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Chapter 9 : Stable Isotope Probing Techniques and Bioremediation

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Abstract:

This chapter summarizes the state of the art for applications of stable isotope probing (SIP) to bio-degradation and bioremediation research. SIP is one of the many emerging tools of inquiry used by environmental microbiologists. The goals of this chapter are to catalog and analyze trends exhibited by the majority of studies published to date that are pertinent to biodegradation and bioremediation. C-based phospholipid fatty acid (PLFA)-SIP showed chromatographic profiles related to but distinct from known type II methanotrophs. Using PLFA-SIP analyses, a variety of comparisons were made between forest, shrubland, and pasture soils; type II methanotrophs were dominant in forest and shrubland, while type I methanotrophs dominated pasture soil. When suitable probes are available, fluorescent in situ hybridization (FISH) is an effective means of microscopic identification of microorganisms and can be combined with techniques using radioactive and stable isotopes to identify metabolically active microorganisms. The combined microscopic approaches of FISH and secondary ion mass spectrometry (SIMS) have tremendous potential to aid investigations examining the roles of bacteria in biogeochemical processes and in the biodegradation of organic pollutants. SIP is a means toward the goal of improved pollution-control technology. In general, no single technique or piece of evidence is sufficient to advance the discipline of environmental microbiology. But SIP is inherently heuristic—results have the potential to create new information and hypotheses that can be tested and confirmed with multidisciplinary approaches.

Citation: Madsen E. 2011. Stable Isotope Probing Techniques and Bioremediation, p 165-201. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch9

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Environmental Microbiology
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Microbial Ecology
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Restriction Fragment Length Polymorphism
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Denaturing Gradient Gel Electrophoresis
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FIGURE 1

Overview of SIP procedures. Biomarkers (nucleic acids are the example) from only a small subset of the microbial community become labeled.

Citation: Madsen E. 2011. Stable Isotope Probing Techniques and Bioremediation, p 165-201. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch9
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Tables

Generic image for table
TABLE 1.

Defining biodegradation and bioremediation

Citation: Madsen E. 2011. Stable Isotope Probing Techniques and Bioremediation, p 165-201. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch9
Generic image for table
TABLE 2.

Survey of studies using SIP techniques to examine microbial populations responsible for biodegradation of aromatic compounds

Citation: Madsen E. 2011. Stable Isotope Probing Techniques and Bioremediation, p 165-201. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch9
Generic image for table
TABLE 3.

Survey of studies using SIP techniques to examine microbial populations responsible for biodegradation of C1 compoundsa

Citation: Madsen E. 2011. Stable Isotope Probing Techniques and Bioremediation, p 165-201. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch9
Generic image for table
TABLE 4.

Survey of studies using SIP techniques to examine microbial populations responsible for biodegradation of organic acids, sugars, and other compounds

Citation: Madsen E. 2011. Stable Isotope Probing Techniques and Bioremediation, p 165-201. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch9
Generic image for table
TABLE 5.

Experimental issues confronted by investigators when implementing SIP assays

Citation: Madsen E. 2011. Stable Isotope Probing Techniques and Bioremediation, p 165-201. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch9

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