Microbial oxidation and reduction processes presently impact global biogeochemical cycling of sulfur, an essential element for life. Sulfur is considered an early substrate for ancient microbial life as the evolution of sulfur metabolism predates photosynthesis. Public access databases are a wellspring of hundreds of thousands of high-quality, structurally and functionally annotated genomes. This project mined the KEGG and PATRIC databases to explore the phylogenetic distribution of sulfur oxidation and reduction traits within sequenced microbial genomes. It was hypothesized that conservatism would follow the number of genes underlying a trait (molecular complexity) and predicted that the most complex would be the most conserved. Several custom BASH language shell programs were used to gather sequence and gene count data. The previously published algorithm consenTRAIT was applied to determine trait depth (τƊ), the Fritz and Purvis test determined phylogenetic Dispersion (D, phylogenetic signal); together these metrics elucidated the levels of conservatism for four key biological sulfur cycle pathways of oxidation and reduction across phyla. Contrary to predictions, the molecularly complex Sox Sulfur Oxidation pathway is the least clumped of all traits analyzed (τƊ = 0.016, D = 0.029). The moderately molecularly complex Assimilatory and Dissimilatory Sulfur Reduction pathways match predictions based on molecular complexity (τƊ = 0.0232, D = -0.0075; τƊ = 0.039, D = -0.350). The most complex pathway, Dissimilatory Sulfur Oxidation, was deeply conserved and also matched predictions based on molecular complexity (τƊ = 0.048, D = -0.3504). The results of this work have elucidated the phylogenetic distribution and conservatism of four biological sulfur cycle pathways for sulfur metabolism across prokaryotes and how molecular complexity of trait affects both distribution and conservatism.
Some files may require a special program or browser plug-in. More Information
|Advisor:||Berlemont, Renaud, Dillon, Jesse|
|School:||California State University, Long Beach|
|School Location:||United States -- California|
|Source:||MAI 82/6(E), Masters Abstracts International|
|Subjects:||Microbiology, Genetics, Bioinformatics, Molecular chemistry, Biogeochemistry, Organic chemistry|
|Keywords:||Comparative genomics, Extreme environments, Phylogenetic signal, Sox, Sulfur metabolism, Sulfur oxidation|
Copyright in each Dissertation and Thesis is retained by the author. All Rights Reserved
The supplemental file or files you are about to download were provided to ProQuest by the author as part of a
dissertation or thesis. The supplemental files are provided "AS IS" without warranty. ProQuest is not responsible for the
content, format or impact on the supplemental file(s) on our system. in some cases, the file type may be unknown or
may be a .exe file. We recommend caution as you open such files.
Copyright of the original materials contained in the supplemental file is retained by the author and your access to the
supplemental files is subject to the ProQuest Terms and Conditions of use.
Depending on the size of the file(s) you are downloading, the system may take some time to download them. Please be