Abstract

Ecologists and ecosystem managers often base their understanding of trophic dynamics on consumer and resource biomass. However, the factors that alter the relative nutritional value of resources are often poorly understood, despite their potential to decouple trophic interactions. Recent population declines in pelagic fishes of the upper San Francisco Estuary were not accompanied by an equivalent decrease in zooplankton biomass, which are the main resource for the fish and their larvae. It was hypothesized that changes in zooplankton nutritional conditions following the establishment of invasive species caused food‐quality related limitations for these higher‐order consumers. Using stable isotopes, elemental stoichiometry and fatty acid analyses for all dominant invasive and native zooplankton taxa and seston, we characterized the plankton community structure in the estuary and demonstrated taxon‐specific differences in their nutritional value. We then quantified the temporal dynamics in meso‐zooplankton proportions of docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), polyunsaturated fatty acids (PUFA), and ratio of n3:n6 fatty acids. We found temporal increase in the community‐level DHA, n3 to n6 fatty acid ratio, decrease in the community‐level EPA and PUFA in the brackish water region, but no change in the bulk PUFA proportions in the freshwater region of the estuary. These changes were caused mainly by declines of native cladocerans that are rich in EPA and by an increase in the dominance of invasive taxa with high DHA concentrations, similar to that of native taxa. Although we showed temporal shifts in individual fatty acid classes, the proportion of the essential fatty acids remained relatively high, suggesting that nutritional prey availability for fish remained unchanged with the shift in species composition. We argue that the nutritional content of resource communities should be considered when analyzing the long‐term trophic dynamics and designing effective management and restoration strategies.

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