Identification, enumeration, and diversity of ammonia-oxidizing archaea in the Laurentian Great Lakes

Date of Award


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Biological Sciences

First Advisor

George Bullerjahn

Second Advisor

William O'Brien (Committee Member)

Third Advisor

Robert Mckay (Committee Member)

Fourth Advisor

Scott Rogers (Committee Member)

Fifth Advisor

Zhaohui Xu (Committee Member)


Nitrification is a major process of the global nitrogen cycle in which ammonia is oxidized to nitrate. Previously it was assumed that bacteria (e.g., Nitrosomonas and Nitrobacter) are responsible for this process. Over the past decade, researchers have discovered different groups of nitrifying archaea, specifically Thaumarchaeota Groups I.1a, and I.1b, in both marine and freshwater environments. The physiological characteristics of these organisms are best suited to the levels of ammonia found in aquatic systems. Since 1900, Lake Superior has seen a steady increase in nitrate, yielding a severe stoichiometric imbalance of nitrogen to phosphorus. Stable isotopic analyses indicate that nitrate increases result from in-lake biological processes. By contrast, mesotrophic Lake Erie is prone to transient hypoxia, yielding nitrogen losses to the atmosphere via denitrification and anammox. In this study, I examined these unique nitrifiers contributing to nitrification in both lakes. Phylogenetics of amoA sequences from lake seston reveals that ammonia oxidizing archaea (AOA) dominate the Superior pelagic microbial community, although AOA diversity in Lake Superior was observed to be low, indicating only a few key ecotypes can survive the extreme oligotrophic conditions prevalent in the lake. CARD-FISH probes specific for AOA, ammonia oxidizing bacteria (AOB) and nitrite oxidizers (NOB) allow their enumeration in samples obtained from 2010-12. During the stratified period in Superior, AOA and NOB are detectable in the hypolimnion and oxic sediments (up to 7 x 104 mL-1), and absent in the epilimnion. AOB are not detectable(<101 mL-1) in Superior, but dominate in Erie samples. For summer 2010, AOA abundance reflects parallel assays of nitrification rates. This study concludes that Thaumarchaeota (AOA) dominate the ammonia-oxidizing microbial population in Lake Superior, whereas, the ammonia oxidizing bacterial population is negligible in the lake. In contrast, Thaumarchaeota are almost absent or negligible in Lake Erie, whereas, the ammonia oxidizing bacterial are the dominant nitrifiers in the lake, indicating towards a possible association of the AOA in environments with lower ammonium concentrations, whereas that of the AOBs with environments with higher ammonium concentrations. Thaumarchaeota (AOA), in spite of being so abundant in Lake Superior, tend to be less diverse in the lake, indicating that only few species of these ammonia-oxidizers can survive the extreme oligotrophic conditions of the lake. All the ammonia oxidizers, irrespective of whether they are bacteria or archaea, tend to be absent from surface waters, whereas their abundance increases with depth of water column in the lakes.