Biology Ph.D. Dissertations


Detection and Characterization of a Unique Ammonia Oxidizing Archaea; Cultured from Lake Superior

Date of Award


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Biological Sciences

First Advisor

George Bullerjahn (Advisor)

Second Advisor

Michael McKay (Committee Member)

Third Advisor

Scott Rogers (Committee Member)

Fourth Advisor

Paul Morris (Committee Member)

Fifth Advisor

John Snyder (Other)


In the past century Lake Superior has seen a 5-fold increase in nitrate levels. Previous research has shown this increase to be due to as of yet undescribed in-lake oxidation processes. It has recently been shown that ammonia oxidizing archaea (AOA) in marine and freshwater environments belonging to the phylum Thaumarchaeota have the ability to oxidize ammonium, and are specifically suited to the low NH4¿ /oligotrophic environment of Lake Superior. In this study isolation and enrichment of these unique freshwater ammonia oxidizing archaea from Lake Superior has enabled the direct measurement of NO2¯ and N2O production and NH4¿ metabolism. In the search for in-lake nitrifying organisms we have identified and described a novel group of freshwater ammonia oxidizing archaea using the ammonia monooxygenase alpha (amoA) subunit gene as a diagnostic tool for microbes capable of ammonia oxidation. Flow cytometry was used to determine cell abundances and ideal incubation times and temperatures for these AOA taken from these Lake Superior. These data along with nitrification measurements enabled us to determine per cell nitrification rates for our AOA enrichment cultures, which have shown that they do indeed account for a major component of in-lake nitrification processes. With the exception of the marine archaeon Nitrosopumilus maritimus, most research has been focused on culture-independent methods for the characterization of nitrifying microbes. This study is among the first of these culture dependent studies to describe methods for culturing a freshwater ammonia oxidizing archaea.