Skip to main content

Advertisement

SpringerLink
Log in

Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants

  • Review Article
  • Published:
Environmental Science and Pollution Research Aims and scope Submit manuscript

Abstract

Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today’s scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Abram F (2015) Systems-based approaches to unravel multi-species microbial community functioning. Comput Struc Biotechnol J 13:24–32

    Article  CAS  Google Scholar 

  • Adebusoye SA, Ilori MO, Picardal FW, Amund OO (2008) Cometabolic degradation of polychlorinated biphenyls (PCBs) by axenic cultures of Ralstonia sp. strain SA-5 and Pseudomonas sp. strain SA-6 obtained from Nigerian contaminated soils. World J Microb Biot 24:61–68

    Article  CAS  Google Scholar 

  • Admire B, Lian B, Yalkowsky SH (2014) Estimating the physicochemical properties of polyhalogenated aromatic and aliphatic compounds using UPPER: Part 2. Aqueous solubility, octanol solubility and octanol–water partition coefficient. Chemosphere 119:1441–1446

    Article  CAS  Google Scholar 

  • Afzal M, Khan QM, Sessitsch A (2014) Endophytic bacteria: prospects and applications for the phytoremediation of organic pollutants. Chemosphere 117:232–242

    Article  CAS  Google Scholar 

  • Agency for toxic substances and disease registry (ATSDR) (2002) Public Health Statement for DDT, DDE, and DDD. http://www.atsdr.cdc.gov/phs/phs.asp?id=79&tid=20. Accessed 21 Jan 2015

  • Allocati N, Federici L, Masulli M, Di Ilio C (2009) Glutathione transferases in bacteria. Febs J 276:58–75

    Article  CAS  Google Scholar 

  • Ang EL, Zhao H, Obbard JP (2005) Recent advances in the bioremediation of persistent organic pollutants via biomolecular engineering. Enzyme Microb Technol 37:487–496

    Article  CAS  Google Scholar 

  • Arber W (2000) Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 24:1–7

    Article  CAS  Google Scholar 

  • Arslan M, Imran A, Khan QM, Afzal M (2015) Plant–bacteria partnerships for the remediation of persistent organic pollutants. Environ Sci Pollut Res 1–15, [Epub ahead of print]

  • Aslanzadeh J, Hedrick HG (1985) Search for Mirex-degrading soil microorganisms. Soil Science 139:369–374

    Article  CAS  Google Scholar 

  • Aso Y, Miyamoto Y, Harada KM, Momma K, Kawai S, Hashimoto W (2006) Engineered membrane superchannel improves bioremediation potential of dioxin-degrading bacteria. Nat Biotechnol 24:188–9

    Article  CAS  Google Scholar 

  • Bala K, Sharma P, Lal R (2010) Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH) degrading bacterium isolated from an HCH-contaminated soil. IJSEM 60:429–43

    CAS  Google Scholar 

  • Barriault D, Plant MM, Sylvestre M (2002) Family shuffling of a targeted bphA region to engineer biphenyl dioxygenase. J Bacteriol 184:794–800

    Article  CAS  Google Scholar 

  • Bedard DL (2008) A case study for microbial biodegradation: anaerobic bacterial reductive dechlorination of polychlorinated biphenyls-from sediment to defined medium. Annual Rev Microbiol 62:253–270

    Article  CAS  Google Scholar 

  • Beunink J, Rehm HJ (1988) Synchronous anaerobic and aerobic degradation of DDT by an immobilized mixed culture system. Appl Microbiol Biotechnol 29:72–80

    Article  CAS  Google Scholar 

  • Black JG (1999) Bioremediation. En: Microbiology: Principles and Explorations, 4th edn. Prentice Hall Publishers, Upper Saddle River, pp 751–752

    Google Scholar 

  • Borgeest C, Greenfeld C, Tomic D, Flaws JA (2002) The effects of endocrine disrupting chemicals on the ovary. Front Biosci 7:1941–1948

    Article  Google Scholar 

  • Bruhlmann F, Chen W (1999) Turning biphenyl dioxygenase for extended substrate specificity. Biotechnol Bioeng 63:544–51

    Article  CAS  Google Scholar 

  • Bumpus JA, Tien M, Wright D, Aust SD (1985) Oxidation of persistent environmental pollutants by a white rot fungus. Science 228:1434–1436

