Sulfate-reducing bacteria. Desulfovibrio species are microbes of interest based on their ability to immobilize heavy toxic metals such as uranium through precipitation and/or changing of the redox state. Desulfovibrio are also industrially important because of their ability to corrode ferrous metals and produce toxic sulfides. An understanding of the intrinsic mechanisms by which these sulfate reducers regulate metabolism is needed for both industrial and environmental remediation purposes. Since many contaminated environments require physiological adaptation for cell survival, information about stress tolerance is particularly pertinent for successful remediation strategies. One of my research interests focuses on iron metabolism and the Fur (ferric uptake regulator) protein in Desulfovibrio. Very little information is currently available on the metabolism of iron in anaerobic bacteria, especially since iron is predicted to be abundant, biologically available, and less toxic under anaerobic conditions. However, Desulfovibrio produce sulfide as a by-product of their metabolism creating iron-precipitates. Does this precipitation create a limitation for bioavailable iron? Since the Fur proteins of the delta-Proteobacteria form a distinct phylogenetic lineage and are predicted to recognize a DNA sequence quite different from other Gram-negative bacteria, do sulfate-reducing bacteria intricately regulate iron uptake in the same manner as aerobic bacteria? Desulfovibrio also contain a large number of iron containing electron transport proteins posited to be involved in metal reduction and ferrous iron corrosion. What role if any does the Fur protein play in regulating these processes? To address these questions and further study the global regulation of Desulfovibrio, we have developed a genetic system for generating targeted deletions. Current studies are underway in our lab to determine the physiological and regulatory ramifications of deleting the Ferric Uptake Regulator paralogs fur, perR, and zur in D. vulgaris Hildenborough.
Ecology of bacteriophage. Following their initial discovery, bacteriophage were studied as a model system for eukaryotic viruses and due to their relatively simple life cycle, became the foundation of early molecular biology. Traditional bacteriophage studies have also been focused on three areas: use of phage as anti-bacterial agents based on their propensity for infection and killing of specific bacterial strains, use as molecular markers to identify specific pathogenic bacteria, and use as recombinant DNA tools via transduction. However, little to no emphasis has been placed on the diversity or abundance of bacteriophage in the environment until just recently. A little over ten years ago, the first environmental abundance study was performed. This simple microscopic analysis of marine and fresh water systems estimated t-tailed phage abundance to be 1030 globally, thus making bacteriophage the most abundant biological system in the biosphere. This astonishing discovery has opened up a new ecological theme focused on the role the virosphere plays on microbial diversity and shaping of bacterial communities. The shear abundance of bacteriophage alone plays a prominent role in the cycling of organic matter, not to mention the impact these viruses have on bacterial nutrient cycling and energy flow via direct effects on bacterial community structure, stability, and diversity. While bacteriophage influence host community structure and stability via infection and thus morbidity of specific strains, host metabolic diversity is impacted by genome evolution via horizontal transfer of DNA from phage to host (transduction). My specific research interests include gaining a glimpse into the unknown bacteriophage diversity specific to unique environmental niches.
Small RNA Analysis. While on-going microarray analyses under various environmental and stress conditions are providing more targets for regulation studies in bacteria another regulatory mechanism has been severely neglected in bacteria, that of small regulatory RNAs. In the last few years our perception of small regulatory RNAs has changed dramatically. From once being regarded as exceptional additions to the known repertoire of RNA-related functions, these small nucleic acids are now known to be abundantly present in all kingdoms of life performing critical roles in the cellular processes of both eukaryotes and prokaryotes. These non-translated RNAs predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion. However, some molecules have been shown to regulate by binding proteins directly thus affecting activity. To target small RNAs, techniques using shotgun cloning of small RNA as well as computational strategies have been developed and used in both eukaryotes and prokaryotes. While the present techniques have proven informative with Escherichia coli and Archaeoglobus fulgidus, little data is present from other prokaryotes. I am interested in focusing on both the bioinformatics and RNomics approaches to identify putative small regulatory RNAs from environmentally and medically significant bacterial species.
