Nitrosomonas

Nitrosomonas
N. eutropha
Scientific classification
Domain:	Bacteria
Phylum:	Pseudomonadota
Class:	Betaproteobacteria
Order:	Spirillales
Family:	Nitrosomonadaceae
Genus:	Nitrosomonas Winogradsky, 1892
Type species
Nitrosomonas europaea
Species
"Nitrosomonas aestuarii" Koops et al. 1991 "Nitrosomonas communis" Koops et al. 1991 "Nitrosomonas cryotolerans" Jones et al. 1988 Nitrosomonas europaea Winogradsky 1892 "Nitrosomonas eutropha" Koops et al. 1991 "Nitrosomonas halophila" Koops et al. 1991 "Nitrosomonas javanensis" Winogradsky 1892 "Nitrosomonas marina" Koops et al. 1991 "Nitrosomonas mobilis" Garrity et al. 2003 "Nitrosomonas nitrosa" Koops et al. 1991 "Nitrosomonas oligotropha" Koops et al. 1991 Nitrosomonas stercoris Nakagawa and Takahashi 2017 Nitrosomonas supralitoralis Urakawa et al. 2023 "Nitrosomonas ureae" Koops et al. 1991

Nitrosomonas is a genus of Gram-negative bacteria, belonging to the Betaproteobacteria. It is one of the five genera of ammonia-oxidizing bacteria and, as an obligate chemolithoautotroph, uses ammonia (${\ce {NH3}}$) as an energy source and carbon dioxide (${\ce {CO2}}$) as a carbon source in the presence of oxygen. Nitrosomonas are important in the global biogeochemical nitrogen cycle, since they increase the bioavailability of nitrogen to plants and in the denitrification, which is important for the release of nitrous oxide, a powerful greenhouse gas. This microbe is photophobic, and usually generate a biofilm matrix, or form clumps with other microbes, to avoid light. Nitrosomonas can be divided into six lineages: the first one includes the species Nitrosomonas europea, Nitrosomonas eutropha, Nitrosomonas halophila, and Nitrosomonas mobilis. The second lineage presents the species Nitrosomonas communis, N. sp. I and N. sp. II. The third lineage includes only Nitrosomonas nitrosa. The fourth lineage includes the species Nitrosomonas ureae and Nitrosomonas oligotropha. The fifth and sixth lineages include the species Nitrosomonas marina, N. sp. III, Nitrosomonas estuarii, and Nitrosomonas cryotolerans.

Morphology

All species included in this genus have ellipsoidal or rod-shaped cells which have extensive intracytoplasmic membranes displaying as flattened vesicles.

Most species are motile with a flagellum located in the polar region of the cell. Three basic morphological types of Nitrosomonas were studied, which are: short rods Nitrosomonas, rods Nitrosomonas, and Nitrosomonas with pointed ends. Nitrosomonas species cells have different criteria of size and shape:

• N. europaea cells appear as short rods with pointed ends, with a size of 0.8–1.1 x 1.0–1.7 μm; motility has not been observed.
• N. eutropha cells present as rod to pear shaped cells with one or both ends pointed, with a size of 1.0–1.3 x 1.6–2.3 μm. They show motility.
• N. halophila cells have a coccoid shape and a size of 1.1–1.5 x 1.5–2.2 μm. Motility is possible because of a tuft of flagella.
• N. communis has large rods with rounded end cells with a size of 1.0–1.4 x 1.7–2.2 μm. Motility has not been observed in this species.
• N. nitrosa, N. oligotropha, and N. ureae cells are spheres or rods with rounded ends. Motility has not been observed in them as well.
• N. marina presents slender rod cells with rounded ends with a size of 0.7–0.9 x 1.7- 2.2 μm.
• N. aestuarii and N. cryotolerans present as rod shaped cells.

Genome

Genome sequencing of Nitrosomonas species has been important to understand the ecological role of these bacteria.

Among the various species of Nitrosomonas that are known today, the complete genomes of N. ureae strain Nm10 and N. europaea, N.sp. Is79 have been sequenced.

Ammonia-oxidation genes

The presence of the genes for ammonia oxidation characterizes all these species. The first enzyme involved in the ammonia oxidation is ammonia monooxygenase (AMO), which is encoded by the amoCAB operon. The AMO enzyme catalyzes the oxidation from ${\ce {NH3}}$

(ammonia) to ${\ce {NH2OH}}$ (hydroxylamine). The amoCAB operon contains three different genes: amoA, amoB and amoC. While N. europaea presents two copies of the genes, N. sp. Is79 and N. ureae strain Nm10 have three copies of these genes.

