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Inland waters cover about 2.5 percent of our planet and harbor huge numbers of known and unknown microorganisms including viruses. Viruses likely play dynamic, albeit largely undocumented roles in regulating microbial communities and in recycling nutrients in the ecosystem. Phycodnaviruses are a genetically diverse, yet morphologically similar, group of large dsDNA-containing viruses (160- to 560-kb) that inhabit aquatic environments. Members of the genus Chlorovirus are common in freshwater. They replicate in eukaryotic, single-celled, chlorella-like green algae that normally exist as endosymbionts of protists in nature. Very little is known about the natural history of the chloroviruses and how they achieve high-titer and long-term persistence in nature. To study their natural history, we examined chloroviruses over a three-year period to determine their abundance, prevalence, and genetic diversity in a small lake in Nebraska (Chapter II). These studies indicated that the amount of infectious virus particles was seasonal and both host- and site-dependent. Chlorovirus populations persisted year-round, suggesting that the viruses are either very stable or that viral production occurs in an unknown natural host(s). During this study, a new viral group was discovered and characterized, expanding the Chlorovirus genus (Chapter III). This group, designated as Only Syngen viruses (OSy), replicates in Chlorella variabilis (Syngen 2-3) cells. Furthermore, OSy viruses also have non-permissive features in two phylogenetically related C. variabilis sub-species and constitute the first report of a post-infection host mechanism that results in resistance against infection. In Chapter IV, five symbiotic-virus suceptible and four free-living Chlorella species were evaluated for their capabilities to assimilate nutrients. Hierarchical clustering reveals a clear distinction of both groups based on their assimilation of galactose, nitrate, asparagine, proline, and serine. Additionally, genomic and differential expression analyses of symbiotic algae confirm an abundance of amino acid transporter genes, some of which are constitutively expressed when the symbiotic algae either grow axenically or as an endosymbiont within their host. Such similarities indicate a parallel coevolution of shared metabolic pathways across multiple independent symbiotic events and suggest that physiological changes driving the Chlorella symbiotic phenotype also contribute to their natural fitness.
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