The goal of this project was to test and refine a tool, Compound-Specific Isotopic Analyses of Amino Acids (CSIA-AA), for determining the trophic positions (TP) of marine organisms in order to improve models for managing ocean fisheries. According to the CSIA-AA method, TP estimates are determined from the difference between nitrogen isotopic compositions of individual amino acids, some that vary little from nitrogen source to primary producers (typically, phenylalanine) and some that enrich strongly in 15N with each trophic step (typically, glutamic acid). An organismÆs tissue (protein) thus contains information about potential regional differences in the source of nitrogen to production, as well as the number of steps that organism is removed from primary producers in its average diet. For the project overall, a broad range of activities were undertaken, including field sampling, laboratory studies and CSIA-AA analyses of organisms ranging from microbes to zooplankton, mesopelagic, pelagic and reef fishes, and sea turtles. Most analyses relating to higher trophic level animals were done by the University of Hawaii component (P.I.s: Brian Popp and Jeff Drazen). For the SIO component, our specific attention was on organism representing the plankton food-web base (phytoplankton – protozooplankton – mesozooplankton). Field sampling was done in four regions of the Pacific Ocean with distinct differences in biogeochemistry, ecology and source nitrogen. We sampled plankton in the coastal upwelling region off of southern California, the iron-limited region of the central equatorial Pacific, the strong denitrification region of the Costa Rice Dome (eastern tropical Pacific), and an area of summertime nitrogen fixation in the subtropical north Pacific (Station ALOHA, Hawaii Ocean Time series). The key findings were that slopes in isotopic enrichment with zooplankton size class were very similar in all regions, with the variations in absolute values mainly reflecting differences in source nitrogen to the food-web base. The results therefore show an underlying similarity in zooplankton trophic structure among contrasting ecological systems, which will be useful in ocean ecosystem modeling. However, the data do not support a common assumption of models that predator and prey in marine plankton systems are related by a mean body size (length) ratio of 10:1. We also use historical samples collected in the California Current during a major El Niño/La Niña transition in 1998-1999 to assess how plankton trophic structure responded to a large environmental perturbation. Comparing samples among three years representing El Niño, La Niña and "normal" conditions, we found a significant 15N enrichment of ~2 ‰ at the base of the food web for all AAs and all zooplankton groups during the 1998 El Niño. Overall, the observed patterns of δ15N values in bulk tissues for CCE zooplankton were driven mainly by changes in source δ15N to phytoplankton, rather than by marked alteration of dietary composition (enhanced carnivory) or increased food web length to the zooplankton. However, the krill species Euphasia pacifica, an important prey for baleen whales, did show a significantly elevated TP, implying increased carnivory, more trophic steps and potentially less energy transfer to krill during 1998. This study also broadened the AA-CSIA method by developing Linear Mixed Effect models to incorporate δ15N values for all measured amino acids, providing greater statistical power for hypothesis testing than the typical approach of using only phenylalanine and glutamic acid. In laboratory experiments, we used a model two-stage chemostat system with a heterotrophic dinoflagellate feeding on a green alga to investigate whether rapid nitrogen cycling within the microbial food web might explain low TP estimates (indicating direct herbivory) for mesozooplank...