Browsing by Author "Becraft, Eric Daniel"

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The ecology and evolution of thermophilic Synechococcus species
(Montana State University - Bozeman, College of Agriculture, 2014) Becraft, Eric Daniel; Chairperson, Graduate Committee: David M. Ward; Frederick M. Cohan, Michael Kuhl, Sheila I. Jensen and David M. Ward were co-authors of the article, 'Fine-scale distribution patterns of Synechococcus ecological diversity in the microbial mat of Mushroom Spring, Yellowstone National Park' in the journal 'Applied and Environmental Microbiology' which is contained within this thesis.; Frederick M. Cohan, Jason M. Wood, Doug B. Rusch, Michael Kuhl, Sheila I. Jensen and David M. Ward were co-authors of the article, 'Pyrosequencing analyses of Synechococcus ecological species inhabiting the microbial mat of Mushroom Spring, Yellowstone National Park' submitted to the journal 'International Society for Microbial Ecology Journal' which is contained within this thesis.
To understand the ecology of any environment, the fundamental species-like units that interact with the biotic and abiotic components of that environment must be understood. Previous research conducted in the Ward Lab has shown that 16S rRNA genotypes have unique distributions along the effluent flow path, and that 16S-23S rRNA internal transcribed spacer region genotypes had unique distributions along vertical gradients at some temperatures. However, out of concern that these genetic markers were too conserved to accurately detect ecological species, in this dissertation I analyzed Synechococcus cyanobacterial diversity in Yellowstone National Park using the more highly-resolving psaA (Photosystem I reaction center protein) locus and an evolutionary simulation based on the Stable Ecotype Model to demarcate putative ecotype populations that are hypothesized to be ecologically distinct species. I used denaturing gradient gel electrophoresis to examine fine-scale distributions of predicted ecotypes along flow and vertical gradients. Because this approach was not sequence-based, and was limited in depth of sequence sampling and habitat coverage, I employed next-generation sequencing technologies (e.g. Ti454-barcoding and sequencing), which was based on sequence information and allowed much deeper sampling and habitat coverage. I used Ti454-barcoding to extend fine-scale distribution studies, examine temporal differences in ecotype-specific gene expression, population-specific responses to environmental perturbations and to examine within-ecotype population genetics. Additionally, I used Ti454-barcoding to analyze frozen samples collected in previous Ward Lab studies, which enabled examination of (i) the biogeographic distributions of Synechococcus sequence variants across the Northwestern United States, (ii) the long-term stability of ecological populations in Octopus Spring and Mushroom Spring, and (iii) the initial colonization of disturbed mats. I was also able to use this technology to contribute to other ongoing Ward Lab studies, including (iv) testing the purity of Synechococcus isolate cultures before genome sequencing, (v) distribution analyses of loci used in previous population genetics studies, and (vi) linking psaA distributions to ecotype-specific genomes. I was able to confirm that many abundant Synechococcus putative ecotypes predicted by Ecotype Simulation are ecologically distinct populations, containing ecologically homogeneous individuals. The conclusion of my research supports applying the ecological species concept to hot spring Synechococcus cyanobacterial populations.