An optimized eDNA protocol for fish tracking in estuarine environments.

Area of Science:

• Environmental DNA (eDNA) analysis
• Aquatic biodiversity assessment
• Estuarine ecosystem monitoring

Background:

• Environmental DNA (eDNA) is a powerful, noninvasive tool for biodiversity research.
• Estuarine systems present unique challenges for eDNA, including PCR inhibition and low fish DNA recovery.
• Existing eDNA methods struggle to accurately assess fish communities in turbid, productive estuarine environments.

Purpose of the Study:

• To develop and present an optimized approach for detecting fish eDNA in challenging estuarine systems.
• To improve the accuracy and efficiency of fish biodiversity assessments in complex aquatic environments.

Main Methods:

• A hybrid eDNA workflow was implemented, combining bead-based extraction with inhibition removal.
• High-fidelity DNA polymerase (Platinum SuperFi II) and multiplexed universal MiFish primers were utilized.
• The method was tested on diverse estuarine samples known to cause PCR inhibition.

Main Results:

• The optimized eDNA approach more than doubled the number of recovered fish species compared to standard methods.
• Significant reduction in off-target amplification was observed, improving data reliability.
• Successful detection of fish species in previously challenging, inhibited estuarine samples.

Conclusions:

• This enhanced eDNA workflow effectively overcomes limitations in analyzing estuarine samples.
• The method provides a more comprehensive and reliable assessment of fish biodiversity in complex aquatic ecosystems.
• This approach advances the application of eDNA for effective environmental monitoring and conservation.