**10. Bioinformatics in bioremediation**

MetaRouter is a system for maintaining heterogeneous information related to Biodegradation in a framework that allows its administration and mining (application of methods for extract‐

information on most known microbial catabolic reaction types and the organic functional groups they transform. Having reached its first goals, it is ready to move beyond them. It is poised to grow in many different ways, including mirror sites; fold prediction for its sequenced enzymes; closer ties to genome and microbial strain databases; and the prediction of biode‐

Scientific Swift in Bioremediation: An Overview

http://dx.doi.org/10.5772/56409

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The rise of genomic technologies and systems biology provide fresh approaches to currently untactable biological processes that are at the root of serious environmental problems. One formidable challenge in this respect is the biological fate of the nearly 8 operons, etc. implicated in this process. The biodegradation database of the University of Minnesota documented new chemical compounds (~40 000 predominant) which are common in modern Organic and Industrial Chemistry. A large number of microbial strains are able to grow on environmental pollutants (about 800 today). Bioremediation was studied from a molecular biology point of view, characterizing the chemical reactions, genes; University of Minnesota has made a pioneering effort in putting together nearly every aspect of our current knowledge on biodegradation pathways and in developing systems for dealing with that data e.g. to learn rules for predicting biodegradative features. Yet, most information available in the literature of microbial biodegradation of xenobiotics and recalcitrant chemicals deals with duos con‐ sisting of one pollutant versus one strain and thus, lacks essential aspects of the natural scenarios, like the interchange of genes between bacteria or their metabolic cooperation. This study of genomes and 'functionomes' from a community point of view (in contrast to organism point of view) is leading, for example, to the sequencing of 'genomes' of communities and ecosystems, instead of single organisms. These circumstances expose the need to qualify and to represent the information available in biodegradation databases in a fashion in which the entire known biodegradative potential of the microbial world can be crossed with the whole collection of compounds known to be partially or totally degraded through (mostly) bacterial

The application of omic sciences to the study of bioremediation is clearly in its infancy. There are many technical issues that will need to be addressed before some of the more novel approaches, such as environmental genome sequencing and arrays. To elucidate the function of most genes recovered from the environment, it will be necessary to recover the relevant organisms and study gene function in pure culture. Microorganisms closely related to those that predominate in some contaminated environments are already available in culture, and the careful replication of environmental conditions during isolation will probably yield more. Microorganisms that typically comprise about one-fourth of the marine microbial community, but the presence of which had only previously been detected from 16S rRNA sequences. This

gradation pathways for compounds it does not contain ( Ellis et al. 2000).

**11. Approaches of systems biology**

action (Kitano 2002).

**12. Conclusion**

**Figure 3.** Omic technologies using a systematic biology approach to track the insights of bioremediation. DNA is di‐ rectly extracted from contaminant environmental sites and from organisms will end up on transcriptomics (DNA mi‐ croarrays). Transcriptomics will expend towards proteomics followed by interactomics. Extraction of protein from pure culture using 2-DE and protein microarray platforms will allow us to explore the new molecules of interest during min‐ eralization process.

ing new data). It is an application intended for laboratories working in this area which need to maintain public and private data, linked internally and with external databases, and to extract new information from it. The system has an open and modular architecture adaptable to different customers. This multiplatform program, implemented in Postgre SQL (standard language for relational databases) and using SRS as an indexing system (used to connect and query Molecular Biology databases), works using a client/server architecture that allows the program to run on the user station or on the company server, so it can be accessed from any place in a secure way just by having a web browser.

The University of Minnesota Biocatalysts/Biodegradation Database (http:// www.labmed.umn.edu/umbbd) begins its fifth year having met its initial goals. It contains approximately 100 pathways for microbial catabolic metabolism of primarily xenobiotic organic compounds, including information on approximately 650 reactions, 600 compounds and 400 enzymes, and containing approximately 250 microorganism entries. It includes information on most known microbial catabolic reaction types and the organic functional groups they transform. Having reached its first goals, it is ready to move beyond them. It is poised to grow in many different ways, including mirror sites; fold prediction for its sequenced enzymes; closer ties to genome and microbial strain databases; and the prediction of biode‐ gradation pathways for compounds it does not contain ( Ellis et al. 2000).
