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.
Highlights
Over the past decade, the study of environmental DNA coupled with next-generation sequencing (NGS) has emerged as a promising means to assess and monitor the biodiversity of a habitat which may in turn influence conservation action and intervention
Despite the low read count for several samples, alpha-diversity rarefaction analysis suggested our method were sufficient to assess progress in recovering representative medusozoan environmental DNA (eDNA) by sample location, given our sequencing depth (Supplementary Figures 5,6)
We have successfully demonstrated the efficacy of our fieldable environmental DNA sequencing (FeDS) kit which leverages the portable MinION sequencer to enable rapid, onsite metabarcoding of eDNA corresponding to 53 medusozoan taxa in the Florida Keys
Summary
The study of environmental DNA (eDNA) coupled with next-generation sequencing (NGS) has emerged as a promising means to assess and monitor the biodiversity of a habitat which may in turn influence conservation action and intervention. These techniques, which have been commonly used in microbial ecology studies for some time, are being. And accurate assessments of organisms in their native habitats are critical to understanding the dynamics of population trends with respect to normal conditions and potentially disruptive environmental events. EDNA-based investigations have proven to be as valuable as traditional survey methods that require capture and subsampling of target organisms. Marine-derived eDNA has been likened to a “barometer of disturbance” with respect to its potential to assess anthropogenic effects on ecosystems (Dibattista et al, 2020)
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