UC San Diego

The focus of this dissertation is to observe and quantify the contribution of bacteria and their habitats to the nutrient cycling in marine environments. As a result of the complex exchanges between ocean physics, chemistry, and biology, the formation and distribution of microbial communities, their metabolisms, and their microenvironments is invariably influenced. Current research is beginning to reveal the heterogeneity of microbial growth, community/species composition, and habitats in the natural marine environment. However, little is currently know about how the mechanisms and interactions of these parameters influence each other. These topics were addressed through the application of microscopy and various fluorescence staining techniques, and following several oceanographic research cruises. After developing a staining protocol of seawater derived microbes and organic matter concentrated on a polycarbonate filter, it was found that an abundant and unclassified type of transparent organic particle exists in coastal and open ocean environments. These structures were termed filter fluorescing particles (FFP) based on their staining characteristics. In addition to their small size of a few to hundreds of micrometers in length, the particles are occasionally associated with heterotrophic bacteria, cyanobacteria, and phytoplankton. Several oceanographic research cruises confirmed the widespread presence of these particles, and suggest that these particles are relatively more abundant in oligotrophic waters containing enhanced concentrations of refractory organic matter. The discovery of these particles adds to our current knowledge of transparent exopolymer particles (TEP), DAPI yellow particles (DYP), and Coomassie stained particles (CSP). The spatial characteristics and dynamics of a deep-water oceanic frontal zone made it possible to study the influence of submesoscale processes on the microscale responses of microbes and organic matter. The strong gradient created at this site created distinct zones of microbial activity, abundance, and size characterized by elevated primary and secondary production at the front. Further, the non-living material comprising the particulate and dissolved organic mater pools was enhanced as well due to elevated the production of the phyto- and bacterioplankton. The abundance and size of FFP and TEP were also monitored, and found to coincide with water mass features as well, presumably due to the physical-biological interactions acting at the front. Lastly, a method was established to simultaneously visualize and quantify the protein synthesis rates of single heterotrophic bacterial cells in order to identify growth ranges and relative biogeochemical contributions in natural populations. This approach relied on the bioorthogonal amino acid homopropargylglycine (HPG), a methionine analog functionalized with an alkyne group. After incubation of natural seawater with HPG followed by fixation and cell immobilization on a filter, the HPG incorporated into the cellular protein of active cells was fluorescently labeled with Alexa Fluor 488 via click chemistry. A conversion factor to measure single-cell protein synthesis was generated from laboratory culture grown in natural seawater. Applying this factor to labeled cells from the Scripps Pier revealed a large range of rates, and highlighted the sensitivity of the method to measure very low activity cells, growth of cells attached to particles, and the continuum of activities that characterize natural heterotrophic bacterial assemblages