Efficiency of Scleractinian-Specific eDNA Metabarcoding Using Specimens from Okinawa Churaumi Aquarium, Japan

Scleractinian-specific eDNA metabarcoding (eDNA-M), based on amplification of mitochondrial 12S rDNA, has become an effective tool for comprehensive monitoring of zooxanthellate scleractinians at the generic level, but several questions remain about its efficiency. Taking advantage of coral culturing tanks at Okinawa Churaumi Aquarium, Japan, we examined the robustness of this metabarcoding technique. Our eDNA-M system can theoretically identify 53 scleractinian genera. Without knowing genera and numbers of colonies in a large, indoor exhibition tank, eDNA-M identified 29 genera in tank effluent and one genus that requires further bioinformatic improvement for detection. Later, aquarium staff informed us that the tank contains 37 genera. Colony numbers in the tank were also provided. Tank population data revealed that mitochondrial 12S rDNA of the seven missing genera had not been sequenced yet. Those seven taxa were sequenced thereafter, with the result that at the end, 36 of the 37 genera were identified. Even three genera with only one colony in the tank were detected. Surveys of outdoor culture tanks yielded comparable results, with additional genera that may have been detected due to contamination in incurrent natural seawater. We conclude that this scleractinian-specific eDNA metabarcoding is robust for coral monitoring, although further mitochondrial 12S rDNA sequences are needed for additional scleractinian genera.