Omics in bioremediation: A consolidated overview

A pure environment gives a quality of life on earth. In ancient times, it was believed that people on earth had an unlimited abundance of land and resources; today, however, the resources in the world show, in greater or lesser degree, our carelessness and negligence in using them. In many parts of the globe the problems associated with contaminated sites are now growing up. The actual cause of this scenario is result from past industrial activities when awareness of the health and environmental effects connected with the production, use, and disposal of hazardous substances were less well recognized than today. It became a global complication when the estimated number of contaminated sites became significant[9]. There are several traditional methods which have been applied to overcome this inconvenience. From the list of ideas which have been applied the best ones are to completely demolish the pollutants if possible, or at least to transform them to innoxious substances. Different kinds of techniques have been applied like high-temperature incineration and various types of chemical decomposition. Bagging several drawbacks like technological complexity, the cost for small-scale application, and the lack of public acceptance, especially for incineration that may increase the exposure to contaminants for both the workers at the site and nearby residents, these are effective at reducing levels of a range of contaminants. Bioremediation is an option that utilizes microbes to remove many contaminants from the environment by a diversity of enzymatic processes. It shows up some positive shades such as, comparatively low-cost, lowtechnology techniques, which generally have a high public acceptance and can often be carried out on site. However, it will not always be suitable as the range of contaminants on which it is effective is limited, the time scales involved are relatively long, and the residual contaminant levels achievable may not always be appropriate. Varying degrees of success bioremediation has been used at a number of sites worldwide. Here, we attempted to assist by providing information how the bioremediation is linked with cutting edge sciences like genomics,transcriptomics, proteomics, interactomics and bioinformatics.

[1]  J. Ramos,et al.  Proteomic Analysis Reveals the Participation of Energy- and Stress-Related Proteins in the Response of Pseudomonas putida DOT-T1E to Toluene , 2005, Journal of bacteriology.

[2]  M. Ebert,et al.  Advances in clinical cancer proteomics: SELDI-ToF-mass spectrometry and biomarker discovery. , 2005, Briefings in functional genomics & proteomics.

[3]  Wen-Tso Liu,et al.  Environmental microbiology-on-a-chip and its future impacts. , 2005, Trends in biotechnology.

[4]  R. Reinhardt,et al.  Substrate-Dependent Regulation of Anaerobic Degradation Pathways for Toluene and Ethylbenzene in a Denitrifying Bacterium, Strain EbN1 , 2005, Journal of bacteriology.

[5]  Brian Raught,et al.  Advances in protein complex analysis using mass spectrometry , 2005, The Journal of physiology.

[6]  Joshua LaBaer,et al.  Protein microarrays as tools for functional proteomics. , 2005, Current opinion in chemical biology.

[7]  Katherine H. Kang,et al.  Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes , 2005, Science.

[8]  Boris Zybailov,et al.  Principles and applications of Multidimensional Protein Identification Technology , 2004, Expert review of proteomics.

[9]  Eduardo Díaz,et al.  Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. , 2004, International microbiology : the official journal of the Spanish Society for Microbiology.

[10]  T. Knigge,et al.  Surface‐enhanced laser desorption/ionization‐time of flight‐mass spectrometry approach to biomarker discovery in blue mussels (Mytilus edulis) exposed to polyaromatic hydrocarbons and heavy metals under field conditions , 2004, Proteomics.

[11]  B. Coulombe,et al.  Interaction Networks of the Molecular Machines That Decode, Replicate, and Maintain the Integrity of the Human Genome * , 2004, Molecular & Cellular Proteomics.

[12]  L. Eyers,et al.  Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics , 2004, Applied Microbiology and Biotechnology.

[13]  Jizhong Zhou,et al.  Detection of Genes Involved in Biodegradation and Biotransformation in Microbial Communities by Using 50-Mer Oligonucleotide Microarrays , 2004, Applied and Environmental Microbiology.

[14]  K. Timmis,et al.  Genome sequence completed of Alcanivorax borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems. , 2003, Journal of biotechnology.

[15]  Donald R. Metzler,et al.  Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer , 2003, Applied and Environmental Microbiology.

[16]  Derek R. Lovley,et al.  Cleaning up with genomics: applying molecular biology to bioremediation , 2003, Nature Reviews Microbiology.

[17]  Vincent J. Denef,et al.  Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. , 2003, Environmental microbiology.

[18]  S. Datta,et al.  Whole-Genome DNA Microarray Analysis of a Hyperthermophile and an Archaeon: Pyrococcus furiosus Grown on Carbohydrates or Peptides , 2003, Journal of bacteriology.

[19]  K. Scow,et al.  Naturally Occurring Bacteria Similar to the Methyl tert-Butyl Ether (MTBE)-Degrading Strain PM1 Are Present in MTBE-Contaminated Groundwater , 2003, Applied and Environmental Microbiology.

[20]  E. A. Greene,et al.  Analysis of environmental microbial communities by reverse sample genome probing. , 2003, Journal of microbiological methods.

[21]  K. M. Ritalahti,et al.  Complete Detoxification of Vinyl Chloride by an Anaerobic Enrichment Culture and Identification of the Reductively Dechlorinating Population as a Dehalococcoides Species , 2003, Applied and Environmental Microbiology.

[22]  R. Fulthorpe,et al.  Monitoring Gene Expression in Mixed Microbial Communities by Using DNA Microarrays , 2003, Applied and Environmental Microbiology.