    Article  CAS  Google Scholar 

  • Bunge M, Adrian L, Kraus A, Lorenz WG, Andreesen JR, Gorisch H, Lechner U (2003) Reductive dehaogenation of chlorinated dioxins by the anaerobic bacterium Dehalococcoides ethenogenes genes sp. strain CBDBI. Nature 421:357–360

    Article  CAS  Google Scholar 

  • Bunge M, Ballerstedt H, Lechner U (2001) Regiospecific dechlorination of spiked tetra and trichlorodibenzo-p-dioxins by anaerobic bacteria from PCDD/F-contaminated Spittelwasser sediments. Chemosphere 43:675–681

    Article  CAS  Google Scholar 

  • Bylaska EJ, Dixon DA, Felmy AR, Aprà E, Windus TL, Zhan CG, Tratnyek PG (2004) The energetics of the hydrogenolysis, dehydrohalogenation, and hydrolysis of 4, 4′-dichloro-diphenyl-trichloroethane from ab initio electronic structure theory. J Phys Chem A 108(27):5883–5893

    Article  CAS  Google Scholar 

  • Chanama M, Chanama S (2011) Expression of pentachlorophenol-degradative genes of Sphingobium chlorophenolica ATCC39723 in Escherichia coli. Asia J Public Health 2:78–83

    Google Scholar 

  • Chakraborty J, Das S (2014) Biosurfactant based bioremediation of toxic metals. In: Microbial Biodegradation and Bioremediation. Elsevier, pp 167–201

  • Chakraborty J, Das S (2016) Characterization of the metabolic pathway and catabolic gene expression in biphenyl degrading marine bacterium Pseudomonas aeruginosa JP-11. Chemosphere 144:1706–1714

    Article  CAS  Google Scholar 

  • Chattaraj PK, Sarkar U, Roy DR (2006) Electrophilicity index. Chem Rev 106:2065–2091

    Article  CAS  Google Scholar 

  • Chaudhry GR, Chapalamadugu S (1991) Biodegradation of halogenated organic compounds. Microbiol Rev 55:59–79

    CAS  Google Scholar 

  • Chavez FP, Lunsdorf H, Jerez CA (2004) Growth of polychlorinated biphenyl degrading bacteria in the presence of biphenyl and chlorobiphenyls generates oxidative stress and massive accumulation of inorganic polyposhphate. Appl Environ Microbiol 70:3064–3072

    Article  CAS  Google Scholar 

  • Chowdhury A, Pradhan S, Saha M, Sanyal N (2008) Impact of pesticides on soil microbiological parameters and possible bioremediation strategies. Indian J Microbiol 48:114–127

    Article  CAS  Google Scholar 

  • Covaci A, Harrad S, Abdallah MAE, Ali N, Law RJ, Herzke D, de Wit CA (2011) Novel brominated flame retardants: a review of their analysis, environmental fate and behaviour. Environ Int 37:532–556

    Article  CAS  Google Scholar 

  • Culligan EP, Sleator RD, Marchesi JR, Hill C (2014) Metagenomics and novel gene discovery: promise and potential for novel therapeutics. Virulence 5:399–412

    Article  Google Scholar 

  • Cvančarová M, Křesinová Z, Filipová A, Covino S, Cajthaml T (2012) Biodegradation of PCBs by ligninolytic fungi and characterization of the degradation products. Chemosphere 88:1317–23

    Article  CAS  Google Scholar 

  • Cvitkovitch DG, Li YH, Ellen RP (2003) Quorum sensing and biofilm formation in Streptococcal infections. J Clin Invest 112:1626–1632

    Article  CAS  Google Scholar 

  • Das S, Dash HR, Chakraborty J (2016) Genetic basis and importance of metal resistant genes in bacteria for bioremediation of contaminated environments with toxic metal pollutants. Appl Microbiol Biotechnol 100:2967–2984

    Article  CAS  Google Scholar 

  • de Carvalho CCCR, Wick LY, Heipieper HJ (2009) Cell wall adaptations of planktonic and biofilm Rhodococcus erythropolis cells to growth on C5 to C16 n-alkane hydrocarbons. Appl Microbiol Biotechnol 82:311–320

    Article  CAS  Google Scholar 

  • De J, Ramaiah N, Sarkar A (2006) Aerobic degradation of highly chlorinated polychlorobiphenyls by a marine bacterium, Pseudomonas CH07. World J Microbiol Biotechnol 22:1321–1327

    Article  CAS  Google Scholar 

  • DeWeerd KA, Mandelco L, Tanner RS, Woese CR, Suflita JM (1990) Desulfomonile tiedjei gen nov and a novel anaerobic dehalogenating sulfate-reducing bacterium. Arch Microbiol 154:23–30

