Polyploidy or whole-genome duplication (WGD) is a ubiquitous phenomenon in the evolutionary history of land-plants. As WGD often induces many new novel, adaptive, or transgressive phenotypes, it can have cascading ecological effects on biotic interactions and potentially the microbiome. There is a growing body of research on the impact that the microbiome plays in plant ecology, but few studies have looked at the potential interactions between ploidy, microbiomes, and pathogens in shaping the ecology of newly established polyploids. This study uses synthetic auto-tetraploid Arabidopsis accessions and a synthetic microbiome representative of natural commensal bacteria in order to assay how these interactions impact host phenotype with respect to pathogen response.

In Chapter 1, I describe how the induction of polyploidy does not change the beta diversity of the phyllosphere but does alter the selection of various taxa of the synthetic community. In Chapter 2, I describe a phenomenon whereby polyploids fare better than diploids when treated with a pathogen regardless of inoculation with a protective microbiome, but where diploids treated with a microbiome better arrest the growth of pathogens than the non-treated diploids. In Chapter 3, I perform an RNA-Seq experiment and find a pattern where defense-associated genes are expressed less in diploid accessions than in polyploids when treated with a microbiome. Together, these chapters for the first time demonstrate that a potential consequence of whole genome duplication may be a loss of control over the composition of the microbiome. Finally in chapter 4, I review and synthesize the literature on somatic polyploidy to assess whether endopolyploidy and whole-genome duplication have shared underlying evolutionary rules.