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Chapter 11 : Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species

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Abstract:

This chapter attempts to place the physiology and biochemistry of nitrite-oxidizing bacteria (NOB) into context with information derived from the annotated genomes. Daims et al. provide an excellent review of insights gained into the physiology and ecology of that were obtained primarily by using genomics tools and other cultivation-independent methods. The genome of is the largest of the Nitrobacter genomes and appears to have maintained a greater level of metabolic flexibility and adaptability than the other sequenced representative. The genes on the largest plasmid, pPB13, appear to be biased toward carbon/energy metabolism. A discussion of the current status of knowledge about carboxysomes is presented in this chapter. The chapter talks about genomic evidence for a potentially different mechanism of CO fixation by '' Nitrospira defluvii'' presented by Daims et al. The glyoxylate pathway genes were annotated, and several genes encoding for enzymes that facilitate metabolism of pyruvate, acetate, and glycerol were identified. The genome analysis of has provided some new and confirmatory insights into the biology of this genus.

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11

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Nitrobacter winogradskyi
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Figures

Image of FIGURE 1
FIGURE 1

Global gene conservation in Each circle represents the total number of gene types in each genome. Overlapping regions depict the number of gene types shared between the respective genomes. The numbers outside the circles indicate the total number of genes identified in each genome, including paralogs/gene duplications. (Reproduced from [ ] with permission.)

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
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Image of FIGURE 2
FIGURE 2

Electron micrographs of and (A) Nb255 (image by William Hickey). (B) spp. enriched from activated sludge. (C) 231 (images in panels B and C by Eva Spieck).

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
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Image of FIGURE 3
FIGURE 3

Electron micrographs of and (A) 347. (B) 6678 (images by Eva Spieck).

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
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Image of FIGURE 4
FIGURE 4

Electron micrographs of “ Nitrospira bockiana.” (a) Planktonic cells. (b) Planktonic cell surrounded by EPS. (c) Microcolony surrounded in EPS. (d) Pleomorphic microcolony. Bars, 0.25 µm (panels a to c) or 0.5 µm (panel d). (Reproduced from the [ ] with permission from the Society of General Microbiology.)

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
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Image of FIGURE 5
FIGURE 5

Organization of NXR operons of and species. Each arrow represents one gene. Locus numbers are indicated within the arrows, and putative gene names are indicated above each arrow.

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
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Image of FIGURE 6
FIGURE 6

Putative organization of NXR and associative electron transport in the cytoplasmic membrane of a sp. Many details remain unknown or uncertain. Although the quinone pool plays a key role in most prokaryotic electron transport and transmembrane H translocation schemes, a complete biosynthetic pathway for menaquionone or ubiquinone biosynthesis could not be annotated in The details of the NO /NO transport mechanism are unknown. The stoichiometry of proton translocation by cytochrome oxidase is unknown. The interrelationships between the members of the electron transport scheme involved with NXR for carrying out NO oxidation versus dissimilatory NO reduction are unknown. The specific mechanism of association of NXR with the cytoplasmic membrane is unknown.

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
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Image of FIGURE 7
FIGURE 7

Model of NirK function and NO metabolism in (A) In the presence of O, most electrons are thought to be directed toward respiration. (B) Under low-oxygen conditions, NirK expression increases, promoting the potential for NO -dependent NO production and favoring electron flux toward reductant generation. Excess reductant would be consumed via nitrite reduction and PHB synthesis to maintain a balanced redox state. Cyt, cytochrome oxidase; NirK, nitrite reductase; I, NADH dehydrogenase (Complex I). (Reproduced from [ ] and the Society for Applied Microbiology/Blackwell Publishing with permission.)

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
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Image of FIGURE 8
FIGURE 8

(A) Carboxysome shell protein structure and function. (B) RuBisCO and carboxysome gene arrangement in CsoS1 forms hexamers that pack into a two-dimensional molecular layer. CsoS4 forms the vertices of the shell. Electrostatic pores (positively charged) through CsoS1 may function to transport bicarbonate (negatively charged) into and out of the carboxysome. Within the CsoS1/CsoS4 protein shell, the carboxysome encapsulates the CO-fixing enzymes, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO; CbbLS) and carbonic anhydrase (CA; CsoS3), to enhance the efficiency of CO fixation and the formation of two molecules of 3-phosphoglycerate (PGA). The function of CsoS2 is unknown. (Assembled from images provided by Todd Yeates.)

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
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Tables

Generic image for table
TABLE 1

Differentiating properties among the genera of NOB

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
Generic image for table
TABLE 2

General genomic characteristics of NOB

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11
Generic image for table
TABLE 3

Unique genes and putative functional biases in the genus

Citation: Starkenburg S, Spieck E, Bottomley P. 2011. Metabolism and Genomics of Nitrite-Oxidizing Bacteria: Emphasis on Studies of Pure Cultures and of Species, p 267-293. In Ward B, Arp D, Klotz M (ed), Nitrification. ASM Press, Washington, DC. doi: 10.1128/9781555817145.ch11

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