Hidden complexities in the base of the pelagic food web: correlates between zooplankton and chlorophyll vary by functional feeding group.

Zooplankton in estuaries provide an important link between primary production and fish. Resource managers in the San Francisco Estuary have several initiatives designed to increase phytoplankton production, expecting zooplankton increases to follow. However, it is not always clear if an increase in phytoplankton biomass will lead to an increase in zooplankton biomass. We used data from twenty years of zooplankton and chlorophyll- a monitoring in the estuary to create linear models of zooplankton abundance versus chlorophyll- a concentration, salinity, turbidity, and microzooplankton biomass (rotifers and copepod nauplii) for twelve of the most abundant zooplankton taxa, categorized by functional feeding guilds (herbivores, omnivores, predators). We then used fifty years of zooplankton data to assess changes in relative abundance of the three feeding guilds, over time and by salinity. We found that herbivorous taxa were positively related to chlorophyll- a concentration, whereas predatory taxa were not, and omnivorous taxa had mixed results. There were positive correlations between microzooplankton and abundance of most of the target taxa. We also documented dominance of herbivores in freshwater regions while omnivorous and predatory taxa dominate in brackish water. There has been an increase in abundance of omnivorous taxa in all salinity zones over time, and an increase in predatory taxa in brackish water. Taken together, these results indicate that management actions designed to increase phytoplankton abundance may be effective in freshwater areas where herbivorous taxa dominate but may be less effective in brackish water areas where predatory and omnivorous taxa dominate. The increase in predatory copepods in brackish water areas may increase food chain length and therefore decrease trophic efficiency in the transfer of carbon to fishes at the top of the food web.