Comparative transcriptome analysis of the heterotrophic nitrifying bacterium Alcaligenes faecalis

Alcaligenes faecalis is a heterotrophic nitrifying bacterium that can oxidize ammonia and generates nitrite and nitrate. When A. faecalis was cultivated in a medium containing pyruvate and ammonia as sole carbon and nitrogen sources, respectively, high concentrations of nitrite accumulated in the medium whose carbon/nitrogen (C/N) ratio was lower than 10 during the exponential growth phase, while the accumulation was not observed in the medium whose C/N ratio was higher than 15. Comparative transcriptome analysis was performed using the bacterial cells cultivated under low and high C/N ratio conditions (5 and 20, respectively) for comprehensive evaluation of the fluctuations of the gene expression levels during induction of heterotrophic nitrification. Expression levels of genes involved in a primary metabolism did not change significantly in the cells at the exponential growth phase under both conditions. We observed significant increase of the expression levels of four gene clusters, pod cluster containing the gene encoding pyruvic oxime dioxygenase (POD), podh cluster containing the gene encoding a POD homologous protein, suf cluster involved in the biosynthesis of iron-sulfur centers, and dnf cluster involved in a novel hydroxylamine oxidation pathway. The result demonstrates that the four gene clusters participate in a heterotrophic nitrification.