7.1 Metabolomics, Metametabolomics, and Fluxomics
Metabolomics is analysis of all the cellular metabolites in a cell and their interactions
in the microbial community. Analysis of cellular metabolites within a cell and
community over a time period in real time is known as fluxomics (Wiechert et al.
2007). Information on factors regulating growth and metabolism of microbial
communities can be accessed by metabolomics, and fluxomics can provide the
missing links in the regulatory pathways involved in metabolism of environmental
pollutants. A microbial cell releases a number of low molecular weight primary and
secondary metabolites in response to an environment challenge or stress. The
influence of the local environment on the metabolome of an organism or community
can be exploited in bioremediation to characterize the effects of xenobiotic compounds. Metabolites can be characterized by mass spectrometry and various spectroscopic techniques. Villas-Boas and Bruheim (2007) have discussed the scenario
of metabolome analysis in bioremediation. The application of metabolomics can
significantly extend and enhance the power of existing bioremediation approaches
by providing a better understanding of the biodegradation process (Villas-Boas and
Bruheim 2007). Keum et al. (2008) studied the metabolic profiles of Sinorhizobium
sp. C4 using mass spectrometry and gas chromatography during the degradation of
phenanthrene in comparison to natural carbon sources. Tang et al. (2009) also
performed a fluxomics analysis on Shewanella sp. known to have co-metabolic
pathways for bioremediation of halogenated organic compounds, toxic metals, and
radionuclides. In addition, they analyzed that a mixed bacterial consortium can
degrade benzene and its derivatives and other aromatic ring organic members
more than 97%. Maphosa et al. (2010) studied organ halide-catabolizing bacteria
and its molecular diagnostics with mass-balancing and kinetic modeling in an in situ
dechlorinating bioreactor and showed its application in monitoring bioremediation.
7.2 Improvement of the Biodegradation Process via
Metabolic Engineering
Recombinant DNA technology can drastically improve metabolic engineering
(ME) and thus improve cellular properties or introduce new ones (Stephanopoulas
et al. 1998). The metabolic engineering (ME) approach has been successfully used
for the improvement of industrial microorganisms. However, the use of ME tools
and principles is also relevant for bioremediation, as potential natural microbial
populations to degrade contaminations are found in fewer numbers (Urgun-Demitras
et al. 2006; Pieper and Reineke 2000; Rui et al. 2004). Accumulation of contaminants in the environment represents a potential pollution problem because many
such are highly toxic, mutagenic, or carcinogenic. Metabolic engineering can lead to
both the introduction of novel biodegradation pathways and to modification and
extension of a substrate range of enzymes in existing degradation pathways in the
18 Molecular Technologies for Assessment of Bioremediation and. . .
461
Metabolomics is analysis of all the cellular metabolites in a cell and their interactions
in the microbial community. Analysis of cellular metabolites within a cell and
community over a time period in real time is known as fluxomics (Wiechert et al.
2007). Information on factors regulating growth and metabolism of microbial
communities can be accessed by metabolomics, and fluxomics can provide the
missing links in the regulatory pathways involved in metabolism of environmental
pollutants. A microbial cell releases a number of low molecular weight primary and
secondary metabolites in response to an environment challenge or stress. The
influence of the local environment on the metabolome of an organism or community
can be exploited in bioremediation to characterize the effects of xenobiotic compounds. Metabolites can be characterized by mass spectrometry and various spectroscopic techniques. Villas-Boas and Bruheim (2007) have discussed the scenario
of metabolome analysis in bioremediation. The application of metabolomics can
significantly extend and enhance the power of existing bioremediation approaches
by providing a better understanding of the biodegradation process (Villas-Boas and
Bruheim 2007). Keum et al. (2008) studied the metabolic profiles of Sinorhizobium
sp. C4 using mass spectrometry and gas chromatography during the degradation of
phenanthrene in comparison to natural carbon sources. Tang et al. (2009) also
performed a fluxomics analysis on Shewanella sp. known to have co-metabolic
pathways for bioremediation of halogenated organic compounds, toxic metals, and
radionuclides. In addition, they analyzed that a mixed bacterial consortium can
degrade benzene and its derivatives and other aromatic ring organic members
more than 97%. Maphosa et al. (2010) studied organ halide-catabolizing bacteria
and its molecular diagnostics with mass-balancing and kinetic modeling in an in situ
dechlorinating bioreactor and showed its application in monitoring bioremediation.
7.2 Improvement of the Biodegradation Process via
Metabolic Engineering
Recombinant DNA technology can drastically improve metabolic engineering
(ME) and thus improve cellular properties or introduce new ones (Stephanopoulas
et al. 1998). The metabolic engineering (ME) approach has been successfully used
for the improvement of industrial microorganisms. However, the use of ME tools
and principles is also relevant for bioremediation, as potential natural microbial
populations to degrade contaminations are found in fewer numbers (Urgun-Demitras
et al. 2006; Pieper and Reineke 2000; Rui et al. 2004). Accumulation of contaminants in the environment represents a potential pollution problem because many
such are highly toxic, mutagenic, or carcinogenic. Metabolic engineering can lead to
both the introduction of novel biodegradation pathways and to modification and
extension of a substrate range of enzymes in existing degradation pathways in the
18 Molecular Technologies for Assessment of Bioremediation and. . .
461