Recommendations for the preservation of environmental samples in diatom metabarcoding studies

By

Baricevic, Ana
Chardon, Cécile
Kahlert, Maria
Karjalainen, Satu Maaria
Pfannkuchen, Daniela Maric
Pfannkuchen, Martin
Rimet, Frederic
Tankovic, Mirta Smodlaka
Trobajo, Rosa
Vasselon, Valentin
Zimmermann, Jonas
Bouchez, Agnès

Type

Article

Date of Publication

2022-11-24

Original Publication

Metabarcoding and metagenomics

Volume

6

Pages

1--17

Subjects

biomonitoring , diatom assemblages , DNA metabarcoding , European Water Framework Directive , methods , sample preservation

Contributed by

Pensoft Publishers

Language

English

Published by

Bulgaria Pensoft Publishers 2017-

Identifiers

DOI: https://doi.org/10.3897/mbmg.6.85844

 

Abstract

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 (< 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, accompanied by operational standards, the method will be ready to be confidently deployed and prescribed in future regulatory monitoring.