Temporal and spatial dynamics within an ammonia-oxidising community from intertidal, freshwater sediments were studied in
microcosms simulating flooding twice a day with fresh, brackish and marine waters. The microcosms had been filled with the upper
5 cm of intertidal freshwater sediment from the river Scheldt. Changes in community composition were examined by denaturing
gradient gel electrophoresis of amplified DNA from the community. In the first week of incubation the initially present members
of the Nitrosomonas oligotropha lineage were replaced by other members of the same lineage in the top layer of the sediment subjected
to flooding with freshwater. Prolonged incubation extended niche differentiation to a depth of 5 cm. In the microcosms
flooded with saline media, the initially present members of the N. oligotropha lineage were replaced by strains belonging to the Nitrosomonas
marina lineage, but only in the top 1 cm. Shift in community composition occurred earlier in the marine microcosms than in
the brackish microcosms and was slower than the change in the freshwater microcosms. Irrespective of the nature of the flooding
medium, shifts in community composition were always consistent among replicate microcosms. We conclude that salinity is an
important steering factor in niche differentiation among ammonia-oxidising bacteria and also that changes within the community
of this functional group of bacteria may occur at different rates
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