The responses of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to mercury (Hg) stress were investigated through a short-term incubation experiment. Treated with four different concentrations of Hg (CK, Hg25, Hg50, and Hg100, denoting 0, 25, 50, and 100 mg Hg/kg dry soil, respectively), samples were harvested after 3, 7, and 28 day incubation. Results showed that the soil potential nitrification rate (PNR) was significantly inhibited by Hg stress during the incubation. However, lower abundances of AOA (the highest in CK: 9.20 × 10 7 copies/g dry soil; the lowest in Hg50: 2.68 × 10 7 copies/g dry soil) and AOB (the highest in CK: 2.68 × 10 7 copies/g dry soil; the lowest in Hg50: 7.49 × 10 6 copies/g dry soil) were observed only at day 28 of incubation ( P < 0.05). Moreover, only the community structure of soil AOB obviously shifted under Hg stress as seen through DGGE profiles, which revealed that 2–3 distinct AOB bands emerged in the Hg treatments at day 28. In summary, soil PNR might be a very useful parameter to assess acute Hg stress on soil ecosystems, and the community structure of soil AOB might be a realistic biological indicator for the assessment of heavy metal stress on soil ecosystems in the future. [ABSTRACT FROM AUTHOR]