Experimental investigations of diverse interactions between an aquatic crustacean and associated environmental bacteria

All animals spend their lives in contact with diverse communities of microorganisms termed their microbiota, and the full range of effects these interactions have on animal ecology and evolution is only beginning to be appreciated. This thesis presents a series of experiments investigating the relationship between the water flea Daphnia magna and the environmental microbes with which it naturally coexists. These experiments lay a foundation for further investigations into host-microbiota interactions in aquatic settings.
The Introduction (Chapter 1) gives a brief overview of the conceptual issues raised by current studies of host-microbe interactions and introduces the ecological model organism Daphnia. In Part I of the thesis, I use newly developed methods for raising bacteria-free Daphnia to investigate the roles of bacterial microbiota in animal functioning. First, we examined the effect of bacteria-free conditions on basic Daphnia life history traits. We found that absence of microbiota has consistent, strong negative effects on Daphnia survival, growth and reproduction (Chapter 2). The effects of microbiota were generally robust to experimental conditions, but variation in the responses observed prompted further investigation into environment-specific benefits of these bacteria. We find that the magnitude of the beneficial effect of microbiota depends on diet (Chapter 3). In addition, we find that bacteria have a positive effect on embryonic development of resting eggs under warmed temperature conditions (Chapter 4). These results indicate a diversity of beneficial effects of Daphnia-associated bacteria.
In Part 2 of the thesis, I investigate how Daphnia-microbiota associations are formed in light of specific ecological characteristics of the host, namely diapause and genetically variable sediment browsing behavior. We find that diapausing stages of Daphnia are associated with beneficial bacteria even after years of dormancy, and use next-generation sequencing of bacterial taxonomic markers to characterize these bacterial communities (Chapter 5). We also investigated the effect of behavior on the composition of host-associated microbiota (Chapter 6), concluding that differences in microbiota diversity between host genotypes may be partially determined by genetic variation in behavior.
In Chapter 7, I argue that the evolution of host-microbe associations cannot be understood without attention to the effect of the interaction on the microbial symbiont community, and furthermore encourage re-framing the effects of complex microbiota as questions of community ecology and ecosystem function, rather than as a simple mutualism between two entities. I conclude with a list of specific research hypotheses raised by my work, and suggest approaches for answering them (Chapter 8).
Taken together, these results suggest that bacteria play fundamental, often cryptic roles in Daphnia biology, and that these relationships arose as a result of the omnipresence of bacteria throughout the history of Daphnia evolution.