The overall goal of this study was to determine the molecular and metabolic responses of chemostat cultures of model nitrifying bacteria to imposition of and recovery from transient anoxic conditions. Based on the study, a specific directionality in nitrous oxide (N(2)O) and nitric oxide (NO) production was demonstrated. N(2)O production was only observed during recovery to aerobic conditions after a period of anoxia and correlated positively with the degree of ammonia accumulation during anoxia. NO, on the other hand, was emitted mainly under anoxia. The production of NO was linked to a major imbalance in the expression of the nitrite reductase gene, which was overexpressed during transient anoxia. In contrast, genes coding for ammonia and hydroxylamine oxidation and nitric oxide reduction were generally under-expressed during transient anoxia. These results are different from the observed parallel expression and activity of nitrite and nitric oxide reductase in heterotrophic bacteria subjected to transient oxygen cycling. Unlike NO, the production of N(2)O could not be solely correlated to gene expression patterns and likely involved responses at the enzyme activity or metabolic levels. Based on experimental data, the propensity of the nitrifying cultures for N(2)O production is related to a shift in their metabolism from a low specific activity (q < q(max)) toward the maximum specific activity (q(max)).