Invertebrate declines are widespread in terrestrial ecosystems, and pesticide use is often cited as a causal factor. Here, we report that aquatic systems are threatened by the high toxicity and persistence of neonicotinoid insecticides. These effects cascade to higher trophic levels by altering food web structure and dynamics, affecting higher-level consumers. Using data on zooplankton, water quality, and annual fishery yields of eel and smelt, we show that neonicotinoid application to watersheds since 1993 coincided with an 83% decrease in average zooplankton biomass in spring, causing the smelt harvest to collapse from 240 to 22 tons in Lake Shinji, Shimane Prefecture, Japan. This disruption likely also occurs elsewhere, as neonicotinoids are currently the most widely used class of insecticides globally.

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Seagrass beds are a target for conservation worldwide and are frequently the focus of bioassessment and biomonitoring surveys. However, these surveys often employ destructive methods and involve considerable effort and cost. Recently, environmental DNA (eDNA) techniques have been attracting attention as a low-impact alternative for evaluating species diversity. However, the relationship between the detection ability of eDNA metabarcoding and the ecology of the organisms from which eDNA is derived has not been explicitly investigated. In this study, we examined this relationship for fishes in 2 eelgrass Zostera marina beds in temperate Japan, with a focus on 2 ecological characteristics (swimming position and appearance frequency in seagrass beds). We used eDNA metabarcoding to identify fish DNA collected from seawater samples and compared species inventories between 2 sampling positions (within vs. above eelgrass meadows) and 2 survey methods (eDNA vs. sledge-net sampling). Our results show that eDNA metabarcoding is much more effective than sledge-net sampling in detecting fish species, and that the detection ability of eDNA metabarcoding differs with water-sampling position. In particular, the relationship between fish ecology and survey detection ability appears to differ between the 2 eelgrass beds. Our results indicate that prior consideration of the spatial structure and fish communities of eelgrass beds is necessary for a reliable estimation of fish diversity in vegetated marine habitats.