Species-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization

Ecology and Evolution
Gert-Jan JeunenNeil J Gemmell

Abstract

DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding-based biodiversity studies is gaining popularity as a noninvasive, time-efficient, and cost-effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under-surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA-related publications have come a wide array of capture and extraction methods. Without visual species confirmation, inconsistent use of laboratory protocols hinders comparability between studies because the efficiency of target DNA isolation may vary. We determined an optimal protocol (capture and extraction) for marine eDNA research based on total DNA yield measurements by comparing commonly employed methods of seawater filtering and DNA isolation. We compared metabarcoding results of both targeted (small taxonomic group with species-level assignment) and universal (broad taxonomic group with genus/family-level assignment) approaches obtained from replicates treated with the optimal and a low-performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. F...Continue Reading

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Citations

Aug 12, 2020·Molecular Ecology·Luna M van der Loos, Reindert Nijland
Feb 24, 2021·Communications Biology·Cindy BesseyOliver Berry
Jul 3, 2021·Animals : an Open Access Journal From MDPI·Philjae KimSook Shin
Aug 17, 2021·Molecular Ecology Resources·Anastasija ZaikoXavier Pochon

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Methods Mentioned

BETA
Assay
PCR
Illumina sequencing

Software Mentioned

Qubit
PEAR
USEARCH
BLASTn
Geneious
R
BLAST

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