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Denitrification is an important microbial process in aquatic ecosystems that can reduce the effects of eutrophication. Here, quantification and pyrosequencing of  nirS ,  nirK , and  nosZ  genes encoding for nitrite and nitrous oxide reductases was performed in sediment samples from four boreal lakes to determine the structure and seasonal stability of denitrifying microbial populations. Sediment quality and nitrate concentrations were linked to the quantity and diversity of denitrification genes, the abundance of denitrifying populations ( nirS  and  nosZ  genes) correlated with coupled nitrification-denitrification (Dn), and the denitrification of the overlying water NO 3  -  (Dw) correlated with the  nirS/nirK  ratio. The number of core  nirS ,  nirK , and  nosZ  operational taxonomical units (OTUs) was low (6, 7, and 3, respectively), and most of these core OTUs were shared among the lakes. Dominant  nirK  sequences matched best with those of the order  Rhizobiales , which was one of the main bacterial orders present in the sediment microbiomes, whereas the dominant  nirS  sequences were affiliated with the order  Burkholderiales . Over half of the  nosZ  sequences belonged to a single OTU of the order  Burkholderiales , but coupled nitrification–denitrification rate correlated with another dominant  nosZ  OTU assigned to the order  Rhodospirillales . The study indicates that a few core proteobacterial clusters may drive denitrification in boreal lake sediments, as the same  Alpha - and  Betaproteobacteria  denitrifier clusters were present in different lakes and seasons.

Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes