The increase of cyanobacteria and benthic diatoms over 43 years in upper San Francisco Estuary, California

The quality and quantity of phytoplankton carbon available at the base of the aquatic food web is critical to fish production in estuaries. Therefore, a decrease in chlorophyll a concentration, an estimate of phytoplankton carbon, in upper San Francisco Bay estuary over the last 43 years is hypothesized to be an important contributing factor to a long-term decline in fish production. Although a decrease in the chlorophyll a concentration is well documented for the upper estuary, the quality of carbon available to the food web due to change in the phytoplankton community composition is not. The relative change in the phytoplankton community composition and how it impacted carbon transfer within the lower San Joaquin River, lower Sacramento River and Suisun Bay, was determined with data from 6 stations sampled at 2-week to 4-week intervals between 1975 and 2017. Analysis of similarity (ANOSIM) comparisons confirmed that the relative change in carbon among phytoplankton genera across time affected the food quality index and the size structure of the phytoplankton food resource in the estuary. Between the first and last decades, phytoplankton carbon shifted from large volume cells and diatoms to small volume cells and cyanobacteria. There was also a shift from pelagic to epibenthic and benthic-pelagic diatoms between these two periods. Only 21 phytoplankton genera were responsible for most of this change based on similarity percentage analysis (SIMPER). Single and multivariate analyses confirmed a link between the phytoplankton community carbon and environmental conditions, particularly an increase in Sechhi disk depth. These analyses suggest that a full understanding of the estuarine food web dynamics over time in upper San Francisco Estuary depends on knowing the phytoplankton community composition and how it varies within pelagic and benthic habitats. •Identification of shifts in percent carbon, size structure and food quality of 43-year estuarine phytoplankton record.•Correlated a long-term change in water clarity with a shift in epibenthic and benthic-pelagic growth forms.•Demonstrated methodological considerations and approaches to “messy” phytoplankton datasets.•Application of nonparametric analyses (nMDS, SIMPER, BEST, ANOSIM and GAM) analysis to long-term phytoplankton data.