Graduation Year


Document Type




Degree Name

Doctor of Philosophy (Ph.D.)


Microbiology, Molecular Biology and Biochemistry

Degree Granting Department

Cell Biology, Microbiology and Molecular Biology

Major Professor

James R. Garey, Ph.D.

Committee Member

Randy Larsen, Ph.D.

Committee Member

Kathleen Scott, Ph.D.

Committee Member

David Merkler, Ph.D.


anoxic marine pits, environmental microbiology, extremophiles, shallow-water hydrothermal vents


The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal vent that extended 120 m away from the vent. Previous studies have shown that the geochemistry of the system is heavily influenced by arsenic which is toxic to most organisms. In this study, macro- and meiofauna were collected and scored and combined with bacterial sequence data collected along the length of the transect. It was found that near vent sites harbored biological communities more similar than sites further from the vent. Many species were found only at sites near the hydrothermal vent. Near-vent communities were less diverse than those away from the vent, and biodiversity generally increased as distance from the vent increased. Distinct correlations between thermophilic organisms and temperature were observed. The metabolic repertoire of the microbial communities suggests that many strategies are used to obtain energy and carbon. The relative abundance of bacteria containing genes to reduce arsenic was comparable to those able to reduce sulfur compounds. Primary production appeared to be a mix of chemo- and phototrophy. Food webs and association analysis suggest a complex interplay between macrofaunal, meiofaunal and bacterial communities. While the system is heavily influenced by arsenic, no specific correlation between the relative abundance of arsenic metabolizing organisms and the amount of arsenic in the system could be drawn. This is likely due to the fact that most of the arsenic produced by the system is readily adsorbed onto iron oxyhydroxides, reducing the arsenic's bioavailability.

The anoxic conditions at Jewfish sink provide a different hurdle than the hot arsenic conditions found in Papua New Guinea. The anoxic conditions are shared by other pit features found in karst geography, but the metabolic processes between Jewfish sink and these other karst habitats are different. The blue holes and black holes of the Bahamas are some of the most well-studied of these karstic pits. In these features, which are large circular pits with diameters of over 300 m, light and sulfur are used as a means of energy acquisition. Jewfish sink, having an opening only 6 m in diameter, is light restricted compared to these systems. As a result, the strategy of organisms dwelling in the anoxic conditions of the sink is different than those found at the well-studied holes in the Bahamas. Geochemical measurements were recorded over two time periods spanning a combined total of 6 years. The anoxic bottom waters of Jewfish sink remain stable and contained high levels of sulfide throughout most of the seasons studies. Sequence analysis of prokaryotes within the sink showed that sulfur reducers had the highest relative abundance compared to other functional guilds. To monitor the changes of the microbial communities within the sink, bacterial communities were examined at 4 depths within the sink at 9 different intervals over a period of 685 days. Denaturing Gradient Gel Electrophoresis (DGGE) was used to fingerprint 16s rRNA bacterial communities and dissimilatory sulfite reducing communities by targeting the 16s rRNA bacterial gene and the dsr gene associated with dissimilatory sulfite reducing bacteria and archaea. The lowest depth studied within the sink (40 m) remained stable chemically and biologically until a turnover event occurred within the second winter of the study. This turnover event disrupted the biological communities at 40 m and led to a reestablished community comprised of different species that those found prior to the event. Upper waters within the sink show that clines establish themselves seasonally and partition zones that confine bacterial communities that are more similar to each other within these zones while excluding bacterial communities that are outside of these zones. Oxygenated water was shown to not contain prokaryotes containing the dsr gene. As the oxycline changed seasonally, dissimilatory sulfite reducing prokaryotes containing the dsr gene remained in the anoxic zone and required time to reestablish themselves whenever oxygenated water displaced them.