Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2013.Cataloged from PDF version of thesis.Includes bibliographical references (p. 143-154).The physical environment in the oceans dictates not only how phytoplankton cells are dispersed and their populations intermingled, but also mediates the supply of nutrients to the surface mixed layer. In this thesis I explore both of these aspects of the interaction between phytoplankton ecology and ocean physics, and have approached this topic in two distinct but complementary ways, working with a global ocean ecosystem model, and collecting data at sea. In the first half of the thesis, I examine the role of mesoscale physical features in shaping phytoplankton community structure and influencing rates of primary production. I compare the output of a complex marine ecosystem model coupled to coarse resolution and eddy-permitting physical models. Explicitly resolving eddies resulted in marked regional variations in primary production, zooplankton and phytoplankton biomass. The same phytoplankton phenotypes persisted in both cases, and were dominant in the same regions. Global phytoplankton diversity was unchanged. However, levels of local phytoplankton diversity were markedly different, with a large increase in local diversity in the higher resolution model. Increased diversity could be attributed to a combination of enhanced dispersal, environmental variability and nutrient supply in the higher resolution model. Diversity "hotspots" associated with western boundary currents and coastal upwelling zones are sustained through a combination of all of these factors. In the second half of the thesis I describe the results of a fine scale ecological and biogeochemical survey of the Kuroshio Extension Front. I found fine scale patterns in physical, chemical and biological properties that can be linked back to both the large scale horizontal and smaller scale vertical physical dynamics of the study region. A targeted genomic analysis of samples focused on the ecology of the picoeukaryote Ostreococcus clade distributions strongly supports the model derived hypotheses about the mechanisms supporting diversity hotspots. Strikingly, two distinct clades of Ostreococcus co-occur in more than half of the samples. A "hotspot" of Ostreococcus diversity appears to be supported by a confluence of water masses containing either clade, as well as a local nutrient supply at the front and the mesoscale variability of the region.by Sophie Anne Clayton.Ph.D.