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The potentially toxic diatom genus  Pseudo-nitzschia  is a common component of the microalgal assemblage in the northern Gulf of Mexico. We characterized community structure in Mobile Bay and the adjacent littoral Gulf in a bloom year (2005) and non-bloom year (2006). In both cases, a shift from domination by eukaryotes to cyanobacteria was correlated with seasonal changes in temperature, whereas the overall biomass was correlated with total nutrient concentrations down the estuarine salinity gradient. The bloom of  Pseudo-nitzschia  spp .  followed a period of high discharge from local aquifers that are highly contaminated with nitrate. The diatom assemblage in both bloom and non-bloom years was dominated by a suite of 12 common genera that formed three distinct clusters. The first cluster contained a single centric genus and dominated only a small fraction of samples. The second comprised four benthic and tychopelagic genera and was most common inside the shallow waters of Mobile Bay. The third comprised seven planktonic genera, including  Pseudo-nitzschia  spp . , which was most closely associated with two well-described bloom-forming genera,  Chaetoceros  and  Skeletonema . We argue that these occupy a ruderal niche, blooming after peaks in discharge of submarine groundwater along the littoral Gulf of Mexico. The 2005 bloom of  Pseudo-nitzschia  spp .  was toxic, with domoic acid concentrations reaching 8.0 μg L −1  and mean cell toxin quotas reaching 4.9 pg cell −1 . The mean cell toxin quotas were highly correlated ( R  = 0.97) with a multivariate statistic based on environmental data and were maximal at low silicate concentration, high salinity and dissolved inorganic carbon, and high irradiance. The correlations are consistent with photoacclimative status, with toxicity being highest under conditions likely to lead to excess “photon pressure”, an imbalance between generation of photosynthetic reductant and its consumption downstream.

Environmental correlates of community composition and toxicity during a bloom of Pseudo-nitzschia spp. in the northern Gulf of Mexico