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

Siegenthaler, A, Wangensteen, OS ORCID: https://orcid.org/0000-0001-5593-348X, Soto, AZ, Benvenuto, C ORCID: https://orcid.org/0000-0002-8378-8168, Corrigan, L and Mariani, S ORCID: https://orcid.org/0000-0002-5329-0553 2018, 'Metabarcoding of shrimp stomach content: harnessing a natural sampler for fish biodiversity monitoring' , Molecular Ecology Resources, 19 (1) , pp. 206-220.

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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 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.

Item Type: Article
Schools: Schools > School of Environment and Life Sciences > Ecosystems and Environment Research Centre
Journal or Publication Title: Molecular Ecology Resources
Publisher: Wiley
ISSN: 1755-0998
Related URLs:
Funders: Natural Environment Research Council (NERC)
Depositing User: USIR Admin
Date Deposited: 11 Oct 2018 13:14
Last Modified: 12 Sep 2019 14:22
URI: http://usir.salford.ac.uk/id/eprint/48628

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