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Investigating the spring bloom in San Francisco Bay: Links between water chemistry, metal cycling, mercury speciation, and phytoplankton community composition This dissertation addresses the relationship between two problems facing estuaries nationwide: nutrient enrichment and metal contamination. The focus is on the southern reach of San Francisco Bay, where high nutrient concentrations can control the magnitude of the predictably occurring spring phytoplankton bloom. The bloom in this study, in spring 2003, was one of the largest blooms on record, exceeding 150 μg L -1 of chlorophyll α. As the bloom grew, diatoms (e.g. Thalassiosira punctigera ) depleted dissolved nutrients from the water column, including the silicate required for their frustules. Along with nutrients, the bloom depleted dissolved Mn, Ni, Pb, and methyl mercury (MeHg). That depletion was statistically significant when the water chemistry data were reduced into three factors by principal component analysis, and the effect of those factors on trace metal concentrations was examined. Algal uptake of trace metals could entrain those metals within the estuary and affect their bioavailability to higher trophic levels through bloom dilution. Consistent with bloom dilution, we calculated that McHg concentrations in phytoplankton decreased when the bloom peaked. However, that decrease was a transient event, caused by depletion of McHg from the water column. Concentrations of McHg and other dissolved metals returned to pre-bloom values, and even exceeded those values, as phytoplankton decayed. The decomposition of phytoplankton presumably caused suboxic conditions in surficial sediments and led to release of trace metals from historically contaminated sediments. Because sediments contain large reservoirs of metals, the most important impact of the recently observed increase in algal biomass in the estuary could be release of metals from sediments during algal decomposition. As the diatoms decayed following nutrient depletion, small phytoplankton (e.g., Synechocystis sp. ) increased. Statistical analyses (multidimensional scaling) found significant spatial and temporal differences in phytoplankton communities. Those community patterns were linked to water temperature and dissolved ammonium concentrations, demonstrating the myriad effects of nutrient enrichment in this system. However, algal community composition was not related to dissolved metal concentrations. This research shows that nutrient enrichment affects the magnitude of the bloom and thereby alters metal cycling, but the relationship is unidirectional because metals do not shape algal community composition.