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Chapter 90 : Characterization of Microeukaryota in Natural Environments

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Abstract:

Microeukaryotes, including fungi and protists, are important members of communities within natural environments. This chapter focuses exclusively on available molecular approaches for investigating microeukaryote assemblages within various natural environments. Oligotrophic environments generally require more sampling effort to obtain adequate biomass for molecular characterization than do more nutrient-rich environments. Sediment sampling achieved by the implementation of sterile mud samplers and coring devices has been described for hydrothermal sediments and anoxic sediments. The 18S rRNA gene contains both conserved and variable regions that can be exploited for characterization of the microeukaryote assemblages within an environment. Multiple PCRs containing amplicons of expected size can be pooled to minimize bias from single reactions. Immunological approaches have proven useful in ecological studies for the detection and enumeration of microeukaryotes. Quantitative real-time PCR uses the rate of accumulation of amplified target DNA during the PCR to estimate the copy number of the target in the original sample. Denaturing gradient gel electrophoresis is a PCR-based method in which the amplified 18S rRNA gene fragments are separated by polyacrylamide gel electrophoresis containing a linearly increasing gradient of denaturant.

Citation: Strap J. 2007. Characterization of Microeukaryota in Natural Environments, p 1112-1121. 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.ch90

Key Concept Ranking

Microbial Ecology
0.55837876
Bacteria and Archaea
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Denaturing Gradient Gel Electrophoresis
0.54199654
Confocal Laser Scanning Microscopy
0.4552771
Restriction Fragment Length Polymorphism
0.4552771
Confocal Laser Scanning Microscopy
0.4552771
0.55837876
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Tables

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TABLE 1

18S rRNA gene primers

Citation: Strap J. 2007. Characterization of Microeukaryota in Natural Environments, p 1112-1121. 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.ch90

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