Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria

The presence of a copper-containing dissimilatory nitrite reductase gene (n irK) was discovered in several isolates of P-subdivision ammonia-oxidizing bacteria using PCR and DNA sequencing. PCR primers Cunir3 and Cunir4 were d esigned based on published nirK sequences from denitrifying bacteria and us ed to amplify a 540-bp fragment of the nirK gene from Nitrosomonas marina a nd five additional isolates of ammonia-oxidizing bacteria. Amplification pr oducts of the expected size were cloned and sequenced. Alignment of the nuc leic acid and deduced amino acid (AA) sequences shows significant similarit y (62 to 75% DNA, 58 to 76% AA) between nitrite reductases present in these nitrifiers and the copper-containing nitrite reductase found in classic he terotrophic denitrifiers. While the presence of a nitrite reductase in Nitr osomonas europaea is known from early biochemical work preliminary sequence data from its genome indicate a rather low similarity to the denitrifier n irKs. Phylogenetic analysis of the partial nitrifier nirK sequences indicat es that the topology of the nirK tree corresponds to the 16S rRNA and amoA trees. While the role of nitrite reduction in the metabolism of nitrifying bacteria is still uncertain, these data show that the nirK gene is present in closely related nitrifying isolates from many oceanographic regions and suggest that nirK sequences retrieved from the environment may include sequ ences from ammonia-oxidizing bacteria.