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

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 s..., Literature Selection
Using standard systematic review protocols (Moher et al., 2015), we conducted a literature search of peer-reviewed articles indexed in Web of Science, PubMed, and Scopus (see Figure 1). On all platforms, we used the search string (“environmental DNA” OR eDNA) AND (marine OR ocean* OR seawater OR saltwater OR sea) across titles, abstracts, and keywords to broadly identify articles using eDNA in marine environments, published up to 31 December 2020. Using this search strategy, we were only selecting for articles that self-identified as studying “environmental DNA,” rather than articles using the same, or similar, methods. Because many eDNA articles are published in the journal Environmental DNA, which at the time of searching was not yet indexed in any of the databases above, we additionally searched that journal’s corpus using the same search string and date range and added the returned articles to our sample. After removing duplicates using the systematic review org...,