USC Microbial Observatory and Dimensions of Biodiversity Project

The USC Microbial Observatory and the Dimensions of Biodiversity Project focuses on exploratory investigation of prokaryotic and unicellular eukaryotic diversity in the San Pedro Channel, California, with a focus on time-dependent changes in community composition in relation to environmental parameters. It also includes focused studies of particular microbial groups.

The project has been running since 2000. Our primary sampling site is located midway between Los Angeles and the USC Wrigley Marine Laboratory on Santa Catalina in approximately 900 m of water. This site is visited monthly by ship for sampling to 890 m depth. Additional sampling is conducted on an ad hoc basis in coastal water near the lab on Catalina Island.

Our monthly routine sampling includes oceanographic as well as microbial data and sample collection. In addition to basic oceanographic parameters measured by the Wrigley Institute for Environmental Studies as part of the San Pedro Ocean Time Series (temperature, salinity, chlorophyll, inorganic nutrients and dissolved oxygen), we monitor the abundance of the microbial assemblages by flow cytometry (Synechococcus, Prochlorococcus, total prokaryotes, phototrophic picoeukaryotes), microscopical analysis (phototrophic and heterotrophic nanoplankton, microplankton, prokaryotes), prokaryotic activity by incorporation of labeled leucine and thymidine, and the diversity by an array of molecular-based techniques. These techniques provide abundance and biomass estimates of the entire microbial community, including bacteria, archaea and eukaryotes. Molecular biological analyses of these samples provide culture-independent estimates of microbial diversity.

These monthly measurements make up the core data set for the project. An important part of the project is to use these data to determine the time-dependent changes in microbial community composition and to try to learn what physical, chemical, and biological factors regulate that composition. While most of the microbial work is broad-based, meaning it looks at the entire community, we also have studies that focus on particular taxa or functional groups. For example, we use genetic analysis to examine the time-dependent change in aerobic anoxygenic photosynthetic bacteria, and proteobacteria that possess genes for nitrogen fixation. Culture efforts with eukaryotes are focused on obtaining representative protistan taxa in laboratory culture, and linking genetic signatures to morphotypes of these species.