We studied controls on nitrification in an undisturbed water-limited ecosystem by inhibiting autotrophic nitrifying bacteria in soils with varying levels of vegetative cover. The activity of nitrifying bacteria was disrupted using nitrapyrin, 2-chloro-6-(trichloromethyl)-pyridine, under field conditions in three microenvironments (underneath shrubs, next to grasses and in bare soil). Ammonia-oxidising bacteria were detected by PCR analysis of DNA in soils. The inhibition of nitrification changed the concentrations of NO 3 2 and NH 4 ĂŸ in the soil, while the microenvironment was most important in determining the response of bacteria to the inhibitor. Nitrapyrin application resulted in a significant Ă°p , 0:05Ă reduction in soil NO 3 2 concentration (39%) and a significant increase Ă°p , 0:001Ă in soil NH 4 ĂŸ concentration (41%). Untreated bare-soil microenvironments had the lowest concentrations of NH 4 ĂŸ (1.57 mg/g of dry soil) and NO 3 2 (0.49 mg/g of dry soil) when compared to the other microenvironments, and showed the highest impacts of nitrification inhibition. For example, NH 4 ĂŸ concentrations increased 288%and NO 3 2 concentrations decreased 60% in inhibited bare-soil microenvironments. In contrast, untreated microenvironments underneath shrubs had the highest levels of NH 4 ĂŸ (10.01 mg/g of dry soil) and NO 3 2 (0.69 mg/g of dry soil), but showed no significant effects of inhibition of nitrification on soil nitrogen concentrations. q