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, Alcaligenes , Bacillus and others. File:Pseudomonas stutzeri.jpg

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.{{Cite journal|last1=Ji|first1=Bin|last2=Yang|first2=Kai|last3=Zhu|first3=Lei|last4=Jiang|first4=Yu|last5=Wang|first5=Hongyu|last6=Zhou|first6=Jun|last7=Zhang|first7=Huining|s2cid=85744076|date=August 2015|title=Aerobic denitrification: A review of important advances of the last 30 years|journal=Biotechnology and Bioprocess Engineering|language=en|volume=20|issue=4|pages=643–651|doi=10.1007/s12257-015-0009-0|issn=1226-8372}}

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.

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.{{Cite journal|last1=Ettwig|first1=Katharina F.|last2=Shima|first2=Seigo|last3=van de Pas-Schoonen|first3=Katinka T.|last4=Kahnt|first4=Jörg|last5=Medema|first5=Marnix H.|last6=op den Camp|first6=Huub J. M.|last7=Jetten|first7=Mike S. M.|last8=Strous|first8=Marc|date=November 2008|title=Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea|journal=Environmental Microbiology|volume=10|issue=11|pages=3164–3173|doi=10.1111/j.1462-2920.2008.01724.x|pmid=18721142|bibcode=2008EnvMi..10.3164E |issn=1462-2912|hdl=2066/72144|hdl-access=free}} 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.{{Cite journal|last1=Deutzmann|first1=Joerg S.|last2=Stief|first2=Peter|last3=Brandes|first3=Josephin|last4=Schink|first4=Bernhard|date=2014-12-03|title=Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake|journal=Proceedings of the National Academy of Sciences|volume=111|issue=51|pages=18273–18278|doi=10.1073/pnas.1411617111|pmid=25472842|pmc=4280587|bibcode=2014PNAS..11118273D|issn=0027-8424|doi-access=free}}

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.{{Cite journal|last1=Raghoebarsing|first1=Ashna A.|last2=Pol|first2=Arjan|last3=van de Pas-Schoonen|first3=Katinka T.|last4=Smolders|first4=Alfons J. P.|last5=Ettwig|first5=Katharina F.|last6=Rijpstra|first6=W. Irene C.|last7=Schouten|first7=Stefan|last8=Damsté|first8=Jaap S. Sinninghe|last9=Op den Camp|first9=Huub J. M.|last10=Jetten|first10=Mike S. M.|last11=Strous|first11=Marc|date=April 2006|title=A microbial consortium couples anaerobic methane oxidation to denitrification|journal=Nature|volume=440|issue=7086|pages=918–921|doi=10.1038/nature04617|pmid=16612380|bibcode=2006Natur.440..918R|hdl=1874/22552|s2cid=4413069|issn=0028-0836|url=https://repository.ubn.ru.nl//bitstream/handle/2066/36167/36167.pdf |hdl-access=free}} 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.{{Cite journal|last1=Anenberg|first1=Susan C.|last2=Schwartz|first2=Joel|last3=Shindell|first3=Drew|last4=Amann|first4=Markus|last5=Faluvegi|first5=Greg|last6=Klimont|first6=Zbigniew|last7=Janssens-Maenhout|first7=Greet|last8=Pozzoli|first8=Luca|last9=Van Dingenen|first9=Rita|last10=Vignati|first10=Elisabetta|last11=Emberson|first11=Lisa|date=June 2012|title=Global Air Quality and Health Co-benefits of Mitigating Near-Term Climate Change through Methane and Black Carbon Emission Controls|journal=Environmental Health Perspectives|volume=120|issue=6|pages=831–839|doi=10.1289/ehp.1104301|pmid=22418651|pmc=3385429|bibcode=2012EnvHP.120..831A |issn=0091-6765}} 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.{{Cite journal|last1=Testa|first1=Jeremy Mark|last2=Kemp|first2=W. Michael|date=May 2012|title=Hypoxia-induced shifts in nitrogen and phosphorus cycling in Chesapeake Bay|journal=Limnology and Oceanography|volume=57|issue=3|pages=835–850|doi=10.4319/lo.2012.57.3.0835|bibcode=2012LimOc..57..835T|issn=0024-3590|doi-access=free}}

