Daphnia -associated bacterial communities are influenced by infection status, environmental conditions and diet quantity across natural epidemics

Microbiomes associated with zooplankton play an important role for host health and contribute to ecosystem functions, such as nutrient cycling. Yet, few studies have assessed how environmental gradients and biotic interactions, such as parasitism and diet, shape the microbiome composition of wild zooplankton. Here, we used 16S rRNA gene sequencing and a long-term field dataset to investigate the microbiomes of water fleas belonging to the Daphnia longispina species complex, across six sampling events spanning 13 years. Sampling coincided with epidemics of the virulent eukaryotic gut parasite Caullerya mesnili. We further surveyed phytoplankton and zooplankton communities in the lake to explore associations between Daphnia microbiome composition and diet (phytoplankton density), as well as zooplankton density and community composition. We observed temporal variation and infection-dependent shifts in Daphnia microbiome composition. Importantly, host microbiome compositions co-varied with infection prevalence, indicating a correlation between host microbiome composition and epidemic size. Furthermore, environmental factors including temperature, dissolved oxygen and cyanobacterial abundance, previously found to drive Caullerya epidemics, were associated with distinct host microbiome compositions. Dominant bacterial taxa in the Daphnia microbiome correlated with Daphnia density, whereas the phylogenetic composition of rare bacterial taxa correlated with total zooplankton density. Lastly, Daphnia microbiome composition correlated with the density of green algae, protists and cyanobacteria in lake water, but not with their community composition. Our findings show the dynamic nature of Daphnia -associated microbiomes and suggest potential mechanisms through which they may mediate host disease dynamics, including associations with temperature, host density and diet quantity.