    Article  CAS  Google Scholar 

  • Dileep K (2008) Biodegradation and bioremediation of pesticide in soil: concept, method and recent developments. Indian J Microbiol 48:35–40

    Article  Google Scholar 

  • Don RH, Pemberton JM (1981) Properties of six pesticides degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutrophus. J Bacteriol 145:681–686

    CAS  Google Scholar 

  • Dumont MG, Murrell JC (2005) Stable isotope probing-linking microbial identity to function. Nat Rev Microbiol 3:499–504

    Article  CAS  Google Scholar 

  • El Fantroussi S, Agathos SN (2005) Is bioaugmentation a feasible strategy for pollutant removal and site remediation? Curr Opin Microbiol 8:268–275

    Article  CAS  Google Scholar 

  • Erickson BD, Mondello FJ (1992) Nucleotide sequencing transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated biphenyl degrading enzyme in Pseudomonas strain LB400. Appl Environ Microbiol 174:2903–12

    CAS  Google Scholar 

  • Erickson BD, Mondello FJ (1993) Enhanced biodegradation of polychlorinated-biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl Environ Microbiol 59:3858–62

    CAS  Google Scholar 

  • Fan X, Liu X, Huang R, Liu Y (2012) Identification and characterization of a novel thermostable pyrethroid-hydrolyzing enzyme isolated through metagenomic approach. Microb Cell Fact 11:1

    Article  CAS  Google Scholar 

  • Fang H, Cai L, Yang Y, Ju F, Li X, Yu Y, Zhang T (2014) Metagenomic analysis reveals potential biodegradation pathways of persistent pesticides in freshwater and marine sediments. Sci Total Environ 470:983–992

    Article  CAS  Google Scholar 

  • Francino MP (2012) The ecology of bacterial genes and the survival of the new. Int J Evol Biol 2012:394026

    Article  Google Scholar 

  • Fries GR, Marrow GS, Gordon CH (1969) Metabolism of o, p’-and p, p’-DDT by rumen microorganism. J Agri Food Chem 17:860–862

    Article  CAS  Google Scholar 

  • Fritsche W and Hofrichter M (2000) Aerobic degradation by microorganisms, in environmental processes. Soil decontamination J Klein Ed. Wiley-VCH Weinheim Germany pp. 146–155

  • Fritsche W and Hofrichter M (2004) Aerobic degradation of recalcitrant organic compounds by microorganisms. Environmental Biotechnology. Concepts and Applications. (eds HJ Jördening and J Winter), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG

  • Fukuda K, Nagata S, Taniguchi H (2002) Isolation and characterization of dibenzofuran-degrading bacteria. FEMS Microbiol Lett 208:179–185

    Article  CAS  Google Scholar 

  • Furukawa K (2000) Engineering dioxygenases for efficient degradation of environmental pollutants. Curr Opin Biotechnol 11:244–9

    Article  CAS  Google Scholar 

  • Furukawa K, Fujihara H (2008) Microbial degradation of polychlorinated biphenyls: biochemical and molecular features. J Biosc Bioeng 105:433–449

    Article  CAS  Google Scholar 

  • Futagami T, Goto M, Furukawa K (2008) Biochemical and genetic bases of dehalorespiration. The Chem Rec 8:1–12

    Article  CAS  Google Scholar 

  • Galvão TC, Mohn WW, de Lorenzo V (2005) Exploring the microbial biodegradation and biotransformation gene pool. Trends Biotechnol 23:497–506

    Article  CAS  Google Scholar 

  • Garg N, Bala K, Lal R (2012) Sphingobium lucknowense sp. nov. a hexachlorocyclohexane (HCH)-degrading bacterium isolated from HCH-contaminated soil. IJSEM 62:618–623

    CAS  Google Scholar 

  • George SE, Claxton LD (1988) Biotransformation of chlordecone by Pseudomonas species. Xenobiotica 18:407–416

    Article  CAS  Google Scholar 

  • Ghazali FM, Rahman RNZA, Salleh AB, Basri M (2004) Biodegradation of hydrocarbons in soil by microbial consortium. Int Biodeter Biodegr 54:61–67

    Article  CAS  Google Scholar 

  • Gibson DT, Cruden DL, Haddock JD, Zylstra GJ, Brand JM (1993) Oxidation of polychlorinated-biphenyls by Pseudomonas sp. strain LB400 and Pseudomonas pseudoalcaligenes KF707. J Bacteriol 175:4561–4564

