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

Siegenthaler, A, Wangensteen, OS, Soto, AZ, Benvenuto, C, Corrigan, L and Mariani, S (2018) Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring. Molecular Ecology Resources, 19 (1). pp. 206-220. ISSN 1755-098X

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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 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 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
Uncontrolled Keywords: 06 Biological Sciences
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Divisions: Biological & Environmental Sciences (new Sep 19)
Publisher: Wiley
Related URLs:
Date Deposited: 06 Mar 2020 10:49
Last Modified: 06 Mar 2020 11:00
DOI or Identification number: 10.1111/1755-0998.12956
URI: http://researchonline.ljmu.ac.uk/id/eprint/12415

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