In situ trophic ecology of benthic marine suspension feeders using metabarcodingBiogeochemical Cycling

Aline Gangnery¹, Flavia Nunes¹, Lucie Caradec¹, Justine Evrard¹, Chloé Jamin¹, Cyril Noel¹, Stéphane Pouvreau^1,3, Hélène Hegaret^2,3, Anne Doner¹, Tania Hernandez-Farina¹

¹Ifremer, France - ²CNRS, France - ³UMR LEMAR, France

Much like the physical habitat (i.e. available space), trophic resources have an important influence on the structure and functioning of coastal benthic communities. Suspension feeders, which dominate these communities, show great trophic plasticity, with phytoplankton and resuspended microphytobenthos representing a major food source. In addition, the various co-occurring groups/species use more or less sophisticated physiological mechanisms to capture them effectively. Several methods are used to study in situ diets, from direct observation of stomach contents or their analysis using molecular approaches to indirect biological markers such as stable isotopes or fatty acids. They are complementary and each has its advantages and limitations. The use of molecular methods on marine macro-organisms has grown considerably over the past decade, enhanced by ongoing improvements in sequencing techniques, helping to reduce costs. Metabarcoding is able to detect DNA from degraded prey, provides better taxonomic resolution down to genus and sometimes species level and gives insights on short-term feeding patterns (almost the diet of the day). So far, however, only a dozen articles using DNA techniques have been published on suspension feeders, and several technical steps remain critical. In this work, we investigated several of these aspects for using metabarcoding to study the trophic ecology of suspension feeders: which biological compartments or tissues to analyse, which marker gene to target, how to exclude host DNA, which sequence database to use, which taxonomic resolution to expect, and how to use metabarcoding data to describe diets. The results showed that the analysis of the 18S gene associated with non-metazoan primers in three biological compartments (seawater, gut and feces) proved effective in identifying phytoplankton species that were ingested and assimilated by four species of suspension feeders. Several indicators can be used to represent their trophic niche as well as diet overlap between them.