A comparison of visual observation and DNA metabarcoding to assess the diet of juvenile sea turtle Caretta caretta in the French Mediterranean sea
Jessica Martin A , Delphine Gambaiani A , Marie-Aurélia Sabatte A , Jacques Pelorce B , Alice Valentini C , Tony Dejean C , Gaëlle Darmon A and Claude Miaud
A *
+ Author Affiliations
- Author Affiliations
A CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Biogeography and Vertebrate Ecology team, Montpellier, France.
B Le Grau-du-Roi, France.
C SPYGEN eDNA laboratory, Le Bourget-du-Lac, France.
Marine and Freshwater Research 73(4) 552-560 https://doi.org/10.1071/MF21179
Submitted: 12 April 2021 Accepted: 17 November 2021 Published: 15 December 2021
© 2021 The Author(s) (or their employer(s)). Published by CSIRO Publishing.
Abstract
The contents of the digestive tracts of 21 loggerhead turtles (20 juveniles and 1 adult) collected along the French Mediterranean coast were extracted during necropsies. Hard and soft items were collected and identified by visual observation. A 15-mL sample of the liquid from the rinsed contents of each digestive tract was collected and dietary DNA (dDNA) was extracted and amplified with a 18S universal eukaryotic primers. The obtained reads were compared with taxonomic DNA reference database. Ten taxonomic groups (annelids, cnidarians, crustaceans, echinoderms, fish, insects, molluscs, plants, poriferans and tunicates) were identified with visual observation and eight (ctenophores, cnidarians, crustaceans, fish, molluscs, poriferans, tunicates and plants) with dDNA metabarcoding. Annelids, echinoderms and insects were detected only with visual observation, whereas ctenophores were detected only with dDNA. The two methods were complementary to cover the range of prey, with more soft-bodied organisms detected by dDNA and more hard-shelled organisms detected by visual observation. The increased use of the dDNA metabarcoding method will help compare sea turtle diets of the different stages such as juveniles and adults, or specimens living in different areas, despite the limitations and complexity associated with its use.
Keywords: Caretta caretta, diet, DNA metabarcoding, French Mediterranean sea, loggerhead turtle, marine turtle, methodology, trophic ecology.
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