Nitrification in nature is a two-step oxidation process of ammonium () or ammonia () to nitrite () and then to nitrate () catalyzed by two ubiquitous bacterial groups growing together. The first reaction is oxidation of ammonium to nitrite by ammonia oxidizing bacteria (AOB) represented by members of
Betaproteobacteria and
Gammaproteobacteria. Further organisms able to oxidize ammonia are
Archaea (
AOA). The second reaction is oxidation of nitrite () to nitrate by nitrite-oxidizing bacteria (NOB), represented by the members of
Nitrospinota,
Nitrospirota,
Pseudomonadota, and
Chloroflexota. This two-step process was described already in 1890 by the Ukrainian
microbiologist Sergei Winogradsky. Ammonia can be also oxidized completely to nitrate by one
comammox bacterium.
Ammonia-to-nitrite mechanism Ammonia oxidation in autotrophic nitrification is a complex process that requires several
enzymes as well as
oxygen as a reactant. The key enzymes necessary for releasing energy during oxidation of ammonia to nitrite are
ammonia monooxygenase (AMO) and
hydroxylamine oxidoreductase (HAO). The first is a transmembrane copper protein which catalyzes the oxidation of ammonia to hydroxylamine () taking two electrons directly from the quinone pool. This reaction requires O2. The second step of this process has recently fallen into question. For the past few decades, the common view was that a trimeric multiheme c-type HAO converts hydroxylamine into nitrite in the periplasm with production of four electrons (). The stream of four electrons is channeled through cytochrome c554 to a membrane-bound cytochrome c552. Two of the electrons are routed back to AMO, where they are used for the oxidation of ammonia (quinol pool). The remaining two electrons are used to generate a proton motive force and reduce NAD(P) through reverse electron transport. Recent results, however, show that HAO does not produce nitrite as a direct product of catalysis. This enzyme instead produces nitric oxide and three electrons. Nitric oxide can then be oxidized by other enzymes (or oxygen) to nitrite. In this paradigm, the electron balance for overall metabolism needs to be reconsidered. proposes a new hypothetical model of NOB electron transport chain and NXR mechanisms. Here, in contrast to earlier models, the NXR would act on the outside of the plasma membrane and directly contribute to a mechanism of proton gradient generation as postulated by Spieck and coworkers. Nevertheless, the molecular mechanism of nitrite oxidation is an open question.
Comammox bacteria The two-step conversion of ammonia to nitrate observed in ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria (such as
Nitrobacter) is puzzling to researchers. Complete nitrification, the conversion of ammonia to nitrate in a single step known as
comammox, has an energy yield (∆G°′) of −349 kJ mol−1 NH3, while the energy yields for the ammonia-oxidation and nitrite-oxidation steps of the observed two-step reaction are −275 kJ mol−1 NH3, and −74 kJ mol−1 NO2−, respectively. These values indicate that it would be energetically favourable for an organism to carry out complete nitrification from ammonia to nitrate (
comammox), rather than conduct only one of the two steps. The evolutionary motivation for a decoupled, two-step nitrification reaction is an area of ongoing research. In 2015, it was discovered that the
species Nitrospira inopinata possesses all the enzymes required for carrying out complete nitrification in one step, suggesting that this reaction does occur.
Table of characteristics == See also ==