This research used culture-based studies of model marine microorganisms to guide environmental analyses of the significance of ammonia-oxidizing microorganisms in shaping the activity and structure of plankton in the upper ocean. By using the most recent technological advances in molecular characterization and analytical chemistry this research established that the greater part of nitrification (the microbiological conversion of ammonia to nitrate) in the North Pacific and coastal areas is controlled primarily by the ammonia-oxidizing archaea (AOA), and served to identify specific biotic and abiotic factors controlled by, and controlling, the activities of the AOA. By better quantifying the contribution of AOA to regenerated nitrate in the upper water column it should now be possible to improve estimates of new ocean production ("biological pump"), an estimate that has been based on nitrate assimilation and the assumption that there is very little endogenous production of nitrate in regions of active photosynthetic production. These analyses have also provided new information about environmental and biological controls of the production of nitrous oxide and methane in the upper ocean, both potent greenhouse gases, and forced a reevaluation of the use of AOA lipids preserved in marine sediments to inform historical excursions in ocean surface water temperature associated with past climates. Together the results of this work have significantly advanced understanding of environmental variables influencing the coupling of marine nitrogen and carbon cycles, and offer new insights into microbial processes relevant to past and future climates. These studies should ultimately provide a better understanding of the impact of human activity on critical marine nutrient cycles. Last Modified: 02/15/2018 Submitted by: David A Stahl