Dietary analysis of three important mariculture species in South Korea using DNA metabarcoding in fecal samples

Knowledge of dietary composition is crucial for understanding the trophic ecology of a mariculture species and the available food in aquafarms, which is fundamental for assessing ecosystem health status and determining ecological response to ecosystem variation to develop a better management plan for marine farming. For suspension-feeding invertebrates, the growth and development rely heavily on the availability and quality of phytoplankton. However, their growth rate can be severely impacted by food deficiency or exposure to harmful algae blooms (HABs) and pathogenic parasites, which are major causes of mass mortality in mariculture. This study aimed to conduct a dietary analysis of three important mariculture species — Magallana gigas, Halocynthia roretzi, and Mizuhopecten yessoensis — on three farms in South Korea using DNA metabarcoding. Sequence processing and filtering generated 304 validated amplicon sequence variants from six fecal samples, taxonomically identifying 15 phyla, 18 classes, 32 orders, 39 families, 43 genera, and 46 species. The DNA recovery of Dinoflagellata was predominantly detected in all fecal samples, followed by Apicomplexa, Bacillariophyta, and Ciliophora. Of the three mariculture species, the fecal assemblage of M. gigas exhibited the highest richness and diversity, with a high read proportion of phytoplankton (specifically Dinoflagellata), while such proportions were relatively low in the M. yessoensis samples. Excessive read proportions of parasites (Apicomplexa) were detected in the fecal samples of two H. roretzi, indicating a possible link to as substantial decrease in H. roretzi production observed in South Korea. A total of 27 key species were detected in six fecal samples, including a high read proportion of Prorocentrum triestinum, which is responsible for HABs in Korean coastal waters. These results emphasize the potential of fecal DNA metabarcoding in the genetic monitoring of aquaculture farms/ecosystems and could be a useful reference for develop effective management plans to guarantee sustainable mariculture production.