Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed

doi:10.1128/9781555818036.ch4

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

Authors: Lawrence P. Wackett¹, C. Douglas Hershberger²

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Affiliations: 1: Department of Biochemistry, Molecular Biology & Biophysics and Biological Process Technology Institute, University of Minnesota, St. Paul, Minnesota 55108-1030; 2: Biological Process Technology Institute University of Minnesota, St. Paul, Minnesota 55108-1030

Content Type: Textbook

Publication Year: 2001

Category: Applied and Industrial Microbiology; Environmental Microbiology

Book DOI: 10.1128/9781555818036

Chapter DOI: 10.1128/9781555818036.ch4

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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, Saccharomyces and Schizosaccharomyces 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 Cunninghamella elegans, 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

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Polycyclic Aromatic Hydrocarbons: 0.49226928
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16s rRNA Sequencing: 0.4309943
Gram-Negative Bacteria: 0.41779307

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Figures

Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed

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Figure 4.1

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

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Figure 4.1

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

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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 44 with permission.)

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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 44 with permission.)

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Figure 4.3

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

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Figure 4.3

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

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Figure 4.4

Continuous acrylamide production by P. chlororaphis B23 in a fed-batch reactor. (From reference 42 with kind permission from Kluwer Academic Publishers.)

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Figure 4.4

Continuous acrylamide production by P. chlororaphis B23 in a fed-batch reactor. (From reference 42 with kind permission from Kluwer Academic Publishers.)

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Figure 4.5

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

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Figure 4.5

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

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Figure 4.6

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

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Figure 4.6

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

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Figure 4.7

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

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Figure 4.7

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

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Figure 4.8

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

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Figure 4.8

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

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Tables

Microbial Diversity: Catabolism of Organic Compounds Is Broadly Distributed

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Table 4.1

Niches and numbers of prokaryotes on Earth a

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Table 4.1

Niches and numbers of prokaryotes on Earth a

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Table 4.2

Phyla and classes of fungi active in hydroxylation reactions a

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Table 4.2

Phyla and classes of fungi active in hydroxylation reactions a

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Table 4.3

Fungal hydroxylation of steroid substrates a

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Table 4.3

Fungal hydroxylation of steroid substrates a

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Table 4.4

Industrially important enzymes produced by fungi

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Table 4.4

Industrially important enzymes produced by fungi

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Table 4.5

Reclassification of bacterial strains previously classified as Pseudomonas species

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Table 4.5

Reclassification of bacterial strains previously classified as Pseudomonas species

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Table 4.6

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

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Table 4.6

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

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Table 4.7

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

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Table 4.7

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

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Table 4.8

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

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Table 4.8

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

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Table 4.9

Compounds known or proposed to be oxidized by P. putida F1 a

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Table 4.9

Compounds known or proposed to be oxidized by P. putida F1 a