Recommendations for the preservation of environmental samples in diatom metabarcoding studies
2022
Baricevic, Ana | Chardon, Cécile | Kahlert, Maria | Karjalainen, Satu Maaria | Pfannkuchen, Daniela Maric | Pfannkuchen, Martin | Rimet, Frederic | Smodlaka Tankovic, Mirta | 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 phytobenthos samples preserved with ethanol. Diatom diversity was not affected and their taxonomic composition predominantly reflected the site origin. Only rare taxa (
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