eDNA and microscopy reveal traits underlying long-term zooplankton community change

Zooplankton form a vital link between phytoplankton and higher trophic levels, including commercially exploited fish, making recent declines in copepods and increases in meroplankton a major concern. To investigate underlying mechanisms, we compared weekly, high-resolution net (microscope analysis: 35 years) and surface water (eDNA: 11 years) from Station L4 in the Western English Channel. The two methods showed strong agreement for holoplanktonic crustaceans and gelatinous predators, but weaker correspondence for meroplankton. The far greater taxonomic insight from meroplankton groups provided by eDNA revealed a shift towards higher relative sequence abundance of soft sediment (mainly sublittoral) fauna, rather than from rocky nearshore. Trait-based analysis showed long-term increases were mainly fine filter feeders, including many meroplankton larvae. This suggests that changes in water column processes, linked to declining nutrient supply and a shift towards smaller phytoplankton, were contributing to broader changes in the pelagic food web and benthic-pelagic coupling.