Foesel, B.U., Department of Biological Sciences, Microbiology, University of Aarhus, Aarhus, Denmark, Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany, Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Germany
Gieseke, A., Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
Schwermer, C., Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
Stief, P., Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
Koch, L., Volcani Center, Institute for Soil, Water and Environmental Sciences, ARO, Bet-Dagan, Israel
Cytryn, E., Volcani Center, Institute for Soil, Water and Environmental Sciences, ARO, Bet-Dagan, Israel, Faculty of Agricultural, Food and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot, Israel, Department of Soil Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN, United States
De La Torré, J.R., Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
Van Rijn, J., Faculty of Agricultural, Food and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot, Israel
Minz, D., Volcani Center, Institute for Soil, Water and Environmental Sciences, ARO, Bet-Dagan, Israel
Drake, H.L., Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
Schramm, A., Department of Biological Sciences, Microbiology, University of Aarhus, Aarhus, Denmark, Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany, Department of Biological Sciences, University of Aarhus, Building 1540, Ny Munkegade, DK-8000 Aarhus C, Denmark

Zero-discharge marine aquaculture systems are an environmentally friendly alternative to conventional aquaculture. In these systems, water is purified and recycled via microbial biofilters. Here, quantitative data on nitrifier community structure of a trickling filter biofilm associated with a recirculating marine aquaculture system are presented. Repeated rounds of the full-cycle rRNA approach were necessary to optimize DNA extraction and the probe set for FISH to obtain a reliable and comprehensive picture of the ammonia-oxidizing community. Analysis of the ammonia monooxygenase gene (amoA) confirmed the results. The most abundant ammonia-oxidizing bacteria (AOB) were members of the Nitrosomonas sp. Nm143-lineage (6.7% of the bacterial biovolume), followed by Nitrosomonas marina-like AOB (2.2% of the bacterial biovolume). Both were outnumbered by nitrite-oxidizing bacteria of the Nitrospira marina-lineage (15.7% of the bacterial biovolume). Although more than eight other nitrifying populations were detected, including Crenarchaeota closely related to the ammonia-oxidizer 'Nitrosopumilus maritimus', their collective abundance was below 1% of the total biofilm volume; their contribution to nitrification in the biofilter is therefore likely to be negligible. © 2007 Federation of European Microbiological Societies.