Comparative Genomics of Freshwater Bloom-Forming Cyanobacteria and Associated Organisms Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/rb68xf16d

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  • The advent of improved DNA sequencing technologies has allowed the analysis of various microbial communities. Bloom-forming freshwater cyanobacteria can produce toxins and taste-and-odor compounds that can negatively affect drinking water supplies. Here, I have employed second- and third-generation sequencing technologies to characterize bloom-forming freshwater cyanobacterial genomes and their associated heterotrophic bacteria and viruses. These include nine novel fresh- water Nostocaceae genomes, three genomes from heterotrophic bacteria associated with Aphanizomenon in a communal culture, and two novel Microcystis phage genomes. • The genomes of three novel heterotrophic bacteria associated with Apha- nizomenon flos-aquae in culture were sequenced and assembled to finished quality with long-read sequencing. These genomes were sequenced together, highlighting the potential for using long-read sequencing towards metage- nomics of low-diversity microbial communities. These genomes were ana- lyzed to assess interactions between Aphanizomenon flos-aquae and these heterotrophs in culture. The presence of an ammonium-importer gene in two of these genomes suggests a putative dependency on fixed nitrogen from Aphanizomenon flos-aquae. • The genomes of nine novel Nostocaceae genomes were sequenced and assem- bled to draft quality. Five of these genomes were assembled and extracted directly from three separate environmental short-read shotgun metagenomes. The remaining four strains were cultured, one of which was from this study (Aphanizomenon MDT14) and three that were provided by Gregory Dick’s lab at the University of Michigan (Anabaena CPCC64, Anabaena LE011- 02, and Anabaena AL09). All novel genomes were characterized relative to the rest of the Nostocaceae family to analyze evolutionary relationships and identify differences in gene content to evaluate potential phenotypic pat- terns/differences. Genes involved in toxin synthesis and sulfur metabolism are variably present in these genomes, with no patterns relative to phyloge- nomic relationships. Conversely, functionally diverse genes are present in genomes with close phylogenomic relationships. • The genomes of two novel Microcystis phages were sequenced and assem- bled to finished quality from two separate environmental short-read shotgun metagenomes. These novel genomes were similar to the previously sequenced Microcystis phages Ma-LMM01 and MaMV-DC, and all four genomes were characterized together to identify patterns of gene conservation in this ge- ographically distributed phage group. Additionally, one of the completed phages was present in samples across a 6-week time series of environmental short-read shotgun metagenomes. Patterns of gene gain/loss and divergence were then analyzed in this Microcystis phage across the time series. Host-like genes involved in photosynthesis and phosphate starvation are present in all genomes, while presence of other host-like genes is less conserved. Genomes from the environmental time-series contain differences in presence/absence of several hypothetical genes, as well as sequence divergence in the tail collar gene, which may have implications for infection in the environment.
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