The second enzyme involved in the ammonia oxidation is hydroxylamine oxidoreductase (HAO), encoded by the hao operon. This enzyme catalyzes the oxidation from ${\ce {NH2OH}}$ to ${\ce {NO}}$, a highly reactive radical intermediate that can be partitioned into both of the main AOB products: ${\ce {N2O}}$, a potent greenhouse gas, and ${\ce {NO2-}}$, a form of nitrogen more bioavailable for crops, but that conversely washes away from fields faster. The hao operon contains different genes such as the haoA, which encodes for the functional cytochrome c subunit, the cycA which encodes for cytochrome c554, and cycB that encodes for quinone reductase. These genes are present in different copies in various species; for instance, in Nitrosomonas sp. Is79 there are only three copies, while in N. ureae there are four.

Denitrification genes

The discovery of genes that encode for enzymes involved in the denitrification process includes the first gene nirK which encodes for a nitrite reductase with copper. This enzyme catalyzes the reduction form ${\ce {NO2}}$(nitrite) to ${\ce {NO}}$ (nitric oxide). While in N. europaea, N. eutropha, and N. cryotolerans, nirK is included in a multigenetic cluster; in Nitrosomonas sp. Is79 and N. sp. AL212, it is present as a single gene. A high expression of the nirK gene was found in N.ureae and this has been explained with the hypothesis that the NirK enzyme is also involved in the oxidation of ${\ce {NH2OH}}$ in this species. The second gene involved in denitrification is norCBQD which encodes a nitric-oxide reductase that catalyze the reduction from ${\ce {NO}}$ (nitric oxide) to ${\ce {N2O}}$ (nitrous oxide). These genes are present in N. sp. AL212, N.cryotolerans, and N. communis strain Nm2. In Nitrosomonas europaea, these genes are included in a cluster. These genes are absent in N. sp. Is79 and N. ureae. Recently, it was found that the norSY gene encodes for a nitric-oxide reductase with copper in N. communis strain Nm2 and Nitrosomonas AL212.

Carbon fixation genes

Nitrosomonas uses the Calvin-Benson cycle as a pathway for Carbon fixation. For this reason, all of the species have an operon that encodes for the RuBisCO enzyme. A peculiarity is found in N. sp Is79 in which the two copies of the operon encode for two different forms of the RuBisCO enzyme: the IA form and the IC form, where the first one has a major affinity with the Carbon dioxide. Other species present different copies of this operon that encodes only for the IA form. In N. europaea, an operon is characterized by five genes (ccbL, ccbS, ccbQ, ccbO, and ccbN) that encode for the RuBisCO enzyme. ccbL encodes for the major subunit while ccbS encodes for the minor subunit; these genes are also the most expressed within the operon. ccbQ and ccbO genes encode for a number of proteins involved in the mechanisms of processing, folding, assembling, activation, and regulation of the RuBisCO enzyme. Instead, ccbN encodes for a protein of 101 amino acids, whose function is not known yet. A putative regulatory gene, cbbR, was found 194 bases upstream of the start codon of cbbL and is transcribed in the opposite direction of other genes).

Transporter genes

Since Nitrosomonas are part of the ammonia-oxidizing bacteria (AOB), ammonia carriers are important to them. Bacteria adapted to high concentrations of ammonia can absorb it passively by simple diffusion. Indeed, N. eutropha, that is adapted to high levels of ammonia, does not present genes that encode for an ammonia transporter. Bacteria adapted to low concentrations of ammonia have a transporter (transmembrane protein) for this substrate. In Nitrosomonas, two different carriers for ammonia have been identified, differing in structure and function. The first transporter is the Amt protein (amtB type) encoded by amt genes and was found in Nitrosomonas sp. Is79. The activity of this ammonia carrier depends on the membrane potential. The second was found in N. europaea, wherein the rh1 gene encodes an Rh-type ammonia carrier. Its activity is independent from the membrane potential. Recent research has also linked the Rh transmembrane proteins with ${\ce {CO2}}$transport, but this is not clear yet.

Metabolism

Nitrosomonas is one of the genera included in AOB and use ammonia as an energy source and carbon dioxide as the main source of carbon. The oxidation of ammonia is a rate-limiting step in nitrification and plays a fundamental role in the nitrogen cycle, because it transforms ammonia, which is usually extremely volatile, into less volatile forms of nitrogen.

