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 of inorganic nitrogen compounds. [1] 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 enzymes in nitrification: ammonia monooxygenase (which oxidizes ammonia to hydroxylamine), hydroxylamine oxidoreductase (which oxidizes hydroxylamine to nitric oxide - which is further oxidized to nitrite by a currently unidentified enzyme), and nitrite oxidoreductase (which oxidizes nitrite to nitrate). [2]

Contents

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). [3] 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 (NH+4) or ammonia (NH3) to nitrite (NO−2) and then to nitrate (NO−3) 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). [4]

The second reaction is oxidation of nitrite (NO−2) to nitrate by nitrite-oxidizing bacteria (NOB), represented by the members of Nitrospinota, Nitrospirota, Pseudomonadota, and Chloroflexota. [5] [6]

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

Molecular mechanism of ammonium oxidation by AOB Ammonia oxidation.tif
Molecular mechanism of ammonium oxidation by AOB

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 ( 1.1 ) taking two electrons directly from the quinone pool. This reaction requires O2.

The second step of this process has recently fallen into question. [7] 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 ( 1.2 ). 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. [8]

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. [7]

NH3 + O2 → NO−2 + 3H+ + 2e−

 

 

 

 

(1)

NH3 + O2 + 2H+ + 2e− → NH2OH + H2O

 

 

 

 

(1.1)

NH2OH + H2O → NO−2 + 5H+ + 4e−

 

 

 

 

(1.2)

Nitrite-to-nitrate mechanism

Nitrite produced in the first step of autotrophic nitrification is oxidized to nitrate by nitrite oxidoreductase (NXR) ( 2 ). 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.[ citation needed ] 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) [9] proposes a new hypothetical model of NOB electron transport chain and NXR mechanisms. Here, in contrast to earlier models, [10] 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 [11] and coworkers. Nevertheless, the molecular mechanism of nitrite oxidation is an open question.

NO−2 + H2O → NO−3 + 2H+ + 2e−

 

 

 

 

(2)

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. [12] [13] 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. [12] 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. [12] [13]

Table of characteristics

GenusPhylogenetic groupDNA (mol% GC)HabitatsCharacteristics

Nitrifying bacteria that oxidize ammonia [5] [14]

Nitrosomonas Beta45-53Soil, sewage, freshwater, marineGram-negative short to long rods, motile (polar flagella) or nonmotile; peripheral membrane systems
Nitrosococcus Gamma49-50Freshwater, marineLarge cocci, motile, vesicular or peripheral membranes
Nitrosospira Beta54SoilSpirals, motile (peritrichous flagella); no obvious membrane system

Nitrifying bacteria that oxidize nitrite [5] [14]

Nitrobacter Alpha59-62Soil, freshwater, marineShort rods, reproduce by budding, occasionally motile (single subterminal flagella) or non-motile; membrane system arranged as a polar cap
Nitrospina Delta58MarineLong, slender rods, nonmotile, no obvious membrane system
Nitrococcus Gamma61MarineLarge cocci, motile (one or two subterminal flagellum) membrane system randomly arranged in tubes
Nitrospira Nitrospirota50Marine, soilHelical to vibroid-shaped cells; nonmotile; no internal membranes

Comammox bacteria [15] [16] [17]

Nitrospira inopinata Nitrospirota 59.23Microbial mat in hot water pipes (56 °C, pH 7.5)Rods

See also

Related Research Articles

<span class="mw-page-title-main">Nitrogen cycle</span> Biogeochemical cycle by which nitrogen is converted into various chemical forms

The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biological and physical processes. Important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification. The majority of Earth's atmosphere (78%) is atmospheric nitrogen, making it the largest source of nitrogen. However, atmospheric nitrogen has limited availability for biological use, leading to a scarcity of usable nitrogen in many types of ecosystems.

<span class="mw-page-title-main">Nitrification</span> Biological oxidation of ammonia/ammonium to nitrate

Nitrification is the biological oxidation of ammonia to nitrite followed by the oxidation of the nitrite to nitrate occurring through separate organisms or direct ammonia oxidation to nitrate in comammox bacteria. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.

