The increased frequency and intensity of drought with climate change may cause an increase in the magnitude and toxicity of freshwater cyanobacteria harmful algal blooms (CHABs), including Microcystis blooms, in San Francisco Estuary, California. As the fourth driest year on record in San Francisco Estuary, the 2014 drought provided an opportunity to directly test the impact of severe drought on cyanobacteria blooms in SFE. A field sampling program was conducted between July and December 2014 to sample a suite of physical, chemical, and biological variables at 10 stations in the freshwater and brackish reaches of the estuary. The 2014 Microcystis bloom had the highest biomass and toxin concentration, earliest initiation, and the longest duration, since the blooms began in 1999. Median chlorophyll a concentration increased by 9 and 12 times over previous dry and wet years, respectively. Total microcystin concentration also exceeded that in previous dry and wet years by a factor of 11 and 65, respectively. Cell abundance determined by quantitative PCR indicated the bloom contained multiple potentially toxic cyanobacteria species, toxic Microcystis and relatively high total cyanobacteria abundance. The bloom was associated with extreme nutrient concentrations, including a 20-year high in soluble reactive phosphorus concentration and low to below detection levels of ammonium. Stable isotope analysis suggested the bloom varied with both inorganic and organic nutrient concentration, and used ammonium as the primary nitrogen source. Water temperature was a primary controlling factor for the bloom and was positively correlated with the increase in both total and toxic Microcystis abundance. In addition, the early initiation and persistence of warm water temperature coincided with the increased intensity and duration of the Microcystis bloom from the usual 3 to 4 months to 8 months. Long residence time was also a primary factor controlling the magnitude and persistence of the bloom, and was created by a 66% to 85% reduction in both the water inflow and diversion of water for agriculture during the summer. We concluded that severe drought conditions can lead to a significant increase in the abundance of Microcystis and other cyanobacteria, as well as their associated toxins.

The impact of the toxic cyanobacterium Microcystis aeruginosa on estuarine food web production in San Francisco Estuary is unknown. It is hypothesized that Microcystis contributed to a recent decline in pelagic organisms directly through its toxicity or indirectly through its impact on the food web after 1999. In order to evaluate this hypothesis, phytoplankton, cyanobacteria, zooplankton, and fish were collected biweekly at stations throughout the estuary in 2005. Concentrations of the tumor-promoting Microcystis toxin, microcystin, were measured in water, plankton, zooplankton, and fish by a protein phosphatase inhibition assay, and fish health was assessed by histopathology. Microcystis abundance was elevated in the surface layer of the western and central delta and reached a maximum of 32 × 10⁹ cells l⁻¹ at Old River in August. Its distribution across the estuary was correlated with a suite of phytoplankton and cyanobacteria species in the surface layer and 1 m depth including Aphanizomenon spp., Aulacoseira granulata, Bacillaria paradoxa, Rhodomonas spp., and Cryptomonas spp. Shifts in the phytoplankton community composition coincided with a decrease in the percentage of diatom and green algal carbon and increase in the percentage of cryptophyte carbon at 1 m depth. Maximum calanoid and cyclopoid copepod carbon coincided with elevated Microcystis abundance, but it was accompanied by a low cladocera to calanoid copepod ratio. Total microcystins were present at all levels of the food web and the greater total microcystins concentration in striped bass than their prey suggested toxins accumulated at higher trophic levels. Histopathology of fish liver tissue suggested the health of two common fish in the estuary, striped bass (Morone saxatilis), and Mississippi silversides (Menidia audens), was impacted by tumor-promoting substances, particularly at stations where total microcystins concentration was elevated. This study suggests that even at low abundance, Microcystis may impact estuarine fishery production through toxic and food web impacts at multiple trophic levels.