Host associated microbial communities can provide a broad set of functions to the organisms they inhabit. However, while these communities can be critically important to host health and development, the interactions and mechanisms that underly these functions, as well as the context in which they matter, are less well understood. The work presented here seeks to provide a better understanding of these host-microbial interactions by utilizing a plant phyllosphere (the bacteria inhabiting the aboveground portion of the plant) model system, and a model microbial community (Synthetic Community) that is a simplified representation of the bacteria that would interact with the plant in a natural setting.

This research begins by outlining the development of the Synthetic Community that will be used throughout the rest of the work to investigate these host-microbe interactions. This chapter highlights the methods used to build the community, the resources that were developed to aid in the use of the community, and a selection of experiments in which the community is initially used. These initial experiments show the importance of understanding functional potential when predicting interactions among species, as well as the ability of individually protective species to work synergistically to yield better outcomes when their host is challenged by a pathogen.

In the following chapter, the Synthetic Community is used to investigate the importance of the phyllosphere to the development and reproductive success of the host plant, specifically looking at colonization and growth of tomato plants. This begins with the hypothesis that phyllosphere interactions will be disrupted in a greenhouse setting where microbial dispersal is limited, and that adding the synthetic community will yield important benefits to the host plant, allowing for a better understanding of the role of these bacteria in plant development. In a series of experiments taking place over several trials, I confirm that greenhouse-grown plants have a depauperate phyllosphere microbiome and that the addition of the Synthetic Community is responsible for a clear and repeatable increase in fruit production in this setting, but not in the field. I further show that this effect is synergistic with the addition of micronutrient-based soil amendments, and that modulating nutrition through conventional fertilizer can alter the protective capacity of these communities. These results suggest that greenhouse environments have poor phyllosphere microbiome establishment, with negative impacts on the plant. The results also implicate the phyllosphere microbiome as a key component of plant fitness, emphasizing that these communities have a clear role to play in the ecology and evolution of plant communities.

In the final chapter, I focus on the role that host condition plays in modulating the reliance on the microbiome. To do this, I look at the effect of whole-genome duplication in Arabidopsis thaliana on the phyllosphere microbiome, using the Synthetic Community, and determine the interacting impacts of ploidy and microbiome on disease outcome. This chapter shows polyploids fare better against the pathogen than diploids, regardless of microbial inoculation, while diploids harboring an intact microbiome have lower pathogen densities than those without. In addition, diploids have elevated numbers of defense-related genes that are differentially expressed in the presence of their phyllosphere microbiota, while polyploids exhibit some constitutively activated defenses regardless of colonization by the synthetic community. These results imply that whole-genome duplication can enhance immunity resulting in a decreased dependence on the microbiome for protection against pathogens.