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Nitrous oxide (N 2 O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N 2 O is the nitrous oxide reductase, encoded by the  nosZ  gene, which is present among bacteria and archaea capable of either complete denitrification or only N 2 O reduction to di-nitrogen gas. To determine whether the occurrence of  nosZ , being a proxy for the trait N 2 O reduction, differed among taxonomic groups, preferred habitats or organisms having either NirK or NirS nitrite reductases encoded by the  nirK  and  nirS  genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, the association of different co-occurrence patterns with enzymes reducing nitric oxide to N 2 O encoded by  nor  genes was examined. We observed that co-occurrence patterns of denitrification genes were not randomly distributed across taxa, as specific patterns were found to be more dominant or absent than expected within different taxonomic groups. The  nosZ  gene had a significantly higher frequency of co-occurrence with  nirS  than with  nirK and  the presence or absence of a  nor  gene largely explained this pattern, as  nirS  almost always co-occurred with  nor . This suggests that  nirS  type denitrifiers are more likely to be capable of complete denitrification and thus contribute less to N 2 O emissions than  nirK  type denitrifiers under favorable environmental conditions .  Comparative phylogenetic analysis indicated a greater degree of shared evolutionary history between  nosZ  and  nirS.  However 30% of the organisms with  nosZ  did not possess either  nir  gene, with several of these also lacking  nor , suggesting a potentially important role in N 2 O reduction. Co-occurrence patterns were also non-randomly distributed amongst preferred habitat categories, with several habitats showing significant differences in the frequencies of  nirS  and  nirK  type denitrifiers. These results demonstrate that the denitrification pathway is highly modular, thus underpinning the importance of community structure for N 2 O emissions.

Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions