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Abstract A quantitative understanding of the mesopelagic zooplankton food web is key to development of accurate carbon budgets and geochemical models in marine systems. Here we use compound specific nitrogen stable isotope analysis of amino acids to quantify the trophic structure of the microzooplankton and mesozooplankton community during summer in the subarctic northeast Pacific Ocean during the EXport Processes in the Ocean from Remote Sensing (EXPORTS) field campaign. Source amino acid values in particles and zooplankton provide strong evidence that basal resources for the mesopelagic zooplankton food web were primarily small (), suspended or slow‐sinking particles, but that surface organic matter delivered by vertically migrating zooplankton may have also been important. Comparisons of values of source and trophic amino acids provide estimates of food web length, which decrease significantly with depth and suggest that protistan microzooplankton are key components of the food web from the surface to at least 500. These results emphasize the importance of small particles as a source of carbon and nitrogen to mesopelagic communities in this region, support observations of an inverse relationship between zooplankton vertical migration and small particles as sources of carbon to deep‐sea food webs in low productivity environments, and document the role of heterotrophic protists as key trophic intermediaries in the mesopelagic zone at this location. 

Abstract Particulate organic matter settling out of the euphotic zone is a major sink for atmospheric carbon dioxide and serves as a primary food source to mesopelagic food webs. Degradation of this organic matter encompasses a suite of mechanisms that attenuate flux, including heterotrophic metabolic processes of microbes and metazoans. The relative contributions of microbial and metazoan heterotrophy to flux attenuation, however, have been difficult to determine. We present results of compound specific nitrogen isotope analysis of amino acids of sinking particles from sediment traps and size‐fractionated particles from in situ filtration between the surface and 500 m at Ocean Station Papa, collected during NASA EXPORTS (EXport Processes in the Ocean from RemoTe Sensing). With increasing depth, we observe: (1) that, based on theδ¹⁵N values of threonine, fecal pellets dominate the sinking particle flux and that attenuation of downward particle flux occurs largely via disaggregation in the upper mesopelagic; (2) an increasing trophic position of particles in the upper water column, reflecting increasing heterotrophic contributions to the nitrogen pool and the loss of particles via remineralization; and (3) increasingδ¹⁵N values of source amino acids in submicron and small (1–6μm) particles, reflecting microbial particle solubilization. We further employ a Bayesian mixing model to estimate the relative proportions of fecal pellets, phytodetritus, and microbially degraded material in particles and compare these results and our interpretations of flux attenuation mechanisms to other, independent methods used during EXPORTS.