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, 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.{{Cite journal|last1=Powell|first1=Shane M.|last2=Ferguson|first2=Susan H.|last3=Snape|first3=Ian|last4=Siciliano|first4=Steven D.|date=March 2006|title=Fertilization Stimulates Anaerobic Fuel Degradation of Antarctic Soils by Denitrifying Microorganisms|journal=Environmental Science & Technology|volume=40|issue=6|pages=2011–2017|doi=10.1021/es051818t|pmid=16570629|bibcode=2006EnST...40.2011P|issn=0013-936X}}

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. 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,{{Cite journal|last1=Boucher|first1=Olivier|last2=Friedlingstein|first2=Pierre|last3=Collins|first3=Bill|last4=Shine|first4=Keith P|date=October 2009|title=The indirect global warming potential and global temperature change potential due to methane oxidation|journal=Environmental Research Letters|volume=4|issue=4|pages=044007|doi=10.1088/1748-9326/4/4/044007|bibcode=2009ERL.....4d4007B|issn=1748-9326|doi-access=free}} and freshwaters are a major contributor of global methane emissions.

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 considered 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.{{Cite journal|last1=Wu|first1=M. L.|last2=van Teeseling|first2=M. C. F.|last3=Willems|first3=M. J. R.|last4=van Donselaar|first4=E. G.|last5=Klingl|first5=A.|last6=Rachel|first6=R.|last7=Geerts|first7=W. J. C.|last8=Jetten|first8=M. S. M.|last9=Strous|first9=M.|last10=van Niftrik|first10=L.|date=2011-10-21|title=Ultrastructure of the Denitrifying Methanotroph "Candidatus Methylomirabilis oxyfera," a Novel Polygon-Shaped Bacterium|journal=Journal of Bacteriology|volume=194|issue=2|pages=284–291|doi=10.1128/jb.05816-11|pmid=22020652|pmc=3256638|issn=0021-9193}}

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.

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.

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 ecological processes if left untreated. Many physical, chemical, and biological methods have been used to remove the nitrogenous compounds and purify wastewaters.{{Cite journal|last1=Huang|first1=Ting-Lin|last2=Zhou|first2=Shi-Lei|last3=Zhang|first3=Hai-Han|last4=Zhou|first4=Na|last5=Guo|first5=Lin|last6=Di|first6=Shi-Yu|last7=Zhou|first7=Zi-Zhen|date=2015-04-10|title=Nitrogen Removal from Micro-Polluted Reservoir Water by Indigenous Aerobic Denitrifiers|journal=International Journal of Molecular Sciences|volume=16|issue=4|pages=8008–8026|doi=10.3390/ijms16048008|issn=1422-0067|pmc=4425064|pmid=25867475|doi-access=free}} The process and methods vary, but it generally involves converting ammonium to nitrate via the 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.{{Cite journal|last1=Park|first1=Hee-Deung|last2=Noguera|first2=Daniel R|date=August 2004|title=Evaluating the effect of dissolved oxygen on ammonia-oxidizing bacterial communities in activated sludge|journal=Water Research|language=en|volume=38|issue=14–15|pages=3275–3286|doi=10.1016/j.watres.2004.04.047|pmid=15276744|bibcode=2004WatRe..38.3275P }} 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.{{Citation|last1=Ni|first1=Bing-Jie|title=Chapter 16. Denitrification Processes for Wastewater Treatment|date=2016|work=Metallobiology|pages=368–418|editor-last=Moura|editor-first=Isabel|publisher=Royal Society of Chemistry|doi=10.1039/9781782623762-00368|isbn=978-1-78262-334-2|last2=Pan|first2=Yuting|last3=Guo|first3=Jianhua|last4=Virdis|first4=Bernardino|last5=Hu|first5=Shihu|last6=Chen|first6=Xueming|last7=Yuan|first7=Zhiguo|editor2-last=Moura|editor2-first=José J G|editor3-last=Pauleta|editor3-first=Sofia R|editor4-last=Maia|editor4-first=Luisa B}}

• Nitrifying bacteria
• Nitrogen Cycle

{{Reflist}}

Category:Bacteria

Category:Nitrogen cycle

Category:Soil biology

Category:Fishkeeping

Category:Aquariums