Integrating host-microbiota dynamics with disease ecology in the model Daphnia

Abstract

Host microbiomes play an important role in host-parasite interaction, but few studies integrate host-parasite-microbiome tripartite interactions in the wild. In this thesis, I combine field and laboratory experiments using the water flea Daphnia to investigate the role of host microbiomes in host-parasite interactions. In Chapter I, I surveyed with my co-authors the bacterial communities of eight Daphnia galeata genotypes isolated from Lake Greifensee and found host genotype-specific variation. We additionally found no correlation between host genetic distances based on whole genome sequencing of the hosts, and bacterial community composition, suggesting that host genetic distances do not predict divergence in bacterial communities. In Chapter II, we compared the bacterial communities of Daphnia sp. in Lake Greifensee between hosts infected or not infected with the virulent, eukaryotic gut parasite Caullerya mesnili. We found that infection associates with reduced alpha diversity in the gut (the site of infection) and altered community composition in both the gut and body. In Chapter III we tested long-term dynamics of host-parasite-bacterial community associations between Daphnia and Caullerya in Lake Greifensee. For this, we compared infected and uninfected Daphnia across six natural epidemics spanning 13 years. Here we found that Daphnia bacterial community composition showed substantial temporal variation in both dominant bacterial taxa as well as rare taxa, but that infection by Caullerya only altered the composition of rare taxa. Host bacterial community composition also correlated with parasite infection prevalence, i.e. years with larger epidemics had distinct host bacterial communities than those with smaller epidemics. We further found that the environmental abiotic conditions temperature, dissolved oxygen content and cyanobacterial abundance in lake water, all previously known to drive epidemics all associated with distinct host bacterial community compositions. In Chapter IV, we tested the directionality of infection and host microbiome interaction in a laboratory experiment with Daphnia magna and the fungal parasite Metschnikowia bicuspidata. We found that initial parasite exposure drives host genotype specific changes in bacterial community compositions that correlate with the parasite’s life stage. We also found that successful infection drives a loss of bacterial community diversity and abundance shifts in dominant bacterial taxa in the host gut. Overall, the results of this thesis indicate that Daphnia bacterial communities play a significant role in host-parasite interaction.