Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring

Abstract

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 is 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-throughput 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 surveybased 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.

Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river

“…Clustering of strictly identical sequences was performed using obiuniq and a chimera removal step was applied in vsearch (Rognes, Flouri, Nichols, Quince, & Mahé, 2016) through the uchime-denovo algorithm (Edgar, Haas, Clemente, Quince, & Knight, 2011 (Boyer et al, 2016) was used for the subsequent taxonomic assignment, with a custom reference database including all known vertebrate sequences for the sequenced 12S fragment (Siegenthaler et al, 2018). Ambiguous taxonomic assignments after ecotag were checked using BLAST against the Genbank nucleotide database.…”

Cobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems

“…Metabarcoding has been successfully applied in a number of studies as a powerful and repeatable method for characterizing biodiversity (Hänfling et al, ; Leray & Knowlton, ). The flexibility of metabarcoding protocols allows the analyses of a wide range of sample types (sediment: Guardiola et al, , substrate: Wangensteen et al, , seawater: Bakker et al, , bulk invertebrate samples: Elbrecht & Leese, , stomach contents: Siegenthaler, Wangensteen, Benvenuto, Campos, & Mariani, and scat: Berry et al, ), to more recent approaches that utilize natural environmental samplers as a tool to survey marine biodiversity such as utilizing the diet profiles of benthic scavengers to assess fish diversity or harnessing water‐filtering sponges to sample environmental DNA (natural sampler DNA—nsDNA; Mariani, Baillie, Colosimo, & Riesgo, ; Siegenthaler, Wangensteen, Soto, et al, ). While metabarcoding of environmental samples has many limitations associated with primer performance, bioinformatic workflows and study design (Elbrecht, Hebert, & Steinke, ), it overcomes many morphology‐based challenges in identifying species at different levels (e.g.…”

Metabarcoding for stomach‐content analyses of Pygmy devil ray (Mobula kuhlii cf. eregoodootenkee): Comparing tissue and ethanol preservative‐derived DNA

“…For instance, a dietary study of the Lionfish ( Pterois volitans ) contributed to identifying 39 species from digested liquiform samples, whose identification would be difficult using traditional methods (Harms‐Tuohy, Schizas, & Appeldoorn, ). Interestingly, stomach‐content analysis of the brown shrimp ( Crangon crangon), a generalist/scavenger feeder, has been used recently as a natural sampler to monitor estuarine biodiversity through DNA metabarcoding (Siegenthaler, Wangensteen, Soto et al, ). Therefore, future dietary studies should consider the importance of fine‐tuning a methodology to allow accurate recovery and identification of the full range of prey.…”

“…Soto et al, 2018). Therefore, future dietary studies should consider the importance of fine-tuning a methodology to allow accurate recovery and identification of the full range of prey.…”