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

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.