Recent studies have demonstrated that aquatic animals including fishes shed their genetic material into the environment as metabolic waste, damaged tissue, or sloughed skin cells. Such genetic material is known as “environmental DNA (eDNA)” and this study presents a novel high-throughput multispecies identification system using eDNA from fishes. This multispecies identification system is called “metabarcoding” and we developed universal PCR primers that are essential for metabarcoding eDNA from a diverse range of fishes comprising >30,000 species. The new primers detected >230 subtropical fish species in water samples from four aquarium tanks with known species compositions and nearby natural seawater in an open ecosystem. The new metabarcoding platform has the potential to serve as an alternative tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
To test versatility of the new primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera.
Research Director: Masaki Miya (Principal Research Scientist, Natural History Museum and Institute, Chiba)
Dr. Masaki Miya is a leader of one of the five teams in the research program “Application of environmental DNA for quantitative monitoring of fish community and ecosystem assessment” led by Prof. Michio Kondo at Ryukoku University (Project period: Oct. 1, 2013 - Mar 31, 2019).
M. Miya, Y. Sato, T. Fukunaga, T. Sado, J.Y. Poulsen, K. Sato, T. Minamoto, S. Yamamoto, H. Yamanaka, H. Araki, M. Kondoh, and W. Iwasaki. “MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species” Royal Society Open Science, doi: 10.1098/rsos.150088.
Masaki Miya, Ph.D.
Principal Research Scientist, Department of Zoology, Natural History Museum and Institute, Chiba
955-2, Aoba-cho, Chuo-ku, Chiba 260-8682, Japan
Department of Innovation Research, JST