The community of organisms that associate with plants are vital to both the survival of the host plant but also the diseases which may kill it. The processes by which this community, called the microbiome, assemble and function can contribute to the traits of the host, including plants that humans rely on for food, resources, and ecosystems services. This thesis focuses on understanding the assembly of microbiomes at the scale of microbe-microbe interactions and traits of individual microbes, as well as how characters of the host may change this process. I first address this by examining the in vitro and in planta interactions within small synthetic communities of root-inhabiting bacteria and fungi and with the plant host and viral disease of the host. While intermicrobial interactions in vitro were not predictive of in planta interactions, adding host disease or additional organisms to the system altered the assembly process. I then show the development and applications of the CONSTAX2 classifier, a taxonomic assignment tool for metabarcoding studies, which offers improved accuracy and ease of use for conducting metabarcoding studies exploring the diversity and structure of microbial communities. Last, I present a study testing which factors affected the composition of forest fungal communities to understand the ecology of litter-inhabiting fungi and improve methodologies for sampling leaf-associated fungal communities. The factors affecting the assembly of plant microbiomes are complex and varied but connecting individual interactions to community composition and ultimately function may improve our abilities to predict and manage microbiome processes.
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