Fish environmental DNA in lake sediment overcomes the gap of reconstructing past fauna in lake ecosystems

Underwater sediments are a natural archive of biological information. Reconstruction of past fauna has been conducted for various taxonomic groups using morphological remains and DNA derived from these remains. However, information on past occurrences of fish species, the top predator of lake ecosystems, could have been reproduced only in exceptional environments, and past quantitative information on fish, particularly in lake ecosystems, has been a knowledge gap in reconstructing past fauna. Tracking the quantitative fluctuations of fish is essential for reconstructing multiple trophic levels of organisms in lake ecosystems.To acquire past quantitative fish information from lake sediments, we collected approximately 30 cm-length of underwater sediments in Lake Biwa. We extracted sedimentary environmental DNA (eDNA) and measured temporal fluctuations in the eDNA concentration of the native and fishery target species Plecoglossus altivelis and Gymnogobius isaza. For P. altivelis, we examined the possibility of tracking quantitative fluctuations by comparing sedimentary eDNA with recorded catch per unit effort (CPUE).The chronology of the sediments allowed us to obtain information on sediments collected in Lake Biwa over the past 100 years. The deepest depths at which sedimentary eDNA was detected were 30 and 13 cm for P. altivelis and G. isaza from the surface, corresponding to approximately 100 and 30 years ago, respectively. In the comparison of sedimentary eDNA concentrations and biomass, we found a significant correlation between the CPUE of P. altivelis and its sedimentary eDNA concentration adjusted to compensate for DNA degradation. Sedimentary eDNA fluctuations were observed in P. altivelis, possibly reflecting the abundance fluctuation due to variations in the main food resources of zooplankton.Our findings provide essential pieces for the reconstruction of past fauna of lake ecosystems. The addition of quantitative information on fish species will reach a new phase, for instance, by investigating population shifts or biological interactions in the reconstruction of past fauna in lake ecosystems.