Nitrification
Nitrification is the biological
.Microbiology
Ammonia oxidation
The process of nitrification begins with the first stage of ammonia oxidation, where ammonia (NH3) or ammonium (NH4+) get converted into nitrite (NO2-). This first stage is sometimes known as nitritation. It is performed by two groups of organisms, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA[2]).
Ammonia-Oxidizing Bacteria
Ammonia-Oxidizing Bacteria (AOB) are typically Gram-negative bacteria and belong to Betaproteobacteria and Gammaproteobacteria[3] including the commonly studied genera including Nitrosomonas and Nitrococcus. They are known for their ability to utilize ammonia as an energy source and are prevalent in a wide range of environments, such as soils, aquatic systems, and wastewater treatment plants.
AOB possess enzymes called ammonia monooxygenases (AMOs), which are responsible for catalyzing the conversion of ammonia to hydroxylamine (NH2OH), a crucial intermediate in the process of nitrification.[4] This enzymatic activity is sensitive to environmental factors, such as pH, temperature, and oxygen availability.
AOB play a vital role in soil nitrification, making them key players in nutrient cycling. They contribute to the transformation of ammonia derived from organic matter decomposition or fertilizers into nitrite, which subsequently serves as a substrate for nitrite-oxidizing bacteria (NOB).
Ammonia-Oxidizing Archaea
Prior to the discovery of archaea capable of ammonia oxidation, ammonia-oxidizing bacteria (AOB) were considered the only organisms capable of ammonia oxidation. Since their discovery in 2005,[5] two isolates of AOAs have been cultivated: Nitrosopumilus maritimus[6] and Nitrososphaera viennensis.[7] When comparing AOB and AOA, AOA dominate in both soils and marine environments,[2][8][6][9][10][11] suggesting that Nitrososphaerota (formerly Thaumarchaeota) may be greater contributors to ammonia oxidation in these environments.[2]
Crenarchaeol, which is generally thought to be produced exclusively by AOA (specifically Nitrososphaerota), has been proposed as a biomarker for AOA and ammonia oxidation. Crenarchaeol abundance has been found to track with seasonal blooms of AOA, suggesting that it may be appropriate to use crenarchaeol abundances as a proxy for AOA populations[12] and thus ammonia oxidation more broadly. However the discovery of Nitrososphaerota that are not obligate ammonia-oxidizers[13] complicates this conclusion,[14] as does one study that suggests that crenarchaeol may be produced by Marine Group II Euryarchaeota.[15]
Nitrite oxidation
The second step of nitrification is the oxidation of nitrite into nitrate. This process is sometimes known as nitratation. Nitrite oxidation is conducted by nitrite-oxidizing bacteria (NOB) from the taxa Nitrospirota,[16] Nitrospinota,[17] Pseudomonadota[18] and Chloroflexota.[19] NOB are typically present in soil, geothermal springs, freshwater and marine ecosystems.
Complete ammonia oxidation
Ammonia oxidation to nitrate in a single step within one organism was predicted in 2006[20] and discovered in 2015 in the species Nitrospira inopinata. A pure culture of the organism was obtained in 2017,[21] representing a revolution in our understanding of the nitrification process.
History
The idea that oxidation of ammonia to nitrate is in fact a biological process was first given by Louis Pasteur in 1862.[22] Later in 1875, Alexander Müller, while conducting a quality assessment of water from wells in Berlin, noted that ammonium was stable in sterilized solutions but nitrified in natural waters. A. Müller put forward, that nitrification is thus performed by microorganisms.[23] In 1877, Jean-Jacques Schloesing and Achille Müntz, two French agricultural chemists working in Paris, proved that nitrification is indeed microbially mediated process by the experiments with liquid sewage and artificial soil matrix (sterilized sand with powdered chalk).[24] Their findings were confirmed soon (in 1878) by Robert Warington who was investigating nitrification ability of garden soil at the Rothamsted experimental station in Harpenden in England.[25] R. Warington made also the first observation that nitrification is a two-step process in 1879[26] which was confirmed by John Munro in 1886.[27] Although at that time, it was believed that two-step nitrification is separated into distinct life phases or character traits of a single microorganism.
