Theses and Dissertations at Montana State University (MSU)
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Item Comparative genomic analyses of Yellowstone hot spring microbial mat Synechococcus spp.(Montana State University - Bozeman, College of Agriculture, 2015) Olsen, Millie Helen Thornton; Chairperson, Graduate Committee: David M. Ward; Shane Nowack, Jason M. Wood, Eric D. Becraft, Kurt LaButti, Anna Lipzen, Joel Martin, Wendy S. Schackwitz, Douglas B. Rusch, Frederick M. Cohan, Donald A. Bryant and David M. Ward were co-authors of the article, 'Comparative genomics of Synechococcus isolates with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat' submitted to the journal 'Frontiers in microbiology' which is contained within this thesis.The question of "What is a microbial species?" has been a highly debated issue in the field of microbiology. Many have accepted a molecular species demarcation approach, that any two organisms with a high enough 16S rRNA sequence similarity are members of the same species. However, the Ward lab has shown that there are many ecologically distinct Synechococcus spp. inhabiting hot springs of the Lower Geyser Basin in Yellowstone National Park, WY, that would be defined as members of the same species using the molecular demarcation approach. Using a theory-based species demarcation approach with a conserved photosystem gene (psaA), evidence of the existence of putative ecotypes, or predicted ecologically distinct species, has been found in the microbial mat, distributed along both temperature and light gradients. Isolates representative of these ecologically distinct populations have also been shown to have distinct temperature adaptations and light adaptations. I obtained the genomes of these isolates, which include representatives of populations with different temperature distributions and different vertical distributions, and replicate isolates within individual putative ecotypes. Using these genome sequences, I compared the psaA gene phylogeny and multi-locus sequence phylogenies with a phylogeny created using genes shared among the genomes to explore the effects of recombination on phylogenies of closely-related organisms. I then explored the underlying genetic mechanisms of the niche adaptations of these ecotypes by (i) comparing the isolate gene content, diel transcription patterns, and positive selection evidence of putative ecotypes with different vertical distributions in the mat and different light adaptations, (ii) comparing the gene content and evidence of positive selection among isolates representative of populations with different temperature distributions, and (iii) comparing the gene content and evidence of positive selection among replicate isolates within individual putative ecotypes. I found that, while recombination may have caused the inaccurate demarcation of genetically distinct isolates into a single PE, there is genomic evidence that species of Synechococcus that are ecologically distinct from one another exist, along both temperature and vertical gradients. Members of a species are ecologically homogenous, though there is evidence of some genetic heterogeneity within a species.Item The distribution of cultivated and uncultivated cyanobacteria and green non-sulfur bacteria in hot spring microbial mats(Montana State University - Bozeman, College of Agriculture, 1993) Ruff-Roberts, Alyson L.Item Control of bacterioplankton activity in a eutrophic lake emphasizing relationships among bacteria, cyanobacteria and nutrients(Montana State University - Bozeman, College of Letters & Science, 1992) Wang, LizhuItem Biogeography of thermophilic cyanobacteria and the importance of isolation to the evolution of microorganisms(Montana State University - Bozeman, College of Agriculture, 2002) Papke, Robertson ThaneItem Molecular analysis of hot spring microbial mats to study bacterial diversity and physiology(Montana State University - Bozeman, College of Agriculture, 1996) Nold, Stephen CharlesItem Glycolate production and consumption in a hot spring cyanobacterial mat(Montana State University - Bozeman, College of Agriculture, 1985) Bateson, Mary MargaretItem Physical and chemical factors promoting cyanobacterial abundance in eutrophic a reservoir(Montana State University - Bozeman, College of Letters & Science, 1994) Briggs, Michael A.Item Influence of inorganic and organic nutrient enrichment on blue-green algal activity and relative biomass in a eutrophic southwest Montana reservoir(Montana State University - Bozeman, College of Letters & Science, 1991) Miller, Thomas DavidItem Identification and distributions of dominant bacterial populations in hot spring Synechococcus mats(Montana State University - Bozeman, College of Agriculture, 1997) Ferris, Michael JosephItem Niche character in a temporally varying environment(Montana State University - Bozeman, College of Letters & Science, 2014) Nowack, Shane Patrick; Chairperson, Graduate Committee: Isaac Klapper; Isaac Klapper and David M. Ward were co-authors of the article, 'Consequences of temporal frequency regime on optimal behavior' submitted to the journal 'Journal of theoretical biology' which is contained within this thesis.; Millie T. Olsen, Eric D. Becraft, Donald A. Bryant, and David M. Ward were co-authors of the article, 'Evidence of closely related Synechococcus species inhabiting the microbial mats of Mushroom Spring, Yellowstone National Park' submitted to the journal 'Applied and environmental microbiology' which is contained within this thesis.One of the major goals in the field of ecology is to understand the connection between an organism and its environment. In this thesis both theoretical and empirical approaches were used to investigate the effects of environmental variation on niche structure. A mathematical model was developed to make predictions about the consequences of temporal frequency regime on optimal behavior. Three different time scales of environmental variation were studied: faster than the growth rate, slower than growth rate, and similar to growth rate. The model results predicted that (i) optimal behavior appears to be independent of fast environmental variation, (ii) niche width is largely determined by slow environmental variation, and (iii) biological clocks may have evolved from environmental variations that occur with a frequency that is comparable to the growth rate of the organism. Representatives of the predominant organisms inhabiting the microbial mats found in the effluent channels of Mushroom Spring, Yellowstone National Park, were cultivated, and the growth rates of the isolated strains were measured with respect to light, temperature, and availability of dissolved inorganic carbon. The growth rate measurements suggested that closely-related Synechococcus species with distinct ecological adaptations exist within the Mushroom Spring community, and may explain the genetic diversity found in situ. The results also suggested that the fundamental light niche is interconnected with other environmental parameters, such as temperature and dissolved inorganic carbon availability. To compare the results of the mathematical and microbiological approaches, environmental light data that were collected in the vicinity of Mushroom Spring were incorporated into the mathematical model. The optimal fundamental light niche that was predicted by the model and the measured light niche of one of the cultivated strains exhibited qualitative similarities. Collectively, this interdisciplinary approach has led to the identification of several environmental characteristics that are hypothesized to be important in determining niche structure.