Denitrifying bacteria

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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. [1] Denitrification is performed by a variety of denitrifying bacteria that are widely distributed in soils and sediments and that use oxidized nitrogen compounds such as nitrate and nitrite in the absence of oxygen as a terminal electron acceptor. [2] They metabolize nitrogenous compounds using various enzymes, including nitrate reductase (NAR), nitrite reductase (NIR), nitric oxide reductase (NOR) and nitrous oxide reductase (NOS), turning nitrogen oxides back to nitrogen gas () or nitrous oxide ().

Contents

Diversity of denitrifying bacteria

There is a great diversity in biological traits. [1] 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. [3]

Denitrifying include for example several species of Pseudomonas , Alcaligenes , Bacillus and others.

Pseudomonas stutzeri, a species of denitrifying bacteria Pseudomonas stutzeri.jpg
Pseudomonas stutzeri, a species of denitrifying bacteria

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. [1] 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. [1] 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. [4]

Denitrification mechanism

Denitrifying bacteria use denitrification to generate ATP. [5]

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. [5]

Oxidation of methane and denitrification

Anaerobic oxidation of methane coupled to denitrification

Anaerobic denitrification coupled to methane oxidation was first observed in 2008, with the isolation of a methane-oxidizing bacterial strain found to oxidize methane independently. [6] 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. [7]

The process of anaerobic denitrification may contribute significantly to the global methane and nitrogen cycles, especially in light of the recent influx of both due to anthropogenic changes. [8] The extent to which anthropogenic methane affects the atmosphere is known to be a significant driver of climate change, and considering it is multiple times more potent than carbon dioxide. [9] 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. [7] Anaerobic denitrification as a mechanism has been shown to be capable of removing the excess nitrate caused by fertilizer runoff, even in hypoxic conditions. [10]

Additionally, microorganisms which employ this type of metabolism may be employed in bioremediation, as shown by a 2006 study of hydrocarbon contamination in the Antarctic, [9] as well as a 2016 study which successfully increased the rates of denitrification by altering the environment housing the bacteria. [10] 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. [11]

Role of denitrifying bacteria as a methane sink

Denitrifying bacteria have been found to play a significant role in the oxidation of methane (CH4) (where methane is converted to CO2, water, and energy) in deep freshwater bodies of water. [7] This is important because methane is the second most significant anthropogenic greenhouse gas, with a global warming potential 25 times more potent than that of carbon dioxide, [12] and freshwaters are a major contributor of global methane emissions. [7]

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. [7] M. oxyfera-like bacteria are bacteria similar to Candidatus Methylomirabilis oxyfera, which is a species of bacteria that acts as a denitrifying methanotroph. [13]

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. [7] 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 and the cyanobacteria. 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 depleting species and N2O is a potent greenhouse gas which can contribute to global warming. [3]

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 or nitrate), 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. [14] The process and methods vary, but it generally involves converting ammonium to nitrate via nitrification process with ammonium oxidizing bacteria (AOB, NH4+→NO2-) and nitrite oxidizing bacteria (NOB, NO2-→NO3-), and finally to nitrogen gas via denitrification. 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. [15] Since denitrifying bacteria are heterotrophic, an organic carbon source is supplied to the bacteria in an anoxic basin. With no available oxygen, denitrifying bacteria use the redox of nitrate to oxidize the carbon. This leads to the creation of nitrogen gas from nitrate, which then bubbles up out of the wastewater. [16]

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 nitrate via the intermediary nitrite. Nitrification is an important step in the nitrogen cycle in soil. The process of complete nitrification may occur through separate organisms or entirely within one organism, as in comammox bacteria. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.

<span class="mw-page-title-main">Nitrous acid</span> Chemical compound

Nitrous acid is a weak and monoprotic acid known only in solution, in the gas phase, and in the form of nitrite salts. It was discovered by Carl Wilhelm Scheele, who called it "phlogisticated acid of niter". Nitrous acid is used to make diazonium salts from amines. The resulting diazonium salts are reagents in azo coupling reactions to give azo dyes.

The nitrite ion has the chemical formula NO−
2. Nitrite is widely used throughout chemical and pharmaceutical industries. The nitrite anion is a pervasive intermediate in the nitrogen cycle in nature. The name nitrite also refers to organic compounds having the –ONO group, which are esters of nitrous acid.

Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.

<span class="mw-page-title-main">Denitrification</span> Microbially facilitated process

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 denitrification as a type of respiration that reduces oxidized forms of nitrogen in response to the oxidation of an electron donor such as organic matter. The preferred nitrogen electron acceptors in order of most to least thermodynamically favorable include nitrate (NO3−), nitrite (NO2−), nitric oxide (NO), nitrous oxide (N2O) finally resulting in the production of dinitrogen (N2) completing the nitrogen cycle. Denitrifying microbes require a very low oxygen concentration of less than 10%, as well as organic C for energy. Since denitrification can remove NO3−, reducing its leaching to groundwater, it can be strategically used to treat sewage or animal residues of high nitrogen content. Denitrification can leak N2O, which is an ozone-depleting substance and a greenhouse gas that can have a considerable influence on global warming.

<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.

<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.

In atmospheric chemistry, NOx is shorthand for nitric oxide and nitrogen dioxide, the nitrogen oxides that are most relevant for air pollution. These gases contribute to the formation of smog and acid rain, as well as affecting tropospheric ozone.

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.

Paracoccus denitrificans, is a coccoid bacterium known for its nitrate reducing properties, its ability to replicate under conditions of hypergravity and for being a relative of the eukaryotic mitochondrion.