The first pure nitrifier (ammonia-oxidizing) was most probably isolated in 1890 by Percy Frankland and Grace Frankland, two English scientists from Scotland.[28] Before that, Warington,[25] Sergei Winogradsky[29] and the Franklands were only able to enrich cultures of nitrifiers. Frankland and Frankland succeeded with a system of serial dilutions with very low inoculum and long cultivation times counting in years. Sergei Winogradsky claimed pure culture isolation in the same year (1890),[29] but his culture was still co-culture of ammonia- and nitrite-oxidizing bacteria.[30] S. Winogradsky succeeded just one year later in 1891.[31]
In fact, during the serial dilutions ammonia-oxidizers and nitrite-oxidizers were unknowingly separated resulting in pure culture with ammonia-oxidation ability only. Thus Frankland and Frankland observed that these pure cultures lose ability to perform both steps. Loss of nitrite oxidation ability was observed already by R. Warington.[26] Cultivation of pure nitrite oxidizer happened later during 20th century, however it is not possible to be certain which cultures were without contaminants as all theoretically pure strains share same trait (nitrite consumption, nitrate production).[30]
Ecology
Part of a series on |
Biogeochemical cycles |
---|
Both steps are producing energy to be coupled to ATP synthesis. Nitrifying organisms are
In most environments, organisms are present that will complete both steps of the process, yielding nitrate as the final product. However, it is possible to design systems in which nitrite is formed (the Sharon process).
Nitrification is important in agricultural systems, where fertilizer is often applied as ammonia. Conversion of this ammonia to nitrate increases nitrogen leaching because nitrate is more water-soluble than ammonia.
Nitrification also plays an important role in the removal of nitrogen from municipal wastewater. The conventional removal is nitrification, followed by denitrification. The cost of this process resides mainly in aeration (bringing oxygen in the reactor) and the addition of an external carbon source (e.g., methanol) for the denitrification.
Nitrification can also occur in drinking water. In distribution systems where chloramines are used as the secondary disinfectant, the presence of free ammonia can act as a substrate for ammonia-oxidizing microorganisms. The associated reactions can lead to the depletion of the disinfectant residual in the system.[33] The addition of chlorite ion to chloramine-treated water has been shown to control nitrification.[34][35]
Together with
Nitrification in the marine environment
In the
Nitrification, as stated above, is formally a two-step process; in the first step
In the second step, nitrite is oxidized to nitrate. In the oceans, this step is not as well understood as the first, but the bacteria Nitrospina[17][40] and Nitrobacter are known to carry out this step in the ocean.[36]
Chemistry and enzymology
Nitrification is a process of nitrogen compound oxidation (effectively, loss of electrons from the nitrogen atom to the oxygen atoms), and is catalyzed step-wise by a series of enzymes.
OR
In Nitrosomonas europaea, the first step of oxidation (ammonia to hydroxylamine) is carried out by the enzyme ammonia monooxygenase (AMO).
The second step (hydroxylamine to nitrite) is catalyzed by two enzymes.
Another currently unknown enzyme converts nitric oxide to nitrite.
The third step (nitrite to nitrate) is completed in a distinct organism.
Factors Affecting Nitrification Rates
Soil conditions
Due to its inherent microbial nature, nitrification in soils is greatly susceptible to soil conditions. In general, soil nitrification will proceed at optimal rates if the conditions for the microbial communities foster healthy microbial growth and activity. Soil conditions that have an effect on nitrification rates include:
- Substrate availability (presence of NH4+)
- Aeration (availability of O2)
- Soil moisture content (availability of H2O)
- pH (near neutral)
- Temperature
Inhibitors of nitrification
Nitrification
The environmental concerns of nitrification also contribute to interest in the use of nitrification inhibitors: the primary product, nitrate, leaches into groundwater, producing toxicity in both humans[44] and some species of wildlife and contributing to the eutrophication of standing water. Some inhibitors of nitrification also inhibit the production of methane, a greenhouse gas.
The inhibition of the nitrification process is primarily facilitated by the selection and inhibition/destruction of the bacteria that
The conversion of ammonia to hydroxylamine is the first step in nitrification, where AH2 represents a range of potential electron donors.
- NH3 + AH2 + O2 → NH2OH + A + H2O
This reaction is catalyzed by AMO. Inhibitors of this reaction bind to the active site on AMO and prevent or delay the process. The process of oxidation of ammonia by AMO is regarded with importance due to the fact that other processes require the co-oxidation of NH3 for a supply of reducing equivalents. This is usually supplied by the compound hydroxylamine oxidoreductase (HAO) which catalyzes the reaction:
- NH2OH + H2O → NO2− + 5 H+ + 4 e−
The mechanism of inhibition is complicated by this requirement. Kinetic analysis of the inhibition of NH3 oxidation has shown that the substrates of AMO have shown kinetics ranging from
Mechanism based inhibitors can be defined as compounds that interrupt the normal reaction catalyzed by an enzyme. This method occurs by the inactivation of the enzyme via
Sulfur-containing compounds, including ammonium thiosulfate (a popular inhibitor) are found to operate by producing volatile compounds with strong inhibitory effects such as carbon disulfide and thiourea.
