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Chapter 11 : Physiological Profiling of Microbial Communities

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Abstract:

While novel methods to discover new types and characterize microbial diversity are valuable, alternative approaches for describing microbial communities in ecologically relevant terms are needed to provide insight into the spatial and temporal patterns in both natural and man-made ecosystems. This chapter concludes with a synthesis of the various community-level physiological profiling (CLPP) approaches, including comparison of their relative strengths and weaknesses, discussion of appropriate applications, and definition of future areas of research. The CLPP assay is a sensitive, simple, rapid, and relatively inexpensive means of discriminating among microbial communities in environmental samples. A number of factors (high substrate concentrations, indirect evaluation of respiration via the redox chemistry, and presence of unknown proprietary ingredients) limit the ability of the Biolog CLPP to examine functionally relevant shifts in microbial communities. Alternative techniques developed to improve functional relevance involve direct measurement of respiration, either based on substrate consumption (O) or product appearance (CO), eliminating bias in the Biolog assay as a result of cells that cannot take up or are inhibited by the redox dye. While further incorporation of new technologies to continually improve CLPP is encouraged, the existing techniques represent valuable tools for evaluating factors affecting the metabolic state of heterotrophic microbial communities.

Citation: Garland J, Campbell C, Mills A. 2007. Physiological Profiling of Microbial Communities, p 126-138. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch11

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Figures

Image of FIGURE 1
FIGURE 1

Time course of color development for several wells in a Biolog plate plotted along with the AWCD. Although only a few of the wells are shown, the AWCD at each point was calculated as the average of all 95 wells in the plate.

Citation: Garland J, Campbell C, Mills A. 2007. Physiological Profiling of Microbial Communities, p 126-138. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch11
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Image of FIGURE 2
FIGURE 2

Schematic of multiple-SIR approach for performing CLPP.

Citation: Garland J, Campbell C, Mills A. 2007. Physiological Profiling of Microbial Communities, p 126-138. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch11
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Image of FIGURE 3
FIGURE 3

Schematic of MicroResp approach for performing CLPP.

Citation: Garland J, Campbell C, Mills A. 2007. Physiological Profiling of Microbial Communities, p 126-138. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch11
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Image of FIGURE 4
FIGURE 4

Schematic of dissolved oxygen microtiter-based systems for performing CLPP.

Citation: Garland J, Campbell C, Mills A. 2007. Physiological Profiling of Microbial Communities, p 126-138. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch11
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Tables

Generic image for table
TABLE 1

Comparison of different approaches for CLPP

Citation: Garland J, Campbell C, Mills A. 2007. Physiological Profiling of Microbial Communities, p 126-138. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch11

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