Data from: Metabarcoding of shrimp stomach content: harnessing a natural sampler for fish biodiversity monitoring

Given their positioning and biological productivity, estuaries have long
represented key providers of ecosystem services, and consequently remain
under remarkable pressure from numerous forms of anthropogenic impact. The
monitoring of fish communities in space and time are one of the most
widespread and established approaches to assess the ecological status of
estuaries and other coastal habitats, but traditional fish surveys are
invasive, costly, labour intensive and highly selective. Recently, the
application of metabarcoding techniques, on either sediment or aqueous
environmental DNA, has rapidly gained popularity. Here, we evaluate the
application of a novel, high through-put DNA-based monitoring tool to
assess fish diversity, based on the analysis of the gut contents of a
generalist predator/scavenger, the European brown shrimp, Crangon crangon.
Sediment and shrimp samples were collected from eight European estuaries
and DNA metabarcoding (using both 12S and COI markers) was carried out to
infer fish assemblage composition. We detected 32 teleost species (16 and
20, for 12S and COI respectively). Twice as many species were recovered
using metabarcoding than by traditional net surveys. By comparing and
interweaving trophic, environmental DNA and traditional survey-based
techniques, we show that the DNA-assisted gut content analysis of a
ubiquitous, easily accessible, generalist species may serve as a powerful,
rapid and cost-effective tool for large scale, routine estuarine
biodiversity monitoring.