobulomycetes, Geoglossomycetes, Mucoromycetes, Pucciniomycetes, Rhizophlyctidomycetes, Archaeorhizomycetes, Arthoniomycetes, Agaricomycetes, Cystobasidiomycetes, Ascomycota_cls_Incertae_sedis, Rozellomycotina_cls_Incertae_sedis, Zoopagomycetes, Pezizomycetes, Basidiobolomycetes, Leotiomycetes, Orbiliomycetes |
| Order | Leucosporidiales, Pezizomycotina_ord_Incertae_sedis, Microthyriales, Filobasidiales, Myrmecridiales, Agaricomycetes_ord_Incertae_sedis, Eurotiomycetidae_ord_Incertae_sedis, Lichenostigmatales, Trichosphaeriales, Microbotryomycetes_ord_Incertae_sedis, Auriculariales, Sordariales, Leotiomycetes_ord_Incertae_sedis, Rhizophlyctidales, Cladosporiales, Mytilinidiales, Orbiliales, Onygenales, Verrucariales, Helicobasidiales, Exobasidiomycetes_ord_Incertae_sedis, Malasseziales, Tremellodendropsidales, Microascales, Cystofilobasidiales, Trichosporonales, Sebacinales, Dothideomycetes_ord_Incertae_sedis, Geminibasidiales, Corticiales, Geoglossales, Acrospermales, Mortierellales, Pseudodactylariales, Rhytismatales, Asterinales, Helotiales, Mucorales, Chaetosphaeriales, Agaricales, GS11, Cephalothecales, Atheliales, Trechisporales, Entorrhizales, Annulatascales, Rozellomycota_ord_Incertae_sedis, Basidiobolomycota_ord_Incertae_sedis, Candelariales, Pleosporales, Umbelopsidales, Pezizales, Glomerellales, Kriegeriales, Spizellomycetales, Polyporales, Sporidiobolales, Zoopagales, Mycosphaerellales, Eurotiales, Capnodiales, Patellariales, GS27_ord_Incertae_sedis, Hymenochaetales, Sclerococcales, Xylariales, Russulales, Hypocreales, Atractiellales, Botryosphaeriales, Tremellales, Chaetothyriales, Venturiales, Exobasidiales, Thelebolales, Tubeufiales, Magnaporthales, Thelephorales, Rhizophydiales, Leotiales, Gloniales, Lobulomycetales, Saccharomycetales, Boletales, Ascomycota_ord_Incertae_sedis, Archaeorhizomycetales, Coniochaetales, Cantharellales, Basidiobolales, Cystobasidiales, Phacidiales, Chaetomellales, Dothideales, Amphisphaeriales |
Sampling Methods
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. Seed 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.
| Study Extent | 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. |
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| Quality Control | 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). Re-annotation against UNITE database took place before publication of this dataset (2026-03-30). |
Method step description:
- 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. Sequence 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.
Additional Metadata
| Introduction | |
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| Getting Started | |
| Purpose | |
| Alternative Identifiers | d19074ea-f1cf-42ba-9109-e99a5e6a50a5 |
| https://www.gbif.se/ipt/resource?r=pyrola-its2-2011-2012 |