Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs

Environmental DNA (eDNA) analysis has seen rapid development in the last
decade, as a novel biodiversity monitoring method. Previous studies have
evaluated optimal strategies, at several experimental steps of eDNA
metabarcoding, for the simultaneous detection of fish species. However,
optimal sampling strategies, especially the season and the location of
water sampling, have not been evaluated thoroughly. To identify optimal
sampling seasons and locations, we performed sampling monthly or at
two-monthly intervals throughout the year in three dam reservoirs. Water
samples were collected from 15 and 9 locations in the Miharu and Okawa dam
reservoirs in Fukushima Prefecture, respectively, and 5 locations in the
Sugo dam reservoir in Hyogo Prefecture, Japan. One liter of water was
filtered with glass-fiber filters and eDNA was extracted. By performing
MiFish metabarcoding, we successfully detected a total of 21, 24, and 22
fish species in Miharu, Okawa, and Sugo reservoirs, respectively. From
these results, the eDNA metabarcoding method had a similar level of
performance compared to conventional long-term data. Furthermore, it was
found to be effective in evaluating entire fish communities. The number of
species detected by eDNA survey peaked in May in Miharu and Okawa
reservoirs, and in March and June in Sugo reservoir, which corresponds
with the breeding seasons of many of fish species inhabiting the
reservoirs. In addition, the number of detected species was significantly
higher in shore, compared to offshore samples in the Miharu reservoir, and
a similar tendency was found in the other two reservoirs. Based on these
results, we can conclude that the efficiency of species detection by eDNA
metabarcoding could be maximized by collecting water from shore locations
during the breeding seasons of the inhabiting fish. These results will
contribute in the determination of sampling seasons and locations for fish
fauna survey via eDNA metabarcoding, in the future.