As in the case of nirS, the nirK gene was amplified
from activated sludge and peat with the majority of the
primer combinations (Table 1). It was more difficult
with the soil samples. Only primer combinations
F1aCu:R3Cu and nirK1F:nirK5R amplified all environmental
samples. Both of these sets generate amplicons
of almost the right size for DGGE, but we chose to
use the F1aCu:R3Cu set because it yields an amplicon
that is ca. 40 bp shorter and less than 500 bp. Moreover,
the results from PCR with the strains were better and
the three base insert in the primer site of nirK1F is
avoided.
I.N. Throb€ack et al. / FEMS Microbiology Ecology 49 (2004) 401–417 409
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