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 based on ITS1-amplicon sequencing, which assesses the structure of fungal assemblages associated with three different zooplankton groups (Cladocera, Copepoda, and Rotifera) inhabiting the same water column during a single growing season. Compared with water-column fungal communities, zooplankton-associated assemblages showed higher genus richness, particularly in Copepoda and Rotifera, but lower diversity and evenness. We identified 190 genera spanning eight fungal phyla, the majority of which were copiotrophic yeasts—organisms favoring nutrient-rich conditions and rapid growth—and predominantly soil-, plant litter–, or wood-associated saprotrophs.. The zooplankton taxonomic identity at the species level, as well as at higher taxonomic levels, was the most significant factor structuring the associated fungal assemblages, explaining 6.5% and 4.0% of the variation, respectively, followed by fungal spore size and precipitation. We found a high prevalence of soil- and plant-associated fungal sequences in zooplankton samples, a strong correlation between fungal community composition and precipitation events—indicative of terrestrial inputs—and the absence of gut-specific taxa. Together, these results suggest that zooplankton graze on fungal cells or propagules in the water column, many of which originate from allochthonous sources. Our results indicate a previously unexplored link across the terrestrial-aquatic ecosystem boundary, warranting further detailed study exploring the role of allochthonous fungi as a food source for zooplankton.