Environmental DNA metabarcoding of benthic brittle stars (Echinodermata: Ophiuroidea) from Ise Bay, central Japan, targeting the 16S rRNA genes

Abstract

The ocean covers 70% of the Earth’s surface, and understanding environmental changes in the ocean is directly related to understanding the global environment. Environmental DNA (eDNA) metabarcoding has become a widely used method for monitoring marine biodiversity, complementing traditional visual surveys; each approach has its own strengths and limitations. However, benthic organisms have rarely been targeted, as many eDNA studies—especially in Japan—have focused on fish. In this study, we sampled 5 L of seawater each from the bottom and surface waters at 17 m and 34 m of Ise Bay, central Japan (in total 20 L), and carried out metabarcoding targeting the mitochondrial 16S rRNA gene (brittle star-specific primer set “16SOph1”) for the water samples. Brittle stars, with about 2,100 known species found from shallow coasts to 8,000 m depths worldwide, are highly diverse and abundant benthic animals. Our results showed that the metabarcoding detected five species of brittle stars, compared to two species by direct collection, and that eDNA obtained from surface water contained DNA of species inhabiting the sea bottom, which indicate that (1) metabarcoding of brittle stars can be performed in tens of meters deep, and (2) eDNA of benthic species can be detected even in surface waters. Further research is needed to confirm the extent of vertical eDNA transport.