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Chapter 4 : Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed

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Abstract:

This chapter focuses on microbial diversity and the catabolism of nonintermediary chemical compounds by disparate genera of prokaryotes. It describes the role that prokaryotes and fungi play collectively in biodegradation and how their extensive biocatalytic potential derives from a long evolutionary history. But microbial diversity also implies that individual bacteria and fungi are metabolically unique. In this context, it is useful to think of microbes as metabolic machines, dependent on gathering chemicals from their environment to obtain carbon, other elements, and energy to compete favorably against other microbes. Fungi are prominent in many environmental biodegradation processes and also in industrial biocatalysis. Four of the five major phyla of fungi are commonly used in industry. Of the ascomycota, and are the major fungal genera used in alcoholic-beverage fermentations. Many of the best-studied prokaryotes are aerobic proteobacteria and the high-G + C gram-positive bacteria. These, along with the fungus , are the examples discussed in the chapter. It is important to point out that some of the extensive catabolic activities of this class are based on the broad substrate specificities of a few oxygenases and related enzymes which handle the oxygenated intermediates.

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4

Key Concept Ranking

Chemicals
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Polycyclic Aromatic Hydrocarbons
0.49226928
Gram-Positive Bacteria
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16s rRNA Sequencing
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Gram-Negative Bacteria
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Figures

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Figure 4.1

Divergence in the metabolism of aromatic hydrocarbons by prokaryotes and eukaryotes.

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
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Figure 4.2

Taxonomic tree of the bacteria with groups heavily represented in the UM-BBD highlighted in green. (From reference with permission.)

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
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Image of Figure 4.3
Figure 4.3

Part of the carbon cycle showing the metabolism of single-carbon compounds and reactions which feed into the cycle.

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
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Figure 4.4

Continuous acrylamide production by B23 in a fed-batch reactor. (From reference with kind permission from Kluwer Academic Publishers.)

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
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Image of Figure 4.5
Figure 4.5

Metabolic pathway for the microbial desulfurization of dibenzothiophene. Substrate and enzyme (green) names are shown in boxes.

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
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Image of Figure 4.6
Figure 4.6

Dioxygenase-catalyzed oxidation of indene to yield -(l ,2 )-dihydroxyindan, useful for the production of the anti-HIV drug indinavir.

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
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Figure 4.7

Consortial metabolism of atrazine, with reactions catalyzed by different bacteria in separate boxes.

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
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Figure 4.8

Output of the UM-BBD “create a pathway” function starting with nitrobenzene.

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
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Tables

Generic image for table
Table 4.1

Niches and numbers of prokaryotes on Earth

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
Generic image for table
Table 4.2

Phyla and classes of fungi active in hydroxylation reactions

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
Generic image for table
Table 4.3

Fungal hydroxylation of steroid substrates

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
Generic image for table
Table 4.4

Industrially important enzymes produced by fungi

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
Generic image for table
Table 4.5

Reclassification of bacterial strains previously classified as species

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
Generic image for table
Table 4.6

Microbial genera known to biodegrade organic compounds, represented in the UM-BBD on 15 August 1999

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
Generic image for table
Table 4.7

Taxonomic distribution of bacteria for which biodegradation reactions were depicted on the UM-BBD as of 15 August 1999

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
Generic image for table
Table 4.8

Prokaryotes from taxonomic groups underrepresented in the biodegradation literature, recently reported to catalyze biodegradation reactions

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4
Generic image for table
Table 4.9

Compounds known or proposed to be oxidized by F1

Citation: Wackett L, Hershberger C. 2001. Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed, p 39-69. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch4

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