Data from: DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

Morphology-based profiling of benthic communities has been extensively
applied to aquatic ecosystems' health assessment. However, it remains
a low-throughput, and sometimes ambiguous, procedure. Despite DNA
metabarcoding has been applied to marine benthos, a comprehensive approach
providing species-level identifications for estuarine macrobenthos is
still lacking. Here we report a combination of experimental and field
studies to assess the aptitude of COI metabarcoding to provide robust
species-level identifications for high-throughput monitoring of estuarine
macrobenthos. To investigate the ability of metabarcoding to detect all
species present in bulk DNA extracts, we contrived three phylogenetically
diverse communities, and applied four different primer pairs to generate
PCR products within the COI barcode region. Between 78-83% of the species
in the contrived communities were recovered through HTS. Subsequently, we
compared morphology and metabarcoding-based approaches to determine the
species composition from four distinct estuarine sites. Our results
indicate that species richness would be considerably underestimated if
only morphological methods were used: globally 27 species identified
through morphology versus 61 detected by metabarcoding. Although further
refinement is required to improve efficiency and output of this approach,
here we show the great aptitude of COI metabarcoding to provide high
quality and auditable species identifications in estuarine macrobenthos
monitoring.