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Chapter 8 : Measuring Diversity

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Abstract:

This chapter deals with the molecular, cultivation, and a few other techniques to evaluate microbial diversity in natural systems. It provides an outline of the various approaches that are used to determine diversity of bacteria and archaea in natural habitats and some guidelines regarding which methods may be most appropriate for specific environments and specific scientific questions. Several of the techniques described rely on the ability to identify particular preselected components of the microbial community. The oldest method for obtaining microbial diversity information is to examine the sample with a microscope and characterize the microbes by their morphology. A major benefit is that the sequences can be used to make probes for quantitative composition analyses of microbial communities. This can prove to be a very powerful approach and can be being augmented by inclusion of 23S rRNA data as well. A related and powerful application has been the use of fingerprinting methods that give a snapshot of the entire microbial community at once, with the ability to tentatively identify different components. An important feature of the fingerprinting methods, such as T-RFLP, length heterogeneity PCR (LHPCR), and ARISA, is that the results are in the form of data on the amount of different PCR products of particular fragment lengths. Some authors have developed tools to “recruit” environmental sequences to known microbial genomes, showing how various relatives of previously sequenced organisms are distributed along the transect, based on all genes and not just phylogenetic markers like 16S rRNA.

Citation: Fuhrman J. 2008. Measuring Diversity, p 131-151. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch8

Key Concept Ranking

Bacteria and Archaea
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Restriction Fragment Length Polymorphism
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Denaturing Gradient Gel Electrophoresis
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Restriction Fragment Length Polymorphism
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Denaturing Gradient Gel Electrophoresis
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Tables

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TABLE 1

General summary of methods to assess diversity and community structure of natural microbial communities: features of the most common applications of the various approaches (Note that these are broad generalizations and do not apply in all instances [see text].)

Citation: Fuhrman J. 2008. Measuring Diversity, p 131-151. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch8

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