Denitrifying bacteria are a diverse group of

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

that encompass many different phyla. This group of bacteria, together with denitrifying fungi and

archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeba ...

, is capable of performing

denitrification Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denit ...

as part of the

nitrogen cycle 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 biolo ...

. 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

nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...

ous compounds using various enzymes, turning

nitrogen oxide Nitrogen oxide may refer to a binary compound of oxygen and nitrogen, or a mixture of such compounds: Charge-neutral *Nitric oxide (NO), nitrogen(II) oxide, or nitrogen monoxide * Nitrogen dioxide (), nitrogen(IV) oxide * Nitrogen trioxide (), or ...

s back to nitrogen

gas Gas is one of the four fundamental states of matter (the others being solid, liquid, and plasma). A pure gas may be made up of individual atoms (e.g. a noble gas like neon), elemental molecules made from one type of atom (e.g. oxygen), or ...

(N2) or

nitrous oxide Nitrous oxide (dinitrogen oxide or dinitrogen monoxide), commonly known as laughing gas, nitrous, or nos, is a chemical compound, an oxide of nitrogen with the formula . At room temperature, it is a colourless non-flammable gas, and ha ...

(N2O).

Diversity of denitrifying bacteria

There is a great diversity in biological traits.Zumft, W. G. (1997). ''Cell biology and molecular basis of denitrification.'' Microbiology and Molecular Biology Reviews, 61(4), 533–616 Denitrifying bacteria have been identified in over 50 genera with over 125 different species and are estimated to represent 10-15% of bacteria population in water, soil and sediment.Eldor, A. (2015). ''Soil microbiology, ecology, and biochemistry'' (4th ed.). Chapter 14 Amsterdam: Elsevier. Denitrifying include for example several species of ''

Pseudomonas ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able t ...

'', ''

Alcaligenes ''Alcaligenes'' is a genus of Gram-negative, aerobic, rod-shaped bacteria. The species are motile with amphitrichous flagella and rarely nonmotile. It is a genus of non-fermenting bacteria (in the family Alcaligenaceae). Additionally, some str ...

'' , ''

Bacillus ''Bacillus'' (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum '' Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural ''Bacill ...

'' and others. Pseudomonas stutzeri

The majority of denitrifying bacteria are facultative aerobic heterotrophs that switch from aerobic respiration to denitrification when oxygen as an available terminal electron acceptor (TEA) runs out. This forces the organism to use nitrate to be used as a TEA. Because the diversity of denitrifying bacteria is so large, this group can thrive in a wide range of habitats including some extreme environments such as environments that are highly saline and high in temperature. Aerobic denitrifiers can conduct an aerobic respiratory process in which nitrate is converted gradually to N₂ (NO₃⁻ →NO₂⁻ → NO → N₂O → N₂ ), using nitrate reductase (Nar or Nap), nitrite reductase (Nir), nitric oxide reductase (Nor), and nitrous oxide reductase (Nos). Phylogenetic analysis revealed that aerobic denitrifiers mainly belong to α-, β- and γ-''Proteobacteria''.

Denitrification mechanism

Denitrifying bacteria use denitrification to generate ATP.Bothe, H., Ferguson, S., & Newton, W. (2007). ''Biology of the nitrogen cycle.'' Amsterdam: Elsevier. The most common denitrification process is outlined below, with the nitrogen oxides being converted back to gaseous nitrogen: 2 NO₃⁻ + 10 e⁻ + 12 H⁺ → N₂ + 6 H₂O The result is one molecule of nitrogen and six molecules of water. Denitrifying bacteria are a part of the N cycle, and consists of sending the N back into the atmosphere. The reaction above is the overall half reaction of the process of denitrification. The reaction can be further divided into different half reactions each requiring a specific enzyme. The transformation from nitrate to nitrite is performed by nitrate reductase (Nar) NO₃⁻ + 2 H⁺ + 2 e⁻ → NO₂⁻ + H₂O Nitrite reductase (Nir) then converts nitrite into nitric oxide 2 NO₂⁻ + 4 H⁺ + 2 e⁻ → 2 NO + 2 H₂O Nitric oxide reductase (Nor) then converts nitric oxide into nitrous oxide 2 NO + 2 H⁺ + 2 e⁻ → N₂O + H₂O Nitrous oxide reductase (Nos) terminates the reaction by converting nitrous oxide into dinitrogen N₂O + 2 H⁺ + 2 e⁻ → N₂ + H₂O It is important to note that any of the products produced at any step can be exchanged with the soil environment.

Oxidation of methane and denitrification

Anaerobic oxidation of methane coupled to denitrification

Anaerobic Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to: * Anaerobic adhesive, a bonding a ...

denitrification coupled to methane oxidation was first observed in 2008, with the isolation of a methane-oxidizing bacterial strain found to oxidize methane independently. This process uses the excess electrons from methane oxidation to reduce nitrates, effectively removing both fixed nitrogen and methane from aquatic systems in habitats ranging from sediment to peat bogs to stratified water columns. The process of anaerobic denitrification may contribute significantly to the global methane and

s, especially in light of the recent influx of both due to

anthropogenic Anthropogenic ("human" + "generating") is an adjective that may refer to: * Anthropogeny, the study of the origins of humanity Counterintuitively, anthropogenic may also refer to things that have been generated by humans, as follows: * Human i ...

changes. The extent to which anthropogenic methane affects the atmosphere is known to be a significant driver of

climate change In common usage, climate change describes global warming—the ongoing increase in global average temperature—and its effects on Earth's climate system. Climate change in a broader sense also includes previous long-term changes to ...

