The importance of the trophic link between <200-µm protistan microzooplankton and mesozooplankton is a cornerstone of modern understanding of foodweb structure of marine pelagic ecosystems that is well demonstrated in experimentally measured contributions of protistan consumers to mesozooplankton diets, in constrained global budgets, and in regional studies that show the inadequacies of meeting zooplankton metabolic requirements by herbivory alone. Nonetheless, protistan trophic steps are poorly reflected in stable isotope analyses by standard methods and systematically neglected in fisheries-related trophic research, which focuses instead on interactions that can be measured in stomach contents. Here, we apply recent advances in compound-specific isotope analysis of amino acids (CSIA-AA) based on alanine as a trophic indicator of protistan foodweb steps to evaluate the implications of lower foodweb structure on trophic position (TP) estimates of tunas. CSIA-AA results for mesozooplankton of the subtropical North Pacific suggest that tuna TPs are underestimated by 0.9, which give rise to new TP estimates of 4.7–5.4 for the three main tuna species of that region. These, in turn, are used to compute a trophic enrichment factor (TEF = 4.45) based on alanine that includes 15N enrichments for protistan consumers and can be applied more broadly in the region. Accounting for the magnitude and variability of protistan trophic steps in the foodwebs supporting pelagic fisheries has important implications for understanding regional variability in energy flows and foodweb structure and their temporal responses to climate change.

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