UBC Theses and Dissertations
Genomic characterization of viruses infecting freshwater polar cyanobacteria Chénard, Caroline
There is wide recognition that cyanobacteria are major primary producers in polar freshwater regions. Filamentous cyanobacteria are commonly found in benthic mats and biofilms at the bottom of lakes, ponds and streams, while picocyanobacteria dominate the planktonic communities of many polar lakes. However, no representative viruses infecting this group of organisms have been characterized. This dissertation, which is a culmination of experiments and genomic and metagenomic analyses, presents the first characterization of viruses infecting freshwater polar cyanobacteria and the discovery of previously unknown groups of viruses. First, I isolated and genetically characterized a polar freshwater cyanophage (S-EIV1) that represents a new evolutionary lineage of bacteriophages that are globally widespread and abundant. Second, I described a new group of viruses (Cyanophage A-1 and Cyanophage N-1) infecting freshwater filamentous cyanobacteria that contain a distinct DNA polymerase. Third, during genomic analysis of Cyanophage N-1, I identified a DNA repeat region similar to a Clustered Regularly Interspaced Short Palindromic (CRISPR) array. The CRISPR array had direct repeats with high similarity to those commonly found in filamentous cyanobacteria. I showed that the viral-encoded CRISPR was transcribed and have the potential be viral-mediated transferred to its host. Finally, DNA-stable isotope probing (DNA-SIP) was used to recover and sequence viruses infecting primary producers in a polar cyanobacterial mat. Arctic freshwater systems are some of the most threatened environments because of rapid climate change, and viruses encompass the greatest genetic and biological diversity on Earth. This work presents previously unknown groups of viruses and a newly discovered virus-host system that provide new tools for investigating host-virus interactions and examining arctic viral diversity.
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Attribution-NonCommercial-NoDerivs 2.5 Canada