, and considering it is multiple times more potent than carbon dioxide. Removing methane is widely considered to be beneficial to the environment, although the extent of the role that denitrification plays in the global flux of methane is not well understood. Anaerobic denitrification as a mechanism has been shown to be capable of removing the excess nitrate caused by fertilizer runoff, even in hypoxic conditions. Additionally, microorganisms which employ this type of metabolism may be employed in

bioremediation Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi, and plants), living or dead, is employed for removing environmental pollutants from air, water, soil, flue gasses, industrial effluent ...

, as shown by a 2006 study of

hydrocarbon In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons are examples of group 14 hydrides. Hydrocarbons are generally colourless and hydrophobic, and their odors are usually weak or ...

contamination in the Antarctic, as well as a 2016 study which successfully increased the rates of denitrification by altering the environment housing the bacteria. Denitrifying bacteria are said to be high quality bioremediators because of their adaptability to a variety of different environments, as well as the lacking any toxic or undesirable leftovers, as are left by other metabolisms.

Role of denitrifying bacteria as a methane sink

Denitrifying bacteria have been found to play a significant role in the

oxidation Redox (reduction–oxidation, , ) is a type of chemical reaction in which the oxidation states of substrate change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is the gain of electrons or ...

of methane (CH₄) (where methane is converted to CO₂, water, and energy) in deep freshwater bodies of water. This is important because methane is the second most significant anthropogenic greenhouse gas, with a

global warming potential Global warming potential (GWP) is the heat absorbed by any greenhouse gas in the atmosphere, as a multiple of the heat that would be absorbed by the same mass of carbon dioxide (). GWP is 1 for . For other gases it depends on the gas and the time ...

25 times more potent than that of carbon dioxide, and freshwaters are a major contributor of global

methane emissions Increasing methane emissions are a major contributor to the rising concentration of greenhouse gases in Earth's atmosphere, and are responsible for up to one-third of near-term global heating. During 2019, about 60% (360 million tons) of methane r ...

. A study conducted on Europe’s Lake Constance found that anaerobic methane oxidation coupled to denitrification - also referred to as nitrate/nitrite-dependent anaerobic methane oxidation (n-damo) - is a dominant sink of methane in deep lakes. For a long time, it was believed that the mitigation of methane emissions was only due to aerobic methanotrophic bacteria. However, methane oxidation also takes place in anoxic, or oxygen depleted zones, of freshwater bodies. In the case of Lake Constance, this is carried out by M. oxyfera-like bacteria. M. oxyfera-like bacteria are bacteria similar to Candidatus Methylomirabilis oxyfera, which is a species of bacteria that acts as a denitrifying methanotroph. The results from the study on Lake Constance found that nitrate was depleted in the water at the same depth as methane, which suggests that methane oxidation was coupled to denitrification. It could be inferred that it was M. oxyfera-like bacteria carrying out the methane oxidation because their abundance peaked at the same depth where the methane and nitrate profiles met. This n-damo process is significant because it aids in decreasing methane emissions from deep freshwater bodies and it aids in turning nitrates into nitrogen gas, reducing excess nitrates.

Denitrifying bacteria and the environment

Denitrification effects on limiting plant productivity and producing by-products

The process of denitrification can lower the fertility of soil as nitrogen, a growth-limiting factor, is removed from the soil and lost to the atmosphere. This loss of nitrogen to the atmosphere can eventually be regained via introduced nutrients, as part of the nitrogen cycle. Some nitrogen may also be fixated by species of

nitrifying bacteria 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 oxidat ...

and the

cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...

. Another important environmental issue concerning denitrification is the fact that the process tends to produce large amounts of by-products. Examples of by-products are nitric oxide (NO) and nitrous oxide (N₂O). NO is an

ozone Ozone (), or trioxygen, is an inorganic molecule with the chemical formula . It is a pale blue gas with a distinctively pungent smell. It is an allotrope of oxygen that is much less stable than the diatomic allotrope , breaking down in the l ...

depleting species and N₂O is a potent greenhouse gas which can contribute to global warming.

Denitrifying bacteria use in wastewater treatment

Denitrifying bacteria are an essential component in treating wastewater. Wastewater often contains large amounts of nitrogen (in the form of

ammonium The ammonium cation is a positively-charged polyatomic ion with the chemical formula or . It is formed by the protonation of ammonia (). Ammonium is also a general name for positively charged or protonated substituted amines and quaterna ...

nitrate Nitrate is a polyatomic ion with the chemical formula . Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are soluble in water. An example of an insolu ...

), which could be damaging to human health and ecological processes if left untreated. Many physical, chemical, and biological methods have been used to remove the nitrogenous compounds and purify polluted waters. The process and methods vary, but it generally involves converting ammonium to nitrate, and finally to nitrogen gas. One example of this is ammonia-oxidizing bacteria which have a metabolic feature that, in combination with other nitrogen-cycling metabolic activities, such as nitrite oxidation and denitrification, remove nitrogen from wastewater in activated sludge. Since denitrifying bacteria are

heterotroph A heterotroph (; ) is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but ...

ic, an organic carbon source is supplied to the bacteria in an anoxic basin. With no available oxygen, denitrifying bacteria use the oxygen present in the nitrate to oxidize the carbon. This leads to the creation of nitrogen gas from nitrate, which then bubbles up out of the wastewater.

References

{{Reflist Bacteria Nitrogen cycle Soil biology Fishkeeping Aquariums