Molecular analysis of ammonia oxidation and denitrification in natural environments

This review summarizes aspects of the curl ent knowledge about the ecology of ammonia-oxidizing and denitrifying bacteria. The development of molecula r techniques has contributed enormously to the rapid recent progress in the field. Different techniques for doing so ale discussed. The characterizati on of ammonia-oxidizing and -denitrifying bacteria by sequencing the genes encoding 16S rRNA and functional proteins opened the possibility of constru cting specific probes. II is now possible to monitor the occurrence of a pa rticular species of these bacteria in any habitat and to get an estimate of the relative abundance of different types, even if they are not culturable as yet. These data indicate that the composition of nitrifying and denitri fying communities is complex and apparently subject to large fluctuations, both in time and in space. More attempts are needed to enrich and isolate t hose bacteria which dominate the processes, and to characterize them by a c ombination of physiological, biochemical and molecular techniques. While PC R and probing with nucleotides or antibodies are primarily used to study th e structure of nitrifying and denitrifying communities, studies of their fu nction in natural habitats, which require quantification at the transcripti onal level, are currently not possible. (C) 2000 Federation of European Mic robiological Societies. Published by Elsevier Science B.V. All rights reser ved.