In particular, thiophosphoryl triamide has been a notable addition where it has the dual purpose of inhibiting both the production of
N-heterocyclic compounds are also highly effective nitrification inhibitors and are often classified by their ring structure. The mode of action for these compounds is not well understood: while nitrapyrin, a widely used inhibitor and substrate of AMO, is a weak mechanism-based inhibitor of said enzyme, the effects of said mechanism are unable to correlate directly with the compound's ability to inhibit nitrification. It is suggested that nitrapyrin acts against the monooxygenase enzyme within the bacteria, preventing growth and CH4/NH4 oxidation.[46] Compounds containing two or three adjacent ring N atoms (pyridazine, pyrazole, indazole) tend to have a significantly higher inhibition effect than compounds containing non-adjacent N atoms or singular ring N atoms (pyridine, pyrrole).[47] This suggests that the presence of ring N atoms is directly correlated with the inhibition effect of this class of compounds.
Methane oxidation inhibition
Some enzymatic nitrification inhibitors, such as nitrapyrin, can also inhibit the oxidation of methane in
Environmental concerns
Nitrification inhibitors are also of interest from an environmental standpoint because of the production of nitrates and nitrous oxide from the process of nitrification. Nitrous oxide (N2O), although its atmospheric concentration is much lower than that of CO2, has a global warming potential of about 300 times greater than carbon dioxide and contributes 6% of planetary warming due to greenhouse gases. This compound is also notable for catalyzing the breakup of ozone in the stratosphere.[50] Nitrates, a toxic compound for wildlife and livestock and a product of nitrification, are also of concern.
Soil, consisting of
Wildlife such as amphibians, freshwater fish, and insects are sensitive to nitrate levels, and have been known to cause death and developmental anomalies in affected species.
See also
- f-ratio
- Haber process
- Nitrifying bacteria
- Nitrogen fixation
- Simultaneous nitrification-denitrification
- Comammox
References
- ^ Nitrification Network. "Nitrification primer". nitrificationnetwork.org. Oregon State University. Archived from the original on 2 May 2018. Retrieved 21 August 2014.
- ^ PMID 22923400.
- PMID 11097916.
- PMID 32086308.
- PMID 16309395.
- ^ S2CID 4340386.
- PMID 21525411.
- S2CID 6789859.
- PMID 16894176.
- (PDF) from the original on 2016-06-11. Retrieved 2016-05-18.
- PMID 23060870.
- (PDF) from the original on 2023-05-22. Retrieved 2022-08-27.
- PMID 21930919.
- PMID 28142226.
- PMID 24946804.
- PMID 11679356.
- ^ PMID 23804152.
- PMID 18031541.
- PMID 31624340.
- from the original on 2020-10-19. Retrieved 2021-01-21.
- PMID 28847001.
- ^ Pasteur L (1862). "Etudes sur les mycoderme". C. R. Acad. Sci. 54: 265–270.
- ^ Müller A (1875). "Ammoniakgehalt des Spree- und Wasserleitungs wassers in Berlin". Fortsetzung der Vorarbeiten zu einer zukünftigen Wasser-Versorgung der Stadt Berlin ausgeführt in den Jahren 1868 und 1869.: 121–123.
- ^ Schloesing T, Muntz A (1877). "Sur la nitrification pas les ferments organisés". C. R. Acad. Sci. 84: 301–303.
- ^ ISSN 0368-1645.
- ^ from the original on 2021-06-12. Retrieved 2021-03-12.
- ISSN 0368-1645.
- ISSN 0264-3839.
- ^ a b Winogradsky S (1890). "Sur les organisms de la nitrification". Ann. Inst. Pasteur. 4: 215–231.
- ^ PMID 32849473.
- ^ Winogradsky S (1891). "Sur les organisms de la nitrification". Ann. Inst. Pasteur. 5: 92–100.
- S2CID 6245255.
- S2CID 96988652.
- S2CID 93321500.
- S2CID 101973325.
- ^ S2CID 23018410.
- ^ (PDF) from the original on 2017-10-19. Retrieved 2018-10-18.
- from the original on 2018-10-18. Retrieved 2018-10-18.
- S2CID 1692603.
- PMID 31118472.
- PMID 28716929.
- ]
- .
- ISSN 2190-5487.
- S2CID 38059676.
- S2CID 34551923.
- S2CID 38059676.
- PMID 16346465.
- PMID 2496288.
- S2CID 128612680.
- PMID 10504145.
External links
- Nitrification at the heart of filtration at fishdoc.co.uk
- Nitrification at University of Aberdeen · King's College
- Nitrification Basics for Aerated Lagoon Operators at lagoonsonline.com