Seventeen sites in Florida Bay were sampled on a monthly basis for 51 months to describe the spatial and temporal patterns of phytoplankton blooms. The study focused on the picoplanktonic cyanobacterium Synechococcus. The greatest frequency and intensity of blooms was observed in the north‐central region of Florida Bay, where cellular biovolumes of this species regularly exceeded 10 × 106μm3 ml−1 and chlorophyll a concentrations were frequently >20 mg m−3. Synechococcus blooms were often restricted to this region of the bay, in part because of the network of shallow mudbanks and islands that restrict water exchange with other regions and outlying waters of the Atlantic Ocean and Gulf of Mexico. The most severe blooms occurred in the summer and fall (May–December). High concentrations of Synechococcus also appeared during the fall in the south‐central region of the bay. The appearance of blooms in this region coincided with the onset of seasonal cold fronts, whose strong northerly and northwesterly winds appear to drive bloom‐laden water from the north‐central region into adjacent parts of the bay. A number of physical and chemical factors appear to contribute to the remarkably high phytoplankton biovolumes observed in the north‐central region of Florida Bay. Physical factors include the shallowness and hydrological isolation of the region. The dominance of Synechococcus in the center of the bay may be attributable to several of the unique physicochemical characteristics of this species, including its small size, cyanobacterial metabolism, euryhaline character, buoyancy, and tolerance to high light intensity.

1. Variations in the relative biovolumes of dominant cyanobacterial taxa were evaluated in the context of environmental conditions using canonical correlation analysis (CCorrA) and Redundancy Analysis (RDA). The objective was to test a conceptual model in which underwater irradiance determines dominance by bloom‐forming (high light adapted) or non‐blooming (low light adapted) taxa. 2. The data set consisted of 404 contiguous observations, collected over a 3‐year period at eight pelagic sites, in shallow Lake Okeechobee, Florida, U.S.A. Data included species biovolumes, total phosphorus (TP), total nitrogen (TN), dissolved oxygen (DO) and chlorophyll a concentrations, as well as two indices: underwater irradiance (Secchi depth) and the ratio of Secchi:total depth. 3. The first environmental canonical variable was strongly correlated with the two light‐related indices, and negatively correlated with TP. This reflects the predominant role of resuspended P‐rich lake sediments in controlling underwater irradiance in the shallow lake. The first species canonical variable displayed a strong negative correlation with Lyngbya limnetica and L. contorta, and positive correlations with Anabaena circinalis, Aphanizomenon flos aquae and Microcystis spp. The results support the conceptual model; the first pair of canonical variables explained 55% of the variation in the species–environmental data set. RDA results provided further support for the hypothesis that irradiance was the major force controlling community structure. 4. One unexpected result was a positive association between Oscillatoria spp. dominance and indicators of high irradiance. This conflicts with past research indicating that Oscillatoria is a low light adapted taxon, and the finding that it is the most abundant taxon in Lake Okeechobee. This may reflect the fact that the two Lyngbya taxa were more strongly associated with low light conditions than Oscillatoria. CCorrA results indicated that Oscillatoria densities are strongly controlled by water temperature. There is a need for more detailed studies of cyanobacteria ecophysiology in order to explain fully the seasonality of phytoplankton in this and other shallow subtropical lakes.

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Over the last half of the 20th century Pyrodinium bahamense var. bahamense has been observed in a variety of locations in the western North Atlantic. Recent evidence of the toxinproducing capacity of this variety of P. bahamense has heightened interest in its habitat requirements and preferences. The objective of this study was to examine the environmental factors that relate to the spatial and temporal patterns of the distribution and abundance of P. bahamense var. bahamense. Based on the results of this study we view the factors as operating in one or more ways: (1) ecophysiological limitations for survival and successful reproductive cycle, (2) environmental regulation of growth and standing crop, and (3) competitive advantages in relation to other species. The focus of the study was the Florida peninsula, but information from other environments in the tropical Atlantic and Gulf of Mexico was included in the interpretation of the results. In terms of physiological limitations, 20°C appears to be the lower temperature limit for a significant presence of P. bahamense var. bahamense, and the salinity tolerance ranged from 10 to 45. The bloom potential of P. bahamense var. bahamense was most closely associated with shallow ecosystems with long water residence times, and peak biomass levels were correlated to nutrient concentrations in regions of high abundance. The ability of P. bahamense var. bahamense to compete effectively for habitat with other euryhaline warm-water phytoplankton is viewed in terms of existing theories on succession and competition, including Margalef's Mandala, Reynolds' Intaglio and C-S-R life-form strategies proposed by Smayda & Reynolds.

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