Investigation of molecular diversity of important functional genes in marine bacteria Principal Investigator: Wade H. Jeffrey, PhD Support Agency: University of West Florida Location of Study: Southeastern Pacific Ocean

The oceans cover 70% of Earth's surface containing an extraordinary diversity of life. The components (i.e. the structure) of the marine food web mediate the transformation of energy and cycling of elements (i.e. the function) in the oceans and atmosphere. Our ignorance of marine microbial communities is vast. For example, less than 1% of the bacterial species in the oceans have been cultured and there are often a million of these unknown cells per ml of seawater. Microbial processes centrally influence all ocean biogeochemistry in today's oceans yet we do not understand how many species contribute to these processes, what their individual biochemical 'roles' are, and what mechanisms guide the assembly and dynamics of these communities. Understanding the gene functions in these organisms in their communities will help us to ascertain the structure and function of these complex systems. Once we can describe the activities of these ecosystems at the molecular level, we can begin to understand what questions are important to ask at the higher levels of organization of these ecosystems.
In the summer of 2000 samples were collected during a transect between Punta Arenas, Chile and the Gulf of Mexico. In addition to standard analysis of community structure via 16S rRNA sequencing, we also collected samples to study the molecular diversity of the genes which carry out significant processes in the worlds' oceans. These processes include biogeochemical and nutrient cycling (eg nitrogen and carbon cycling) and as well as stress response (ultraviolet radiation and oxidative damage). Polymerase Chain Reaction (PCR) based analysis will be used to investigate these functional gene sequences collected over such a geographically diverse region. Resulting PCR products are being analyzed for diversity in several ways including Denaturing Gradient Gel Electrophoresis (DGGE) and Terminal Restriction Fragment Length Polymorphism (TRFLP). Although the specifics are complex, these protocols may be thought of as similar to "DNA fingerprinting." Ultimate resolution of gene similarity may be determined by DNA sequencing with comparison to known sequences in databases.