The first distribution, biomass and toxicity study of a newly established bloom of the colonial cyanobacteria Microcystis aeruginosa was conducted on October 15, 2003 in the upper San Francisco Bay Estuary. Microcystis aeruginosa was widely distributed throughout 180 km of waterways in the upper San Francisco Bay Estuary from freshwater to brackish water environments and contained hepatotoxic microcystins at all stations. Other cyanobacteria toxins were absent or only present in trace amounts. The composition of the microcystins among stations was similar and dominated by demethyl microcystin-LR followed by microcystin-LR. In situ toxicity computed for the >75 lm cell diameter size fraction was well below the 1 lg l )1 advisory level set by the World Health Organization for water quality, but the toxicity of the full population is unknown. The toxicity may have been greater earlier in the year when biomass was visibly higher. Toxicity was highest at low water temperature, water transparency and salinity. Microcystins from the bloom entered the food web and were present in both total zooplankton and clam tissue. Initial laboratory feeding tests suggested the cyanobacteria was not consumed by the adult copepod Eurytemora affinis, an important fishery food source in the estuary.

A bloom of the cyanobacteria Microcystis aeruginosa was sampled over the summer and fall in order to determine if the spatial and temporal patterns in cell density, chlorophyll a (chl a) concentration, total microcystins concentration, and percent microcystins composition varied with environmental conditions in San Francisco Estuary. It was hypothesized that the seasonal variation in Microcystis cell density and microcystin concentration was ecologically important because it could influence the transfer of toxic microcystins into the aquatic food web. Sampling for Microcystis cell density, chl a concentration, total microcystins concentration and a suite of environmental conditions was conducted biweekly at nine stations throughout the freshwater tidal and brackish water regions of the estuary between July and November 2004. Total microcystins in zooplankton and clam tissue was also sampled in August and October. Microcystis cell density, chl a concentration and total microcystins concentration varied by an order of magnitude and peaked during August and September when P B m and a B were high. Low streamflow and high water temperature were strongly correlated with the seasonal variation of Microcystis cell density, total microcystins concentration (cell) -1 and total microcystins concentration (chl a) -1 in canonical correlation analyses. Nutrient concentrations and ratios were of secondary importance in the analysis and may be of lesser importance to seasonal variation of the bloom in this nutrient rich estuary. The seasonal variation of Microcystis density and biomass was potentially important for the structure and function of the estuarine aquatic food web, because total microcystins concentration was high at the base of the food web in mesozooplankton, amphipod, clam, and worm tissue during the peak of the bloom.

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.

Human effects on estuaries are often associated with major decreases in abundance of aquatic species. However, remediation priorities are difficult to identify when declines result from multiple stressors with interacting sublethal effects. The San Francisco Estuary offers a useful case study of the potential role of contaminants in declines of organisms because the waters of its delta chronically violate legal water quality standards; however, direct effects of contaminants on fish species are rarely observed. Lack of direct lethality in the field has prevented consensus that contaminants may be one of the major drivers of coincident but unexplained declines of fishes with differing life histories and habitats (anadromous, brackish, and freshwater). Estuaries and Coasts (2012) 35:603-621 DOI 10.1007/s12237-011-9459-6 indicates that examining the effects of contaminants and other stressors on specific life stages in different seasons and salinity zones of the estuary is critical to identifying how several interacting stressors could contribute to a general syndrome of declines. Moreover, warming water temperatures of the magnitude projected by climate models increase metabolic rates of ectotherms, and can hasten elimination of some contaminants. However, for other pollutants, concurrent increases in respiratory rate or food intake result in higher doses per unit time without changes in the contaminant concentrations in the water. Food limitation and energetic costs of osmoregulating under altered salinities further limit the amount of energy available to fish; this energy must be redirected from growth and reproduction toward pollutant avoidance, enzymatic detoxification, or elimination. Because all of these processes require energy, bioenergetics methods are promising for evaluating effects of sublethal contaminants in the presence of other stressors, and for informing remediation. Predictive models that evaluate the direct and indirect effects of contaminants will be possible when data become available on energetic costs of exposure to contaminants given simultaneous exposure to non-contaminant stressors.

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 9 10 9 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.

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Primary productivity, community respiration, chlorophyll a concentration, phytoplankton species composition, and environmental factors were compared in the Yolo Bypass floodplain and adjacent Sacramento River in order to determine if passage of Sacramento River through floodplain habitat enhanced the quantity and quality of phytoplankton carbon available to the aquatic food web and how primary productivity and phytoplankton species composition in these habitats were affected by environmental conditions during the flood season. Greater net primary productivity of Sacramento River water in the floodplain than the main river channel was associated with more frequent autotrophy and a higher P:R ratio, chlorophyll a concentration, and phytoplankton growth efficiency (a B ). Total irradiance and water temperature in the euphotic zone were positively correlated with net primary productivity in winter and early spring but negatively correlated with net primary productivity in the late spring and early summer in the floodplain. In contrast, net primary productivity was correlated with chlorophyll a concentration and streamflow in the Sacramento River. The flood pulse cycle was important for floodplain production because it facilitated the accumulation of chlorophyll a and wide diameter diatom and green algal cells during the drain phase. High chlorophyll a concentration and diatom and green algal biomass enabled the floodplain to export 14-37% of the combined floodplain plus river load of total, diatom and green algal biomass and wide diameter cells to the estuary downstream, even though it had only 3% of the river streamflow. The study suggested the quantity and quality of riverine phytoplankton biomass available to the aquatic food web could be enhanced by passing river water through a floodplain during the flood season.