Alternative Bioenergy: Updates to and Challenges in Nitrification Metalloenzymology

Biological ammonia (NH3) oxidation to nitrate (NO3-)-nitrification-is a critical pathway of the biogeochemical nitrogen cycle. Additional products and by-products of this pathway include nitrite (NO2), nitric oxide (NO), nitrous oxide (N-2(-)), and nitrogen dioxide (NO2), several of which are pollutants. How these species are generated during nitrification is not entirely clear, but pathways toward their generation have drawn substantial research effort. The cumulative evidence shows several parallel biological pathways comprising the net nitrification process. Bacteria were long thought to mediate all nitrification transformations; however, archaeal nitrifiers are now recognized. Furthermore, nitrification was thought to require two distinct microbial classes: NH3 oxidizers to oxidize NH3 to NO2-, and NO2 oxidizers that oxidize NO2 to NO(3)Comammox bacteria, which effect complete oxidation of NH3 to NO3, were recently discovered. This Perspective summarizes the current understanding of nitrification biochemistry and highlights exciting opportunities for future research.