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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
Figures
Ammonia-Oxidizing Bacteria: Their Biochemistry and Molecular Biology
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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
/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.
10.1128/9781555817145/f0012-01_thmb.gif
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.
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
/content/10.1128/9781555817145.ch02.ch02fig02
FIGURE 2
Catabolism of ammonia: proteins involved, product and flow of electrons.
10.1128/9781555817145/f0014-01_thmb.gif
10.1128/9781555817145/f0014-01.gif
FIGURE 2
Catabolism of ammonia: proteins involved, product and flow of electrons.
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
/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.)
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
/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).
10.1128/9781555817145/f0018-01_thmb.gif
10.1128/9781555817145/f0018-01.gif
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).
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
/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).
10.1128/9781555817145/f0022-01_thmb.gif
10.1128/9781555817145/f0022-01.gif
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).
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
/content/10.1128/9781555817145.ch02.ch02fig06
FIGURE 6
Central carbon metabolism in N. europaea under oxic conditions.
10.1128/9781555817145/f0027-01_thmb.gif
10.1128/9781555817145/f0027-01.gif
FIGURE 6
Central carbon metabolism in N. europaea under oxic conditions.
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
/content/10.1128/9781555817145.ch02.ch02fig07
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).
10.1128/9781555817145/f0029-01_thmb.gif
10.1128/9781555817145/f0029-01.gif
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).
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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