Applied and Environmental Microbiology, May 2001, p. 2213-2221, Vol. 67, No. 5
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.5.2213-2221.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Department of Geosciences, Princeton University, Princeton, New Jersey 08544
Received 6 September 2000/Accepted 20 February 2001
The presence of a copper-containing dissimilatory nitrite reductase
gene (nirK) was discovered in several isolates of
-subdivision ammonia-oxidizing bacteria using PCR and DNA
sequencing. PCR primers Cunir3 and Cunir4 were designed based on
published nirK sequences from denitrifying bacteria and
used to amplify a 540-bp fragment of the nirK gene from
Nitrosomonas marina and five additional isolates of
ammonia-oxidizing bacteria. Amplification products of the expected size
were cloned and sequenced. Alignment of the nucleic acid and deduced
amino acid (AA) sequences shows significant similarity (62 to 75% DNA,
58 to 76% AA) between nitrite reductases present in these nitrifiers
and the copper-containing nitrite reductase found in classic
heterotrophic denitrifiers. While the presence of a nitrite reductase
in Nitrosomonas europaea is known from early biochemical
work, preliminary sequence data from its genome indicate a rather low
similarity to the denitrifier nirKs. Phylogenetic analysis
of the partial nitrifier nirK sequences indicates 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
sequences from ammonia-oxidizing bacteria.
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