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Optimising Zooplankton DNA Metabarcoding: Methodological Considerations for Large-Scale Monitoring.

Elizaveta Ershova-Menze^1,2, Jon-Ivar Westgaard², Helene Hjellnes²

¹Akvaplan-Niva, Bergen, Norway.

Molecular Ecology Resources

|May 22, 2026

Summary

DNA metabarcoding for plankton monitoring shows robust biodiversity patterns across methods. Standardizing protocols, like using Tris-EDTA-SDS buffer and curated databases, enhances reliability for ecological studies.

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Area of Science:

Marine biology
Molecular ecology
Environmental DNA (eDNA)

Background:

DNA metabarcoding is widely used for plankton monitoring but suffers from inconsistent methodologies.
Lack of standardization hinders biodiversity trend analysis and data integration across studies.

Purpose of the Study:

To assess the impact of methodological choices on DNA metabarcoding results for plankton.
To provide a roadmap for improving reliability and reproducibility in marine zooplankton monitoring.

Main Methods:

Controlled experimental comparisons of different metabarcoding protocols.
Comprehensive literature synthesis of existing studies.
Analysis of COI metabarcoding data, including sample preservation, DNA extraction, sequencing, and taxonomic assignment.

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Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

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Published on: November 25, 2016

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Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

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Main Results:

Biodiversity and community patterns are robust across various tested methods.
Tris-EDTA-SDS buffer with at-sea homogenization is a viable alternative to ethanol preservation.
Integrating multiple classification methods and reference databases improves diversity estimates.
Stricter filtering thresholds enhance data robustness but may exclude rare taxa.

Conclusions:

DNA metabarcoding patterns are generally comparable across studies, despite methodological variations.
Standardization of key steps, such as sample preservation and taxonomic assignment, is crucial.
This study offers practical guidance to improve the consistency and reliability of plankton monitoring using DNA metabarcoding.