FRESHBAR – Barcoding of freshwater organisms for improved assessment of biodiversity

The ultimate aim of FRESHBAR was 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 were also be compared, to resolve taxonomic uncertainties of closely related species.

Reports & results

• Final report: Kahlert, M., Johnson, R.K., Goedkoop, W., Brodin, Y., Lyrholm, T., Zimmermann, J. 2024. FRESHBAR – Streckkodning av sötvattenorganismer för förbättrade bedömningar av biodiversitet. Rapport 7130, Naturvårdsverket (in Swedish with English summary)
• Video by DNAquaNet: Environmental DNA (eDNA) bioassessment in a nutshell (YouTube)
• 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.
• 312 diatom monoclonal diatom cultures (strains) were established using single-cell isolation, of which 258 strains were successfully sequenced with Sanger technique for barcodes rbcL and 18S. A selection of strains were sent alive for long-term storage to diatom culture collections. The morphological identification of the strains is ongoing (~50 species), and vouchering is prepared.
• Metabarcoding of invertebrates of 12 lakes identified 78 chironomid species, which was a marked increase in taxonomic resolution compared to the routine method, where only ~20 species are separated. Analyses of old samples showed no systematic difference in results compared to recent samples. COI was sufficient to identify most 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 was conducted in two workpackages in cooperation with national and international partners, including the former 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) were responsible for WP1 on diatoms, Willem Goedkoop and Richard Johnson (SLU) for WP2 on invertebrates.