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Summary: The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations. [ABSTRACT FROM AUTHOR]

Phytoplankton influence the composition of bacterial communities, but the taxonomic specificity of algal-bacterial interactions is unclear due to the aggregation of ecologically distinct bacterial populations by community characterization methods. Here we examine whether phytoplankton seasonal succession affects the composition of subtypes within the cosmopolitan freshwater bacterial genus P olynucleobacter. Changes in the composition of P olynucleobacter subtypes were characterized in samples collected weekly from May to August in 2003 and 2008 from three humic lakes using terminal restriction fragment length polymorphism fingerprinting of the protein-encoding cytochrome c oxidase cco N gene. Changes in phytoplankton population abundances explained, on average, 30% of temporal variation in the composition of P olynucleobacter subtypes and the interaction between phytoplankton and the environment explained an additional 18% of temporal variation. The effect of phytoplankton on specific P olynucleobacter subtypes was experimentally confirmed by changes in P olynucleobacter subtype composition following incubation with different phytoplankton assemblages or a no-phytoplankton control. Phytoplankton-associated subtypes and differentiation in substrate use among subtypes likely contribute to the effects of phytoplankton on P olynucleobacter subtype composition. Interactions between unique P olynucleobacter populations and phytoplankton highlight the ecological significance and specificity of species interactions in freshwater communities. [ABSTRACT FROM AUTHOR]

Shifts in the composition of dissolved organic matter ( DOM) may be a principal factor effecting changes in bacterial community composition. Emerald Lake, a high-elevation lake with DOM dominated by terrestrial sources in the spring with increasing phytoplankton-derived inputs throughout the ice-free season, provided a natural experiment with which to investigate the importance of resource-mediated drivers. Glycolate-utilizing bacteria, a subset of the bacterial community able to use algal exudates, were characterized using DNA analysis of glycolate oxidase subunit D ( glcD) genes from Emerald Lake samples collected approximately biweekly from ice-cover ( June) through fall turnover ( September). glcD genes were not detected in early-season samples when the lake was ice-covered and phytoplankton-derived resources were scarce. Following this period, glcD gene composition exhibited significant changes through time, which were strongly correlated with the combination of fluorescence index, an indicator of the proportion of lake vs. terrestrially derived DOM, and dissolved inorganic nitrate + nitrite. These results suggest that seasonal shifts in DOM source and environmental variables that affect the composition of algal-derived dissolved resources drive changes in the relative abundance and composition of putative glycolate-utilizing bacteria. These findings strengthen the evidence for shifts in DOM structuring bacterial communities. [ABSTRACT FROM AUTHOR]