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Chapter 6 : Monitoring Bioremediation

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Abstract:

The needs for monitoring of bioremediation projects clearly start even before technology selection. In flame atomic absorption spectrometry (FAAS), the sample solution is sprayed as a fine mist into a flame, commonly air-acetylene or nitrous oxide-acetylene, where it is vaporized at temperatures in excess of 2,400°C into constituent atoms prior to light absorption. The inductively coupled plasma (ICP) optical emission spectrometer uses an ICP source (usually argon) to dissociate aspirated samples and standards into their constituent atoms or ions, exciting them to a level where they emit light of a characteristic wavelength detected electronically (e.g., with a photomultiplier tube or charge-coupled device). When analytical laboratory procedures are used to measure the concentrations of organic contaminants, the first task for the laboratory analyst is the extraction of the pollutants from the samples supplied. The chapter discusses different types of chromatography including gas chromatography, mass spectrometry, and headspace gas chromatography. Several investigations have demonstrated an increase in numbers of hydrocarbon-oxidizing bacteria (HOB) in habitats that suffer from oil pollution. Also it appears that the addition of an artificial oil slick causes a shift to the isolation of a greater percentage of HOB. Molecular methods including such as PCR, 16S Ribosomal DNA and denaturing gradient gel electrophoresis (DGGE) are discussed. Modern monitoring approaches employ both traditional chemical analyses and a variety of biological methods, ranging from community structure analyses to the use of reporter genes that can visually demonstrate the presence of specific microorganisms and their metabolic activities in field samples.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6

Key Concept Ranking

Microbial Ecology
0.912299
Environmental Microbiology
0.89137274
Microbial Communities in Environment
0.5205528
Denaturing Gradient Gel Electrophoresis
0.4449804
Aliphatic Hydrocarbon Degrading Bacteria
0.43833894
Chemicals
0.43077788
Aromatic Hydrocarbon Degrading Bacteria
0.43000287
0.912299
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Figures

Image of FIGURE 6.1
FIGURE 6.1

The filter pad method for growing HOB.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.2
FIGURE 6.2

Bacterial colonies growing on an agar plate with a thin film of phenanthrene applied by the spray-plate technique. The cleared halo surrounding colonies is evidence of phenanthrene biotransformation.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.3
FIGURE 6.3

Illustration of a five-“tube” MPN result for a marine sediment sample obtained by the sheen screen method. The 10 and 10 dilutions are all positive for crude oil emulsifications, four of five of the 10 dilution tubes are scored positive, and one of five of the 10 dilution tubes scored positive. Courtesy of Ed Brown, University of Northern Iowa.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.4
FIGURE 6.4

DGGE principle. conc., concentration. After Iwamoto and Nasu (55).

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.5
FIGURE 6.5

DGGE profile for samples taken from a groundwater diesel remediation system. Each band in theory represents a single taxonomic unit. Courtesy of Lena Ciric.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.6
FIGURE 6.6

Output from LH-PCR (top) and tRFLP (bottom). Both outputs correspond to lane 20 on the DGGE gel in Fig. 6.5 . Courtesy of Lena Ciric.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.7
FIGURE 6.7

tRFLP principle. After Iwamoto and Nasu ( ).

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.8
FIGURE 6.8

The appearance of natural (C) and heavy (C-labeled) RNA shown in RNA-SIP. The top gradient fractions contain the natural-weight RNA, and the heavy RNA becomes apparent as one moves down the fractions ( ). H, heavy; L, light. Courtesy of Andrew S. Whiteley.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.9
FIGURE 6.9

Bioluminescent bacteria. (a) A shake flask liquid culture. (b) Bioluminescent transposon mutants in daylight (top right) and in the dark room (bottom right). Courtesy of Andrew S. Whiteley.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of BOX FIGURE 6.1.1
BOX FIGURE 6.1.1

Toxmap, a toxicity map for a contaminated site generated by using toxicity biosensors. Courtesy of Remedios Ltd., Aberdeen, United Kingdom.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.10
FIGURE 6.10

Sample output data for a genetically modified toxicity biosensor. On contact with 3,5-dichlorophenol (3,5-DCP), this biosensor shows increasing light reduction with concentration (conc.), which can be transformed to a linear plot by probit transformation, allowing the user to input data to software to compute an effective concentration that reduces light output by 50%. After Philp et al. ( ).

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.11
FIGURE 6.11

Mercury detoxification system.

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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Image of FIGURE 6.12
FIGURE 6.12

The naphthalene regulatory system of HK44. After Simpson et al. ( ).

Citation: Philp J, Whiteley A, Ciric L, Bailey M. 2005. Monitoring Bioremediation, p 237-268. In Atlas R, Philip J (ed), Bioremediation. ASM Press, Washington, DC. doi: 10.1128/9781555817596.ch6
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