Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

Abstract

Recent advances in molecular sequencing technology and the increased availability of fieldable laboratory equipment have provided researchers with the opportunity to conduct real-time or near real-time gene-based biodiversity assessments of aquatic ecosystems. In this study, we developed a workflow and portable kit for fieldable environmental DNA sequencing (FeDS) and tested its efficacy by characterizing the breadth of jellyfish (Medusozoa) taxa in the coastal waters of the Upper and Lower Florida Keys. Environmental DNA was isolated from seawater collection events at eight sites and samples were subjected to medusozoan 16S rRNA gene and metazoan mitochondrial cytochrome oxidase 1 gene profiling via metabarcoding onsite. In total, FeDS yielded 175,326 processed sequence reads providing evidence for 53 medusozoan taxa. Our most salient findings revealed eDNA from: (1) two venomous box jellyfish (Cubozoa) species, including taxa whose stings cause the notorious Irukandji envenomation syndrome; (2) two species of potentially introduced stalked jellyfish (Staurozoa); and (3) a likely cryptic species of upside-down jellyfish (Scyphozoa). Taken together, the results of this study highlight the merits of FeDS in conducting biodiversity surveys of endemic and introduced species, and as a potential tool for assessing envenomation and/or conservation-related threats.

Analyses of Stalked Jellyfish in Kitsunezaki, Japan: Calvadosia nagatensis, and Two Lineages of Haliclystus inabai with Early Life Stages Observed in an Aquarium in Canada

“…Recently, eDNA (environmental DNA) signatures of two staurozoan species, Calvadosia cruxmelitensis and Haliclystus cf. tenuis, were detected in the Florida Keys (Key Largo and Fleming Key, FL, USA) [23], where they had not been reported previously, suggesting that these cryptic animals may have more widespread distributions than previously appreciated. Novel approaches to eDNA detection (e.g., [38]) should aid our understanding of global distribution paths of staurozoans and their underlying mechanisms of dispersal.…”

“…PCR (polymerase chain reaction) was used to amplify the two molecular targets in a thermal cycler (BentoLab, Bioworks, London, UK or Takara Bio, Kusatsu, Shiga, Japan). Cycling profile for 16S primers included initial denaturation at 94 • C for 3 minutes, followed by 38 cycles of denaturation, annealing and extension (94 • C for 30 s, 54 • C for 30 s, and 72 • C for 45 s), and a final extension at 72 • C for 10 minutes [23]. Cycling profile for COI primer included denaturation at 94 • C for 5 minutes, followed by 38 cycles of denaturation, annealing, and extension (94 • C for 30 s, 46 • C for 30 s, and 72 • C for 1 min), and a final extension at 72 • C for 10 minutes.…”

Environmental Dna in an Ocean of Change: Status, Challenges and Prospects

“…Recently, a study compared the zooplankton taxa recovered with nets and with eDNA of filtered water samples, and demonstrated eDNA to be particularly suitable for revealing gelatinous diversity (Govindarajan et al, 2021). However, eDNA studies focusing on gelatinous zooplankton still remain relatively scarce (Ames et al, 2021;Gaynor et al, 2017;Minamoto et al, 2017;Takasu et al, 2019).…”

A review of applications of environmental DNA for reptile conservation and management

“…This was achieved with high accuracy (>99%) in under 24 h under challenging field conditions (e.g., inconsistent electricity), illustrating how “mobile laboratories that fit in a single backpack” can be used in a conservation context in developing countries (Pomerantz et al, 2018 ). The MinION has carried over into the field of eDNA (Ames et al, 2021 ; Egeter et al, 2022 ; Truelove et al, 2019 ); for example, eDNA in seawater was sequenced, and annotated results for white sharks ( Carcharodon carcharias ) were available in 48 h, which is a substantial reduction in typical eDNA turnaround times (Truelove et al, 2019 ).…”