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

Lewis Ames, Cheryl and Ohdera, Aki H. and Colston, Sophie M. and Collins, Allen G. and Fitt, William K. and Morandini, André C. and Erickson, Jeffrey S. and Vora, Gary J. (2021) Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States. Frontiers in Marine Science, 8 . Art. No. 640527. ISSN 2296-7745. https://resolver.caltech.edu/CaltechAUTHORS:20210528-094925416

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.3389/fmars.2021.640527DOIArticle
https://github.com/aohdera/Ames_et_al_2020Related ItemData/Code
ORCID:
AuthorORCID
Lewis Ames, Cheryl0000-0003-1132-6834
Ohdera, Aki H.0000-0003-4417-905X
Collins, Allen G.0000-0002-3664-9691
Morandini, André C.0000-0003-3747-8748
Vora, Gary J.0000-0002-0657-8597
Additional Information:© 2021 Ames, Ohdera, Colston, Collins, Fitt, Morandini, Erickson and Vora. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Received: 11 December 2020; Accepted: 22 March 2021; Published: 13 April 2021. We are grateful to Mónica Medina, whose assistance in establishing the Cassiopea model meeting in Key Largo (FL, United States) allowed us to conduct this research, and the meeting attendees for their assistance with collecting. Additionally, we acknowledge technical support received from Vanessa Molina, NRL Key West, and CPT Brett Ambroson, Diving Medical Officer, Special Forces Underwater Operations School, Key West, for logistical assistance in Fleming Key (FL, United States). Finally, we are grateful to two reviewers and the Editor for their constructive comments. This is a contribution of NP-BioMar USP. The opinions and assertions contained herein are those of the authors and are not to be construed as those of the U.S. Navy, military service at large or U.S. Government. Data Availability Statement: Filtered and trimmed 16S and COI MinION data sets have been made available at: https://github.com/aohdera/Ames_et_al_2020. Nanopore sequences for medusozoans (16S; classes Scyphozoa, Cubozoa, and Staurozoa) have been separately accessioned into GenBank (see Table 2). All code and data sets used in this study are provided as Supplementary Data Sheet 1: https://github.com/aohdera/Ames_et_al_2020. Author Contributions: CA conceived, designed, and carried out sample collection, and all steps in the FeDS workflow in Key Largo and Fleming Key, conducted bioinformatic analyses and phylogenetic analyses, coauthored the first draft of the manuscript, and prepared figures and tables. AO carried out sample collection and MinION sequencing in Key Largo, conducted bioinformatic analyses, prepared figures and tables, and coauthored the first draft. SC helped to design the experiments, provided training in MinION technology, assisted with MinION read processing, and prepared figures and tables. AC conducted phylogenetic analyses and interpretation of results, historical data assessment and synopsis, prepared figures and tables, and coauthored the first draft. WF assisted with sample collection in Key Largo, provided ecological data related to pre- and post-Irma conditions in Key Largo, and conducted photo-documentation. ACM assisted with sample collection in Key Largo, species identification, and conducted photo-documentation. JE provided technical guidance during experimental design and developing equipment for portability. GV helped to conceive of the experiments, oversaw all aspects of the project from start to finish, assisted with FeDS kit design, and contributed reagents, materials, and analysis tools. All authors provided content for each manuscript draft and approved the final draft. This research was supported by the Office of Naval Research via Naval Research Laboratory core funds (work unit 6B84). CA and SC acknowledge postdoctoral fellowships through the National Research Council’s Research Associateship Program. ACM was supported by FAPESP 2015/21007-9 and CNPq 309440/2019-0. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Edited by: Frank Edgar Muller-Karger, University of South Florida, United States Reviewed by: Chih-Ching Chung, National Taiwan Ocean University, Taiwan Yu Zhang, Shanghai Jiao Tong University, China
Funders:
Funding AgencyGrant Number
Naval Research Laboratory6B84
National Research CouncilUNSPECIFIED
Fundação de Amparo à Pesquisa do Estado de Sao Paulo (FAPESP)2015/21007-9
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)309440/2019-0
Subject Keywords:eDNA, envenomation, upside-down jellyfish, conservation, biodiversity, portable lab kit
Record Number:CaltechAUTHORS:20210528-094925416
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210528-094925416
Official Citation:Ames CL, Ohdera AH, Colston SM, Collins AG, Fitt WK, Morandini AC, Erickson JS and Vora GJ (2021) Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States. Front. Mar. Sci. 8:640527. doi: 10.3389/fmars.2021.640527
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:109302
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:28 May 2021 20:44
Last Modified:28 May 2021 20:44

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