Nitrifying Microorganisms

Ammonia-Oxidizing Bacteria

Nitrification is performed by two functionally defined groups of microbes, referred to together as nitrifiers. The first group of nitrifiers is the ammonia oxidizers, which oxidize ammonia to nitrite. In most natural waters, ammonium is present predominantly as the positively charged ion, ammonium (NH|), but the enzyme responsible for the first step of the reaction uses the gaseous form, NH3, which is usually a minor component at equilibrium. We shall use the term ammonium when we are mainly concerned with the form that is important in the environment, and ammonia when referring to the enzymatic oxidation process of the specific substrate. There are two very different groups of ammonia-oxidizing microbes. One is the well-known bacterial group (ammonia-oxidizing bacteria, AOB), which includes a few different kinds of bacteria that all make a living by generating reducing power (ATP) from the oxidation of ammonia and using that energy to fix carbon dioxide. They are generally considered to be obligate autotrophs, that is, they are unable to utilize or grow on organic carbon to any important extent, and can grow only by fixing their own CO2 using the Calvin cycle. Ammonia is their only energy source, and their main metabolic product is nitrite. Conventional AOB have been cultivated for over 100 years and their description played an important role in the discovery and early research on chemoautotrophy.

Ammonia-Oxidizing Archaea

A second distinct group of ammonia-oxidizing microbes has only recently been recognized and brought into culture only in 2005, and these are not bacteria, but archaea (ammonia-oxidizing archaea, AOA). Little is known about their cellular metabolism, but they appear to use a very similar pathway for ammonia oxidation and they are capable of autotrophic growth, although the pathway used for CO2 fixation is not clear. In addition, is it suspected that the AOA are not obligate autotrophs, rather it seems likely that they are capable of heterotrophic growth at the expense of organic compounds. Much research remains to be done on this group.

Aerobic ammonia oxidation proceeds by the following stoichiometry:

In addition to the net production of nitrite by the above equation, AOB are also capable of producing nitrous oxide (N2O). The mechanism by which the N2O is produced has not been completely elucidated, but most AOB investigated to date possess the genes and enzymes necessary for the partial denitrification pathway that reduces nitrite to nitric oxide (NO) and then to N2O. The genes involved are homologous to those found in denitrifiers, and the process is often referred to as nitrifier denitrifica-tion. The result is the production of N2O, whereas complete denitrification by the usual denitrifying bacteria produces N2O only as a transient intermediate. The proportion of ammonia that is released as N2O during nitrification increases at low oxygen concentrations, implying that nitrifiers use this pathway for anaerobic respiration, just as in denitrifiers. It is not currently known whether AOA are capable of nitrifier denitrification or whether they produce N2O, but this will be an important point to consider in determining the role of AOA in the ocean's biogeochemistry.

Anammox Organisms

A third group of bacteria, members of the Planctomyces phylum, are capable of oxidizing ammonium using nitrite instead of oxygen and producing N2 instead of nitrite. This metabolism is strictly anoxic and the process is known as anaerobic ammonia oxidation, or anammox. Anammox organisms are unique in a number of ways; the pathway for oxidation of ammonium is not very similar to that found in AOB or AOA. Hydrazine, more commonly associated with rocket fuel than with biological systems, is an intermediate, while hydroxylamine, an intermediate in AOB and AOA, is apparently not involved in anammox. Anammox organisms are strict autotrophs, and apparently use the acetyl-CoA pathway for CO2 fixation. Their growth is extremely slow, with generation times on the order of 2 weeks. The cells contain an internal membrane-bound 'organelle' called the anammoxazome, in which the anammox reaction is localized. The cell membranes contain unique lipids called ladderanes, after their diagrammatic appearance as a ladder, which is assumed to lend the cell the strength needed to handle hydrazine as an intermediate. The net reaction for anammox involves a 1:1 combination of ammonium and nitrite in the production of N2.

Thus, unlike conventional nitrification, anammox results in the loss of fixed nitrogen from the system, and is ecologically equivalent to denitrification, rather than to nitrification. Anammox results in the anaerobic removal of ammonium using nitrite, derived from either aerobic ammonium oxidation or partial denitrification, as the oxidant.

Nitrite-Oxidizing Bacteria

The second functionally defined group of nitrifying microbes is the nitrite-oxidizing bacteria (NOB), which include several genera. The best-known cultivated members are chemolithoautotrophic, like the AOBs, using nitrite as an energy source and CO2 as a carbon source via the Calvin cycle. Many strains are known to possess heterotrophic capabilities and are considered mixotrophic or facultative autotrophs. Although they have limited metabolic capabilities for uptake and degradation of organic molecules, they can supplement their growth with organic carbon and, in some cases, grow slowly in the absence of nitrite when certain organic substrates are present. The oxidation of nitrite is even less energy yielding than ammonia oxidation, so perhaps this ability for heterotrophic growth is not surprising. Aerobic nitrite oxidation proceeds by the following stoichiometry:

There are no other pathways, nor any different kinds of bacteria or archaea known to be capable of or involved in nitrite oxidation in the environment. The recent finding of greater diversity among ammonia-oxidizing microbes begs the question, however, of whether additional nitrite oxidation pathways and organisms remain to be discovered.

Heterotrophic Nitrifiers

The ability to nitrify, via pathways involving the inorganic transformations normally associated with the autotrophic nitrifiers described above, or via pathways involving organic intermediates but resulting in the net oxidation of ammonium, has been attributed to some heterotrophic bacteria and fungi. Heterotrophic nitrification does not conserve energy (i.e., is not linked to ATP production) and the rates observed are much slower than rates found in cultivated conventional nitrifiers. Autotrophic nitrifiers are susceptible to inhibition by a number of naturally occurring substances, including secondary metabolites of some trees, for example, AOB are inhibited by acidic conditions, which pertain in some soils. These observations led to the suggestions that heterotrophic nitrification might be particularly important under conditions in some soils that are very unfavorable for known autotrophic nitrifiers. The quantitative importance of heterotrophic nitrification remains uncertain in both aquatic and terrestrial environments.

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