The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers

Abstract

Gene sequence analysis of nirS and nirK, both encoding nitrite reductases, was performed on cultivated denitrifiers to assess their incidence in different bacterial taxa and their taxonomical value. Almost half of the 227 investigated denitrifying strains did not render an nir amplicon with any of five previously described primers. NirK and nirS were found to be prevalent in Alphaproteobacteria and Betaproteobacteria, respectively, nirK was detected in the Firmicutes and Bacteroidetes and nirS and nirK with equal frequency in the Gammaproteobacteria. These observations deviated from the hitherto reported incidence of nir genes in bacterial taxa. NirS gene phylogeny was congruent with the 16S rRNA gene phylogeny on family or genus level, although some strains did group within clusters of other bacterial classes. Phylogenetic nirK gene sequence analysis was incongruent with the 16S rRNA gene phylogeny. NirK sequences were also found to be significantly more similar to nirK sequences from the same habitat than to nirK sequences retrieved from highly related taxa. This study supports the hypothesis that horizontal gene transfer events of denitrification genes have occurred and underlines that denitrification genes should not be linked with organism diversity of denitrifiers in cultivation-independent studies.

Higher diversity and abundance of denitrifying microorganisms in environments than considered previously

“…Previous studies utilized conventional primer sets to analyze nirK and nirS of denitrifiers that belonged primarily to alpha-, beta-, and gamma-proteobacteria from various environmental samples (Braker et al, 2000;Heylen et al, 2006;Smith et al, 2007;Ishii et al, 2011;Palmer et al, 2012). However, our phylogenetic analysis of the available nirK and nirS showed that a greater diversity of microorganisms possess nirK or nirS, including Actinobacteria, Bacteroidetes, Chloroflexi, Nitrospirae, Spirochetes, Planctomycetes, NC10, and even the archaeal phylum Euryarchaeota (Figure 1).…”

Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil

“…However, this did not mean that these nirKharboring denitrifiers belonged to Rhizobiales or Burkholderiales, since the nirK phylogeny was incompatible with the 16S rDNA phylogeny (Heylen et al, 2006;Jones et al, 2008;Philippot et al, 2002;Yoshida et al, 2009). Our results showed that over 80% of NirS clones distributed in clusters I and VI (unknown branch), cluster II (Rhodobacterales).…”

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

“…Major OTUs affiliated with Alphaproteobacterial sequences and were substantially more abundant in cryoturbated peat nirS amplicon libraries than in those from unturbated peat (Figures 4 and 6). nirS-based phylogenies are more congruent with the 16S rRNA-based phylogenies of their hosts than nirK-based phylogenies; thus, the data suggest that uncultured acid-tolerant denitrifiers of the Alphaproteobacteria occur in cryoturbated peat soil (Heylen et al, 2006). Certain nirK harboring acid-tolerant Rhodanobacter strains of the Gammaproteobacteria that are known to be capable of complete denitrification to N 2 at pH 4 were not detected (van den Heuvel et al, 2010).…”

“…NirK and NirS are structurally different but functionally equivalent (Jones et al, 2008). Organisms hosting both types of nitrite reductase are unknown to date (Heylen et al, 2006). The genes coding for the above-named oxidoreductases are commonly used as structural gene markers for the analysis of nitrate reducer and denitrifier communities (Braker et al, 2000;Philippot et al, 2002;Prieme et al, 2002;Rich et al, 2003;Horn et al, 2006;Enwall et al, 2010;Jones and Hallin, 2010;Palmer et al, 2010;Bru et al, 2011).…”