<span class="mw-page-title-main">Anammox</span> Anaerobic ammonium oxidation, a microbial process of the nitrogen cycle

Anammox, an abbreviation for "anaerobic ammonium oxidation", is a globally important microbial process of the nitrogen cycle that takes place in many natural environments. The bacteria mediating this process were identified in 1999, and were a great surprise for the scientific community. In the anammox reaction, nitrite and ammonium ions are converted directly into diatomic nitrogen and water.

Nitrosomonas europaea is a Gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite and lives in several places such as soil, sewage, freshwater, the walls of buildings and on the surface of monuments especially in polluted areas where the air contains high levels of nitrogen compounds.

<i>Nitrosomonas</i> Genus of bacteria

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 as an energy source and carbon dioxide as a carbon source in 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, meanwhile the third lineage includes only Nitrosomonas nitrosa. The fourth lineage includes the species Nitrosomonas ureae and Nitrosomonas oligotropha and the fifth and sixth lineages include the species Nitrosomonas marina, N. sp. III, Nitrosomonas estuarii and Nitrosomonas cryotolerans.

Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. Denitrification is performed by a variety of denitrifying bacteria that are widely distributed in soils and sediments and that use oxidized nitrogen compounds in absence of oxygen as a terminal electron acceptor. They metabolise nitrogenous compounds using various enzymes, turning nitrogen oxides back to nitrogen gas or nitrous oxide.

<i>Nitrobacter</i> Genus of bacteria

Nitrobacter is a genus comprising rod-shaped, gram-negative, and chemoautotrophic bacteria. The name Nitrobacter derives from the Latin neuter gender noun nitrum, nitri, alkalis; the Ancient Greek noun βακτηρία, βακτηρίᾱς, rod. They are non-motile and reproduce via budding or binary fission. Nitrobacter cells are obligate aerobes and have a doubling time of about 13 hours.

Nitrite reductase refers to any of several classes of enzymes that catalyze the reduction of nitrite. There are two classes of NIR's. A multi haem enzyme reduces NO2− to a variety of products. Copper containing enzymes carry out a single electron transfer to produce nitric oxide.

Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.

Nitrospira translate into “a nitrate spiral” is a genus of bacteria within the monophyletic clade of the Nitrospirota phylum. The first member of this genus was described 1986 by Watson et al. isolated from the Gulf of Maine. The bacterium was named Nitrospira marina. Populations were initially thought to be limited to marine ecosystems, but it was later discovered to be well-suited for numerous habitats, including activated sludge of wastewater treatment systems, natural biological marine settings, water circulation biofilters in aquarium tanks, terrestrial systems, fresh and salt water ecosystems, and hot springs. Nitrospira is a ubiquitous bacterium that plays a role in the nitrogen cycle by performing nitrite oxidation in the second step of nitrification. Nitrospira live in a wide array of environments including but not limited to, drinking water systems, waste treatment plants, rice paddies, forest soils, geothermal springs, and sponge tissue. Despite being abundant in many natural and engineered ecosystems Nitrospira are difficult to culture, so most knowledge of them is from molecular and genomic data. However, due to their difficulty to be cultivated in laboratory settings, the entire genome was only sequenced in one species, Nitrospira defluvii. In addition, Nitrospira bacteria's 16s rRNA sequences are too dissimilar to use for PCR primers, thus some members go unnoticed. In addition, members of Nitrospira with the capabilities to perform complete nitrification has also been discovered and cultivated.

<i>Nitrosopumilus</i> Genus of archaea

Nitrosopumilus maritimus is an extremely common archaeon living in seawater. It is the first member of the Group 1a Nitrososphaerota to be isolated in pure culture. Gene sequences suggest that the Group 1a Nitrososphaerota are ubiquitous with the oligotrophic surface ocean and can be found in most non-coastal marine waters around the planet. It is one of the smallest living organisms at 0.2 micrometers in diameter. Cells in the species N. maritimus are shaped like peanuts and can be found both as individuals and in loose aggregates. They oxidize ammonia to nitrite and members of N. maritimus can oxidize ammonia at levels as low as 10 nanomolar, near the limit to sustain its life. Archaea in the species N. maritimus live in oxygen-depleted habitats. Oxygen needed for ammonia oxidation might be produced by novel pathway which generates oxygen and dinitrogen. N. maritimus is thus among organisms which are able to produce oxygen in dark.

