Fact and Fiction of Nitrous Oxide Production By Nitrification

Abstract:

An accepted dogma in nitrification research is that ammonia-oxidizing bacteria (AOB) produce a modicum of nitrous oxide (N2O) during nitritation via incomplete oxidation of hydroxylamine, and substantially more at low oxygen concentrations via nitrifier denitrification.The nitrifier denitrification pathway involves the reduction of nitrite to N2O via nitric oxide and was thought to require activities of a copper-containing nitrite reductase (NirK) and nitric oxide reductase (NorB); inventory encoded in most, but not all AOB genome sequences. The discovery of nirK genes in ammonia-oxidizing Thaumarchaeota (AOA) resulted in a slew of publications stating that AOA must also perform nitrifier denitrification and, due to their high abundance, must control the majority of nitrification-linked N2O emissions. Prior to a publication by Stieglmeier et al. (2014), which definitively showed a lack of nitrifier denitrification by two axenic AOA cultures, other researchers relied on enrichment cultures, negative data, and heavy inferencing without direct demonstration of either a functional pathway or involvement of specific genes or enzymes. AOA genomes lack recognizable nitric oxide reductases and thermophilic AOA also lack nirK genes. Physiological and microrespirometry experiments with axenic AOB and AOA cultures allowed us to demonstrate that: 1) AOB produce N2O via nitrifier denitrification even though some lack annotated nirK and/or norB genes; 2) nitrifier denitrification by AOB is reliant on nitric oxide but ammonia oxidation is not; 3) ammonia oxidation by AOA is reliant on production of nitric oxide; 4) AOA are incapable of generating N2O via nitrifier denitrification; 5) N2O production by AOA is from chemical interactions between NO and media components, most likely not by enzyme activity. Our results reveal operation of different N oxide transformation pathways in AOB and AOA governed by different environmental controls and involving different mechanisms of N2O production. Critical controls on these mechanisms are levels of oxygen and ammonium. Future calculations of relative contributions of AOB and AOA to N2O emissions must take into account physiological, enzymatic, and environmental differences between these two nitrifying microorganisms.