Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

• Published in: Scientific reports Vol. 7; no. 1; p. 40368
• Main Authors: Yamamoto, Satoshi, Masuda, Reiji, Sato, Yukuto, Sado, Tetsuya, Araki, Hitoshi, Kondoh, Michio, Minamoto, Toshifumi, Miya, Masaki
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 12.01.2017; Nature Publishing Group
• Subjects: 631/158/2452; 631/158/2464; 631/158/670; Animals; Bays; Biodiversity; Coastal waters; Community structure; Deoxyribonucleic acid; DNA; DNA - genetics; DNA Barcoding, Taxonomic - methods; Environmental DNA; Environmental Monitoring - methods; Field tests; Fish; Fisheries; Fishes - genetics; Geography; Humanities and Social Sciences; Japan; Marine ecosystems; multidisciplinary; Primers; Science; Science (multidisciplinary); Sequence Analysis, DNA; Species; Species Specificity; Water; Water analysis; Water sampling
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep40368

Environmental DNA (eDNA) metabarcoding has emerged as a potentially powerful tool to assess aquatic community structures. However, the method has hitherto lacked field tests that evaluate its effectiveness and practical properties as a biodiversity monitoring tool. Here, we evaluated the ability of eDNA metabarcoding to reveal fish community structures in species-rich coastal waters. High-performance fish-universal primers and systematic spatial water sampling at 47 stations covering ~11 km 2 revealed the fish community structure at a species resolution. The eDNA metabarcoding based on a 6-h collection of water samples detected 128 fish species, of which 62.5% (40 species) were also observed by underwater visual censuses conducted over a 14-year period. This method also detected other local fishes (≥23 species) that were not observed by the visual censuses. These eDNA metabarcoding features will enhance marine ecosystem-related research, and the method will potentially become a standard tool for surveying fish communities.