| Summary: | Links between nitrification rates and betaproteobacterial ammonia oxidising bacteria (AOB) community structure in estuarine sediments were determined in relation to changes in salinity and substrate concentrations associated with these environments. Sediment was collected from the upper, middle and lower reaches of the estuary and incubated with water amended with either a range of salinities from marine to freshwater, or a range of ammonia concentrations. Ammonia consumption, nitrate and nitrite production were measured at regular intervals as an indicator of nitrification rates and 16S rRNA gene-targeted analysis of betaproteobacterial AOB community structure was carried out by denaturing gradient gel electrophoresis of amplified genes from original sediment, at the beginning of nitrate production, and after a period of incubation. Salinity and ammonia concentrations were shown to influence both nitrification rates and betaproteobacterial AOB community structure in estuarine sediments, in particular increased ammonia concentrations lead to increased nitrification regardless of the origin of the sediment. A shift in the dominant betaproteobacterial AOB community structure was observed in microcosms with both salinity and ammonia treatments, but particular treatments did not lead to the selection of a common community structure. Members of the <i>Nitrosomonas </i>cluster 5 were selected for in most sediments and treatments, regardless of salinity and ammonia treatments, while others, such as members of the <i>Nitrosospira</i>-lineage cluster 1 group, were restricted to low ammonia microcosms. This study indicates that community members are capable of functioning at a wide range of estuarine salinity and ammonia conditions but that these are eventually replaced by community members better suited to these conditions.
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