Graf Daniel R H, Jones Christopher M, Hallin Sara
Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
PLoS One. 2014 Dec 1;9(12):e114118. doi: 10.1371/journal.pone.0114118. eCollection 2014.
Nitrous oxide (N2O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O is the nitrous oxide reductase, encoded by the nosZ gene, which is present among bacteria and archaea capable of either complete denitrification or only N2O reduction to di-nitrogen gas. To determine whether the occurrence of nosZ, being a proxy for the trait N2O 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 N2O 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 N2O 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 N2O 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 N2O emissions.
一氧化二氮（N₂O）是一种强效温室气体，也是主要的臭氧层消耗物质。已知唯一能还原N₂O的酶是一氧化二氮还原酶，由nosZ基因编码，该基因存在于能够进行完全反硝化或仅将N₂O还原为氮气的细菌和古菌中。为了确定作为N₂O还原特性指标的nosZ的出现情况在不同分类群、偏好的栖息地或分别由nirK和nirS基因编码具有NirK或NirS亚硝酸还原酶的生物体之间是否存在差异，对18个门的652个微生物基因组进行了比较。此外，还研究了不同共现模式与由nor基因编码的将一氧化氮还原为N₂O的酶之间的关联。我们观察到反硝化基因的共现模式并非在分类群中随机分布，因为在不同分类群中发现特定模式比预期更占主导或不存在。nosZ基因与nirS共现的频率显著高于与nirK共现的频率，nor基因的存在与否在很大程度上解释了这种模式，因为nirS几乎总是与nor共现。这表明在有利的环境条件下，nirS型反硝化菌比nirK型反硝化菌更有可能能够进行完全反硝化，因此对N₂O排放的贡献更小。比较系统发育分析表明nosZ和nirS之间有更大程度的共同进化历史。然而，30%具有nosZ的生物体既不拥有nir基因，其中一些还缺乏nor，这表明它们在N₂O还原中可能具有重要作用。共现模式在偏好的栖息地类别中也不是随机分布的，有几个栖息地在nirS和nirK型反硝化菌的频率上显示出显著差异。这些结果表明反硝化途径具有高度模块化，从而突出了群落结构对N₂O排放的重要性。
