FRESHBAR – Barcoding of freshwater organisms for improved assessment of biodiversity

Last changed: 10 August 2020
Diatoms in bottles, photo.

DNA can be used to identify freshwater organisms in a lakes or stream using only a water sample. DNA-based assessment methods can provide better insight into the taxonomy of aquatic organisms and increase cost-efficiency of biological monitoring.

The ultimate aim of FRESHBAR is to establish DNA-barcoding techniques in operative national monitoring and improve assessment of biodiversity human-induced stress on freshwater ecosystems. However, several challenges remain before DNA-based methods can be operational in environmental monitoring. One of them is to improve barcode libraries. The barcode is a portion of a specific gene used to identify species, and the library contains information on which barcodes belongs to which species. FRESHBAR aims at improving reference databases by generating many new species’ barcodes.

In FRESHBAR, different molecular methods will also be compared, to resolve taxonomic uncertainties of closely related species.

Specific tasks

  • providing new reference sequences for diatoms and invertebrates that are important for monitoring
  • guaranteeing the taxonomical correctness of new sequence identifications by molecular and morphological taxonomical curation
  • contribute to the development of metabarcoding using long marker sequences (diatoms) and testing shorter barcodes (invertebrates)
  • comparing morphological and DNA-based identifications across environmental gradients
  • depositing results and samples in quality-assured public databases and collections.

FRESHBAR research will be conducted in two workpackages in cooperation with national and international partners, including the COST network DNAqua-Net, and ongoing SLU research project such as DNA barcoding of benthic diatoms. Maria Kahlert (SLU) and Jonas Zimmermann (Freie Universität Berlin, Germany) are responsible for WP1 on diatoms, Willem Goedkoop and Richard Johnson (SLU) for WP2 on invertebrates. 

Reports & results

  • Status report 2019 (in Swedish, .docx)
  • Bonnie Bailet employed as technical assistant for the diatom cultures 2020-21.
  • Guest researcher Demetrio Mora, Freie Universität Berlin & Botanischer Garten und Botanisches Museum, Germany, visiting SLU 20 Jan-13 Mar 2020 under a Short-term scientific mission (STSM) from the EU network COST DNAqua-Net, working within FRESHBAR with the isolation of new diatom species for barcoding, and with developing long-read sequencing (PacBio) for diatoms together with UMBLA. 200 clones are now growing (April 2020).

Facts:

The project is funded by the Swedish Environmental Protection Agency´s Research Grant in collaboration with the Swedish Agency for Marine and Water Management.

Page editor: simon.hallstan@slu.se