BIOWIDE eDNA Fungi dataset
Citation
Frøslev T, Ejrnæs R (2018). BIOWIDE eDNA Fungi dataset. Danish Biodiversity Information Facility. Occurrence dataset https://doi.org/10.15468/nesbvx accessed via GBIF.org on 2024-09-04.Description
The Biowide project (2014-2018) was a project aiming at collecting biodiversity data from 130 terrestrial sampling sites across Denmark. Data was collected with both classical means (observation and trapping) and by eDNA metabarcoding (sequencing of amplified marker genes. Data was also collected on environmental variables. Biowide (Biodiversity in Width and Depth) took place in collaboration between Århus Universiity (main project holder) and the two major Danish natural history museums and the University of Copenhagen, and was supported by the Villum Foundation. During the first two years of the project, a host of professionals and volunteers collected data on the environment from the 130 sample plots – on everything from soil moisture, temperature, nutrients, plant biomass, trees, dead wood, stone and ant hills, expanses of water and flowers. The major effort has been collecting information on plants, mosses, lichens, invertebrates and fungi that live in the surfaces. With the help of volunteers, it was attempted to map as much as possible. As part of the Biowide project bulk soil samples were collected from each sampling site for eDNA metabarcoding (sequencing of amplified marker genes) with various genetic markers, for fungi, plants, insects, nematodes, etc. Sampling was stratified across the three gradients expected to have most importance for terrestrial biodiversity: fertility, humidity and disturbance. The plots represent one of the widest ecological samplings for eDNA to this date, as landscape types as diverse as sand dunes, meadows, bogs, agricultural land and also forest plantations and Danish natural forest are included. The project and methods are described in Brunbjerg et al. (2017)
BIOWIDE eDNA Fungi dataset.
As part of the Biowide project soil was collected for eDNA metabarcoding (sequencing of amplified marker genes) with various genetic markers, for fungi, plants, insects, nematodes, etc. This dataset represents data from the metabarcoding targeting soil fungi with primers (sub-)specific for fungi (gITS7 and ITS4), amplifying the ITS2 region.
Sampling Description
Study Extent
DenmarkSampling
From 130 40x40m plots across Danish nature types bulk soil was sampled, DNA extracted, and amplified and sequenced for fungi.Method steps
- For each of the 130 40x40m sampling sites, 81 soil cores were sampled and poole, homogenized and subsampled, and the subsample frozen.
- DNA was extracted from each of the 130 samples samples with a modified protocol based on PowerMax soil kit (MoBio, now Qiagen), and normalized to 1 ng/µl
- For each DNA extract 1 µl, the ITS2 region was amplified in triplicates with the primers gITS7 and ITS4, using Amplitaq Gold. All pcr reactions were tagged with unique 8-9 bp tags (MIDs)
- All pcr products were build into Illumina sequencing libraries with the TruSeq PCR free kit.
- Sequencing of the 130 samples (390 triplicates) was done with the Illumina MiSeq platform using the V2 kit 250 bp paired end seqencensing. Data from two sequencing runs were pooled.
- Paired reads were demultiplexed and analysed with custom scripts similar to those published in Frøslev et al (2017) using cutadapt, vsearch and dada2, and subsequent 98.5% clustering with vsearch.
- Sequences were annotated by comparison with the UNITE database.
- Taxonomic assignment of the OTUs was done using the 2017 UNITE general FASTA release (http://dx.doi.org/10.15156/BIO/587475). We used 98, 90, 85, 80, 75 and 70% sequence identity as for assigning OTUs to species, genus, family, order, or class and kingdom respectively.
Taxonomic Coverages
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Fungirank: kingdom
Geographic Coverages
Bibliographic Citations
- Frøslev T.G., Kjøller R., Bruun H.H., Ejrnæs R., Hansen A.J., Læssøe T., Heilmann-Clausen J. (2019) Man against machine: Do fungal fruitbodies and eDNA give similar biodiversity assessments across broad environmental gradients?, Biological Conservation, Volume 233, 2019, Pages 201-212, ISSN 0006-3207 - DOI:10.1016/j.biocon.2019.02.038
- Frøslev T.G., Kjøller R., Bruun H.H., Ejrnæs R., Brunbjerg A.K., Pietroni C., Hansen A.J. (2017) Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications volume 8, Article number: 1188 - DOI:10.1038/s41467-017-01312-x
- Brunbjerg A.K., Bruun H.H., Brøndum L., Classen A.T., Fog K., Frøslev T.G., Goldberg I., Hansen M.D.D., Høye T.T, Læssøe T, Newman G, Skipper L., Søchting U., Ejrnæs R. (2017) A systematic survey of regional multitaxon biodiversity: evaluating strategies and coverage. bioRxiv, 158030 - DOI:10.1101/158030
Contacts
Tobias Frøslevoriginator
position: Assistant Professor
Natural History Museum of Denmark
Natural History Museum of Denmark, Øster Voldgade 5-7
Copenhagen
DK
email: tobiasgf@snm.ku.dk
userId: http://orcid.org/0000-0002-3530-013X
Rasmus Ejrnæs
originator
position: Senior researcher
Institut for bioscience
Grenåvej 14 bygning 8416, K106
Rønde
8410
DK
email: rasmus@bios.au.dk
Tobias Frøslev
metadata author
position: Assistant Professor
Natural History Museum of Denmark
Natural History Museum of Denmark, Øster Voldgade 5-7
Copenhagen
DK
email: tobiasgf@snm.ku.dk
Rasmus Ejrnæs
administrative point of contact
position: Senior researcher
INSTITUT FOR BIOSCIENCE
Grenåvej 14 bygning 8416, K106
Rønde
8410
DK
email: rasmus@bios.au.dk