San Francisco Estuary and Watershed Science

Zooplankton provide critical food for threatened and endangered fish species in the San Francisco Estuary (estuary). Reduced food supply has been implicated in the Pelagic Organism Decline of the early 2000s, and further changes in zooplankton abundance, seasonality, and distribution may continue to threaten declining fishes. While we have a wealth of monitoring data, we know little about the abundance trends of many estuary zooplankton species. To fill these gaps, we reviewed past research and then examined trends in seasonality and abundance from 1972 to the present of three key but understudied zooplankton species (Bosmina longirostris, Acanthocyclops spp., and Acartiella sinensis) that play important roles in the estuary food web. We fit Bayesian generalized additive mixed models of each taxon’s relationship with salinity, seasonality, year, and geography on an integrated database of zooplankton monitoring in the upper estuary. We found marked changes in the seasonality and overall abundance of each study species. Bosmina longirostris no longer peaks in abundance in the fall months, Acanthocyclops spp. precipitously declined in all months and lost its strong relationship with salinity, and A. sinensis adult abundance has become more strongly related to salinity while juveniles have developed wider seasonal abundance peaks. Through these analyses, we have documented the relationship of each species with salinity and seasonality since the beginning of monitoring or their introduction, thus increasing our understanding of their ecology and importance in the estuary. These results can inform food-web models, be paired with fish data to model the contributions of these species toward fish abundance trends and be mirrored to elucidate other species’ trends in future studies.