Effect of soybean seed treatments on oomycete evolution and diversity for improved seedling disease management

Soybean (Glycine max L.) is the second most important crop in the United States. Soil conservation efforts combined with earlier planting dates has led to increased crop residue and cooler soil at planting. This exposes seeds and developing seedlings to adverse conditions for extended periods of time, which can increase disease pressure from many oomycete pathogens causing pre- or post-emergence damping-off. In North America, at least 84 oomycete species within the genera Pythium, Phytophthora, Phytopythium, and Aphanomyces are associated with soybean seedlings. The number of oomycete species makes management decisions difficult and seed applied anti-oomycete chemicals (oomicides) are the primary management tool against the majority of these species. Therefore, the overall theme of this dissertation was to determine the effect of soybean seed treatments on oomycete evolution and diversity to improve management recommendations. First, in chapter 1, I provide a review of current literature and background information on soybean seedling disease management, fungicide (including oomicide) resistance theory, Peronosporalean taxonomy and evolution, and review current methods to study oomycete diversity. Secondly, since an essential step in monitoring for oomicide resistance is in vitro testing, I provide clarification of terms and models involved in the analysis of in vitro dose-response data for improved reproducibility (chapter 2). Next, in chapter 3, the level of interspecific variation in mefenoxam and ethaboxam sensitivity was determined using a newly developed high-throughput assay for oomycetes that utilized growth curves and Z'-factor for quality control. This revealed that that interspecific variation in sensitivity to ethaboxam was greater than mefenoxam. Therefore, in chapter 4, the genetic and evolutionary mechanism of ethaboxam insensitivity was investigated. This revealed for the first time that inherent insensitivity to ethaboxam was linked to the convergent evolution of a specific substitution in the target gene, which resulted in lineage-specific insensitivity to ethaboxam. In chapter 5, the effect of location, and seed treatments containing either mefenoxam or ethaboxam and metalaxyl on the recovery of oomycetes from soybean taproot or lateral root tissue. This study demonstrated that oomycete communities were largely structured by location and that the recovery oomycetes from soybeans were dependent on the unique combination of location, tissue, and seed treatment. Finally, in chapter 6, an oomycete metabarcoding approach (amplicon sequencing) was used to study the influence of soybean seed treatment and genotype on oomycete rhizosphere diversity from a location with or without a history of seedling disease. This indicated that oomycete community diversity was driven by location and that an imbalance of oomycete taxa rather than simply the presence-absence of certain taxa might be responsible for differences in disease pressure. Additionally, there was no substantial evidence that genotype or seed treatment influenced oomycete diversity in soybean rhizosphere samples. Finally, in chapter 7, I discuss the overall conclusions and impacts of the studies presented herein. Overall, data from these studies provide essential new information for the management of oomycete communities with soybean seed treatments. Importantly, these studies advance our knowledge about the effect of soybean seed treatments on the evolution and diversity of oomycetes in a soybean agroecosystem.