Kyle, Christopher

White-nose syndrome (WNS) is a skin disease of bats caused by the fungus Pseudogymnoascus destructans (Pd) that damages flight membranes during hibernation and can lead to death. The disease causes mortality of multiple bat species in eastern North America and is spreading into western North America. Future impacts of WNS on naïve bat populations are unknown. Variation in host susceptibility occurs among and within species, but mechanisms driving this variation are unclear. Multiple studies have characterized immunological responses to WNS, but skin physiology as a barrier to pathogens is understudied. The unique ability of Pd to actively penetrate the normal, intact skin of its mammalian host makes WNS an interesting study system to understand skin defenses. Aspects of the mammalian skin environment that can influence disease susceptibility include pH, sebaceous lipids, and microbiomes. I found skin mycobiomes of WNS-susceptible species had significantly lower alpha diversity and abundance compared to bat species resistant to Pd infection. Using these data, I predicted that most naïve bat species in western North America will be susceptible to WNS based on the low diversity of their skin mycobiomes. Some fungi isolated from bat wings inhibited Pd growth in vitro, but only under specific salinity and pH conditions, suggesting the microenvironment on wings can influence microbial interactions and potentially WNS-susceptibility. I measured the wing-skin pH of bats in eastern Canada and found that Eptesicus fuscus (WNS-tolerant) had more acidic skin than M. lucifugus (WNS-susceptible). Differences in sebum quantity and composition among and within mammalian species may help explain variation in skin disease susceptibility and the composition of skin microbiomes. This is due to the antimicrobial properties of sebum and the use of sebum as a nutrition source by microbes. Outcomes of this work further our understanding of inter- and intra-specific differences among bat species and individuals in skin mycobiomes and physiology, which may contribute to variation in WNS-susceptibility. Future research should focus on characterizing the physical and chemical landscape of skin as this is essential for understanding mechanisms structuring skin microbial assemblages and skin disease susceptibility in wildlife.

Author Keywords: bat, fungi, microbiome, mycology, physiology, white-nose syndrome

Puccinia triticina, wheat leaf rust (WLR), is the most economically damaging fungal rust of wheat on a global scale. This study identified transcriptome changes in a recently emerged race of WLR in Ontario with a new virulence type relative to a possible ancestor race. Also, this study focused on detecting variation in candidate virulence genes and uncovering novel insight into WLR virulence evolution. Various race-by-variety interactions were evaluated using RNA-seq experiments. A list of genes with statistically significant expression changes in each comparison was prepared and predicted effectors were retained for further analysis. Proteins with nonsynonymous substitutions were run through BLASTx to identify potential orthologs. Over 100 candidate effectors with a 2-fold or higher change in transcript level were identified. Seven of these candidate effector genes were recognized to contain single nucleotide polymorphisms (SNPs) which altered the amino acid sequence of the resulting protein. The information gained may aid in targeted breeding programs to combat new WLR races as well as provide the basis for functional analysis of WLR using potential orthologs in a model basidiomycete.

Author Keywords: effectors, RNA-seq, rust fungi, SNPs, transcriptome, wheat leaf rust

Trinucleotide repeats (TNRs) are a class of highly polymorphic microsatellites which occur in neutral and non-neutral loci and may provide utility for individual- and population-identification. Exonic trinucleotide motifs, in particular, offer additional advantages for non-human species that typically utilize dinucleotide microsatellite loci. Specifically, the reduction of technical artifacts, greater separation of alleles and greater specificity of amplification products leading to more efficient multiplexing and cross-taxa utilization. This study aims to identify and characterize polymorphic trinucleotide repeats and conserved primer sequences which are conserved across Cervidae (deer) species and their potential for individual identification in forensic wildlife investigations. Chapter one provides a broad introduction to trinucleotide microsatellites, chapter two deals with data-mining TNRs and chapter three applies the identified TNRs as genetic markers for individual identification. Results demonstrate proof-of-concept that exonic TNRs are capable of giving random match probabilities low enough to be employed in individual identification of evidentiary samples.

Author Keywords: DNA typing, Exons, Genetic Markers, Individual Identification, Trinucleotide, Wildlife Forensics