Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility

Author:

Shea Meghan M.1,Kuppermann Jacob2,Rogers Megan P.3,Smith Dustin Summer2,Edwards Paul4,Boehm Alexandria B.5

Affiliation:

1. Emmett Interdisciplinary Program in Environment & Resources (E-IPER), Stanford University, Stanford, CA, United States of America

2. Earth Systems Program, Stanford University, Stanford, CA, United States of America

3. Program in Human Biology, Stanford University, Stanford, CA, United States of America

4. Program in Science, Technology and Society, Stanford University, Stanford, CA, United States of America

5. Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America

Abstract

The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR–findable, accessible, interoperable, and reusable–despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.

Funder

Emmett Interdisciplinary Program in Environment & Resources (E-IPER) Summer Research Grant

Stanford School of Earth, Energy & Environmental Sciences, McGee/Levorsen Research Grant

Stanford Interdisciplinary Graduate Fellowship and an E-IPER Sykes Family Fellowship

Publisher

PeerJ

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

Reference103 articles.

1. Guidance on the use of targeted environmental DNA (eDNA) analysis for the management of aquatic invasive species and species at risk 46;Abbott,2021

2. Uncovering the complete biodiversity structure in spatial networks: the example of riverine systems;Altermatt;Oikos,2020

3. Including digital sequence data in the nagoya protocol can promote data sharing;Ambler;Trends in Biotechnology,2021

4. Environmental DNA (eDNA) metabarcoding: diversity study around the pondok dadap fish landing station, Malang, Indonesia;Andriyono;Biodiversitas,2019

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