DOI: 10.5061/dryad.7498b88
title: Data from: Metabarcoding of shrimp stomach content: harnessing a natural sampler for fish biodiversity monitoring

description: 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.
description: COI sediment and Crangon
 crangon stomach dataTable including the
 taxonomic assignment (using ecotag), the abundances per site and the
 sequence of COI-MOTUs found in sediment and pooled Crangon crangon stomach
 samples collected from 21 sites in the Netherlands, Portugal and United
 Kingdom. Ordered in the following columns: (A) Sample_type (B) id, (C)
 rank, (D) scientific_name, (E) best_identity, (F) superkingdom, (G)
 kingdom, (H) phylum, (I) class, (J) order, (K) family, (L) genus, (M)
 species, (N to AH) abundances in the different sites [ES: Eastern Scheldt,
 WS: Western Scheldt, MI: Minho, AV: Aveiro, ME: Mersey, KE: Kent; 1-4:
 Replicates], (AI) sequence.DATA_COI.csv12S sediment and Crangon crangon stomach dataTable including the taxonomic assignment (using ecotag), the abundances per site and the sequence of 12S-MOTUs found in sediment and pooled Crangon crangon stomach samples collected from 21 sites in the Netherlands, Portugal and United Kingdom. Ordered in the following columns: (A) Sample_type (B) id, (C) rank, (D) scientific_name, (E) best_identity, (F) superkingdom, (G) kingdom, (H) phylum, (I) class, (J) order, (K) family, (L) genus, (M) species, (N to AH) abundances in the different sites [ES: Eastern Scheldt, WS: Western Scheldt, MI: Minho, AV: Aveiro, ME: Mersey, KE: Kent; 1-4: Replicates], (AI) sequence.DATA_12S.csv12S Tweed and Tees (UK) sediment, water and Crangon crangon stomach dataTable including the taxonomic assignment (using ecotag), the abundances per sample and the sequence of 12S-MOTUs found in sediment, water and pooled Crangon crangon stomach samples collected from 2 sites in the United Kingdom (TW: Tweed, TS: Tees). Ordered in the following columns: (A) id, (B) rank, (C) scientific_name, (D) best_identity, (E) superkingdom, (F) kingdom, (G) phylum, (H) class, (I) order, (J) family, (K) genus, (L) species, (M to R) abundances in the different sediment samples, (S to X) abundances in the different water samples, (Y to AC) abundances in the different pooled stomach samples, (AD) sequence.DATA_12S_UK.csv