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

Abstract

AbstractMicrobiomes 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 theDaphnia longispinaspecies complex, across six sampling events spanning 13 years. Sampling coincided with epidemics of the virulent eukaryotic gut parasiteCaullerya mesnili.We further surveyed phytoplankton and zooplankton communities in the lake to explore associations betweenDaphniamicrobiome composition and diet (phytoplankton density), as well as zooplankton density and community composition. We observed temporal variation and infection-dependent shifts inDaphniamicrobiome 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 driveCaulleryaepidemics, were associated with distinct host microbiome compositions. Dominant bacterial taxa in theDaphniamicrobiome correlated withDaphniadensity, whereas the phylogenetic composition of rare bacterial taxa correlated with total zooplankton density. Lastly,Daphniamicrobiome 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 ofDaphnia-associated microbiomes and suggest potential mechanisms through which they may mediate host disease dynamics, including associations with temperature, host density and diet quantity.