Quantifying environmental DNA signals for aquatic invasive species across multiple detection platforms

Area of Science:

• Environmental molecular surveillance
• Aquatic invasive species detection
• Molecular biology techniques

Background:

• Molecular surveillance methods, including environmental DNA (eDNA), offer enhanced sensitivity and efficiency over traditional sampling for aquatic research.
• Advancements in molecular technologies have led to the development of novel detection platforms for eDNA analysis.
• Environmental DNA (eDNA) analysis is increasingly adopted by aquatic researchers and managers for species monitoring.

Purpose of the Study:

• To compare the performance of three eDNA surveillance platforms: traditional polymerase chain reaction (PCR), quantitative PCR (qPCR), and digital droplet PCR (ddPCR).
• To evaluate the sensitivity, efficiency, and cost-effectiveness of ddPCR relative to established methods for aquatic eDNA detection.

Main Methods:

• Water samples were collected over 24 hours from mesocosm experiments with varying densities of invasive species.
• Three eDNA detection platforms were employed: traditional PCR, qPCR, and ddPCR.
• DNA concentrations were estimated and compared across the different platforms.

Main Results:

• All three platforms successfully detected target DNA, even at low organism densities within the first hour of sampling.
• Quantitative PCR (qPCR) and ddPCR yielded comparable estimates of DNA concentrations.
• Digital droplet PCR (ddPCR) analysis was faster and approximately 50% less expensive than qPCR, from sample collection to final analysis.

Conclusions:

• Digital droplet PCR (ddPCR) is a reliable and consistent platform for eDNA surveillance in aquatic environments.
• ddPCR offers a faster and more cost-effective alternative to qPCR for estimating DNA concentrations.
• The adoption of ddPCR is recommended for future aquatic eDNA surveillance applications by researchers and managers.