The enzymatic reactions that occur during nitrification are nature’s means to use ammonia as cellular fuel. Complete understanding of nitrification and related processes are vital to sustainable agriculture and renewable energy technologies."

Source : Proc Natl Acad Sci U S A. 114(31): 8217–8222

The bacterial nitrification process is a constant and ubiquitous natural phenomenon which breaks down ammonia (from animal waste etc) into chemicals vital for plant growth. Until 2013, it was widely believed to be fully explained - but is now in question again.

The paper cited above, for example, describes a previously overlooked step - involving nitric oxide - in the process. The enzymes involved in the nitric oxide step are presently unknown, as is a complete description of the chemistry involved.

The prevailing view of the first phase of nitrification is that ammonia oxidizing bacteria use two enzymes, ammonia monooxygenase and hydroxylamine oxidoreductase, to oxidize ammonia to nitrite via hydroxylamine as an obligate intermediate. Our work reveals nitric oxide as an additional obligate intermediate.
The presented findings necessitate revision of a key biogeochemical process, identify a new bioenergetic role for nitric oxide, predict participation of a third enzyme in the biological oxidation of ammonia to nitrite, and will inform models toward sustainable agriculture.

[source as above]

The molecular mechanism of nitrite oxidation therefore remains an open question.