Rhee SK, Liu X, Wu L, Chong SC, Wan X, Zhou J (2004) Detection of genes involved in
biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70:4303–4317
Richardson RE, Bhupathiraju VK, Song DL, Goulet TA, Alvarez-Cohen L (2002) Phylogenetic
characterization of microbial communities that reductively dechlorinate TCE based upon a
combination of molecular techniques. Environ Sci Technol 36:2652–2662
Rindle E, Troll WJ (1975) Metabolic reduction of benzidine azo dyes to benzidine in the Rhesus
monkey. J Natl Cancer Inst 55:181
Rogers SL, McClure N (2003) In: Head IM, Singleton I, Milner MG (eds) Bioremediation: a
criticial review. Horizon Scientific Press, Wymondham, pp 27–59
Ros M, Rodriguez I, Garcia C, Hernandez T (2010) Microbial communities involved in the
bioremediation of an aged recalcitrant hydrocarbon polluted soil by using organic amendments.
Bioresour Technol 101:6916–6923
Rui L, Kwon YM, Reardon KF (2004) Metabolic pathway engineering to enhance aerobic
degradation of chlorinated ethenes and to reduce their toxicity by cloning a novel glutathione
S-transferase, an evolved toluene o-monooxygenase, and gamma-glutamylcysteine synthetase.
Environ Microbiol 6:491–500
Saleh-Lakha S, Miller M, Campbell RG, Schneider K, Elahimanesh P, Hart MM (2005) Microbial
gene expression in soil: methods, applications and challenges. J Microbiol Methods 63:1–19
Santos PM, Benndorf D, Sa-Correia I (2004) Insights into Pseudomonas putida KT2440 response
to phenol-induced stress by quantitative proteomics. Proteomics 4:2640–2652
Sanz JL, Kochling T (2007) Molecular biology techniques used in waste treatment: an overview.
Process Biochem 42:119–133
Schmalenberger A, Schwieger F, Tebbe CC (2001) Effect of primers hybridizing to different
evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial
community analyses and genetic profiling. Appl Environ Microbiol 67:3557–3563
Schut GJ, Brehm SD, Datta S (2003) Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides. J Bacteriol
185:3935–3947
Segura A, Godoy P, van Dillewijn P (2005) Proteomic analysis reveals the participation of energyand stress-related proteins in the response of Pseudomonas putida DOT-T1E to toluene. J
Bacteriol 187:5937–5945
Simon C, Daniel R (2011) Metagenomic analysis: past and future trends. Appl Environ Microbiol
77:1153–1161
Spiegelman D, Whissell G, Greer CW (2005) A survey of the methods for the characterization of
microbial consortia and communities. Can J Microbiol 51:355–386
Stach JEM, Bathe S, Clapp JP, Burns RG (2001) PCR-SSCP comparison of 16S rDNA sequence
diversity in soil DNA obtained using different isolation and purification methods. FEMS
Microbiol Ecol 36:139–151
Stephanopoulas GN, Aristidou AA, Nielsen J (1998) Metabolic engineering: principles and methodologies. Academic Press, San Diego
Tan G-L, Shu W-S, Zhou W-H, Li X-L, Lan C-Y, Huang L-N (2009) Seasonal and spatial
variations in microbial community structure and diversity in the acid stream draining across
an ongoing surface mining site. FEMS Microbiol Ecol 70:277–285
Tang YJ, Martin HG, Dehal PS, Deutschbauer A, Llora X, Meadows A, Arkin A, Keasling JD
(2009) Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central
carbon metabolism. Biotechnol Bioeng 102:1161–1169
Teira E, Lekunberri I, Gasol JM, Nieto-Cid M, Alvarez-Salgado XA, Figueiras FG (2007) Dynamics of the hydrocarbon-degrading Cycloclasticus bacteria during mesocosm-simulated oil spills.
