González Colmenares, Giovanna M.

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    Using eDNA sampling for species-specific fish detection in tropical oceanic samples: Limitations and recommendations for future use
    (2023-05-13) González Colmenares, Giovanna M.; Alfaro Lozano, Monica; College of Arts and Sciences - Sciences; Schizas, Nikolaos V.; Harms Tuohy, Chelsea; Department of Biology; Santiago Torres, Frances J.
    Environmental DNA (eDNA) is a resourceful tool in conservation and bio-monitoring studies. However, the use of eDNA sampling and application in tropical latitude marine fish studies is limited. Commercially important and over-exploited Caribbean fishes are optimal candidates to explore this method when sampling at their spawning aggregation sites where fish abundance is higher than during other non-reproductive times of the year. This study tests the use of targeted eDNA sampling to detect fish at their known fish spawning aggregation sites (FSAs) off Puerto Rico’s west coast, using CO1 and 12S rRNA primers targeting specific species. DNA concentrations in the eDNA samples varied both between replicates and collection methods, with concentrations ranging from 0.2ng/µL to 88.2ng/µl. Despite primer validation and sample collection during spawning peak, traditional PCR and qPCR failed to detect the target species. A trial was conducted using CO1 primers wherein target fish DNA was spiked at various concentrations into the respective eDNA samples to determine the target species’ DNA concentration detection limit. These samples were below the detection threshold, suggesting a strong DNA signal was not present likely due to insufficient fish abundance at the specific FSA. Biotic and abiotic factors possibly affected DNA persistence and degradation rates. Recommendations were provided for studies attempting FSA monitoring or detection using eDNA sampling in tropical latitudes.