Another DNA microarray-based approach for reading a microbial community is
reverse sample genome probing (RSGP). This technique uses genome microarrays to
research the microbial network composition of the most dominant culturable species
in an environment. RSGP has three steps: isolation of genomic DNA from pure
cultures, hybridization checking to attain DNA fragments with much less than 70%
cross-hybridization and preparation of genome arrays on a strong support, and
random labelling of a defined mixture of general network DNA and general inner
DNA (Greene and Voordouw 2003). This approach has been used to investigate
microbial groups in oil fields and in polluted soils (Greene et al. 2000). As in DNA–
DNA hybridization, RSGP and microarrays have the advantage of not being confounded via PCR biases. Microarrays can incorporate many target gene sequences,
but are handiest in detecting the maximum plentiful species. In this fashion, species
need to be cultured; however, in precept cloned DNA fragments of uncultured
bacteria may also be used. The variety must be minimum, or enriched cultures will
be needed for this approach. Otherwise, pass-hybridization can be intricate. Using
genes or DNA fragments rather than genomes in the microarray removes the need to
maintain cultures of live organisms, because genes can be cloned into plasmids or
PCR can be consistently used to amplify the DNA fragments (Gentry et al. 2006). In
addition, fragments would increase the specificity of hybridization over using
genomes, and useful genes within the community might be assessed (Greene and
Voordouw 2003).
6 Omics in Bioremediation
Various ‘omics’ strategies have opened the way for environmental probing at the
molecular level and have also created a new paradigm in bioremediation design and
control. Ecogenomics – the utility of genomics to ecological and environmental
sciences – defines phylogenetic and functional biodiversity on the DNA, RNA, and
protein levels, with emphasis on the capabilities and interactions of organisms in the
surroundings relative to ecological and evolutionary methods. For effective bioremediation of halo-organic pollution in anaerobic environments, we need the information from catabolic ability and in situ dynamics of organohalide-consuming and
cometabolizing microbes. Current methods of the OMICS pathways are outlined in
Fig. 18.1.
6.1 Genomics
Genomics is a powerful computer-based technology used to understand the structure
and feature of all genes in an organism. Study of pure cultures have become very
easy using the software of genomics to bioremediation. Next-era genome sequencing
strategies will be critical in elaborating the physiological and genomic features of
18 Molecular Technologies for Assessment of Bioremediation and. . .
457
reverse sample genome probing (RSGP). This technique uses genome microarrays to
research the microbial network composition of the most dominant culturable species
in an environment. RSGP has three steps: isolation of genomic DNA from pure
cultures, hybridization checking to attain DNA fragments with much less than 70%
cross-hybridization and preparation of genome arrays on a strong support, and
random labelling of a defined mixture of general network DNA and general inner
DNA (Greene and Voordouw 2003). This approach has been used to investigate
microbial groups in oil fields and in polluted soils (Greene et al. 2000). As in DNA–
DNA hybridization, RSGP and microarrays have the advantage of not being confounded via PCR biases. Microarrays can incorporate many target gene sequences,
but are handiest in detecting the maximum plentiful species. In this fashion, species
need to be cultured; however, in precept cloned DNA fragments of uncultured
bacteria may also be used. The variety must be minimum, or enriched cultures will
be needed for this approach. Otherwise, pass-hybridization can be intricate. Using
genes or DNA fragments rather than genomes in the microarray removes the need to
maintain cultures of live organisms, because genes can be cloned into plasmids or
PCR can be consistently used to amplify the DNA fragments (Gentry et al. 2006). In
addition, fragments would increase the specificity of hybridization over using
genomes, and useful genes within the community might be assessed (Greene and
Voordouw 2003).
6 Omics in Bioremediation
Various ‘omics’ strategies have opened the way for environmental probing at the
molecular level and have also created a new paradigm in bioremediation design and
control. Ecogenomics – the utility of genomics to ecological and environmental
sciences – defines phylogenetic and functional biodiversity on the DNA, RNA, and
protein levels, with emphasis on the capabilities and interactions of organisms in the
surroundings relative to ecological and evolutionary methods. For effective bioremediation of halo-organic pollution in anaerobic environments, we need the information from catabolic ability and in situ dynamics of organohalide-consuming and
cometabolizing microbes. Current methods of the OMICS pathways are outlined in
Fig. 18.1.
6.1 Genomics
Genomics is a powerful computer-based technology used to understand the structure
and feature of all genes in an organism. Study of pure cultures have become very
easy using the software of genomics to bioremediation. Next-era genome sequencing
strategies will be critical in elaborating the physiological and genomic features of
18 Molecular Technologies for Assessment of Bioremediation and. . .
457