Potential graduate students are highly encouraged to contact me to discuss their interests. Below is a short list of potential thesis topics for future students.
Potential Thesis Topics
Metals as micronutrients in low-oxygen environments
Microbial processes that occur in the absence of oxygen, or when oxygen is very low, are important in the carbon and nitrogen cycles. These include methane oxidation, denitrification, anamox and the oxidative degradation of many organic contaminants. Metalloenzymes catalyze most of these processes and require metals like copper or iron. But under reducing (low oxygen) conditions, many of these metals are bound to reduced sulfur compounds and other chelators, rendering them non-bioavailable. So rates of these processes may be controlled by metal availability. A thesis project could involve investigating what processes are influenced by metals, how bacteria acquire the metals they need, and under what conditions metal limitation may occur.
A primary study area for me is the Arabian Sea, one of the most important places in the world for denitrification. However, many of these processes can be studied right at our back door, at the San Pedro Ocean Time Series Station (SPOT) midway between San Pedro and USC's Wrigley Center on Catalina.
Role of Fe limitation in controlling N fixation in the Pacific and Indian Oceans (w. Eric Webb)
Nitrogen fixation requires a lot of iron for the nitrogenase enzyme. Iron is scarce in many of the oligotrophic regimes where N-fixation is important, including vast areas of the Pacific and Indian Oceans. A combination of iron measurements and molecular biological stress markers can be used to assess the spatial and temporal range of Fe limitation, and can be the basis of a thesis project. Stress markers include proteins associated with high-affinity Fe transporters that are up-regulated under Fe stress. An important question is why diazotrophs have a special acquisition pathway for Fe(II) normally found in anaerobes, since Fe(II) is unstable in the presence of oxygen.
Metals and Biology in Mono Lake and other hyperalkaline environments
The pH in Mono Lake is about 10. Under such conditions we expect that iron may be tied up as insoluble hydroxides. It is likely that the active microbial community there has developed strategies to acquire iron, including the production of siderophores. However, many of the most powerful siderophores, like the catechols, are unstable at such high pH values. So microbes in Mono Lake, as well as certain streams in northern California where the pH is even higher, may have evolved novel strategies for Fe acquisition.
I am interested in the idea that there may be a completely novel class of compounds in Mono Lake which may dominate iron chemistry there.
Inputs of contaminants into California coastal waters during episodic events, such as floods, and their ecological impacts
Most pollutants enter coastal waters during floods and heavy rains, especially in southern California, where such events are infrequent but large. They are hard to study, because, as transients, they have a high degree of spatial and temporal variability. Conventional sampling from a boat does not provide the spatial and temporal coverage needed to adequately characterize pollutant transport and fate during such events. In this project, I am interested in using a combination of in situ sensors, passive sampling probes, and short-term physiological responses of macroalgae and invertebrates growing in impacted areas, to study these processes.