Doctor of Philosophy in Botany (PhD)
Microbial interactions with photosynthetic hosts
Animals live with a symbiotic community of bacteria, and some of these bacteria affect host biology. Generally, these bacterial communities are diverse and complex. A key question in microbiome research is whether bacteria are specific to a host and affect host biology. In my dissertation, I use observational and experimental approaches to 1) understand the factors that contribute to composition of host-microbiota, 2) determine the core bacteria of a host by comparing the abundance of host bacteria to the bacteria in environmental bacterial communities, 3) determine the phylogenetic and environmental distribution of core bacteria and their close relatives to better understand their natural history, and 4) test whether core bacteria are correlated with aspects of host biology. Across three host species, I found bacterial communities that were populated by a few common and prevalent core bacteria that are absent from the environment; in most cases, these core bacteria belong to host-associated clades of bacteria. In chapter 2, I characterize the microbiota of the keystone sea star Pisaster ochraceus, identify core bacteria, and use phylogenetic trees to assess the distribution of their relatives. In chapter 3, I study the interactions between the skin microbiota and host innate immunity of Columbia spotted frogs and to determine whether they explain the occurrence of the amphibian pathogen, Batrachochytrium dendrobatidis (Bd). In chapter 4, I characterize the microbiota of wild and captive endangered Oregon spotted frogs (OSF) and whether their skin bacteria are associated with Bd intensity. Lastly, I experimentally test the hypothesis environmental reservoirs of bacteria influence the bacteria on the skins of frogs. Understanding the factors that structure captive communities has substantial conservation implications for captive breeding and head start programs. My results differ from previous studies by comparing the host to their environment and focusing on specific core bacteria.
Macroalgae (seaweeds) have an intimate relationship with their microbial symbionts. Microbial communities associated with macroalgal surfaces (epibiota) are generally host-specific and, historically, there has been great interest in the role of biological compounds and chemical warfare in microbial community assembly on seaweeds. However, the interaction between seaweeds and their environment may also influence community assembly of their microbiota. In my thesis, I conduct two experiments that ask how factors not related to seaweed chemistry influence microbial community assembly. First, I ask whether the interaction between flow and seaweed morphology affects the settlement and structure of microbial biofilms. In this project, I test whether three common algal morphologies select for differential biofilm communities using artificial macroalgae units (AM units) made out of latex. I find that morphology does affect initial microbial settlement and community structure, but that eventual dominance of substrate specialists (in our case a latex degrader) swamps the influence of morphology in long-term biofilms. The second chapter of my thesis asks whether macroalgae affect the microbial epibiota of each other. To test this, I co-incubate Nereocystis leutkeana meristem fragments with different species of mature macroalgae. I find that although water column communities change significantly when incubated with mature macroalgae, seaweed surface communities are far more resistant to change. Overall, these results support the idea that the seaweed surfaces are highly selective, and demonstrate that modulations on seaweed microbiota operate within an overarching paradigm of species specificity. With these experiments, I hope to contribute to the larger body of knowledge on seaweed-microbe associations and improve understanding of how, and why, we find the observed microbiota on seaweed surfaces.
A fundamental goal of microbial ecology is to understand how microbial diversity is distributed over space and time. At broad scales, abiotic factors drive microbial community composition, and salinity plays a particularly important role. Do all microbes respond in the same way? Here I investigate the diversity of two domains encompassed within the blanket term ‘microbes’ the bacteria and protists (unicellular eukaryotes). I examined their diversity and composition across a river to ocean transect and compare the shifts in diversity that occur in these two domains. I collected 122 samples from the Fraser River, its plume and the adjacent coastal water at three time points covering the spring freshet. I used a combined approach of high-throughput sequencing and inverted microscopy to investigate the changes in diversity and community composition. As expected, there was a strong turnover in the community composition of bacteria and protists across the salinity gradient. I found that diversity of both the bacteria and protists was highest in the freshwater and brackish water with low salinity, and decrease with increasing salinity, and observed a high degree of separation between marine and freshwater community composition. However, the shift from communities with predominately fresh to marine water taxa occurs at the higher taxonomic level for bacteria (phylum/class) and lower taxonomic level (family/genus) for protists. Moreover, the inflection point for taxonomic distribution tends to occur around at 20 salinity for bacteria and 10 salinity for protists. Overall, bacteria are distributed more broadly across the salinity gradient than protists and more likely to be present across time points. In contrast, protists tend to be found in a narrower salinity range and are more often restricted to either marine or freshwater, and found at a single time point.