    CAS  Google Scholar 

  • Gienfrada L, Rao MA (2008) Interactions between xenobiotics and microbial and enzymatic soil activity. Crit Rev Environ Sci Technol 38:269–310

    Article  CAS  Google Scholar 

  • Gooch JW, Matsumura F (1985) Evaluation of the toxic components of toxaphene in Lake Michigan lake trout. J Agric Food Chem 33:844–848

    Article  CAS  Google Scholar 

  • Gouin T, Mackaya D, Jones KC, Harner T, Meijer SN (2004) Evidence for the “grasshopper” effect and fractionation during long-range atmospheric transport of organic contaminants. Environ Pollut 128:139–148

    Article  CAS  Google Scholar 

  • Habe H, Chung JS, Lee JH, Kasuga K, Yoshida T, Nojiri H, Omori T (2001) Degradation of chlorinated dibenzofurans and dibenzo-p-dioxins by two types of bacteria having angular dioxygenases with different features. Appl Environ Microbiol 67:3610–3617

    Article  CAS  Google Scholar 

  • Haggblom, MM, Bossert ID (2004) Halogenated organic compounds-a global perspective. In Dehalogenation Springer US pp. 3–29

  • Hay AG, Focht DD (1998) Cometabolism of 1, 1-dichloro-2, 2-bis (4-chlorophenyl)ethylene by Pseudomonas acidovorans M3GY grown on biphenyl. Appl Environ Microbiol 64:2141–6

    CAS  Google Scholar 

  • Hayes JD, Flanagan JU, Jowsey IR (2005) Glutathione transferases. Annu Rev Pharmacol Toxicol 45:51–88

    Article  CAS  Google Scholar 

  • Henderson IR, Owen P, Nataro JP (1999) Molecular switches—the ON and OFF of bacterial phase variation. Mol Microbiol 33:919–932

    Article  CAS  Google Scholar 

  • Henne A, Schmitz RA, Bomeke M, Gottschalk G, Daniel R (2000) Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl Environ Microbiol 66:3113–3116

    Article  CAS  Google Scholar 

  • Hernandez-Raquet G, Soef A, Delgenès N, Balaguer P (2007) Removal of the endocrine disrupter nonylphenol and its estrogenic activity in sludge treatment processes. Water Res 41:2643–2651

    Article  CAS  Google Scholar 

  • Heuer H, Smalla K (2012) Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 36:1083–1104

    Article  CAS  Google Scholar 

  • Hill JE, Fernando WU, Zello GA, Tyler RT, Dahl WJ, Van Kessel AG (2010) Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail. Appl Environ Microbiol 76:4550–4552

    Article  CAS  Google Scholar 

  • Hiraishi A, Yoshida N, Takahashi N (2005) Phylogenetic characterization of a polychlorinated-dioxin dechlorinating microbial community by use of microcosm studies. Appl Environ Microbiol 71:4325–4334

    Article  CAS  Google Scholar 

  • Hofrichter M, Bublitz F, Fritsche W (1994) Unspecific degradation of halogenated phenols by the soil fungus Penicillium frequentans Bi7/2. J Basic Microbiol 34:163–172

    Article  CAS  Google Scholar 

  • Houghton JE, Shanley MS (1994) Catabolic potential of Pseudomonads: a regulatory perspective. In: Chaudhry GR (ed) Biological degradation and bioremediation of toxic chemicals. Dioscorides press, Portland pp, pp 11–32

    Google Scholar 

  • Hrywna Y, Tsoi TV, Maltseva OV, Quensen JF, Tiedje JM (1999) Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls. Appl Environ Microbiol 65:2163–2169

    CAS  Google Scholar 

  • Huang WE, Ferguson A, Singer AC, Lawson K, Thompson IP, Kalin RM, Whiteley AS (2009) Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell Raman-fluorescence in situ hybridization. Appl Environ Microbiol 75:234–41

    Article  CAS  Google Scholar 

  • Huang Y, Wang J (2013) Degradation and mineralization of DDT by the ectomycorrhizal fungi Xerocomus chrysenteron. Chemosphere 92:760–4

    Article  CAS  Google Scholar 

  • Hutz RJ (1999) Reproductive endocrine disruption by environmental xenobiotics that modulate the estrogen-signaling pathway, particularly tetrachlorodibenzo-p-dioxin (TCDD). J Reprod Dev 45:1–12

