Microorganisms play an important role in coral ecology; however, little is known about cold-water coral (CWC) reefs. Microbial abundance in bottom water of Lophelia pertusa-dominated CWC reefs in the Skagerrak, North Sea, was elevated by ca. 40% for prokaryotes and 70 to 90% for viruses compared to bottom water where no corals were present. This indicates that CWCs influence the microbial food web in bottom water. Furthermore, results suggest that microorganisms contributed significantly to the stock of organic nitrogen (13%) and organic phosphorus (32%) in bottom water. Prokaryotic abundances in the coelenteron of freshly collected corals were (2.0 +/- 0.2) x 10(7) cells ml(-1) and viral abundances were (4.0 +/- 0.6) x 10(7) particles ml(-1). Prokaryotic abundances in coral mucus were (7.5 +/- 0.7) x 10(7) cells ml(-1) and viral abundances were (1.7 +/- 0.3) x 10(8) particles ml(-1). Onboard incubations with elevated prokaryotic and viral abundances in the incubation water indicated that (1) corals accumulate microorganisms in the coelenteron as a potential food source and (2) control mechanisms exist for the abundance of prokaryotic cells and viral particles in the mucus. Our data suggest that L. pertusa controls microbial biomass in the CWC reef environment and coral microhabitats.