18S data from: Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea (Hu et al. 2016)
Citation
Andersson A, Karlson B (2023). 18S data from: Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea (Hu et al. 2016). Version 1.9. KTH Royal Institute of Technology. Occurrence dataset https://doi.org/10.15468/5k9w88 accessed via GBIF.org on 2023-11-28. accessed via GBIF.org on 2024-02-27. accessed via GBIF.org on 2024-06-13. accessed via GBIF.org on 2024-08-15.Description
18S rRNA gene metabarcoding data of surface water microbial communities from 21 off-shore stations following a transect from Kattegat to the Gulf of Bothnia in the Baltic Sea. The data was published in: Yue O O Hu, Bengt Karlson, Sophie Charvet, Anders F Andersson. Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea. Front Microbiol. 2016 May 12;7:679. doi: 10.3389/fmicb.2016.00679. This dataset was published via the SBDI ASV portal.Sampling Description
Study Extent
Twenty-one water samples were collected in the Kattegat, the Baltic Proper and the Gulf of Bothnia during 13th–19th of July 2013.Sampling
Twenty-one water samples were collected in the Kattegat, the Baltic Proper and the Gulf of Bothnia using a FerryBox system installed in the ship TransPaper during 13th–19th of July 2013. The ship followed the route: Gothenburg (Sweden)—Kemi (Finland)—Oulu (Finland)—Lübeck (Germany)—Gothenburg. The FerryBox system consists of a pump with a water inlet at 3 m depth, a circuit of multiple sensors for temperature, conductivity, chlorophyll and phycocyanin fluorescence, turbidity, and oxygen as well as automated water sampling devices. A detailed description of the FerryBox system is found in Karlson et al. (in press). Manual water sampling for DNA analysis was carried out both on the Northward and Southward legs. Approximately, 10 L of seawater were collected in a polycarbonate carboy. Subsamples of 200–500 mL were filtered onto 0.22 μm pore-size mixed cellulose ester membrane filters (Merck Millipore co., Cat. No. GSWP04700) to capture plankton. The filters were frozen in liquid nitrogen on board and kept at −20 to −80°C until DNA extraction. Genomic DNA was extracted using the PowerWater® DNA isolation kit (MO-BIO Laboratories Inc, Carlsbad CA, USA) following the instructions provided by the manufacturer. The V4–V5 regions of eukaryotic 18S rRNA genes were PCR amplified with primers 574*F (CGGTAAYTCCAGCTCYV) and 1132R (CCGTCAATTHCTTYAAR) (Hugerth et al., 2014a). A two step PCR procedure was applied (Hugerth et al., 2014a), with 38 (28 + 10) PCR cycles. Between the first and second PCR, and prior to pooling libraries, amplicons were purified with 8.8% PEG 6000 (Polyethylene Glycol 6000) (Merck Millipore co., Cat. No. 528877-1KG) precipitation buffer and CA beads (carboxylic acid-coated superparamagnetic beads) (Dynabeads® MyOne™ Carboxylic Acid, Cat. No. 65012; Lundin et al., 2010). Agilent 2100 Bioanalyzer (Agilent, Technologies, DNA 1000 LabChip kit) and Qubit® 2.0 Fluorometer (Invitrogen, Qubit-IT™ dsDNA HS Assay kit) were used for checking the amplicon fragment sizes and quantification. Equimolar amounts of indexed samples were mixed and sequenced with Illumina MiSeq (Illumina Inc, USA) at NGI/Scilifelab Stockholm. The sequencing reads have been submitted to the European Nucleotide Archive (ENA) under accession numbers PRJEB12362. Sequence processing was not conducted as in the journal publication, but by using the https://nf-co.re/ampliseq pipeline in which the denoising (ASV reconstruction) step was conducted with DADA2.Method steps
- See Sampling Description.
Taxonomic Coverages
Geographic Coverages
Water samples from a transect from Kattegatt to the Gulf of Bothnia
Bibliographic Citations
Contacts
Anders Anderssonoriginator
position: Associate Professor
KTH Royal Institute of Technology
Science for Life Laboratory
Stockholm
SE
email: anders.andersson@scilifelab.se
userId: http://orcid.org/0000-0002-3627-6899
Bengt Karlson
originator
position: Researcher
Swedish Meteorological and Hydrological Institute (SMHI)
Göteborg
SE
email: Bengt.Karlson@smhi.se
Anders Andersson
metadata author
position: Associate Professor
KTH Royal Institute of Technology
Science for Life Laboratory
Stockholm
SE
email: anders.andersson@scilifelab.se
userId: http://orcid.org/0000-0002-3627-6899
Bengt Karlson
metadata author
position: Researcher
Swedish Meteorological and Hydrological Institute (SMHI)
Göteborg
SE
email: Bengt.Karlson@smhi.se
Anders Andersson
administrative point of contact
position: Associate Professor
KTH Royal Institute of Technology
Science for Life Laboratory
Stockholm
SE
email: anders.andersson@scilifelab.se
userId: http://orcid.org/0000-0002-3627-6899
Bengt Karlson
administrative point of contact
position: Researcher
Swedish Meteorological and Hydrological Institute (SMHI)
Göteborg
SE
Anders Andersson
administrative point of contact
position: Associate Professor
KTH Royal Institute of Technology
Science for Life Laboratory
Stockholm
SE
email: anders.andersson@scilifelab.se
userId: http://orcid.org/0000-0002-3627-6899