Fungi Associated With Freshwater Zooplankton Are Taxon-Specific, Temporally Dynamic and Reflect Allochthonous Inputs

The associations between microbes and planktonic invertebrates in freshwater ecosystems are considered key ecological interactions. However, our understanding of the structure, taxonomic specificity, and environmental drivers of zooplankton microbiomes remains poor. Here, we present the results of a field study using ITS1-amplicon sequencing that assesses the structure of fungal assemblages associated with three zooplankton groups (Cladocera, Copepoda and Rotifera) inhabiting the same water column during a single growing season. Compared with fungal communities in the surrounding water, zooplankton-associated assemblages showed higher genus richness, particularly in Copepoda and Rotifera, but lower diversity and evenness. We identified 190 fungal genera spanning eight phyla, dominated by fast-growing yeasts that thrive in nutrient-rich environments and are commonly associated with soil, leaf litter and decaying wood. The taxonomic identity of the zooplankton emerged as the main factor shaping fungal assemblages, followed by spore size and precipitation. Fungal sequences in zooplankton samples were largely derived from taxa typically linked to soils and plants, and the community composition shifted after precipitation events, consistent with terrestrial inputs to the lake. No fungal taxa were found exclusively in zooplankton guts, suggesting that these associations are transient and trophic rather than colonising. Taken together, these patterns indicate that zooplankton feed on suspended fungal cells or spores, many of which originate from surrounding terrestrial habitats. This suggests an overlooked pathway connecting land and freshwater ecosystems, highlighting terrestrial fungi as an under-recognised component of freshwater trophic linkages.