Ammonia-oxidation

Nitrosomonas oxidizes ammonia into nitrite in a metabolic process, known as nitritation (a step of nitrification). This process occurs with the accompanying reduction of an oxygen molecule to water (which requires four electrons), and the release of energy. The oxidation of ammonia to hydroxylamine is catalyzed by ammonia monooxygenase (AMO), which is a membrane-bound, multisubstrate enzyme. In this reaction, two electrons are required to reduce an oxygen atom to water:

NH₃ + O₂ + 2 H⁺ + 2 e^– → NH₂OH + H₂O

Since an ammonia molecule only releases two electrons when oxidized, it has been assumed that the other two necessary electrons come from the oxidation of hydroxylamine to nitrite, which occurs in the periplasm and it is catalyzed by hydroxylamine oxidoreductase (HAO), a periplasm associated enzymes.

NH₂OH + H₂O → NO₂^– + 5 H⁺ + 4 e^–

Two of the four electrons released by the reaction, return to the AMO to convert the ammonia in hydroxylamine. 1,65 of the two remaining electrons are available for the assimilation of nutrients and the generation of the proton gradient. They pass through the cytochrome c552 to the cytochrome caa3, then to O₂, which is the terminal acceptor; here they are reduced to form water. The remaining 0,35 electrons are used to reduce NAD+ to NADH, to generate the proton gradient.

Nitrite is the major nitrogen oxide produced in the process, but it has been observed that, when oxygen concentrations are low, nitrous oxide and nitric oxide can also form, as by-products from the oxidation of hydroxylamine to nitrite.

The species N. europaea has been identified as being able to degrade a variety of halogenated compounds including trichloroethylene, benzene, and vinyl chloride.

Ecology

Habitat

Nitrosomonas is generally found in highest numbers in all habitats in which there is abundance of ammonia (environment with plentiful protein decomposition or in wastewater treatment), thrive in a pH range of 6.0–9.0, and a temperature range of 20–30 °C (68–86 °F). Some species can live and proliferate on a monuments’ surface or on stone buildings’ walls, contributing to erosion of those surfaces.

It is usually found in all types of waters, globally distributed in both eutrophic and oligotrophic freshwater and saltwater, emerging especially in shallow coastal sediments and under the upwelling zones, such as the Peruvian coast and the Arabian Sea, but can also be found in fertilized soils.

Some Nitrosomonas species, such as N.europaea, possess the enzyme urease (which catalyzes the conversion of urea into ammonia and carbon dioxide) and have been shown to assimilate the carbon dioxide released by the reaction to make biomass via the Calvin cycle, and harvest energy by oxidizing ammonia (the other product of urease) to nitrite. This feature may explain enhanced growth of AOB in the presence of urea in acidic environments.

Leaching of soil

In agriculture, nitrification made by Nitrosomonas represents a problem because the oxidized nitrite by ammonia can persist in the soil, leaching and making it less available for plants.

Nitrification can be slowed down by some inhibitors that are able to slow down the oxidation process of ammonia to nitrites by inhibiting the activity of Nitrosomonas and other ammonia-oxidizing bacteria thereby minimizing or preventing the loss of nitrate. (Read more about inhibitors in the section 'Inhibitors of nitrification' on this page Nitrification)

Application

Nitrosomonas is used in activated sludge in aerobic wastewater treatment; the reduction of nitrogen compounds in the water is given by nitrification treatment in order to avoid environmental issues, such as ammonia toxicity and groundwater contamination. Nitrogen, if present in high quantities can cause algal development, leading to eutrophication with degradation of oceans and lakes.

Employing as wastewater treatment, biological removal of nitrogen is obtained at a lower economic expense and with less damage caused to the environment compared to physical-chemical treatments.

Nitrosomonas has also a role in biofilter systems, typically in association and collaboration with other microbes, to consume compounds such as ${\ce {NH4+}}$ or ${\ce {CO2}}$ and recycle nutrients. These systems are used for various purposes but mainly for the elimination of odors from waste treatment.

Other uses

Potential cosmetic benefits

N. europaea is a non-pathogenic bacteria studied in connection with probiotic therapies. In this context, it may give aesthetic benefits in terms of reducing the appearance of wrinkles. The effectiveness of probiotic products has been studied to explore why N. eutropha, which is a highly mobile bacterium, has become extinct from the normal flora of our skin. It has been studied in connection with the idea of having benefits through the repopulation and reintroduction of N. eutropha to the normal flora of human skin.

See also

• Nitrate
• Nitrite
• Nitrobacter
• Nitrobacteraceae
• Nitrogen cycle
• Nitrospira
• Nitrospirota

References

• George M. Garrity: Bergey's manual of systematic bacteriology. 2. Auflage. Springer, New York, 2005, Vol. 2: The Proteobacteria Part C: The Alpha-, Beta-, Delta-, and Epsilonproteobacteria ISBN 0-387-24145-0