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test  Biofilms, the rule rather than the exception in many aquatic environments, are a complex milieu of phototrophic and heterotrophic organisms. How environmental factors alter biofilm composition and determine which planktonic microorganisms colonize new surfaces to form biofilms is poorly understood. In aquatic plankton and biofilm communities, heterotrophic bacteria (hereafter bacteria) derive some to all of their organic carbon (C) from the photoautotrophs (hereafter algae) while simultaneously competing for inorganic nutrients such as phosphorus (P). Therefore, C inputs have the potential to alter the ecology of aquatic microbial communities by increasing the resource space available to heterotrophic bacteria (more C) while decreasing the resource space available to algae (less P). We amended a series of flow-through seawater mesocosms with C and P to achieve four target resource C:P levels. We asked if resource amendments altered the size of the biomass pool of bacteria and/or algae in both plankton and biofilm communities. We then used 454 pyrosequencing of bacterial 16S and 23S plastid genes to ask how shifts in the pool size of each community affected community composition and diversity. We saw pronounced differences between the highest carbon treatment and all other treatments. The highest carbon treatment had the lowest planktonic algal abundance yet highest biofilm biomass and highest planktonic bacterial abundance. Resource amendments did not have a significant effect on alpha diversity in either the planktonic or biofilm communities. Rather the biofilm communities consistently had higher alpha diversity than the planktonic communities for any given time point in all mesocosms. Bacterial plankton and biofilm communities were distinct in all but the highest carbon treatment where biofilm and planktonic communities increasingly resembled each other over time. Algal biofilm and plankton communities displayed distinct microbial membership and structure in all treatments including the highest carbon treatment. Our results suggest that broad ecological dynamics (e.g. shifts in dominance between algal and bacterial biomass) driven by shifts in resource availability have important underlying community membership dynamics that alter the interactions and trophic balance of both planktonic and biofilm mirobial communities.