    Article  CAS  Google Scholar 

  • Ikuma K (2011) The effect of select biological and environmental factors on the horizontal gene transfer and functionality of the TOL plasmid: a case study for genetic bioaugmentation. Duke University, Doctoral dissertation

    Google Scholar 

  • Isken S, de Bont JA (1998) Bacteria tolerant to organic solvents. Extremophiles 2:229–238

    Article  CAS  Google Scholar 

  • Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM (2009) Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J 4:279–285

    Article  CAS  Google Scholar 

  • Jadeja NB, More RP, Purohit HJ, Kapley A (2014) Metagenomic analysis of oxygenases from activated sludge. Bioresour Technol 165:250–256

    Article  CAS  Google Scholar 

  • Jaiswal PK, Thakur IS (2007) Isolation and characterization of dibenzofuran-degrading Serratia marcescens from alkalophilic bacterial consortium of the chemostat. Curr Microbiol 55:447–454

    Article  CAS  Google Scholar 

  • Jayaraman R (2011) Hypermutation and stress adaptation in bacteria. J Genetics 90:383–391

    Article  CAS  Google Scholar 

  • Jefferson KK (2004) What drives bacteria to produce a biofilm? FEMS Microbiol Lett 236:163–173

    Article  CAS  Google Scholar 

  • Jeon JR, Murugesan K, Nam IH, Chang YS (2013) Coupling microbial catabolic actions with abiotic redox processes: a new recipe for persistent organic pollutants (POPs) removal. Biotechnol Adv 31:246–256

    Article  CAS  Google Scholar 

  • Jha SK, Jain P, Sharma HP (2015) Xenobiotic degradation by bacterial enzymes. Int J Curr Microbiol App Sci 4:48–62

    Google Scholar 

  • Joesten MD, Hogg JL, Castellion ME (2006) The world of chemistry: essentials: essentials. Cengage Learning

  • Juhasz A, Naidu R (2000) Enrichment and isolation of non-specific aromatic degraders from unique uncontaminated (plant and fecal material) sources and contaminated soils. J Appl Microbiol 89:642–650

    Article  CAS  Google Scholar 

  • Kaiya S, Utsunomiya S, Suzuki S, Yoshida N, Futamata H, Yamada T, Hiraishi A (2012) Isolation and functional gene analyses of aromatic-hydrocarbon-degrading bacteria from a polychlorinated-dioxin-dechlorinating process. Microbes Environ 27:127–35

    Article  Google Scholar 

  • Kakirde KS, Parsley LC, Liles MR (2010) Size does matter: application-driven approaches for soil metagenomics. Soil Biol Biochem 42:1911–1923

    Article  CAS  Google Scholar 

  • Kamanavalli CM, Ninnekar HZ (2004) Biodegradation of DDT by a Pseudomonas sp. Curr Microbiol 48:10–13

    Article  CAS  Google Scholar 

  • Kao CM, Chen SC, Liu JK, Wu MJ (2001) Evaluation of TCDD biodegradability under different redox conditions. Chemosphere 44:1447–1454

    Article  CAS  Google Scholar 

  • Karigar CS, Rao SS (2011) Role of microbial enzymes in the bioremediation of pollutants: a review. Enz Res 805187

  • Kataoka R, Takagi K, Kamei I, Kiyota H, Sato Y (2010) Biodegradation of dieldrin by a soil fungus isolated from a soil with annual endosulfan applications. Environ Sci Technol 44:6343–9

    Article  CAS  Google Scholar 

  • Keim T, Francke W, Schmidt S, Fortnagel P (1999) Catabolism of 2, 7 dichloro and 2, 4, 8-trichlorodibenzofuran by Sphingomonas sp. strain RW1. J Ind Microbiol Biotechnol 23:359–363

    Article  CAS  Google Scholar 

  • Khan AA, Wang RF, Cao WW, Doerge DR, Wennerstrom D, Cerniglia CE (2001) Molecular cloning, nucleotide sequence and expression of genes encoding a polycyclic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67:3577–3585

    Article  CAS  Google Scholar 

  • Kidd KA, Becher G, Bergman Å, Muir DC, Woodruff TJ (2012) Human and wildlife exposures to EDCs. State of the Science of Endocrine Disrupting Chemicals 1–261

  • Kimbara K (2005) Recent developments in the study of microbial aerobic degradation of polychlorinated biphenyls. Microbes Environ 20:127–134

    Article  Google Scholar 

  • Kimura N, Nishi M, Goto M, Furukawa K (1997) Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J Bacteriol 179:3936–3943

