**9. Comparative analysis of Omics in bioremediation**

aspects of their physiology that are likely to control their growth and activity in contaminated environments. However, before the application of molecular techniques to bioremediation, it was uncertain whether the isolated organisms were important in bioremediation *in situ*,or whether they were 'weeds' that grew rapidly in the laboratory but were not the primary

A significant advance in the field of microbial ecology was the finding that the sequences of highly conserved genes that are found in all microorganisms, most notably the 16S rRNA genes, could provide a phylogenetic characterization of the microorganisms that comprise microbial communities (Pace et al. 1986., Amann et al. 1995).This was a boon to the field of bioremediation because it meant that by analysing 16S rRNA sequences in contaminated environments, it was possible to determine definitively the phylogenetic placement of the microorganisms that are associated with bioremediation processes (Rogers and McClure.

One of the surprises from the application of the 16S rRNA approach to bioremediation has been the finding that, in some instances, microorganisms that predominate during bioreme‐ diation are closely related to organisms that can be cultured from subsurface environments (Lovley. 2001).This contrasts with the general dilemma in environmental microbiology that is, it can be difficult to recover the most environmentally relevant organisms in culture (Amann et al. 1995). For example, in polluted aquifers, in which microorganisms were oxidizing contaminants with the reduction of Fe (m) oxides, there was a significant enrichment in microorganisms with 16S rRNA sequences that were closely related to those of previously cultured Geobacter species (Rooney-varga et al. 1999., Snoeyenbos-West et al. 2000., Roling et al. 2001).Coupled with the fact that Geobacter species in pure culture are capable of oxidizing organic contaminants with the reduction of Fe(III) oxide (Lovley et al. 1989),this indicated that Geobacter species are important in contaminant degradation in situ. Geobacter species can also remove uranium from contaminated water by reducing soluble U(vi) to insoluble U(iv) (Lovley et al. 1991). 16S rRNA sequence analysis showed that, when acetate was added to uranium-contaminated groundwater to promote micro-bial reduction of U(vi), the number of Geobacter species increased by several orders of magnitude, accounting for as much as 85% of the microbial community in the groundwater (Anderson et al. In Press, Holmes et al. 2002) In aquifers in which the indigenous microbial community was degrading the solvent trichlor‐ oethene (TCE), 16S rRNA sequences that are ~99% identical to the 16S rRNA sequence of a pure culture of the TCE-degrader Dehalococcoides ethanogenes, were detected (Fennell et al. 2001., Richardson et al. 2002., Hendrickson et al. 2002).Marine sediments with high rates of anaerobic naphthalene degradation were found to be specifically enriched in microorganisms with 16S rRNA sequences closely related to NaphS2, an anaerobic naphthalene degrader that is available in pure culture (Hayes and Lovley. 2002). There was a close correspondence between the potential for aerobic degradation of the fuel oxygenate methyl tert-butyl ether (MTBE) in groundwater and the number of organisms with 16S rRNA sequences that had more

organisms responsible for the reaction of interest in the environment.

**8. The 16S rRNA approach**

384 Applied Bioremediation - Active and Passive Approaches

2003., Watanabe and Baker. 2000)

Based on an overall analysis of transcriptomics and proteomics, the comprehensive analysis of wholegenome sequencing is especially helpful to understand bioremediation-relevant microorganisms whose physiology has not yet been studied in detail. Global gene expression using DNA microarray technology, very much depends on the degree of coverage of the cellular mRNA and cellular proteins, whereas the coverage of the whole genome represents all the genes of an organism by definition. Cellular mRNA levels do not display as wide a dynamic range as the encoded proteins (Gygi et al. 1999). Thus, whole genome arrays are believed to provide a much more comprehensive overview of the actual gene expression pattern than proteomic studies.

According to global gene expression studies, both transcriptomics and proteomics support the view that the DNA array technologies record changes in gene expression more completely than the proteomics (Muffler et al. 2002., Kuhner et al. 2005., Eymann et al. 2002). Therefore, genomics data is deemed necessary to complement the proteomics approach (Hegde et al. 2003). However, proteomics would retain its central position in functional transcriptomics and/ or genomics. The protein molecules, but not the mRNAs, are the key players in an on-site microbial mineralization reaction; the later are one of the highly unstable transmitters on the path from the genes to the ribosome, but each protein molecule represents the end product of gene expression (Kuhner et al. 2005). Complete protein profiling provides not only information on the individual organism, but also information on the fate and destination of protein molecules inside and outside the cell that can only be discovered via a joint transcriptomics, proteomics and interactomics approach (Figure 3).
