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

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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 NH-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 NH. 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 NH: ammonia monooxygenase (AMO), hydroxylamine oxidoreductase (HAO), and cytochromes c (cyt c) and cm(cyt cm). The electron transport chain of 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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Amino Acid Synthesis
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Carbon monoxide
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Image of FIGURE 1
FIGURE 1

Electron microscopy picture of thin sections of cells of 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
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Image of FIGURE 2
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
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Image of FIGURE 3
FIGURE 3

Model for the oxidation of ammonia and the proteins involved. , complex III; QH, quinol. (Adapted from and 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
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Image of FIGURE 4
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
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Image of FIGURE 5
FIGURE 5

Three-dimensional X-ray crystal structure of hydroxylamine oxidoreductase from 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) ( ) 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
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Image of FIGURE 6
FIGURE 6

Central carbon metabolism in 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
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Image of FIGURE 7
FIGURE 7

Electron microscopy picture of thin sections of 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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