Honors Program Theses


Open Access Honors Program Thesis

First Advisor

Marek Sliwinski, Honors Thesis Advisor


Archaebacteria--South Dakota--Wind Cave National Park; Extreme environments--Microbiology--South Dakota--Wind Cave National Park; Microbial diversity--South Dakota--Wind Cave National Park;


Archaea have the potential to play an essential role in their environment at the base of the food chain. In particular, most of the known species in the phylum Thaumarchaea are autotrophs that can fix their own carbon using energy from ammonia oxidation, that is, they produce their own organic molecules from carbon dioxide by burning nitrogen-based fertilizer. Since their discovery, it has been difficult to learn more about these microbes because they do not grow well in pure laboratory culture. Therefore, much of what is known about them comes from analyzing environmental DNA samples. This allowed researchers to discover that Archaea are ubiquitous in soils and are found even in seemingly barren environments such as the subterranean lakes in Wind Caves National Park. This cave system is one of the most complex in the world and provides an analog for some of the other extreme environments that exist in the solar system. By utilizing molecular techniques such as qPCR and Sanger sequencing of cloned PCR products, we quantified the relative number of archaea in the cave system, as well as identified some of the archaeal species based on their 16S rRNA genes. Our qPCR results revealed that there are fewer archaeal 16S rRNA genes inside of the cave than near the natural entrance to the cave. Our preliminary results of the archaeal clone library identified only thaumarchaeal species suggesting this phylum is the most numerous Archaea in the cave system. In terms of spatial distribution, archaeal DNA was found at all levels of the cave including near the surface and in the deep subterranean cave lakes. Future studies will be able to use our collection of environmental DNA samples to quantify and analyze species diversity using additional molecular techniques such as NGS (next generation sequencing).

Year of Submission



Department of Biology

University Honors Designation

A thesis submitted in partial fulfillment of the requirements for the designation University Honors

Date Original


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1 PDF file (24 pages)

Creative Commons License

Creative Commons Attribution-NonCommercial 4.0 International License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License



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