Ammonia-Oxidizing Bacteria: Their Biochemistry and Molecular Biology

Luis A. Sayavedra-Soto; Daniel J. Arp

doi:10.1128/9781555817145.ch2

Chapter 2 : Ammonia-Oxidizing Bacteria: Their Biochemistry and Molecular Biology

Authors: Luis A. Sayavedra-Soto¹, Daniel J. Arp²

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Affiliations: 1: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; 2: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331

Content Type: Monograph

Publication Year: 2011

Category: Environmental Microbiology

Book DOI: 10.1128/9781555817145

Chapter DOI: 10.1128/9781555817145.ch2

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Abstract:

This chapter covers the current understanding of the biochemical and genetic underpinnings relevant to ammonia oxidation by aerobic bacteria. Ammonia is released into the environment mainly from the decay of organic matter or from the use of NH3-based fertilizers in agriculture and serves as an N supply to plants and microorganisms. Ammonia-oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA), and anaerobic ammonia-oxidizing (anammox) bacteria can derive energy for growth from the oxidation of NH3. Bacterium has the advantages of growing relatively rapid for an AOB and being able to tolerate high concentrations of ammonium (up to 100 mM) and nitrite. The genomes of AOB also show that all encode four specialized proteins perform the oxidation of NH3: ammonia monooxygenase (AMO), hydroxylamine oxidoreductase (HAO), and cytochromes c554 (cyt c554) and cm552 (cyt cm552). The electron transport chain of N. europaea has the same major electron transfer complexes as the electron transport chain of mitochondria.

Citation: Sayavedra-Soto L, Arp D. 2011. Ammonia-Oxidizing Bacteria: Their Biochemistry and Molecular Biology, p 11-37. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch2

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Ammonia-Oxidizing Bacteria: Their Biochemistry and Molecular Biology

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/content/10.1128/9781555817145.ch02.ch02fig01

FIGURE 1

Electron microscopy picture of thin sections of cells of N. europaea, some of which are dividing. Note the ICM in the periphery of the cells.

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10.1128/9781555817145/f0012-01.gif

FIGURE 1

Electron microscopy picture of thin sections of cells of N. europaea, some of which are dividing. Note the ICM in the periphery of the cells.

/content/10.1128/9781555817145.ch02.ch02fig02

FIGURE 2

Catabolism of ammonia: proteins involved, product and flow of electrons.

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FIGURE 2

Catabolism of ammonia: proteins involved, product and flow of electrons.

/content/10.1128/9781555817145.ch02.ch02fig03

FIGURE 3

Model for the oxidation of ammonia and the proteins involved. bc1 , complex III; QH2, quinol. (Adapted from Arp and Stein [2003] and Hooper et al. [1997] with permission.)

10.1128/9781555817145/f0015-01_thmb.gif

10.1128/9781555817145/f0015-01.gif

FIGURE 3

Model for the oxidation of ammonia and the proteins involved. bc1 , complex III; QH2, quinol. (Adapted from Arp and Stein [2003] and Hooper et al. [1997] with permission.)

/content/10.1128/9781555817145.ch02.ch02fig04

FIGURE 4

Reactions catalyzed by AMO are broad in substrate specificity and include oxidation and dehydrogenation (Hoffman and Lee, 1953; Hyman and Wood, 1983; Vanelli and Hooper, 1995; Keener and Arp, 1994).

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FIGURE 4

Reactions catalyzed by AMO are broad in substrate specificity and include oxidation and dehydrogenation (Hoffman and Lee, 1953; Hyman and Wood, 1983; Vanelli and Hooper, 1995; Keener and Arp, 1994).

/content/10.1128/9781555817145.ch02.ch02fig05

FIGURE 5

Three-dimensional X-ray crystal structure of hydroxylamine oxidoreductase from N. europaea. Each subunit is shown in ribbon form of a different shade. The heme molecules are shown as stick structures. The figure was derived from file PDB ID 1FGJ (www.pdb.org) ( Igarashi et al., 1997 ) and MacPyMOLsoftware (www.pymol.org).

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FIGURE 5

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FIGURE 6

Central carbon metabolism in N. europaea under oxic conditions.

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FIGURE 6

Central carbon metabolism in N. europaea under oxic conditions.

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FIGURE 7

Electron microscopy picture of thin sections of N. europaea treated with acid-thiosemicarbazideosmium tetroxide to visualize glycogen granules in the cells (dark spots).

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FIGURE 7

Electron microscopy picture of thin sections of N. europaea treated with acid-thiosemicarbazideosmium tetroxide to visualize glycogen granules in the cells (dark spots).

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