title: 18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species.
abstract: The potential of the 18S rRNA V9 metabarcoding approach for diet assessment was explored using MiSeq paired-end (PE; 2 × 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.
authors.affiliation: Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain.
authors.forename: Aitor
authors.initials: A
authors.lastname: Albaina
authors.affiliation: Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain.
authors.forename: Mikel
authors.initials: M
authors.lastname: Aguirre
authors.affiliation: Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain.
authors.forename: David
authors.initials: D
authors.lastname: Abad
authors.affiliation: Marine Research Division AZTI Tecnalia Herrera Kaia Portualdea z/g P.O. Box 20110 Pasaia Gipuzkoa Spain.
authors.forename: María
authors.initials: M
authors.lastname: Santos
authors.affiliation: Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain.
authors.forename: Andone
authors.initials: A
authors.lastname: Estonba
keywords: 18S rRNA V9; MiSeq paired‐end technology; Sardina pilchardus; Sprattus sprattus; diet analysis; metabarcoding; plankton