Development of a sensitive detection method to survey pelagic biodiversity using eDNA and quantitative PCR: a case study of devil ray at seamounts

Environmental DNA (eDNA) is increasingly being used in aquatic environments for monitoring species, particularly those that are of conservation concern and/or are difficult to visually observe. Quantitative PCR (qPCR) has been employed to detect low abundance species occurring in environmental water samples. However, the qPCR technique has principally been applied to freshwater habitats, with less application to pelagic marine environments. We developed a species-specific eDNA assay for the Chilean devil ray, Mobula tarapacana, to assess the capability of using eDNA to detect transient pelagic marine animals. For this pilot study, seawater samples taken at seamounts around the Azores (NE Atlantic) were tested to determine the suitability of this approach for detecting the target species. Samples were taken at sites where M. tarapacana has been previously observed, in addition to sites where its presence is not known. eDNA detection was compared to observations carried out on the same day as water sampling. The qPCR assay successfully detected M. tarapacana at four of five seamount sampling opportunities where the species was observed, and there is a statistically significant relationship between genetic and visual detection. Target DNA was found at one location between seamounts in the absence of visual observation. Our results highlight the importance of physical environmental factors in relation to sampling eDNA in the ocean, such as currents and eDNA dispersal ability. This method has been shown to be sensitive for detection of M. tarapacana DNA in seawater and, therefore, in the identification of important seamounts requiring conservation.