Abstract
Significant effort is spent on monitoring of benthic ecosystems through government funding or indirectly as a cost of business, and metabarcoding of environmental DNA samples has been suggested as a possible complement or alternative to current morphological methods to assess biodiversity. In metabarcoding, a public sequence database is typically used to match barcodes to species identity, but these databases are naturally incomplete. The North Sea oil and gas industry conducts large-scale environmental monitoring programs in one of the most heavily sampled marine areas worldwide and could therefore be considered a “best-case scenario” for macrofaunal metabarcoding. As a test case, we investigated the database coverage of two common metabarcoding markers, mitochondrial COI and the ribosomal rRNA 18S gene, for a complete list of 1802 macrofauna taxa reported from the North Sea monitoring region IV. For COI, species level barcode coverage was 50.4% in GenBank and 42.4% for public sequences in BOLD. For 18S, species level coverage was 36.4% in GenBank and 27.1% in SILVA. To see whether rare species were underrepresented, we investigated the most commonly reported species as a separate dataset but found only minor coverage increases. We conclude that compared to global figures, barcode coverage is high for this area, but that a significant effort remains to fill barcode databases to levels that would make metabarcoding operational as a taxonomic tool, including for the most common macrofaunal taxa.
Highlights
The objective of this paper is to investigate the current state of publicly accessible barcode repositories, including GenBank, Barcode of Life Data System (BOLD), and SILVA, for metabarcode taxon matching—the barcode repository gap—for the c oxidase subunit I (COI) and 18S genes in marine benthic macrofauna taxa using a large dataset from a densely surveyed area
Validating and updating taxon names and classification in World Register of Marine Species (WoRMS) reduced the number of valid taxa names to 1802 and valid species names to 1474 (Supplementary Table 1)
For the ten most common taxa reported from each station, WoRMS indicated 236 valid taxon names including 184 taxa at the species level (Supplementary Table 2)
Summary
The practice of using estimates of biodiversity change to understand the extent of anthropogenic impact on the environment still routinely uses century-old sampling techniques. Most benthic community impact assessments are based on changes in the macrofauna assemblage sampled by replicate sediment grab samples sieved to retain fauna larger than 0.5 or 1 mm (Bean et al 2017). This fauna is subsequently determined to lowest possible taxonomical level using morphological characters based on available taxonomic expertise and literature
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