Data from: Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers

Background: Copper dependent nitrite reductase, NirK, catalyses the key
step in denitrification, i.e. nitrite reduction to nitric oxide. Distinct
structural NirK classes and phylogenetic clades of NirK-type denitrifiers
have previously been observed based on a limited set of NirK sequences,
however, their environmental distribution or ecological strategies are
currently unknown. In addition, environmental nirK-type denitrifiers are
currently underestimated in PCR-dependent surveys due to primer coverage
limitations that can be attributed to their broad taxonomic diversity and
enormous nirK sequence divergence. Therefore, we revisited reported
analyses on partial NirK sequences using a taxonomically diverse,
full-length NirK sequence dataset. Results: Division of NirK sequences
into two phylogenetically distinct clades was confirmed, with Clade I
mainly comprising Alphaproteobacteria (plus some Gamma- and
Betaproteobacteria) and Clade II harbouring more diverse taxonomic groups
like Archaea, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae,
Firmicutes, Actinobacteria, Planctomycetes and Proteobacteria (mainly Beta
and Gamma). Failure of currently available primer sets to target diverse
NirK-type denitrifiers in environmental surveys could be attributed to
mismatches over the whole length of the primer binding regions including
the 3′ site, with Clade II sequences containing higher sequence divergence
than Clade I sequences. Simultaneous presence of both the denitrification
and DNRA pathway could be observed in 67 % of all NirK-type denitrifiers.
Conclusion: The previously reported division of NirK into two distinct
phylogenetic clades was confirmed using a taxonomically diverse set of
full-length NirK sequences. Enormous sequence divergence of nirK gene
sequences, probably due to variable nirK evolutionary trajectories, will
remain an issue for covering diverse NirK-type denitrifiers in
amplicon-based environmental surveys. The potential of a single organism
to partition nitrate to either denitrification or dissimilatory nitrate
reduction to ammonium appeared to be more widespread than originally
anticipated as more than half of all NirK-type denitrifiers were shown to
contain both pathways in their genome.