Nitrifying bacteria

Nitrifying bacteria are chemoautotrophic or chemolithotrophs depending on the genera (Nitrosomonas, Nitrosococcus, Nitrobacter, Nitrococcus) bacteria that grow by consuming inorganic nitrogen compounds.^[1] 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, and nitrite oxidoreductase, which oxidizes nitrite to nitrate.

Ecology

Nitrifying bacteria are a narrow taxonomic group in the environment, and are found in highest numbers where considerable amounts of ammonia are present (areas with extensive protein decomposition, and sewage treatment plants).^[2] Nitrifying bacteria thrive in lakes and rivers streams with high inputs and outputs of sewage and 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 (NH₄⁺) or ammonia (NH₃) to nitrate (NO₃⁻) catalyzed by two ubiquitous bacterial groups. The first reaction is oxidation of ammonium to nitrite by ammonium oxidizing bacteria (AOB) represented by the "Nitrosomonas" species. The second reaction is oxidation of nitrite (NO₂⁻) to nitrate by nitrite-oxidizing bacteria (NOB), represented by the Nitrobacter species.^[3][4]

First step nitrification - molecular mechanism

Figure 1. Molecular mechanism of ammonium oxidation by AOB

Ammonia oxidation in autotrophic nitrification is a complex process that requires several enzymes, proteins and presence of oxygen. The key enzymes, necessary to obtaining energy during oxidation of ammonium to nitrite are ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase (HAO). First is a transmembrane copper protein which catalyzes the oxidation of ammonium to hydroxylamine (1.1) taking two electrons directly from the quinone pool. This reaction requires O₂. In the second step (1.2), a trimeric multiheme c-type HAO converts hydroxylamine into nitrite in the periplasm with production of four electrons. The stream of four electron are channelled 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). Rest two electrons are used to generate a proton motive force and reduce NAD(P) through reverse electron transport.^[5]

NH₃ + O₂ → NO−
2 + 3H⁺ + 2e⁻ (1)

NH₃ + O₂ + 2H⁺ + 2e⁻ → NH₂OH +  H₂O (1.1)

NH₂OH +  H₂O → NO−
2 + 5H⁺ + 4e⁻ (1.2)

Second step nitrification - molecular 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 molybdoprotein, and is part of an electron transfer chain which channels electrons from nitrite to molecular oxygen. The molecular mechanism of oxidation nitrite is less described than oxidation ammonium. In new research (e.g. Woźnica A. et al., 2013)^[6] proposed new hypothetical model of NOB electron transport chain and NXR mechanism (Figure 2.). It should be noted that, in contrast to earlier models ^[7] the NXR acts on the outside of the plasma membrane, directly contributing to postulated by Spieck ^[8] and coworkers mechanism of proton gradient generation. Nevertheless, the molecular mechanism of nitrite oxidation is an open question.

NO−
2 +  H₂O → NO−
3 + 2H⁺ + 2e⁻ (2)

Characteristic of ammonia and nitrite oxidizing bacteria

Nitrifying bacteria that oxidize ammonia ^[3][9]

Genus	Phylogenetic group	DNA (mol% GC)	Habitats	Characteristics
Nitrosomonas	Beta	45-53	Soil, Sewage, freshwater, Marine	Gram-negative short to long rods, motile (polar flagella)or nonmotile; peripheral membrane systems
Nitrosococcus	Gamma	49-50	Freshwater, Marine	Large cocci, motile, vesicular or peripheral membranes
Nitrosospira	Beta	54	Soil	Spirals, motile (peritrichous flagella); no obvious membrane system

Nitrifying bacteria that oxidize nitrite ^[3][9]

Genus	Phylogenetic group	DNA (mol% GC)	Habitats	Characteristics
Nitrobacter	Alpha	59-62	Soil, Freshwater, Marine	Short rods, reproduce by budding, occasionally motile (single subterminal flagella) or non-motile; membrane system arranged as a polar cap
Nitrospina	Delta	58	Marine	Long, slender rods, nonmotile, no obvious membrane system
Nitrococcus	Gamma	61	Marine	Large Cocci, motile (one or two subterminal flagellum) membrane system randomly arranged in tubes
Nitrospira	Nitrospirae	50	Marine, Soil	Helical to vibroid-shaped cells; nonmotile; no internal membranes

See also

• Root nodule
• Denitrification
• Denitrifying bacteria
• f-ratio
• Nitrification
• Nitrogen cycle
• Nitrogen deficiency
• Nitrogen fixation
• Electron transport chain

References

1. Mancinelli RL (1996). "The nature of nitrogen: an overview". Life support & biosphere science : international journal of earth space 3 (1–2): 17–24. PMID 11539154.
2. Belser LW (1979). "Population ecology of nitrifying bacteria". Annu. Rev. Microbiol. 33: 309–333. doi:10.1146/annurev.mi.33.100179.001521. PMID 386925.
3. Schaechter M. „Encyclopedia of Microbiology", AP, Amsterdam 2009
4. 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.
5. Byung Hong Kim, Geoffrey Michael Gadd (2008). Bacterial Physiology and Metabolism. Cambridge University Press.
6. 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. doi:10.1371/journal.pone.0053484.
7. Ferguson SJ, Nicholls DG (2002). Bioenergetic III. Academic Press.
8. 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.
9. Michael H. Gerardi (2002). Nitrification and Denitrification in the Activated Sludge Process. John Wiley & Sons,.