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Related Experiment Video

Updated: Aug 22, 2025

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

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

Published on: November 25, 2016

Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence-based

Avery McCarthy¹, Hoda Rajabi¹, Beverly McClenaghan¹

¹Centre for Environmental Genomics Applications, eDNAtec Inc., Newfoundland and Labrador, St. John's, Canada.

Molecular Ecology Resources

|November 11, 2022

Summary

Next-generation sequencing (NGS) offers superior sensitivity for environmental DNA (eDNA) detection compared to qPCR. This advanced method is crucial for comprehensive ecological biomonitoring of aquatic species.

Keywords:

environmental DNA fish limit of detection metabarcoding next-generation sequencing qPCR

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Last Updated: Aug 22, 2025

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

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Published on: August 1, 2025

Area of Science:

Ecology
Conservation Biology
Molecular Ecology

Background:

Environmental DNA (eDNA) methods are vital for ecological and conservation biomonitoring.
Quantitative PCR (qPCR) is a standard for species-specific detection from eDNA, particularly for fish.
DNA metabarcoding presents a potential alternative to qPCR for certain eDNA applications.

Purpose of the Study:

To compare the sensitivity of Illumina NovaSeq 6000 next-generation sequencing (NGS) with qPCR TaqMan assays.
To determine the limits of detection for both methods using aquatic eDNA.
To evaluate eDNA analysis from Churchill River and Lake Melville, NL, Canada.

Main Methods:

Collected eDNA samples from water in Churchill River and Lake Melville.
Performed species-specific, targeted NGS assays.
Utilized qPCR TaqMan assays for comparison.
Measured limits of detection for both NGS and qPCR.

Main Results:

Targeted NGS assays demonstrated significantly higher sensitivity than qPCR, with 14- to 29-fold lower limits of detection.
Targeted NGS detected Gadus ogac (Greenland cod) in 29% of samples, compared to 21% with qPCR.
General NGS assays matched qPCR sensitivity while detecting 15 fish species simultaneously.

Conclusions:

Next-generation sequencing (NGS) offers enhanced sensitivity and broader detection capabilities for eDNA analysis compared to traditional qPCR.
Sensitive and parallel eDNA detection methods like NGS are essential for effective regional and global biomonitoring of the planet's diverse fish species.