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As part of a larger investigation, the effect of apex predation on estuarine bacterial community structure, through trophic cascading, was investigated using experimental in situ mesocosms. Through either the removal (filtration) or addition of specific size classes of planktonic groups, four different trophic scenarios were established using estuarine water and its associated plankton. One such treatment represented a "natural" scenario in which stable apex predatory pressure was qualified. Water samples were collected over time from each of the treatments for bacterial community evaluation. These samples were assessed through pyrosequencing of the variable regions 4 and 5 of the bacterial 16S rRNA gene and analysed at the species operational taxonomic unit (OTU) level using a community procedure. The blue-green group dominated the samples, followed by Proteobacteria and Bacteroidetes. Samples were the most similar among treatments at the commencement of the experiment. While the bacterial communities sampled within each treatment changed over time, the deviation from initial appeared to be linked to the treatment trophic scenarios. The least temporal deviation-from-initial in bacterial community was found within the stable apex predatory pressure treatment. These findings are consistent with trophic cascade theory, whereby predators mediate interactions at multiple lower trophic levels with consequent repercussions for diversity.