Using eDNA sampling for species-specific fish detection in tropical oceanic samples: limitations and recommendations
Giovanna M Gonzalez Colmenares1, Alejandro J Gonzalez Montes2, Chelsea A Harms-Tuohy3
1Department of Biology, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, Puerto Rico.
Peerj
|February 8, 2023
Summary
Environmental DNA (eDNA) failed to detect fish spawning aggregations (FSAs) in Puerto Rico due to low DNA concentrations. Further research is needed to optimize eDNA methods for marine fish biomonitoring in tropical waters.
Area of Science:
- Marine Biology
- Conservation Genetics
- Environmental DNA (eDNA) Analysis
Background:
- Environmental DNA (eDNA) is a valuable tool for biomonitoring, but its application in marine fish studies, especially in tropical regions, is limited.
- Commercially important Caribbean fish are overexploited, making them ideal candidates for eDNA biomonitoring, particularly during fish spawning aggregations (FSAs).
- FSAs are critical, predictable, yet ephemeral reproductive events highly susceptible to overfishing.
Purpose of the Study:
- To assess the feasibility of using eDNA water and sediment sampling to detect known FSAs off Puerto Rico.
- To develop and test species-specific primers (targeting CO1 and 12S rRNA) for marine fish detection using traditional PCR and qPCR.
- To evaluate the effectiveness of eDNA methods for monitoring fish populations at FSAs.
Main Methods:
- Collected 290 eDNA samples (water and sediment) from known FSAs.
- Developed and tested 12 primer sets targeting specific marine fish species.
- Utilized traditional PCR and quantitative PCR (qPCR) for eDNA analysis.
- Conducted DNA 'spiking' experiments to determine the limit of detection for target DNA.
Main Results:
- eDNA samples showed variable DNA concentrations across replicates and collection methods.
- Species-specific amplification failed despite validated primers and sampling during peak spawning times.
- Trial experiments indicated that eDNA concentrations in samples were below the detection threshold of the applied methods.
- Factors like non-target DNA, environmental conditions, and DNA degradation may have impacted detection.
Conclusions:
- Current eDNA methods, including PCR and qPCR with tested primers, were insufficient for detecting target species at FSAs in this study.
- Low DNA concentrations in eDNA samples suggest inadequate numbers of fish or rapid DNA degradation.
- Recommendations are provided for improving species-specific fish detection and eDNA monitoring of FSAs in tropical latitudes.
