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Title: 18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species
Authors: Albaina, Aitor; Aguirre, Mikel; Abad, David; Santos, Maria; Estonba, Andone
Citation: ECOLOGY AND EVOLUTION, 2016, 6, 1809-1824
Abstract: The potential of the 18S rRNA V9 metabarcoding approach for diet assessment was explored using MiSeq paired-end (PE; 2 9 150 bp) technology. To critically evaluate the method's performance with degraded/digested DNA, the diets of two zooplanktivorous fish species from the Bay of Biscay, European sardine (Sardina pilchardus) and European sprat (Sprattus sprattus), were analysed. The taxonomic resolution and quantitative potential of the 18S V9 metabarcoding was first assessed both in silico and with mock and field plankton samples. Our method was capable of discriminating species within the reference database in a reliable way providing there was at least one variable position in the 18S V9 region. Furthermore, it successfully discriminated diet between both fish species, including habitat and diel differences among sardines, overcoming some of the limitations of traditional visual-based diet analysis methods. The high sensitivity and semi-quantitative nature of the 18S V9 metabarcoding approach was supported by both visual microscopy and qPCR-based results. This molecular approach provides an alternative cost and time effective tool for food-web analysis.
Keywords: 18S rRNA V9; diet analysis; metabarcoding; MiSeq paired-end technology; plankton; Sardina pilchardus; Sprattus sprattus; REAL-TIME PCR; HIGH-THROUGHPUT; SARDINA-PILCHARDUS; COPY NUMBER; NORTH-SEA; DNA; BIODIVERSITY; COMMUNITIES; DIVERSITY; COPEPODS
Issue Date: 2016
Type: Article
Language: English
DOI: 10.1002/ece3.1986
ISSN: 2045-7758
Funder: projects ECOGENBAY \[MICINN CTM2009-13570-C02-02]
Government of Spain
project ``Bay of Biscay anchovy biomass estimates for year´´
European Commission \[665/2008]
Euskampus Foundation (Euskampus Fundazioa)
Basque Government (UPV/EHU ``ZabaldUz´´ program)
Basque Government \[IT558-10]
Appears in Publication types:Artículos científicos

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