DNA barcoding of benthic diatoms

Last changed: 29 April 2020

The aim of this project is to develop DNA metabarcoding of benthic diatoms for use in environmental assessment in Sweden

DNA barcoding of benthic diatoms can be used for ecological status classification of streams, and CEN standards are under development, but there are many questions that need to be investigated first.

One goal of this projekt is to achieve more complete and correct taxa lists for both traditional and molecular methods as another step for the routine usage of metabarcoding in the future.

In this way, it will be possible to use well-implemented diatom metrics for environmental assessment also with metabarcoding data.

It took 100 years to get a diatom metric that is now commonly and frequently used in Europe, based on an agreed diatom ecology based on morphological taxa
We should take advantage of this knowledge, but can improve it with new knowledge gained by metabarcoding data. New metrics based on metabarcoding data will also be developed and tested.
 

Cooperation

INRA (FR), NIVA (NO), SYKE (FIN), Icelandic Institute of Freshwater Fisheries, The Royal Botanic Garden Edinburgh (UK).

DNAqua-net - genomic tools for routine application of biomonitoring of European water bodies

EDNA - national network to develop DNA methods for monitoring and assessment

PhD student project "New methods improving freshwater conservation and management" Bonnie Bailet funded by Stiftelsen Oscar och Lili Lamms Minne

Publications

Reference library, open access 21.9.2015: http://138.102.89.206/new_rsyst_alg/
Rimet et al. (2016). R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database. DOI: 10.1093/database/baw016.

Groendahl Sophie, Kahlert Maria & Fink Patrick (2017).  The best of both worlds: a combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods.  PLoS ONE,  (12) 12(2),  DOI:10.1371/journal.pone.0172808             

Vasselon, V., et al. (2017). "Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?" Freshwater Science 36(1): 162-177.

Page editor: Simon.Hallstan@slu.se