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Chapter 2 : Selective Isolation of Actinobacteria

Author: Michael Goodfellow
Content Type: Reference
Publication Year: 2010

Category: Applied and Industrial Microbiology

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Abstract:

This chapter deals with the principles and practices currently used to selectively isolate and recognize previously uncultivated taxa. Actinobacteria mainly occur as saprophytes in diverse natural habitats, including soil, the initial focus of selective isolation studies. Various pretreatments can be used to select for different fractions of actinobacterial communities present in environmental samples. Nutrient amendment and baiting techniques are used to increase the populations of specific fractions of actinobacterial communities in environmental samples to facilitate their isolation on nutrient and selective media. Soil amendments with substrates such as chitin and keratin were first used by Jensen to boost the numbers of streptomycetes. This approach has fallen into neglect to some extent, but does provide an effective way of enhancing specific components of actinobacterial communities in soil. Until recently, relatively little effort was made to evaluate the effectiveness of procedures recommended for the isolation of specific fractions of actinobacterial communities present in natural habitats. The assignment of unknown actinobacteria to either formally described or novel taxa is essentially a two-stage process. The identity of representative isolates can also be achieved by using other molecular systematic procedures, notably by the use of taxon-specific 16S rRNA oligonucleotide primers. The application of reliable selective isolation and characterization procedures to surveys of the cultivable actinobacteria in poorly studied and neglected habitats is yielding a steady flow of novel taxa.

Citation: Goodfellow M. 2010. Selective Isolation of Actinobacteria, p 13-27. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch2
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Selective Isolation of Actinobacteria
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Citation: Goodfellow M. 2010. Selective Isolation of Actinobacteria, p 13-27. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch2
/content/10.1128/9781555816827.ch02.ch02fig01
FIGURE 1
Hierarchic classification of the phylum based on 16S rRNA gene sequences and taxon-specific 16S rDNA signature nucleotides (adapted from reference ).
10.1128/9781555816827/f0014-01_thmb.gif
10.1128/9781555816827/f0014-01.gif
Image of FIGURE 1
FIGURE 1

Hierarchic classification of the phylum based on 16S rRNA gene sequences and taxon-specific 16S rDNA signature nucleotides (adapted from reference ).

Citation: Goodfellow M. 2010. Selective Isolation of Actinobacteria, p 13-27. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch2
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Tables

Selective Isolation of Actinobacteria
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Citation: Goodfellow M. 2010. Selective Isolation of Actinobacteria, p 13-27. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch2
/content/10.1128/9781555816827.ch02.ch02tab01
TABLE 1
Selective heat pretreatments for the isolation of actinobacteria
Generic image for table
TABLE 1

Selective heat pretreatments for the isolation of actinobacteria

Citation: Goodfellow M. 2010. Selective Isolation of Actinobacteria, p 13-27. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch2
/content/10.1128/9781555816827.ch02.ch02tab02
TABLE 2
Chemical pretreatments for the selective isolation of actinobacteria
Generic image for table
TABLE 2

Chemical pretreatments for the selective isolation of actinobacteria

Citation: Goodfellow M. 2010. Selective Isolation of Actinobacteria, p 13-27. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch2
/content/10.1128/9781555816827.ch02.ch02tab03
TABLE 3
Antibiotics used in the selective isolation of actinobacterial taxa
Generic image for table
TABLE 3

Antibiotics used in the selective isolation of actinobacterial taxa

Citation: Goodfellow M. 2010. Selective Isolation of Actinobacteria, p 13-27. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch2
/content/10.1128/9781555816827.ch02.ch02tab04
TABLE 4
Selective media based on information mined from phenotypic databases generated in numerical taxonomic studies
Generic image for table
TABLE 4

Selective media based on information mined from phenotypic databases generated in numerical taxonomic studies

Citation: Goodfellow M. 2010. Selective Isolation of Actinobacteria, p 13-27. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch2
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TABLE 5
Integrated procedures for the selective isolation of actinobacterial taxa
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TABLE 5

Integrated procedures for the selective isolation of actinobacterial taxa

Citation: Goodfellow M. 2010. Selective Isolation of Actinobacteria, p 13-27. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch2

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