Significant taxon sampling gaps in DNA databases limit the operational use of marine macrofauna metabarcoding

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.

Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding

“…These results undoubtedly indicate the existence of many new taxa, but it should be noted that the incompleteness of reference database coverage remains a major impediment to taxon assignment in biodiversity surveys. In a recent study based on samples from a well-studied and heavily sampled area of the North Sea, Hestetun et al (2020) estimated that for the 18S rRNA gene, species coverage was 36% for GenBank and 27% for SILVA, which we used in this study (along with the curated, protistfocused PR 2 ). The species coverage in these databases is certain to be substantially lower for the sparsely sampled, species-rich deep sea.…”

A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON)

“…The low overlap between the communities identified by image and genetic analysis (Figure 3) demonstrates the strengths and weaknesses of both conventional and novel identification methods, while it also indicates how these methods complement each other. Genetic identifications are usually confined by incomplete reference libraries (Hestetun et al, 2020), while image-based identifications are confined by the available taxonomic expertise and image resolution. These limitations decline as genetic and image reference libraries continue to grow and computational image-based identification methods improve in the coming years.…”

“…The use of metabarcoding for rapid identification of species in marine communities, however, is not without limitations (e.g., Cahill et al, 2018). One obvious drawback is the still incomplete taxonomic reference databases, which limit positive identifications and can also lead to misidentifications (Meiklejohn et al, 2019;Weigand et al, 2019;Hestetun et al, 2020). It should be noted that alternative morphologicalbased identification also has flaws as the declining number of taxonomic experts and large numbers of cryptic species mean that mis-identification is commonplace, with important consequences especially for non-indigenous species (NIS) detection (e.g., Viard et al, 2019).…”

eDNA metabarcoding vs metagenomics: an assessment of dietary competition in two estuarine pipefishes

“…The efficiency of metabarcoding to identify species relies on wide coverage and high quality of taxon reference records in the DNA repositories (Hestetun et al, 2020; Leite et al, 2020). Our study highlights the fact that a more comprehensive reference database for South African estuarine macroinvertebrates is required to unequivocally identify the prey items consumed by the two pipefish species studied here.…”