Nitrosomonas europaea (ATCC 19718) is one of several nitrifying species that participate in the biological removal of nitrogen front wastewater by oxidizing ammonia to nitrite, the first step in nitrification. Because nitrification is quite sensitive to cyanide, it compound often encountered in wastewater treatment plants, we characterized the physiological and transcriptional responses of N. europaea cells to cyanide. The cells were extremely sensitive to low concentrations of cyanide, with NO, production and ammonia-dependent oxygen uptake rates decreasing by 50% within 30 min of exposure to 1 mu M NaCN. Whole-genome transcriptional responses of cells exposed to 1 mu M NaCN were examined using Affymetrix microarrays to identify stress-induced genes. The transcript levels of 35 genes increased more than 2-fold while transcript levels of 29 genes decreased more than 20-fold. A gene Cluster that included mocZ (NE2353), encoding it rhodanese homologue and thought to be involved in detoxification of cyanide, showed the highest up-regulation (7-fold). The down-regulated genes included genes encoding proteins involved in the sulfate reduction pathway, signal transduction mechanisms, carbohydrate transport, energy production, coenzyme metabolism, and amino acid transport.