The fungal microbiome, or “mycobiome” of plants is diverse and important to host health, but the fluxes of fungi among plant hosts and with the surrounding environment are poorly understood. In chapter two, we employed sterile culture techniques and spatial sampling to examine leaves as possible vectors for transfer of their endophytic fungi from the canopy to substrate on the forest floor, as predicted by the Foraging Ascomycete hypothesis. Some foliar endophytic fungal species are also present as wood-decomposing fungi on the forest floor, that transfer of mycelium across these two life history stages can occur, that endophytic life history stages are buffered from environmental conditions in comparison to wood-decomposing fungi, and that spatial linkages between the two life history stages can be observed. In another study, described in chapter 3, wood and leaf wood endophytes were sampled across a 25 ha plot, to explore landscape patterns of mycobiomes, and to explore the concept of a core microbiome in aerial plant tissues. We found that core microbiomes may be observed in a real ecological setting, but that the concept of core must be carefully defined and that some level of buffering from disturbance may be necessary to allow core microbiomes to assemble. In chapter four, we return to examine some of the assumptions and implications of the Foraging Ascomycete hypothesis, with an agent-based model. We model the conditions under which dispersal through falling leaves may represent a fitness-enhancing dispersal strategy for fungi, and that deforestation as is currently underway throughout the world may have impacts on fungi that rely upon a canopy- inhabiting life stage for dispersal. In chapter five, some challenges associated with environmental sampling of microbes using illumina© MiSeq sequences are critically examined. We find that biases introduced by random sampling at various stages of IVenvironmental DNA extraction and illumina© MiSeq sequencing are not well corrected by currently accepted bioinformatic algorithms. In addition, information loss from differential extraction, PCR amplification, and sequencing success, requires that users of MiSeq read libraries to interpret read abundances carefully. This dissertation includes previously published, co-authored material.