Ammonia oxidizing prokaryotes play key role in the first and rate-limiting step of nitrification. However, the environmental factor shaping their community is largely unknown. In this study, we investigated the influence of salinity and ammonium levels on ammonia oxidizing bacteria (AOB) and archaea (AOA) by monitoring their amo subunit A (amoA) messenger RNA (mRNA) expression. The aerobic mini-continuous stirred-tank reactors (mini-CSTRs) were operated for 48 hours under different salinity or

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... mmonium levels. Archaeal and bacterial amoA mRNA levels were quantified using real-time reverse transcription polymerase chain reaction. To investigate the differential transcriptional responses among AOA species, terminal restriction fragment length polymorphism (T-RFLP) analysis was performed. Both of high salinity and ammonium levels repressed archaeal amoA mRNA expressions, while only high salinity level repressed bacterial mRNA expression. T-RFLP results implied that the influence of salinity and ammonium levels were different among AOA species. Thus, the combination of the short-term mini-CSTRs operations and amoA mRNA-based analyses showed the influence of environmental factors on competition between AOA and AOB and also AOA community structure.