Graduate Thesis Or Dissertation
 

Bioinformatics applied to freshwater cyanobacterial blooms and cyanophage

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https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/x059c944h

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  • Freshwater cyanobacterial blooms are a nuisance and health threat in the Pacific Northwest. The accepted methods of characterizing these blooms by microscopic cell counts cannot differentiate between toxic and non-toxic strains of the cyanobacterium Microcystis. Also, there is limited understanding of freshwater cyanophage that may control bloom dynamics. In order to better understand the cyanobacterial and cyanophage populations of the Klamath River, two studies were conducted. Methods in the studies were largely composed of bioinformatic techniques. First, using clone libraries to genetically track the Microcystis blooms, we found a distinct separation in bloom populations according to whether the toxin microcystin could be produced. The genotypic differences in two bloom cycles were parsed into a graphical representation, useful for describing many closely related organisms. Further investigation of the bloom community led to the isolation of the novel, freshwater Synechococcus-infecting myophage, S-CRM01. The phage is very similar in gene content to marine cyanomyophage, but differs in synteny and nucleotide composition. The bioinformatic techniques used that were either developed or customized to fit our data. Our findings indicate that the use of bioinformatic techniques will greatly increase the resolution of population and genomic studies in freshwater environments. This is apparent in the population differentiation seen throughout the bloom season in the Copco Reservoir as well as the comparative genomics of phage S-CRM01. The results of the research support the use of bioinformatics to acquire and interpret genetic data for cyanobacteria and cyanophage.
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