[23]  A. Kraus,et al.  Reductive dehalogenation of chlorinated dioxins by an anaerobic bacterium , 2003, Nature.

[24]  O. White,et al.  Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis , 2002, Nature Biotechnology.

[25]  James M. Tiedje,et al.  Shewanella—the environmentally versatile genome , 2002, Nature Biotechnology.

[26]  O. Sorgenfrei,et al.  Genome-wide transcription profiling of Corynebacterium glutamicum after heat shock and during growth on acetate and glucose. , 2002, Journal of biotechnology.

[27]  E. Madsen,et al.  Detection in coal tar waste-contaminated groundwater of mRNA transcripts related to naphthalene dioxygenase by fluorescent in situ hybridization with tyramide signal amplification. , 2002, Journal of microbiological methods.

[28]  M. Hecker,et al.  Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis , 2002, Journal of bacteriology.

[29]  Kelly P. Nevin,et al.  Mechanisms for Accessing Insoluble Fe(III) Oxide during Dissimilatory Fe(III) Reduction by Geothrix fermentans , 2002, Applied and Environmental Microbiology.

[30]  Kelly P. Nevin,et al.  Mechanisms for Fe(III) Oxide Reduction in Sedimentary Environments , 2002 .

[31]  J. Tiedje,et al.  Quantitative Detection of Microbial Genes by Using DNA Microarrays , 2002, Applied and Environmental Microbiology.

[32]  D. E. Ellis,et al.  Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe , 2002, Applied and Environmental Microbiology.

[33]  W. Röling,et al.  Relationships between Microbial Community Structure and Hydrochemistry in a Landfill Leachate-Polluted Aquifer , 2001, Applied and Environmental Microbiology.

[34]  D. Lovley,et al.  Anaerobes to the Rescue , 2001, Science.

[35]  D. Fennell,et al.  Assessment of indigenous reductive dechlorinating potential at a TCE-contaminated site using microcosms, polymerase chain reaction analysis, and site data. , 2001, Environmental science & technology.

[36]  R. Ye,et al.  Global Gene Expression Profiles of Bacillus subtilis Grown under Anaerobic Conditions , 2000, Journal of bacteriology.

[37]  Dianne K. Newman,et al.  A role for excreted quinones in extracellular electron transfer , 2000, Nature.

[38]  S. Weinberger,et al.  Recent advancements in surface‐enhanced laser desorption/ionization‐time of flight‐mass spectrometry , 2000, Electrophoresis.

[39]  J. Smith,et al.  A method for application of samples to matrix-assisted laser desorption ionization time-of-flight targets that enhances peptide detection. , 2000, Analytical biochemistry.

[40]  Robert T. Anderson,et al.  Microbial Communities Associated with Anaerobic Benzene Degradation in a Petroleum-Contaminated Aquifer , 1999, Applied and Environmental Microbiology.

[41]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[42]  Denis F. Hochstrasser,et al.  Proteome in Perspective , 1998, Clinical chemistry and laboratory medicine.

[43]  M Schena,et al.  Microarrays: biotechnology's discovery platform for functional genomics. , 1998, Trends in biotechnology.

[44]  C. Kulpa,et al.  The Application of Molecular Techniques in Environmental Biotechnology for Monitoring Microbial Systems , 1998 .

[45]  N. Pace A molecular view of microbial diversity and the biosphere. , 1997, Science.

[46]  T. Barkay,et al.  Detection of the merA gene and its expression in the environment , 1996, Microbial Ecology.

[47]  B. Poolman,et al.  Mechanisms of membrane toxicity of hydrocarbons. , 1995, Microbiological reviews.

[48]  E. Saouter,et al.  merA gene expression in aquatic environments measured by mRNA production and Hg(II) volatilization , 1994, Applied and environmental microbiology.

[49]  G. Sayler,et al.  Quantitative Relationship between Naphthalene Catabolic Gene Frequency and Expression in Predicting PAH Degradation in Soils at Town Gas Manufacturing Sites , 1993 .

[50]  Edward R. Landa,et al.  Microbial reduction of uranium , 1991, Nature.

[51]  Michael Kube,et al.  The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1 , 2004, Archives of Microbiology.

[52]  Kelvin H. Lee,et al.  Applications of affinity chromatography in proteomics. , 2004, Analytical biochemistry.

[53]  Ramon Gonzalez,et al.  DNA Microarrays: Experimental Issues, Data Analysis, and Application to Bacterial Systems , 2004, Biotechnology progress.

[54]  D. Lovley,et al.  Specific 16S rDNA Sequences Associated with Naphthalene Degradation under Sulfate-Reducing Conditions in Harbor Sediments , 2001, Microbial Ecology.

[55]  Lynda B. M. Ellis,et al.  The University of Minnesota Biocatalysis/Biodegradation Database: microorganisms, genomics and prediction , 2000, Nucleic Acids Res..

[56]  K. Watanabe,et al.  Environmentally relevant microorganisms. , 2000, Journal of bioscience and bioengineering.

[57]  M. Wilkins,et al.  Progress with gene‐product mapping of the Mollicutes: Mycoplasma genitalium , 1995, Electrophoresis.

[58]  Derek R. Lovley,et al.  Oxidation of aromatic contaminants coupled to microbial iron reduction , 1989, Nature.

[59]  D. P. McCarty Phylogenetic Characterization of Microbial Communities That Reductively Dechlorinate TCE Based upon a Combination of Molecular Techniques , 2022 .