Chapter 5 : Heterotrophic Nitrification and Nitrifier Denitrification

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This chapter on describes the physiology and biochemical pathways of heterotrophic nitrification and nitrifier denitrification, a description of the genetic and organism diversity involved, and a brief description of techniques to discern one process from another. A final perspective is offered on how anthropogenic input of nitrogen affects microbial transformations of inorganic N with particular emphasis on emissions of gaseous N-oxides to the atmosphere. Ammonia-oxidizing bacteria (AOB) can produce nitrous oxide by two different pathways, hydroxylamine oxidation or nitrifier denitrification. The technical breakthrough to discriminate nitrous oxide production from nitrification, nitrifier denitrification, and denitrification was the detection of individual nitrous oxide isotopomers using isotope ratio mass spectroscopy. The δN of nitrous oxide produced from hydroxylamine oxidation was significantly more positive than that from nitrifier denitrification or denitrification. This study found that the site preference of N in nitrous oxide was significantly different during nitrifier denitrification by AOB versus denitrification by two species of . The chapter touches on largely understudied, but highly significant, processes of inorganic nitrogen metabolism that impact the global nitrogen cycle. Many of the studies cited in this chapter suggest that these processes are strongly influenced by the availability of carbon, nitrogen, and oxygen in the environment. It describes microbial populations and processes that make nitrous oxide in response to increased fertilizer use, nitrogen deposition, and hypoxia.

Citation: Stein L. 2011. Heterotrophic Nitrification and Nitrifier Denitrification, p 95-114. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch5
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Image of FIGURE 1

Pathways of ammonia oxidation and nitrifier denitrification in Dashed lines indicate the direction of electron flow, with thinner lines indicating less electron flow than thicker lines. The question mark above cytochrome c indicates the uncertainty of whether electrons are delivered to this enzyme directly from HAO or via cytochrome c ( ). Similarly, the question mark in the middle of NcgA, NcgBC, and NirK indicates that order of electron transfer among these proteins remains uncharacterized. NorCB, nitric oxide reductase; Ncg, products of cluster genes; Q, quinone.

Citation: Stein L. 2011. Heterotrophic Nitrification and Nitrifier Denitrification, p 95-114. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch5
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Image of FIGURE 2

Putative pathway for heterotrophic nitrification and aerobic denitrification in GB17 (based on model by ). Electron carriers between the putative hydroxylamine oxidase enzyme and members of the denitrification pathway remain uncharacterized. AMO, putative ammonia monooxygenase; HO, putative hydroxylamine oxidase; NorCB, nitric oxide reductase; NAP, periplasmic nitrate reductase; Q, quinone.

Citation: Stein L. 2011. Heterotrophic Nitrification and Nitrifier Denitrification, p 95-114. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch5
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Image of FIGURE 3

Pathway for hybrid respiration of oxygen and nitrate in Denitrification is linked to formate oxidation in the mitochrondria as per the model presented by . FDH, formate dehydrogenase; Nar, nitrate reductase; P450nor, nitric oxide reductase.

Citation: Stein L. 2011. Heterotrophic Nitrification and Nitrifier Denitrification, p 95-114. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch5
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Image of FIGURE 4

Two pathways for nitrous oxide production in : hydroxylamine oxidation pathway and nitrifier denitrification pathway. Lightly shaded enzymes indicate reductases, and darkly shaded enzymes indicate oxidative processes. CytL, cytochrome P460; NorB, nitric oxide reductase implicated in denitrification pathway; NOR, generic nitric oxide reductase (descriptive of multiple enzymes in ).

Citation: Stein L. 2011. Heterotrophic Nitrification and Nitrifier Denitrification, p 95-114. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch5
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Characteristics of putative bacterial hydroxylamine-oxidizing enzymes

Citation: Stein L. 2011. Heterotrophic Nitrification and Nitrifier Denitrification, p 95-114. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch5
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Characteristics of select heterotrophic nitrifying microorganisms

Citation: Stein L. 2011. Heterotrophic Nitrification and Nitrifier Denitrification, p 95-114. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch5
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Methods to discriminate between heterotrophic and chemolithotrophic nitrifiers

Citation: Stein L. 2011. Heterotrophic Nitrification and Nitrifier Denitrification, p 95-114. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch5

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