Ontogenic shift of feeding habit in Manila clam Ruditapes philippinarum after settlement revealed by diatom specific DNA-metabarcoding diet analysis

Abstract

Clarifying the feeding ecology of each life stage of the Manila clam is essential for an accurate assessment of the food environment for this species. However, information on the feeding habit of clams remains insufficient, and also the morphological and ecological characteristics of the diverse microalgal species in the coastal zone on which clams feed remains largely unknown. In this study, we investigated the ontogenic change in feeding habit of clams in natural waters based on chloroplast-targeting DNA metabarcoding. Samples of clams (spats, juveniles, adults), seawater and sediment were collected in three regions in Japan. DNA was extracted from each sample and PCR and DNA metabarcoding were performed using diatom-specific universal primers for chloroplasts (rbcL), after comparison with the universal primer for microalgae (psbA). Then, we calculated compositions of diatom genera in each sample, proportions of planktonic and benthic diatoms in gut contents of clams and similarities of diatom genera compositions between each sample. High proportions of benthic diatoms tended to be detected from spats and small juveniles with a shell length less than 2 mm. On the other hand, high proportions of planktonic diatoms were detected from gut contents of juveniles and adults with a shell length greater than 8 mm, and their composition was similar to that of diatoms in the ambient seawater. This diet shift may be attributed to the developmental completion of the inhalant siphon for filter-feeding at around 2 mm in shell length. From these results, the life history stages of the Manila clam after settlement can be divide into three phases: pedal-feeding phase from the settlement to 2 mm shell length, transition phase from 2 to 8 mm and filter-feeding phase larger than 8 mm.