Occurrence

18s-v1-3-complete-taxonomy

Latest version published by KTH Royal Institute of Technology on 16 December 2022 KTH Royal Institute of Technology
Publication date:
16 December 2022
License:
CC0 1.0

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 6,491 records in English (2 MB) - Update frequency: unknown
Metadata as an EML file download in English (12 KB)
Metadata as an RTF file download in English (10 KB)

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.

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 6,491 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.

Occurrence (core)
6491
ExtendedMeasurementOrFact 
12982
dnaDerivedData 
6491

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:

Andersson A, Karlson B (2022): 18S data from: Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea (Hu et al. 2016). v1.3. KTH Royal Institute of Technology. Dataset/Occurrence. 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.

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is KTH Royal Institute of Technology. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 406a44dc-d814-4017-b59d-418fe81634a7.  KTH Royal Institute of Technology publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Belgian Biodiversity Platform.

Keywords

Occurrence

Contacts

Anders Andersson
  • Metadata Provider
  • Originator
  • Point Of Contact
Associate Professor
KTH Royal Institute of Technology
Science for Life Laboratory
Stockholm
SE
Bengt Karlson
  • Metadata Provider
  • Originator
Researcher
Swedish Meteorological and Hydrological Institute (SMHI)
Göteborg
SE

Geographic Coverage

Water samples from a transect from Kattegatt to the Gulf of Bothnia

Bounding Coordinates South West [53.278, 9.316], North East [66.373, 27.246]

Temporal Coverage

Start Date / End Date 2013-07-13 / 2013-07-19

Project Data

No Description available

Title Diversity of pico-to mesoplankton along the 2000 km salinity gradient of the Baltic Sea
Identifier https://doi.org/10.3389/fmicb.2016.00679

The personnel involved in the project:

Yue Hu
  • Author
Bengt Karlson
  • Author
Sophie Charvet
  • Author

Sampling Methods

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.

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.

Method step description:

  1. See Sampling Description.

Additional Metadata

Alternative Identifiers 406a44dc-d814-4017-b59d-418fe81634a7
https://ipt.gbif.org/resource?r=dwca-kth-2013-baltic-18s-v1-3