Finding Crush: Environmental DNA Analysis as a Tool for Tracking the Green Sea Turtle Chelonia mydas in a Marine Estuary

Abstract

Environmental DNA (eDNA) analysis is a rapid, non-invasive method for species detection and distribution assessment using DNA released into the surrounding environment by an organism. eDNA analysis is recognised as a powerful tool for detecting endangered or rare species in a range of ecosystems. Although the number of studies using eDNA analysis in marine systems is continually increasing, there appears to be no published studies investigating the use of eDNA analysis to detect sea turtles in natural conditions. We tested the efficacy of two primer pairs known to amplify DNA fragments of differing lengths (488 and 253 bp) from Chelonia mydas tissues for detecting C. mydas eDNA in water samples. The capture, extraction, and amplification of C. mydas eDNA from aquaria (Sea World, San Diego, CA, United States) and natural water (San Diego Bay, CA, United States) were successful using either primer set. The primer pair providing the shorter amplicon, LCMint2/H950g, demonstrated the ability to distinguish cross-reactive species by melt curve analysis and provided superior amplification metrics compared to the other primer set (LTCM2/HDCM2); although primer dimer was observed, warranting future design refinement. Results indicated that water samples taken from deeper depths might improve detection frequency, consistent with C. mydas behaviour. Overall, this pilot study suggests that with refinement of sampling methodology and further assay optimisation, eDNA analysis represents a promising tool to monitor C. mydas. Potential applications include rapid assessment across broad geographical areas to pinpoint promising locations for further evaluation with traditional methods.

Environmental DNA is effective in detecting the federally threatened Louisiana Pinesnake (Pituophis ruthveni)

“…The target organism itself can exacerbate low eDNA detection rates and concentration. eDNA can have an extremely heterogeneous spatial distribution in the environment if the target organism does not readily release eDNA (Adams, Hoekstra, Muell, & Janzen, 2019; Harper et al., 2020; Hunter et al., 2015; Tréguier et al., 2014), is at low density (Gasparini et al., 2020; Wacker et al., 2019), exhibits periods of lower activity (Buxton et al., 2018; Hunter et al., 2015; de Souza et al., 2016), and utilizes microhabitats or has a large home range, both of which limit opportunities for eDNA deposition (Goldberg et al., 2018; Harper, Handley, et al, 2019). Spatial heterogeneity is further influenced by the ecosystem the target organism occupies, with eDNA being more patchily distributed in static systems with little mixing or flow/wave dynamics to enable eDNA transport, for example, ponds, lakes, soil (Goldberg et al., 2018; Harper, Handley, et al, 2019; Lawson Handley et al., 2019; Zinger et al., 2020).…”

“…eDNA is trace DNA released by organisms into their environment via secretions (Ficetola, Miaud, Popanon, & Tab erlet, 2008; Jerde, Mahon, Chadderton, & Lodge, 2011), excretions (Anderson et al., 2011; Martellini, Payment, & Villemur, 2005; Thomsen et al., 2012), or even decomposing carcasses (Merkes, McCalla, Jensen, Gaikowski, & Amberg, 2014, but see Curtis & Larson, 2020) that can be harnessed from environmental samples (e.g., soil, water) without observation or direct capture of the target organism itself (Thomsen & Willerslev, 2015). Over the past decade, the utility of eDNA analysis has grown rapidly, and its efficacy has been demonstrated from freshwater, marine, subterranean, terrestrial, and airborne samples (e.g., Franklin et al., 2019; Harper et al., 2020; Johnson, Cox, & Barnes, 2019; Niemiller et al., 2018; Thomsen et al., 2012). Since eDNA analysis was first applied to macrobiota (Ficetola et al., 2008), it has become an important conservation and management tool that is capable of detecting both invasive and imperiled species at low abundances in numerous contexts (e.g., Gasparini, Crookes, Prosser, & Hanner, 2020; Goldberg, Strickler, & Fremier, 2018; Kessler, Ash, Barratt, Larson, & Davis, 2020; de Souza, Godwin, Renshaw, & Larson, 2016; Tréguier et al., 2014; Valentin et al., 2020; Wacker et al., 2019).…”

An experimental assessment of the distribution of environmental DNA along the water column

“…eDNA concentration, composition and spatial distribution is then expected to vary as communities change through depth due to vertical zoning. While some studies conclude that there is a negligible impact on the detection and composition (Cordier et al 2019;Currier et al 2018;Eichmiller et al 2014;Harper et al 2020;Lafferty et al 2020) others report differences (Andruszkiewicz et al 2017;Cordier et al 2019;Hänfling et al 2016;Jeunen et al 2020;Kuehne et al 2020;Lacoursière-Roussel et al 2018;Lor et al 2020;Minamoto et al 2017;Moyer et al 2014;Murakami et al 2019;Sigsgaard et al 2020;Uthicke et al 2018;Yamamoto et al 2016;Zhang et al 2020). These studies, however, vary significantly between the water body architecture, water composition, depth sampled, sampling strategy, target organism, detecting technique, extraction protocol and molecular marker.…”

Disease risk analysis in sea turtles: A baseline study to inform conservation efforts

“…Advanced biodiversity monitoring techniques for sea turtles conservation is gaining popularity including alternative and efficient techniques such as environmental DNA [ 8 , 9 ]. Screening eDNA is considered to be a non-invasive way to assess the population dynamics of sea turtles [ 10 ], along with investigating the causation and progression of diseases such as fibropapillomatosis [ 11 ]. Satellite telemetry is another advanced tool successfully used in sea turtle population assessment and marine parks management [ 12 ].…”