Anaerobic oxidation of methane (AOM) is a methane-consuming microbial process occurring in anoxic marine and freshwater sediments. AOM is known to occur among mesophiles, but also in psychrophiles, thermophiles, halophiles, acidophiles, and alkophiles. During AOM, methane is oxidized with different terminal electron acceptors such as sulfate, nitrate, nitrite and metals, either alone or in syntrophy with a partner organism.

Nitric oxide reductase, an enzyme, catalyzes the reduction of nitric oxide (NO) to nitrous oxide (N2O). The enzyme participates in nitrogen metabolism and in the microbial defense against nitric oxide toxicity. The catalyzed reaction may be dependent on different participating small molecules: Cytochrome c (EC: 1.7.2.5, Nitric oxide reductase (cytochrome c)), NADPH (EC:1.7.1.14), or Menaquinone (EC:1.7.5.2).

<span class="mw-page-title-main">Nitrous-oxide reductase</span> Class of enzymes

In enzymology, a nitrous oxide reductase also known as nitrogen:acceptor oxidoreductase (N2O-forming) is an enzyme that catalyzes the final step in bacterial denitrification, the reduction of nitrous oxide to dinitrogen.

Aerobic denitrification, or co-respiration, the simultaneous use of both oxygen (O2) and nitrate (NO−3) as oxidizing agents, performed by various genera of microorganisms. This process differs from anaerobic denitrification not only in its insensitivity to the presence of oxygen, but also in its higher potential to form nitrous oxide (N2O) as a byproduct.

"Candidatus Scalindua" is a bacterial genus, and a proposed member of the order Planctomycetales. These bacteria lack peptidoglycan in their cell wall and have a compartmentalized cytoplasm. They are ammonium oxidizing bacteria found in marine environments.

<span class="mw-page-title-main">Cattle urine patches</span> Grass damage by cattle urine

Urine patches in cattle pastures generate large concentrations of the greenhouse gas nitrous oxide through nitrification and denitrification processes in urine-contaminated soils. Over the past few decades, the cattle population has increased more rapidly than the human population. Between the years 2000 and 2050, the cattle population is expected to increase from 1.5 billion to 2.6 billion. When large populations of cattle are packed into pastures, excessive amounts of urine soak into soils. This increases the rate at which nitrification and denitrification occur and produce nitrous oxide. Currently, nitrous oxide is one of the single most important ozone-depleting emissions and is expected to remain the largest throughout the 21st century.

Dissimilatory nitrate reduction to ammonium (DNRA), also known as nitrate/nitrite ammonification, is the result of anaerobic respiration by chemoorganoheterotrophic microbes using nitrate (NO3−) as an electron acceptor for respiration. In anaerobic conditions microbes which undertake DNRA oxidise organic matter and use nitrate (rather than oxygen) as an electron acceptor, reducing it to nitrite, and then to ammonium (NO3− → NO2− → NH4+).

An oxygen minimum zone (OMZ) is characterized as an oxygen-deficient layer in the world's oceans. Typically found between 200m to 1500m deep below regions of high productivity, such as the western coasts of continents. OMZs can be seasonal following the spring-summer upwelling season. Upwelling of nutrient-rich water leads to high productivity and labile organic matter, that is respired by heterotrophs as it sinks down the water column. High respiration rates deplete the oxygen in the water column to concentrations of 2 mg/L or less forming the OMZ. OMZs are expanding, with increasing ocean deoxygenation. Under these oxygen-starved conditions, energy is diverted from higher trophic levels to microbial communities that have evolved to use other biogeochemical species instead of oxygen, these species include Nitrate, Nitrite, Sulphate etc. Several Bacteria and Archea have adapted to live in these environments by using these alternate chemical species and thrive. The most abundant phyla in OMZs are Pseudomonadota, Bacteroidota, Actinomycetota, and Planctomycetota.

<i>Methylomirabilis oxyfera</i> Bacteria species

Candidatus "Methylomirabilis oxyfera" is a candidate species of Gram-negative bacteria belonging to the NC10 phylum, characterized for its capacity to couple anaerobic methane oxidation with nitrite reduction in anoxic environments. To acquire oxygen for methane oxidation, M. oxyfera utilizes an intra-aerobic pathway through the reduction of nitrite (NO2) to dinitrogen (N2) and oxygen.

References

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  2. ↑ Averill, B.A.; Tiedje, J.M. (1982-02-08). "The chemical mechanism of microbioal denitrification". FEBS Letters. 138 (1): 8–12. doi: 10.1016/0014-5793(82)80383-9 . PMID   7067831. S2CID   84456021.
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  4. ↑ Ji, Bin; Yang, Kai; Zhu, Lei; Jiang, Yu; Wang, Hongyu; Zhou, Jun; Zhang, Huining (August 2015). "Aerobic denitrification: A review of important advances of the last 30 years". Biotechnology and Bioprocess Engineering. 20 (4): 643–651. doi:10.1007/s12257-015-0009-0. ISSN   1226-8372. S2CID   85744076.
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  16. ↑ Ni, Bing-Jie; Pan, Yuting; Guo, Jianhua; Virdis, Bernardino; Hu, Shihu; Chen, Xueming; Yuan, Zhiguo (2016), Moura, Isabel; Moura, José J G; Pauleta, Sofia R; Maia, Luisa B (eds.), "CHAPTER 16. Denitrification Processes for Wastewater Treatment", Metallobiology, Royal Society of Chemistry, pp. 368–418, doi:10.1039/9781782623762-00368, ISBN   978-1-78262-334-2
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