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

PeerJ. 2023 Mar 24:11:e14993. doi: 10.7717/peerj.14993. eCollection 2023.


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.

Keywords: Best practices; Data accessibility; Data storage; Data usability; Environmental DNA; FAIR data principles; Marine; Metabarcoding; Metadata; Systematic review.

Publication types

  • Systematic Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biodiversity
  • DNA Barcoding, Taxonomic
  • DNA, Environmental*


  • DNA, Environmental

Associated data

  • Dryad/10.5061/dryad.95x69p8pd

Grants and funding

This work was supported by an Emmett Interdisciplinary Program in Environment & Resources (E-IPER) Summer Research Grant and a Stanford School of Earth, Energy & Environmental Sciences McGee/Levorsen Research Grant. Meghan M. Shea is supported by a Stanford Interdisciplinary Graduate Fellowship and an E-IPER Sykes Family Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.