Research Article

Using Environmental DNA metabarcoding to detect clams in lagoons

¹ MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
² MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
³ Argaly, Bâtiment CleanSpace, Sainte-Hélène-du-Lac, France
⁴ Ifremer, IRSI, SeBiMER Service de Bioinformatique de l’Ifremer, Plouzané, France

^* Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

Received: 27 September 2025
Accepted: 15 June 2026

Abstract

Clams are coastal resources widely exploited by both fishing and aquaculture. Most inhabit shallow waters, especially lagoons, that are transitional zones between the sea and land. In the Mediterranean French lagoons, two clam species are usually exploited: the native European clam, Ruditapes decussatus, and the introduced Manila clam, Ruditapes philippinarum, whereas several others are not of fishing interest, such as the golden carpet shell, Polititapes aureus. Those animals are relatively small, spend most of their lives buried, and can be difficult to identify based on shell morphology. Therefore, we tested a metabarcoding approach to detect clam species from environmental DNA (eDNA) samples. After an in silico comparison between a universal and a group-specific metabarcode, we conducted an in vivo experiment to characterise this metabarcode on clams and tested it in situ in two French lagoons. Specifically, we aimed to answer the following questions: (1) Is the group-specific metabarcode developed for freshwater Venerida also usable for marine Venerida and, more specifically, for clam species? (2) What clam species are detected in two French Mediterranean lagoons? (3) Is the intraspecific information of interest in characterising the populations and improving the surveys? The metabarcode proved to be very powerful to detect the targeted clam species and allowed support for a very significant depletion of the European clam in one lagoon and the predominance of the Manila clam in another lagoon. This eDNA metabarcoding protocol allows species identification with an easy deployment on the field and no clam sampling.