The community structure of ammonia-oxidizing bacteria of the beta -subclass Proteobacteria was investigated with respect to environmental gradients along the Schelde, a eutrophic estuary system. A dominance of Nitrosomonas-Like sequences was detected using molecular techniques targeting the 16S rRNA gene on 3 separate sampling dates, and different Nitrosomonas-like populations were most dominant at different locations along the estuary. The most frequently detected ammonia oxidizer-like sequences in the freshwater part of the estuary were associated with a sequence cluster previously designated as Nitrosomonas Cluster 6a. This group, which is closely affiliated with the cultured species N, ureae, has previously been detected as the dominant ammonia-oxidizer group in various freshwater systems, and was also the dominant recovered sequence cluster from a contributory, untreated sewage effluent sample. The 16S rDNA recovered from brackish locations further downstream was dominated by a group of novel Nitrosomonas-like sequences. Nitrosospira-like sequences represented only a small minority of those detected for all samples. The shift in dominant ammonia-oxidizer populations occurred in the estuarine region with the sharpest observed gradients in salinity, oxygen, and ammonia. These results provide evidence in support of the differential selection of physiologically distinct Nitrosomonas-like groups according to the environmental gradients encountered along the estuary
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