Ammonia-oxidizing bacteria were detected by PCR amplification of DNA extracted from filtered water samples throughout the water column of Mono Lake, California. Ammonia-oxidizing members of the  subdivision of the division Proteobacteria (-subdivision Proteobacteria) were detected using previously characterized PCR primers; target sequences were detected by direct amplification in both surface water and below the chemocline. Denaturing gradient gel electrophoresis analysis indicated the presence of at least four different -subdivision ammonia oxidizers in some samples. Subsequent sequencing of amplified 16S rDNA fragments verified the presence of sequences very similar to those of cultured Nitrosomonas strains. Two separate analyses, carried out under different conditions (different reagents, locations, PCR machines, sequencers, etc.), 2 years apart, detected similar ranges of sequence diversity in these samples. It seems likely that the physiological diversity of nitrifiers exceeds the diversity of their ribosomal sequences and that these sequences represent members of the Nitrosomonas europaea group that are acclimated to alkaline, high-salinity environments. Primers specific for Nitrosococcus oceanus, a marine ammonia-oxidizing bacterium in the ␥ subdivision of the Proteobacteria, did not amplify target from any samples.Mono Lake is an alkaline, hypersaline, closed-basin lake in central California just east of the Sierra Nevada Mountains (38°N, 119°W). Exceptionally heavy rainfall in 1982 and 1983 caused a freshening of the surface layer; the resulting largedensity difference between surface and deep waters caused the lake to become ectogenically meromictic (15, 18). The lake became stratified with a chemocline in the vicinity of 15 m (total depth, approximately 30 m) and did not turn over or mix thoroughly until 1988. In the interval, the difference in salinity between the deep water and surface layer gradually decreased (15), due to evaporation and removal of surface water to supply drinking water to southern California. After 1988, the lake resumed its normal pattern of annual winter holomixis (15).The seasonal density stratification leads to stratification in oxygen and other parameters, such as nitrogenous nutrients (16), and this stratification is expected to be reflected in the depth distribution of microbial activities. Both ammonium and methane accumulate in the deep layer (25); the major biological sinks for these compounds are thought to be oxidation by obligately aerobic chemolithotrophic bacteria in the surface layer and, for methane, anaerobic oxidation in the deep layer. The depth distributions of methane and ammonia oxidation, measured by radiotracer experiments, were previously reported (19).Ammonia-oxidizing bacteria are responsible for the oxidation of ammonia to nitrite, the first step in nitrification, in terrestrial and aquatic habitats of all kinds and are found in the  and ␥ subdivisions of the division Proteobacteria. The number of species of ammonia oxidizers that have been descr...