Kahlert, Maria
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
Research article2022Peer reviewedOpen access
Baricevic, Ana; Chardon, Cecile; Kahlert, Maria; Karjalainen, Satu Maaria; Pfannkuchen, Daniela Maric; Pfannkuchen, Martin; Rimet, Frederic; Tankovic, Mirta Smodlaka; Trobajo, Rosa; Vasselon, Valentin; Zimmermann, Jonas; Bouchez, Agnes
Implementation of DNA metabarcoding for diatoms for environmental monitoring is now moving from a research to an operational phase, requiring rigorous guidelines and standards. In particular, the first steps of the diatom metabarcoding process, which consist of sampling and storage, have been addressed in various ways in scientific and pilot studies and now need to be rationalised. The objective of this study was to compare three currently applied preservation protocols through different storage durations (ranging from one day to one year) for phytobenthos and phytoplankton samples intended for diatom DNA metabarcoding analysis. The experimental design used samples from four freshwater and two marine sites of diverse ecological characteristics. The impact of the sample preservation and storage duration was assessed through diatom metabarcoding endpoints: DNA quality and quantity, diversity and richness, diatom assemblage composition and ecological index values (for freshwater samples). The yield and quality of extracted DNA only decreased for freshwater phytoben-thos samples preserved with ethanol. Diatom diversity was not affected and their taxonomic composition predominantly reflected the site origin. Only rare taxa (< 100 reads) differed among preservation methods and storage durations. For biomonitoring purposes, freshwater ecological index values were not affected by the preservation method and storage duration tested (including ethanol preservation), all treatments returning the same ecological status for a site. This study contributes to consolidating diatom metabarcoding. Thus, accompa-nied by operational standards, the method will be ready to be confidently deployed and prescribed in future regulatory monitoring.
biomonitoring; diatom assemblages; DNA metabarcoding; European Water Framework Directive; methods; sample preservation
Metabarcoding and Metagenomics
2022, volume: 6, article number: e85844
Environmental Sciences
https://res.slu.se/id/publ/120501