Data (images) for: New barcodes of freshwater diatoms from Sweden
The published data are images of freshwater diatoms, taken within the national barcoding project FRESHBAR (2019-2023), a research project focusing on the development of DNA methods for national environmental monitoring. The project was financed by the Environmental Protection Agency’s environmental research grant in collaboration with the Swedish Agency for Marine and Water Management. The aim of the project was to establish as many diatom cultures as possible, to generate their barcodes, to identify them to the lowest taxonomical level possible, and to make all results, data and material publicly available for further research and usage within environmental monitoring. FRESHBAR represents the first large-scale effort to generate barcode reference sequences for Nordic freshwater benthic diatoms. The images are part of the results. Images of living and prepared strains are stored with open access (license: CC0) in the e-archive of the Swedish University of Agricultural Sciences (SLU), available under the permanent link https://hdl.handle.net/20.500.12703/6968. Images are stored in different subfolders, grouped by taxon. Information on storage is found when searching in the menu “By subject”, where the metadata are found under “FRESHBAR images” in the file “FRESHBAR picture images SLU archive.xlsx”. Images taken with LM are stored in the subfolder https://hdl.handle.net/20.500.12703/6822, SEM images in the subfolder https://hdl.handle.net/20.500.12703/6823. Metadata are stored in the subfolder https://hdl.handle.net/20.500.12703/6825. In order to find a specific image item, you can locate the handle in the provided mapfiles.txt, and then go to https://hdl.handle.net/[handle], e.g. for https://hdl.handle.net/20.500.12703/6885 for SEM 1C11.
Go to data source
http://hdl.handle.net/20.500.12703/6968
Documentation files
Documentation files
Citation and access
Citation and access
Data access level:
Creator/Principal investigator(s):
Research principal:
Principal's reference number:
- SLU.ma.2025.4.2.IÄ-7
Data contains personal data:
No
Citation:
Language:
Method and outcome
Method and outcome
Time period(s) investigated:
Data format/data structure:
Species and taxons:
Samples/material - Collected from scientific collection/biobank
Samples/material - Collected from scientific collection/biobank
Name:
Herbarium Berolinense (B)
Type(s) of sample:
diatoms
Data collection - Biological tests
Data collection - Biological tests
Mode of collection:
Biological tests
Description of the mode of collection:
Diatoms were isolated from fresh samples taken in coordination with the Swedish national monitoring program in 2019 and 2020. Those samples were taken following the European standard EN 13946:2025 Water quality - Guidance standard for the routine sampling and preparation of benthic diatoms from rivers and lakes. In total, 273 monoclonal cultures were established from single cells using the micropipette method. Cultures were grown in WC (Guillard and Lorenzen 1972), PM (Stosch and Fecher 1979), or L16 (Lindström 1991) medium at room temperature. Photographs were taken from each living culture if possible. The cultures were subsequently harvested and sequenced, and in parallel identified using morphological characters using light microscopy in a first step. Selected cultures were also studied and pictures taken using scanning electronic microscopy. The clones were harvested when the biomass was sufficient for all further project relevant analysis steps, which included DNA barcode sequencing for rbcL and 18SV4.
Time period(s) for data collection:
2020 - 2021
Data collector:
- Swedish University of Agricultural Sciences
Opens a new window at ror.org.
ROR
Source of the data:
- Research data
- Biological samples
- Other
Geographic coverage
Geographic coverage
Geographic location:
Geographic description:
The diatom material has been sampled from 44 different streams in Sweden, geographically distributed over the country from North to South (58.3475 to 65.4433 WGS84).
Administrative information
Administrative information
Responsible department/unit:
Department of Aquatic Sciences and Assessment
Commissioning organisation:
- Swedish Environmental Protection Agency
Opens a new window at ror.org.
ROR
Registration number at commissioning organization:
- 18/171
Identifiers
Identifiers
Handle:
Funding
Funding
Funding agency:
- Swedish Agency for Marine and Water Management
Opens a new window at ror.org.
ROR
Award number:
18/171
Funding agency:
- Swedish Environmental Protection Agency
Opens a new window at ror.org.
ROR
Award number:
18/171
Topic and keywords
Topic and keywords
Swedish Standard Classification of Research Subjects 2025:
Relations
Relations
Publications
Publications
Citation:
Kahlert, M., Mora, D. Kusber, W-H., Abarca, N. & Zimmermann, J. (XXXX) New DNA barcode reference data of freshwater diatoms from Sweden - old acquaintances and new taxa. Environmental DNA. in process
