Abstract
Summary 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 M ay to A ugust 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.