Nanoplastics (NPs) are emerging contaminants of concern that may interact with natural biotic stressors (such as parasites) to disrupt host-associated microbiomes, which play a crucial role in the health and ecological dynamics of aquatic animals. Here, we investigate the effects of polystyrene NP beads and parasite infection on the microbiome diversity and composition of the model plankton organism Daphnia magna. We exposed D. magna to two NP sizes (50 nm and 100 nm) at two concentrations (1 mg L−1 and 5 mg L−1), both with and without infection by the yeast parasite Metschnikowia bicuspidata and sequenced the microbiomes of gut and body tissues using 16S rRNA gene sequencing. High concentrations of 50 nm NPs significantly increased bacterial richness in both gut and body tissue, with shifts exceeding those induced by parasite infection. In the gut, the relative abundances of Burkholderiales and Chitinophagales decreased, while Caulobacterales, Rhizobiales, and Salinisphaerales increased. In body tissues, Chitinophagales declined, whereas Burkholderiales, Caulobacterales, Rhizobiales, and Salinisphaerales were enriched. NP size, concentration and interaction with infection, significantly influenced gut and body microbiome alpha diversity. Bray-Curtis dissimilarity analysis confirmed that 50 nm NPs drove distinct shifts in bacterial community composition, independent of parasite infection. Overall, NP-size and concentration had a stronger influence on the Daphnia microbiome than parasite infection. Given the critical roles of the Daphnia microbiome in nutritional support and stress tolerance, our findings highlight the potential ecological impacts of NPs on aquatic ecosystems.