Environ Microbiol 9(10):2551–2562
Thavamani P, Megharaj M, Naidu R (2012) Bioremediation of high molecular weight polyaromatic
hydrocarbons co-contaminated with metals in liquid and soil slurries by metal tolerant PAHs
degrading bacterial consortium. Biodegradation 23(6):823–35
472
S. K. Shekhar et al.
biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70:4303–4317
Richardson RE, Bhupathiraju VK, Song DL, Goulet TA, Alvarez-Cohen L (2002) Phylogenetic
characterization of microbial communities that reductively dechlorinate TCE based upon a
combination of molecular techniques. Environ Sci Technol 36:2652–2662
Rindle E, Troll WJ (1975) Metabolic reduction of benzidine azo dyes to benzidine in the Rhesus
monkey. J Natl Cancer Inst 55:181
Rogers SL, McClure N (2003) In: Head IM, Singleton I, Milner MG (eds) Bioremediation: a
criticial review. Horizon Scientific Press, Wymondham, pp 27–59
Ros M, Rodriguez I, Garcia C, Hernandez T (2010) Microbial communities involved in the
bioremediation of an aged recalcitrant hydrocarbon polluted soil by using organic amendments.
Bioresour Technol 101:6916–6923
Rui L, Kwon YM, Reardon KF (2004) Metabolic pathway engineering to enhance aerobic
degradation of chlorinated ethenes and to reduce their toxicity by cloning a novel glutathione
S-transferase, an evolved toluene o-monooxygenase, and gamma-glutamylcysteine synthetase.
Environ Microbiol 6:491–500
Saleh-Lakha S, Miller M, Campbell RG, Schneider K, Elahimanesh P, Hart MM (2005) Microbial
gene expression in soil: methods, applications and challenges. J Microbiol Methods 63:1–19
Santos PM, Benndorf D, Sa-Correia I (2004) Insights into Pseudomonas putida KT2440 response
to phenol-induced stress by quantitative proteomics. Proteomics 4:2640–2652
Sanz JL, Kochling T (2007) Molecular biology techniques used in waste treatment: an overview.
Process Biochem 42:119–133
Schmalenberger A, Schwieger F, Tebbe CC (2001) Effect of primers hybridizing to different
evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial
community analyses and genetic profiling. Appl Environ Microbiol 67:3557–3563
Schut GJ, Brehm SD, Datta S (2003) Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides. J Bacteriol
185:3935–3947
Segura A, Godoy P, van Dillewijn P (2005) Proteomic analysis reveals the participation of energyand stress-related proteins in the response of Pseudomonas putida DOT-T1E to toluene. J
Bacteriol 187:5937–5945
Simon C, Daniel R (2011) Metagenomic analysis: past and future trends. Appl Environ Microbiol
77:1153–1161
Spiegelman D, Whissell G, Greer CW (2005) A survey of the methods for the characterization of
microbial consortia and communities. Can J Microbiol 51:355–386
Stach JEM, Bathe S, Clapp JP, Burns RG (2001) PCR-SSCP comparison of 16S rDNA sequence
diversity in soil DNA obtained using different isolation and purification methods. FEMS
Microbiol Ecol 36:139–151
Stephanopoulas GN, Aristidou AA, Nielsen J (1998) Metabolic engineering: principles and methodologies. Academic Press, San Diego
Tan G-L, Shu W-S, Zhou W-H, Li X-L, Lan C-Y, Huang L-N (2009) Seasonal and spatial
variations in microbial community structure and diversity in the acid stream draining across
an ongoing surface mining site. FEMS Microbiol Ecol 70:277–285
Tang YJ, Martin HG, Dehal PS, Deutschbauer A, Llora X, Meadows A, Arkin A, Keasling JD
(2009) Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central
carbon metabolism. Biotechnol Bioeng 102:1161–1169
Teira E, Lekunberri I, Gasol JM, Nieto-Cid M, Alvarez-Salgado XA, Figueiras FG (2007) Dynamics of the hydrocarbon-degrading Cycloclasticus bacteria during mesocosm-simulated oil spills.
Environ Microbiol 9(10):2551–2562
Thavamani P, Megharaj M, Naidu R (2012) Bioremediation of high molecular weight polyaromatic
hydrocarbons co-contaminated with metals in liquid and soil slurries by metal tolerant PAHs
degrading bacterial consortium. Biodegradation 23(6):823–35
472
S. K. Shekhar et al.