Lake fish fauna frequently suffer from multiple pressures such as anthropogenic modifications on physicochemical features of lake and exotic-species invasions. To detect any anomalies triggered by these causes, appropriate methods for continuous and sensitive monitoring of the fish community should be developed. In the case of large bodies of water, conventional monitoring methods such as direct catchment would be ineffective. These methods are too timeconsuming and have intrinsic bias in catchment results, making it unsuitable for long-term and large-scale monitoring.
In this study, we employed an environmental DNA (eDNA) metabarcoding technique for investigating spatiotemporal dynamics of fish community in the littoral zone of Lake Biwa, an ancient lake in Japan. As DNA in the lake water can be used as proxy for species presence, seasonal water samples were collected from the 24 littoral zone sites placed around the lake and a total of 96 extracted DNA samples were served for metabarcoding analysis using a set of universal primers MiFish. Indexed amplicons were Illumina sequenced and the resulting sequence reads were assigned to OTU with reference to a custom database containing >7,000 fish species.
MiFish metabarcoding detected 50 species in total, with 39, 39, 39, and 46 species in fall, winter, spring, and summer, respectively. A permutational multivariate analysis of variance revealed significant effects of site location (latitude) and season on fish community compositions based on the dissimilarities. Inter-site distances positively correlated with the dissimilarity of fish community according to the Mantel test. These results suggest that the fish species community in the littoral zone is strongly characterized by the site location and the season. This would be the outcome of two distinctive lake basins; the shallow, small south basin and the deep, large north basin of the lake.
Interspecific analyses revealed variations in their spatiotemporal distribution. For instance, two dominant invasive species in the lake, largemouth bass and bluegill, and endemic Carrasius carp species showed ubiquitous distributions throughout the year. Meanwhile, occurrences of some other species were spatiotemporally restricted to either north or south basins or to a specific season. This is the first MiFish metabarcoding study that provides us with an unprecedented data set of the littoral fish community of the lake covering four seasons. The data set can be useful for an initial reference to detect new invasion by exotic species and the shrinking of the rate-species distribution in further eDNA monitoring of the lake.