**4. Applications of DNA microarray**

Even with the complete genome sequences of microorganisms with the potential for bioremediation (Golyshin et al. 2003., Tiedje. 2002., Heidelberg et al. 2002., Seshadri et al. 2005., Rabus et al. 2005), studies are not accelerating in a rapid manner. With the complet‐ ed genome sequences, it is possible to analyse the expression of all genes in each ge‐ nome under various environmental conditions using whole-genome DNA microarrays (Gao et al. 2004., Muffler et al. 2002., Schut et al. 2003). Such genome-wide expression analysis provides important data for identifying regulatory circuits in these organisms (Lovley. 2003., Rabus et al. 2005., Muffler et al. 2002). In the past, DNA microarrays have been used to evaluate the physiology of pure environmental cultures (Schut et al. 2003) and to monitor the catabolic gene expression profile in mixed microbial communities (Dennis et al. 2003). More than 100 genes were found to be affected by oxygen-limiting conditions when a DNA microarray was used to study changes in mRNA expression levels in Bacillus subtilis grown under anaerobic conditions (Ye et al. 2000). Sensitivity may often be a part of the problem in PCR-based cDNA microarrays, since only genes from popula‐ tions contributing to more than 5% of the community DNA can be detected. Several parameters were evaluated to validate the sensitivity of spotted oligonucleotide DNA

microarrays and their applicability for bacterial functional genomics (Denef et al. 2003). Optimal parameters were found to be 50-C6- amino-modified 70 mers printed on CMT-GAPS II substrates at a 40 *m*M concentration combined with the use of tyramide signal amplification labelling. Based on most of the known genes and pathways involved in biodegradation and metal resistance, a comprehensive 50-mer-based oligonucleotide microarray was developed for effective monitoring of biodegrading populations (Rhee et al. 2004). This type of DNA microarray was effectively used to analyze naphthaleneamended enrichment, and soil microcosms demonstrated that microflora changed differen‐ tially depending on the incubation conditions (Cho and Tiedje. 2002 ).A global gene expression analysis revealed the co-regulation of several thusfar- unknown genes during the degradation of alkylbenzenes (Kuhner et al. 2005). Besides this, DNA microarrays have been used to determine bacterial species, in quantitative applications of stress gene analysis of microbial genomes and in genome-wide transcriptional profiles (Muffler et al. 2002., Greene and Voordouw. 2003).

**5. Foot prints of proteomics**

and Kim. 2005).

**6. Interaction of interactomics**

The terms 'proteomics' and 'proteome' were introduced in 1995 (Wasinger et al. 1995), which is a key postgenomic feature that emerged from the growth of large and complex genome sequencing datasets. Proteomic analysis is particularly vital because the observed phenotype is a direct result of the action of the proteins rather than the genome sequence.Traditionally, this technology is based on highly efficient methods of separation using two-dimensional polyacrylamide gel electrophoresis (2-DE) and modern tools of bioinformatics in conjunction with mass spectrometry (MS) (Hochstrasser. 1995). However, 2-DE has been considered to be a limited approach for very basic and hydrophobic membrane proteins in compartmental proteomics. In bioremediation, the proteome of the membrane proteins is of high interest, specifically in PAH biodegradation, where many alterations in any site specific bacterium affects cell-surface proteins and receptors (Sikkema et al. 1995). The improvements in 2-DE for use in compartmental proteomics have been made by introducing an alternative approach for multidimensional protein identification technology (MudPIT) (Paoletti et al. 2004). MS has revolutionized the environmental proteomics towards the analysis of small molecules to peptides and proteins that has pushed up the sensitivity in protein identification by several orders of magnitude followed by minimizing the process from many hours to a few minutes (Aebersold and Mann. 2003). The advancement in MS techniques coupled with database

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searching have played a crucial role in proteomics for protein identification.

Matrixassociated laser desorption/ionization time-of-flight MS (MALDI-TOF-MS) is the most commonly used MS approach to identifying proteins of interest excised from 2-DE gels, by generation of peptidemass fingerprinting (Aebersold and Mann. 2003., Aitken and Learmonth. 2002., Landry et al. 2000). Surface-enhanced laser-desorption-ionization MS (SELDI-TOF-MS) is the combination of direct sample fractions on a chip integrated with MALDI-TOF-MS analysis (Merchant and Weinberger. 2000., Seibert et al. 2005). A variety of differentially expressed signature proteins were analysed using SELDITOF- MS in blue mussels (Mytilus edulis) exposed to PAHs and heavy metals (Knigge et al. 2004). The liquid chromatography MS (LC-MS) technique has begun to open a new analytical window for direct detection and identification of potential contaminants in water (Joo and Kim. 2005). In addition, the metab‐ olites and degradation products have been taken into account to assess the fate of organic contaminants such as pesticides, surfactants, algal and cynobacterial toxins, disinfection byproducts or pharmaceuticals in the environment and during water treatment processes (Joo

Genome-wide mRNA profiling is unable to provide any information about the activity, arrangement, or final destination of the gene products, the proteins. Various proteomic approaches, on the other hand, can successfully provide the straight answers. It is very rare that any protein molecule acts as a unique pillar during the physiological response in biore‐

**Figure 1.** Work flow of gene array analysis. Diagrammatic representation of DNA microarray data analysis and relative limitations under each category of data analysis during data mining.
