DNA metabarcoding unveils multi-scale trophic variation in a widespread coastal opportunist

Siegenthaler, A; Wangensteen, OS; Benvenuto, C; Campos, J; Mariani, S

Abstract

A thorough understanding of ecological networks relies on comprehensive information on trophic relationships among species. Since unpicking the diet of many organisms is unattainable using traditional morphology-based approaches, the application of high-throughput sequencing methods represents a rapid and powerful way forward. Here, we assessed the application of DNA-metabarcoding with nearly universal primers for the mitochondrial marker cytochrome c oxidase (COI) in defining the trophic ecology of adult brown shrimp, Crangon crangon, in six European estuaries. The exact trophic role of this abundant and widespread coastal benthic species is somewhat controversial, while information on geographical variation remains scant. Results revealed a highly opportunistic trophic behaviour. We found evidence of the consumption of hundreds of taxa of which 306 were identified as distinct species, belonging to 35 phyla. Twenty species had a mean relative abundance of more than 0.5 %. Predominant species included other abundant coastal and estuarine taxa, such as the shore crab Carcinus maenas and the amphipod Corophium volutator. Jacobs’ selectivity index estimates based on DNA extracted from both shrimp stomachs and sediment samples were used to assess the shrimp’s trophic niche; indicating a generalist diet, dominated by crustaceans, polychaetes and fish. Spatial variation in diet composition, both at regional and local scales, confirmed the highly flexible nature of this trophic opportunist. Furthermore, the detection of a prevalent, possibly endoparasitic fungus (Purpureocillium lilacinum) in the shrimp’s stomach demonstrates the wide range of questions that can be addressed using metabarcoding, towards a more robust reconstruction of ecological networks.

Citation

Siegenthaler, A., Wangensteen, O., Benvenuto, C., Campos, J., & Mariani, S. (2019). DNA metabarcoding unveils multi-scale trophic variation in a widespread coastal opportunist. Molecular Ecology, 28(2), 232-249. https://doi.org/10.1111/mec.14886

• Journal Article Type: Article
• Acceptance Date: Sep 17, 2018
• Online Publication Date: Oct 1, 2018
• Publication Date: Feb 6, 2019
• Deposit Date: Sep 18, 2018
• Publicly Available Date: Oct 5, 2018
• Journal: Molecular Ecology
• Print ISSN: 0962-1083
• Electronic ISSN: 1365-294X
• Publisher: Wiley
• Volume: 28
• Issue: 2
• Pages: 232-249
• DOI: https://doi.org/10.1111/mec.14886
• Publisher URL: https://doi.org/10.1111/mec.14886
• Related Public URLs: https://onlinelibrary.wiley.com/journal/1365294x