Endosymbiosis is a pervasive phenomenon that has been a powerful force in insect evolution. In many well studied insect-bacterial associations, the bacteria can serve as reproductive manipulators, nutritional mutualists or defenders of their hosts. Fungi are also frequently associated with insects, and initial estimates suggest that these fungi are hyperdiverse. Saving a handful of examples, however, the functions of these fungi within insect hosts are largely unknown. This dissertation begins with a review that lays the conceptual groundwork for understanding bacterial and fungal endosymbiosis in insects. I make predictions about why one versus the other microbe might serve the insect, given any unique physiological, ecological or evolutionary conditions. I then aim to derive insights about microbial symbiosis by focusing on a particular system, that of brownbanded cockroaches, Supella longipalpa (Blattaria: Blattellidae) and their specialist wasp parasitoids, Comperia merceti (Hymenoptera: Encyrtidae). Here, I identify the symbiotic community of these two insects by using both culture-dependent and independent methods to characterize the vertically transmitted bacterial and fungal associates. Finally, I show that a heritable fungus in C. merceti, long presumed to be a mutualist, is parasitic under laboratory conditions: infected wasps incur fitness costs for housing the fungal symbiont relative to uninfected wasps. Additionally, although the fungus is not horizontally transmitted sexually, it is readily horizontally transmitted from the offspring of infected females to those of uninfected females that are using the same host.

As one of the most diverse and ecologically important clades of life, fungi are best known as pathogens, saprotrophs, mycorrhizae, and lichens. Yet an enormous amount of previously unknown diversity occurs among endophytic and endolichenic fungi--species-rich, horizontally transmitted fungi that live within asymptomatic photosynthetic structures such as leaves and lichens. Here, I explore the biodiversity of these understudied symbiotrophs and the ecological and biogeographic factors influencing their communities.To evaluate methods currently used in ecological studies of environmental samples of fungi, I assessed inter- and intraspecific divergence of a fast-evolving locus for four genera commonly found as endophytes, and compared analytical methods for identifying and delimiting OTUs. Then I used the most robust methods to show that after soil contact, seeds of a focal tree species contain diverse fungi that are closely related to endophytes and pathogens.To explore the ecological specificity of symbiotrophic fungi, I examined endophytic, endolichenic, and saprotrophic communities inhabiting physically proximate hosts in a biotically rich area of southeastern Arizona. I found that endolichenic fungi are largely distinct from plant-associated fungi, with the exception of a group of ecologically flexible symbionts that occur in lichens and mosses. Although numerous endophytes were found in non-living leaves, fungi that were highly abundant in leaf litter were seldom found as endophytes.To assess symbiotroph biodiversity and ecological specificity at a broad geographic and phylogenetic scale, I isolated>4100 endophytic and endolichenic fungi from diverse communities of plants and lichens across five climatic regions in North America. I found that the abundance, diversity, and composition of these nearly ubiquitous fungi differ as a function of climate, locality, and host. Differences among communities reflect environmental characteristics more strongly than geographic distance.Last, I addressed a series of hypotheses regarding the ecological specificity of fungi inhabiting living and non-living leaves. I show that like endophytes, saprotrophic communities are structured by environmental characteristics, and at small spatial scales by host and leaf status. Yet, differences in communities between living leaves and leaf litter suggest that most endophytes either rapidly complete their life-cycle or are out-competed by robust saprotrophs once leaves senesce.