Kungsängen soil microbial communities
Citation
Rosling A, Eshghi Sahraei S, Furneaux B, Kluting K, Zakieh M (2024). Kungsängen soil microbial communities. Version 1.7. Biology Section, Uppsala University. Occurrence dataset https://doi.org/10.15468/upxbwy accessed via GBIF.org on 2024-11-14.Description
Since Linnaeus's time, the Kungsängen Nature Reserve has drawn frequent visitors because of its vegetation including the largest population of Fritillaria meleagris L. in Sweden. The reserve is a meadow with an abrupt moisture transition, where the wetter part has a Carex acuta dominated plant community with low species richness, visually distinct from the drier part, which has a species rich plant community including a high density of Fritillaria meleagris. To investigate the link between plant and below-ground micro-eukaryotic communities, we amplified and sequenced the ITS and LSU regions of the rDNA operon (1500 bp) from soil using PacBio SMRT sequencing, and evaluated three different methods for generation of operational taxonomic units. We found distinct communities associated with wet and mesic-dry soil conditions but estimated richness was not so different. Both soil conditions host communities dominated by protists, a large fraction of which were taxonomically assigned to Ciliphora (Alveolata), while 30-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of the read clustering method used. However, different clustering methods affect the taxonomic and phylogenetic resolution of community characterization with implications for how well members of the micro-eukaryotic communities can be recognized in the data. This data resource contain amplicon sequence variant (ASV) sequences generated with DADA2 using the Ampliseq pipeline (https://nf-co.re/ampliseq). This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/).Sampling Description
Study Extent
Soil samples were collected on June 7th, 2016, at Kungsängen Nature Reserve (N59°50’, E17°40’). Samples were taken from five locations 30 m apart on each side of the soil moisture transition border separated by 30 m across the transition border.Sampling
Soil samples were taken with a soil corer when possible (5cm diameter x 10 cm depth), or with a hand shovel when soil was to wet (sampling depth and volume estimated to correspond to that of the soil cores). Soil samples were individually placed in plastic bags and kept on ice during sampling before storage at 4degC over night. The day after, soils were homogenized in the plastic bags and subsamples were transferred to 15ml conical centrifuge tubes and frozen at -20degC prior to freeze drying. Approximately 250 to 500 mg of freeze-dried soil was used for total DNA extraction. The entire ITS and partial LSU regions of rDNA, approximately 1500 bp, was amplified using a modified ITS1 primer and the LR5 primer. Both primers were indexed for multiplexing to allow pooling of the samples during sequencing. The pooled library was sequenced at SciLifeLab/NGI (Uppsala, Sweden) on the PacBio RSII sequencing platform.Method steps
- Sequence denoising and ASV creation was performed with DADA2 using the nfcore/ampliseq pipeline (https://nf-co.re/ampliseq), commit 5adaf23d7f. Taxonomy assignment was based on the ITS2 region and performed according to https://docs.biodiversitydata.se/analyse-data/molecular-tools/#taxonomy-annotation, using nf-core/ampliseq commit e1bdbfb623 and the database unite-alleuk=8.3 (UNITE general FASTA release for Eukaryotes - Version 8.3, https://doi.org/10.15156/BIO/1280127)
Taxonomic Coverages
Geographic Coverages
Kungsängen Nature Reserve (N59°50’, E17°40’) is a 12.5-hectare reserve in a larger meadow located in the south of Uppsala, Sweden, along the east shore of the Fyris River. Soil samples were taken across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris.
Bibliographic Citations
Contacts
Anna Roslingoriginator
position: Associate Professor
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
Telephone: +46184716444
email: Anna.Rosling@ebc.uu.se
userId: http://orcid.org/0000-0002-7003-5941
Shadi Eshghi Sahraei
originator
position: PhD student
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
email: shadi.eshghi.sahraei@ebc.uu.se
userId: http://orcid.org/0000-0003-4741-5871
Brendan Furneaux
originator
position: PhD student
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
email: brendan.r.furneaux@jyu.fi
userId: http://orcid.org/0000-0003-3522-7363
Kerri Kluting
originator
position: PhD student
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
email: klutingkl@gmail.com
userId: http://orcid.org/0000-0002-2328-8081
Mustafa Zakieh
originator
position: Associate Professor
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
email: m.zakieh@gmail.com
Anna Rosling
metadata author
position: Associate Professor
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
Telephone: +46184716444
email: Anna.Rosling@ebc.uu.se
userId: http://orcid.org/0000-0002-7003-5941
Shadi Eshghi Sahraei
metadata author
position: Associate Professor
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
email: shadi.eshghi.sahraei@ebc.uu.se
userId: http://orcid.org/0000-0003-4741-5871
Anna Rosling
administrative point of contact
position: Associate Professor
Department of Ecology and Genetics, Uppsala University
Evolutionsbiologiskt centrum, Norbyvägen 18D
Uppsala
752 36
SE
Telephone: +46184716444
email: Anna.Rosling@ebc.uu.se
userId: http://orcid.org/0000-0002-7003-5941