Emerging interactions are key determinants of system productivity and efficiency in plant and animal communities, whereas their importance for planktonic microbial assemblages is unknown. We studied the relationship between two aquatic bacterial strains and a protistan predator with respect to cooperation and system efficiency. While competitive exclusion of one bacterial strain was observed in grazer-free cocultures, the presence of the predator induced the formation of large coaggregates and allowed a coexistence of both strains. The aggregates moreover provided a substrate for attachment of the predators. The interactions in the more complex community, i.e., microbial flocs composed by both bacterial strains and predators, led to a significantly increased transfer efficiency of dissolved organic matter to the higher trophic level than in systems with two species only. Similar emerging interactions might also play a role in complex microbial assemblages in natural aquatic systems, i.e., on suspended organic aggregates.