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The environmental regulation of planktonic food web structure is a key determinant for the efficiency of energy transfer through trophic levels, with direct implications for the amount of energy that is available to top-consumers and deep-sea communities. Yet, the complex trophic interplay between the different components of plankton communities under contrasting environmental conditions remains unresolved. Here, we present a comprehensive field study based on compound-specific isotope analysis of amino acids that aims to explore depth-resolved changes in the trophic strategies of various size-classes of mesozooplankton from distinct habitats across the Southeast Pacific. According to the δ15N values of the so-called source amino acids such as phenylalanine, we first identified a clear shift in nitrogen sources for biological production, from nitrate in the productive upwelling waters of the Humboldt Current System to increased inputs of diazotroph-N within the ultra-oligotrophic South Pacific gyre. These shifts in the productivity and in the source of N at the base of the food web were not accompanied by significant changes in the trophic position (TP) of mesozooplankton, which were mainly omnivores (TP = 2.8 ± 0.3, n = 65) in all ecoregions. However, although the planktonic food web length remained relatively unaltered along the productivity gradient, the microbial contribution to mid-trophic level consumers appeared to be more important at relatively high productivities, likely due to more intense remineralization processes in a late successional stage of the upwelling throughout the coastal-transition zone. Altogether, this research work will contribute to a better understanding of the food web functioning in one of the least explored marine regions of the world's oceans., IF-U was supported by ANID-FONDECYT research projects 3180352 and 11221079 during the field sampling and the writing process, respectively. CSIA-AA analyses were partially funded by ANID-REDES 10039 and ANID-FONDECYT 1181682 projects granted to RE. The authors also acknowledge support from the Millennium Institute of Oceanography (IMO) of ANID Chile (Grant ICN12_019).

The overall objective of cruise M117 was to investigate biochemical processes in upwelling zones. Upwelled water is characterized by re-mineralized nutrients, CO2-supersaturation, cold temperature and enhanced primary productivity. The phenomenon of upwelling is of interest to several research activities of working groups (WP) of the participating research institutes. Therefore, the cruise M117 has been an efficient approach to understand potentially interconnected biochemical processes within upwelling systems of the Baltic Sea. Research activities include phosphorus availability for harmful cyanobacteria blooms (WP1), air-sea CO2 exchange (WP2), marine aerosol formation (WP3), mercury species distribution and Hg sea-air gas exchange (WP4), and energy turnover of zooplankton communities along food quality gradients (WP5). The research activities rely on supplementary data of nutrients and phytoplankton composition. For this reason the research activities during cruise M117 have been combined with monitoring programs conducted regularly by IOW on behalf of the Federal Maritime and Hydrography Agency (BSH) and of the Helsinki Commission (HELCOM)., METEOR-Berichte