Biology ETDs


Daniel Colman

Publication Date



Yellowstone National Park (YNP) thermal springs have been a crucial resource for the discovery and characterization of microbial biodiversity. The use of cultivation-independent methods has documented many new phyla of uncultured Archaea and Bacteria within thermal springs. Here, I describe the phylogenetic diversity and distribution of Archaea within the YNP thermal spring ecosystem and the phylogenetic and physiologic characterization of novel, uncultured hyperthermophilic bacterial lineages from metagenomic data. In chapter two, I evaluated the efficacy of commonly used, 'universal' archaeal-specific 16S rRNA gene PCR primers in detecting archaeal phylogenetic diversity. In chapter three, using the PCR primers that would provide the best representation of archaeal communities, I used high-throughput 454 pyrosequencing to analyze the phylogenetic diversity and distribution of Archaea and Bacteria among 33 YNP springs. The results indicated that Archaea were ubiquitously distributed across YNP springs and exhibited significant taxonomic diversity across springs but were overall less phylogenetically diverse in the YNP system than Bacteria. pH, followed by temperature primarily explained the distribution of both archaeal and bacterial taxonomic distribution. Co-occurence analysis suggested a substantial number of putative interactions across the YNP system between and within domains. The results from these two chapters provide the largest survey of Archaea in any thermal system to date and contribute to our understanding of their phylogenetic diversity and ecology in such systems. In Chapter 4, I report the phylogenetic and physiologic characterization of novel, deep-branching bacterial phylotypes from metagenomic data from two YNP springs. Genome assemblies representing four populations were recovered from Aquificaceae-dominated community metagenomes from two high-temperature, circumneutral YNP springs. Phylogenetic analyses indicated they belonged to two distinct, deep-branching bacterial lineages, one of which has no currently characterized genome references. The lineages appeared to be heteroorganotrophs based on metabolic reconstructions and also were both putatively capable of using energy conserved from organic carbon degradation to fuel aerobic respiration. Analysis of the ecological distribution of these populations confirmed that they are currently restricted to high-temperature circumneutral terrestrial springs, largely within YNP. The characterization of these populations provides important physiologic context for the deepest-branching bacterial lineages and valuable genomic references for uncultured, ubiquitously distributed hyperthermophilic bacteria.




Archaea, Yellowstone National Park, Hot Springs, Thermophile, Microbial Ecology, Microbial Genomics, Extremophiles, PCR Primers, Microbial Diversity, Aquificales, Aigarchaeota

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Department Name

UNM Biology Department

First Committee Member (Chair)

Sinsabaugh, Robert

Second Committee Member

Crossey, Laura

Third Committee Member

Northup, Diana