Nitrite oxidoreductase is an enzyme involved in nitrification. It is the last step in the process of aerobic ammonia oxidation, which is carried out by two groups of nitrifying bacteria: ammonia oxidizers such as Nitrosospira, Nitrosomonas, and Nitrosococcus convert ammonia to nitrite, while nitrite oxidizers such as Nitrobacter and Nitrospira oxidize nitrite to nitrate.

Hydroxylamine oxidoreductase (HAO) is an enzyme found in the prokaryotic genus Nitrosomonas. It plays a critically important role in the biogeochemical nitrogen cycle as part of the metabolism of ammonia-oxidizing bacteria.

<span class="mw-page-title-main">SHARON Wastewater Treatment</span>

SHARON is a sewage treatment process. A partial nitrification process of sewage treatment used for the removal of ammonia and organic nitrogen components from wastewater flow streams. The process results in stable nitrite formation, rather than complete oxidation to nitrate. Nitrate formation by nitrite oxidising bacteria (NOB) is prevented by adjusting temperature, pH, and retention time to select for nitrifying ammonia oxidising bacteria (AOB). Denitrification of waste streams utilizing SHARON reactors can proceed with an anoxic reduction, such as anammox.

Nitrospirota is a phylum of bacteria. It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985. The second member, Nitrospira moscoviensis, was discovered in 1995.

Hydroxylamine dehydrogenase (EC 1.7.2.6, HAO (ambiguous)) is an enzyme with systematic name hydroxylamine:ferricytochrome-c oxidoreductase. This enzyme catalyses the following chemical reaction

Ammonia monooxygenase (EC 1.14.99.39, AMO) is an enzyme, which catalyses the following chemical reaction

Nitrospira moscoviensis was the second bacterium classified under the most diverse nitrite-oxidizing bacteria phylum, Nitrospirae. It is a gram-negative, non-motile, facultative lithoauthotropic bacterium that was discovered in Moscow, Russia in 1995. The genus name, Nitrospira, originates from the prefix “nitro” derived from nitrite, the microbe’s electron donor and “spira” meaning coil or spiral derived from the microbe’s shape. The species name, moscoviensis, is derived from Moscow, where the species was first discovered. N. moscoviensis could potentially be used in the production of bio-degradable polymers.

Comammox is the name attributed to an organism that can convert ammonia into nitrite and then into nitrate through the process of nitrification. Nitrification has traditionally thought to be a two-step process, where ammonia-oxidizing bacteria and archaea oxidize ammonia to nitrite and then nitrite-oxidizing bacteria convert to nitrate. Complete conversion of ammonia into nitrate by a single microorganism was first predicted in 2006. In 2015 the presence of microorganisms that could carry out both conversion processes was discovered within the genus Nitrospira, and the nitrogen cycle was updated. Within the genus Nitrospira, the major ecosystems comammox are primarily found in natural aquifers and engineered ecosystems.

Nitrospira inopinata is a bacterium from the phylum Nitrospirota. This phylum contains nitrite-oxidizing bacteria playing role in nitrification. However N. inopinata was shown to perform complete ammonia oxidation to nitrate thus being the first comammox bacterium to be discovered.

