Scales of diversity in thermophilic microbial communities : from metagenomes to individual cells and viral metagenomes
Abstract/Contents
- Abstract
- Microbial diversity can be queried at several scales within natural environments. On a macroscopic scale, microbial communities are capable of incredible feats: from colonizing the most inhospitable habitats imaginable, to creating ancient stromatolites, or living in intimate symbioses with the human body, inside and out. These complex microbial assemblages are comprised of different microscopic populations, which interact as a whole to stabilize the community ecosystem: selective evolutionary pressures work to shape each population, exquisitely adapting it to succeed in the current environmental conditions. In turn, these populations are comprised of millions of individual cells, each struggling to survive a variety of environmental stressors, to outcompete their closely-related neighbours, and carve out a distinct niche. Single cells wage constant war against predators such as viruses, which exist in large numbers and can effect entire populations, and ultimately the community as a whole. With such a range of complexity within a microbial community, it is essential to view microbial diversity through several tiers, in order to achieve a more complete picture. Only when diversity is viewed from several hierarchical levels, can the connections be made between the biology that is occurring on very fine scales and its effect on the entire system. Thus, this thesis has characterized microbial diversity in the hot spring microbial mats of Yellowstone National Park at multiple scales. There are several reasons why the microbial mats represent the ideal model system in which to query microbial diversity (Chapter 1). The evolution and adaptation of thermophilic Synechococcus sp. across a temperature gradient is queried by the creation of a targeted deep sequencing dataset, revealing statistically significant SNPs that correlate with thermal adaptation (Chapter 2). A second targeted deep sequencing dataset of 90 loci was generated to investigate the microdiversity present between two closely related thermophilic Synechococcus species, confirming the presence of micro-niches in stabilizing diversity across several years (Chapter 3). Successful gene amplification of the T1B CRISPR loci from a single cyanobacterial cell was achieved with the goal of investigating diversity at the single cell level (Chapter 4). Lastly, host-virus co-evolution is characterized by creation of a virome and a novel pipeline to assemble and analyze viral sequences: matching potential host-viral pairs by using CRISPR spacers (Chapter 5).
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2013 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Davison, Michelle René | |
|---|---|---|
| Associated with | Stanford University, Department of Biology. | |
| Primary advisor | Bhaya, Devaki, 1957- | |
| Primary advisor | Fukami, Tadashi, 1972- | |
| Thesis advisor | Bhaya, Devaki, 1957- | |
| Thesis advisor | Fukami, Tadashi, 1972- | |
| Thesis advisor | Batzoglou, Serafim | |
| Thesis advisor | Grossman, Arthur (Arthur R.) | |
| Thesis advisor | Spormann, Alfred M | |
| Advisor | Batzoglou, Serafim | |
| Advisor | Grossman, Arthur (Arthur R.) | |
| Advisor | Spormann, Alfred M |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Michelle René Davison. |
|---|---|
| Note | Submitted to the Department of Biology. |
| Thesis | Ph.D. Stanford University 2013 |
| Location | electronic resource |
Access conditions
- Copyright
- © 2013 by Michelle Rene Davison
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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