Nitrifying Bacteria
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Nitrifying bacteria are chemolithotrophic organisms that include species of genera such as '' Nitrosomonas'', '' Nitrosococcus'', '' Nitrobacter'', '' Nitrospina'', '' Nitrospira'' and '' Nitrococcus''. These bacteria get their energy from the
oxidation Redox ( , , reduction–oxidation or oxidation–reduction) is a type of chemical reaction in which the oxidation states of the reactants change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is ...
of inorganic nitrogen compounds. Types include ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Many species of nitrifying bacteria have complex internal membrane systems that are the location for key
enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...
s in nitrification: ammonia monooxygenase (which oxidizes
ammonia Ammonia is an inorganic chemical compound of nitrogen and hydrogen with the chemical formula, formula . A Binary compounds of hydrogen, stable binary hydride and the simplest pnictogen hydride, ammonia is a colourless gas with a distinctive pu ...
to hydroxylamine), hydroxylamine oxidoreductase (which oxidizes hydroxylamine to
nitric oxide Nitric oxide (nitrogen oxide, nitrogen monooxide, or nitrogen monoxide) is a colorless gas with the formula . It is one of the principal oxides of nitrogen. Nitric oxide is a free radical: it has an unpaired electron, which is sometimes den ...
- which is further oxidized to nitrite by a currently unidentified enzyme), and nitrite oxidoreductase (which oxidizes
nitrite The nitrite polyatomic ion, ion has the chemical formula . Nitrite (mostly sodium nitrite) is widely used throughout chemical and pharmaceutical industries. The nitrite anion is a pervasive intermediate in the nitrogen cycle in nature. The name ...
to
nitrate Nitrate is a polyatomic ion with the chemical formula . salt (chemistry), Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are solubility, soluble in wa ...
).


Ecology

Nitrifying bacteria are present in distinct taxonomical groups and are found in highest numbers where considerable amounts of ammonia are present (such as areas with extensive protein decomposition, and sewage treatment plants). Nitrifying bacteria thrive in lakes, streams, and rivers with high inputs and outputs of sewage, wastewater and freshwater because of the high ammonia content.


Oxidation of ammonia to nitrate

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 ''Betaproteobacteria'' are a class of Gram-negative bacteria, and one of the six classes of the phylum '' Pseudomonadota'' (synonym Proteobacteria). Metabolism The ''Betaproteobacteria'' comprise over 75 genera and 400 species. Together, they ...
and Gammaproteobacteria. Further organisms able to oxidize ammonia are
Archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...
(AOA). The second reaction is oxidation of nitrite () to nitrate by nitrite-oxidizing bacteria (NOB), represented by the members of Nitrospinota, Nitrospirota,
Pseudomonadota Pseudomonadota (synonym "Proteobacteria") is a major phylum of gram-negative bacteria. Currently, they are considered the predominant phylum within the domain of bacteria. They are naturally found as pathogenic and free-living (non- parasitic) ...
, and Chloroflexota.Schaechter M. "Encyclopedia of Microbiology", AP, Amsterdam 2009 This two-step process was described already in 1890 by the Ukrainian
microbiologist A microbiologist (from Greek ) is a scientist who studies microscopic life forms and processes. This includes study of the growth, interactions and characteristics of microscopic organisms such as bacteria, algae, fungi, and some types of par ...
Sergei Winogradsky Sergei Nikolaevich Winogradsky (; ; , Kyiv – 24 February 1953, Brie-Comte-Robert), also published under the name Sergius Winogradsky, was a Ukrainian and Russian microbiologist, ecologist and soil science, soil scientist who pioneered the Biog ...
. 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
enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...
s as well as
oxygen Oxygen is a chemical element; it has chemical symbol, symbol O and atomic number 8. It is a member of the chalcogen group (periodic table), group in the periodic table, a highly reactivity (chemistry), reactive nonmetal (chemistry), non ...
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.


Nitrite-to-nitrate mechanism

Nitrite produced in the first step of autotrophic nitrification is oxidized to nitrate by nitrite oxidoreductase (NXR) (). It is a membrane-associated iron-sulfur molybdo protein and is part of an electron transfer chain which channels electrons from nitrite to molecular oxygen. The enzymatic mechanisms involved in nitrite-oxidizing bacteria are less described than that of ammonium oxidation. Recent research (e.g. Woźnica A. et al., 2013) 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

*
Root nodule Root nodules are found on the roots of plants, primarily legumes, that form a symbiosis with nitrogen-fixing bacteria. Under nitrogen-limiting conditions, capable plants form a symbiotic relationship with a host-specific strain of bacteria known ...
* Denitrification * Denitrifying bacteria * f-ratio * Nitrification *
Nitrogen cycle The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmosphere, atmospheric, terrestrial ecosystem, terrestrial, and marine ecosystems. The conversion of nitrogen can ...
* Nitrogen deficiency *
Nitrogen fixation Nitrogen fixation is a chemical process by which molecular dinitrogen () is converted into ammonia (). It occurs both biologically and abiological nitrogen fixation, abiologically in chemical industry, chemical industries. Biological nitrogen ...
*
Electron transport chain An electron transport chain (ETC) is a series of protein complexes and other molecules which transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples th ...
* Comammox


References

{{reflist Bacteriology Nitrogen cycle Metabolism Soil biology