References

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  2. ↑ Kuypers, MMM; Marchant, HK; Kartal, B (2011). "The Microbial Nitrogen-Cycling Network". Nature Reviews Microbiology. 1 (1): 1–14. doi:10.1038/nrmicro.2018.9. hdl: 21.11116/0000-0003-B828-1 . PMID   29398704. S2CID   3948918.
  3. ↑ Belser LW (1979). "Population ecology of nitrifying bacteria". Annu. Rev. Microbiol. 33: 309–333. doi:10.1146/annurev.mi.33.100179.001521. PMID   386925.
  4. ↑ Könneke, Martin; Bernhard, Anne E.; de la Torre, José R.; Walker, Christopher B.; Waterbury, John B.; Stahl, David A. (September 2005). "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature. 437 (7058): 543–546. Bibcode:2005Natur.437..543K. doi:10.1038/nature03911. ISSN   1476-4687. PMID   16177789. S2CID   4340386.
  5. 1 2 3 Schaechter M. "Encyclopedia of Microbiology", AP, Amsterdam 2009
  6. ↑ Ward BB (1996). "Nitrification and ammonification in aquatic systems". Life Support & Biosphere Science: International Journal of Earth Space. 3 (1–2): 25–9. PMID   11539155.
  7. 1 2 Caranto, Jonathan D.; Lancaster, Kyle M. (2017-07-17). "Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase". Proceedings of the National Academy of Sciences. 114 (31): 8217–8222. Bibcode:2017PNAS..114.8217C. doi: 10.1073/pnas.1704504114 . ISSN   0027-8424. PMC   5547625 . PMID   28716929.
  8. ↑ Byung Hong Kim; Geoffrey Michael Gadd (2008). Bacterial Physiology and Metabolism. Cambridge University Press.
  9. ↑ Woznica A, et al. (2013). "Stimulatory Effect of Xenobiotics on Oxidative Electron Transport of Chemolithotrophic Nitrifying Bacteria Used as Biosensing Element". PLOS ONE. 8 (1). e53484. Bibcode:2013PLoSO...853484W. doi: 10.1371/journal.pone.0053484 . PMC   3541135 . PMID   23326438.
  10. ↑ Ferguson SJ, Nicholls DG (2002). Bioenergetic III. Academic Press.
  11. ↑ Spieck E, et al. (1998). "Isolation and immunocytochemical location of the nitrite-oxidizing system in Nitrospira moscoviensis". Arch Microbiol. 169 (3): 225–230. doi:10.1007/s002030050565. PMID   9477257. S2CID   21868756.
  12. 1 2 3 Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra; Han, Ping; Herbold, Craig; Albertsen, Mads; Jehmlich, Nico; Palatinszky, Marton; Vierheilig, Julia (2015-12-24). "Complete nitrification by Nitrospira bacteria". Nature. 528 (7583): 504–509. doi:10.1038/nature16461. ISSN   0028-0836. PMC   5152751 . PMID   26610024.
  13. 1 2 van Kessel, Maartje A. H. J.; Speth, Daan R.; Albertsen, Mads; Nielsen, Per H.; Op den Camp, Huub J. M.; Kartal, Boran; Jetten, Mike S. M.; Lücker, Sebastian (2015-12-24). "Complete nitrification by a single microorganism". Nature. 528 (7583): 555–559. doi:10.1038/nature16459. ISSN   0028-0836. PMC   4878690 . PMID   26610025.
  14. 1 2 Michael H. Gerardi (2002). Nitrification and Denitrification in the Activated Sludge Process. John Wiley & Sons.
  15. ↑ Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra; Han, Ping; Herbold, Craig; Albertsen, Mads; Jehmlich, Nico; Palatinszky, Marton; Vierheilig, Julia; Bulaev, Alexandr; Kirkegaard, Rasmus H. (December 2015). "Complete nitrification by Nitrospira bacteria". Nature. 528 (7583): 504–509. Bibcode:2015Natur.528..504D. doi:10.1038/nature16461. ISSN   1476-4687. PMC   5152751 . PMID   26610024.
  16. ↑ van Kessel, Maartje A. H. J.; Speth, Daan R.; Albertsen, Mads; Nielsen, Per H.; Op den Camp, Huub J. M.; Kartal, Boran; Jetten, Mike S. M.; Lücker, Sebastian (December 2015). "Complete nitrification by a single microorganism". Nature. 528 (7583): 555–559. Bibcode:2015Natur.528..555V. doi:10.1038/nature16459. ISSN   1476-4687. PMC   4878690 . PMID   26610025.
  17. ↑ Kits, K. Dimitri; Sedlacek, Christopher J.; Lebedeva, Elena V.; Han, Ping; Bulaev, Alexandr; Pjevac, Petra; Daebeler, Anne; Romano, Stefano; Albertsen, Mads; Stein, Lisa Y.; Daims, Holger (September 2017). "Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle". Nature. 549 (7671): 269–272. Bibcode:2017Natur.549..269K. doi:10.1038/nature23679. ISSN   1476-4687. PMC   5600814 . PMID   28847001.
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