    CAS  Google Scholar 

  • Kitagawa W, Takami S, Miyauchi K, Masai E, Kamagata Y, Tiedje JM, Fukuda M (2002) Novel 2, 4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment. J Bacteriol 184:509–18

    Article  CAS  Google Scholar 

  • Klecka GM, Gibson DT (1980) Metabolism of dibenzo-para-dioxin and chlorinated dibenzo-para-dioxins by a Beijerinckia species. Appl Environ Microbiol 39:288–296

    CAS  Google Scholar 

  • Kumar S (2004) Occupational exposure associated with reproductive dysfunction. J Occup Health 46:1–19

    Article  CAS  Google Scholar 

  • Kumari R, Subudhi S, Suar M, Dhingra G, Raina V, Dogra C, Lal R (2002) Cloning and characterization of lin genes responsible for the degradation of hexachlorocyclohexane isomers by Sphingomonas paucimobilis strain B90. Appl Environ Microbiol 68:6021–6028

    Article  CAS  Google Scholar 

  • La Farre M, Pérez S, Kantiani L, Barceló D (2008) Fate and toxicity of emerging pollutants, their metabolites and transformation products in the aquatic environment. TrAC Trend Anal Chem 27:991–1007

    Article  CAS  Google Scholar 

  • Lacayo-Romero M, Quillaguamán J, Van Bavel B, Mattiasson B (2005) A toxaphene-degrading bacterium related to Enterobacter cloacae, strain D1 isolated from aged contaminated soil in Nicaragua. Syst Appl Microbiol 28:632–639

    Article  CAS  Google Scholar 

  • Leadbetter JR (2003) Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory. Curr Opin Microbiol 6:274–281

    Article  CAS  Google Scholar 

  • Ledger T, Pieper DH, Gonzalez B (2006) Chlorophenol hydroxylases encoded by plasmid pJP4 differentially contribute to chlorophenoxyacetic acid degradation. Appl Environ Microbiol 72:2783–2792

    Article  CAS  Google Scholar 

  • Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203–221

    CAS  Google Scholar 

  • Li X, Gao Y, Wang Y, Pan Y (2014) Emerging persistent organic pollutants in Chinese Bohai Sea and its coastal regions. Sci World J 608231

  • Lu XX, Chen CQ, Zhang S, Ou Y, Yin L, Wu W (2012) Microbial degradation of 2, 2′,4, 4′-tetrabrominated diphenyl ether under anaerobic condition. Huan Jing Ke Xue 33:1000–1007

    CAS  Google Scholar 

  • Lu Y, Yu Y, Zhou R, Sun W, Dai C, Wan P, Ren H (2011) Cloning and characterization of a novel 2, 4-dichlorophenol hydroxylase from a metagenomic library derived from polychlorinated biphenyl-contaminated soil. Biotechnol Lett 33:1159–1167

    Article  CAS  Google Scholar 

  • Malandain C, Fayolle-Gulchard F, Vogel TM (2010) Cytochromes P450-mediated degradation of fuel oxygenates by environmental isolates. FEMS Microbiol Ecol 72:289–296

    Article  CAS  Google Scholar 

  • Mangwani N, Shukla SK, Rao TS, Das S (2014) Calcium-mediated modulation of Pseudomonas mendocina NR802 biofilm influences the phenanthrene degradation. Colloids Surf B 114:301–309

    Article  CAS  Google Scholar 

  • Mangwani N, Kumari S, Das S (2015) Involvement of quorum sensing genes in biofilm development and degradation of polycyclic aromatic hydrocarbons by a marine bacterium Pseudomonas aeruginosa N6P6. Appl Microbiol Biotechnol 99:10283–10297

    Article  CAS  Google Scholar 

  • Marcobal AM, Sela DA, Wolf YI, Makarova KS, Mills DA (2008) Role of hypermutability in the evolution of the genus Oenococcus. J Bacteriol 190:564–570

    Article  CAS  Google Scholar 

  • Matsumoto E, Kawanaka Y, Yun SJ, Oyaizu H (2008) Isolation of dieldrin and endrin degrading bacteria using 1, 2 epoxycyclohexane as a structural analog of both compounds. Appl Microbiol Biotechnol 80:1095–1103

    Article  CAS  Google Scholar 

  • Matsuzaki F, Wariishi H (2005) Molecular characterization of cytochrome P450 catalyzing hydroxylation of benzoates from the white-rot fungus Phanerochaete chrysosporium. Biochem Biophys Res Comm 334:1184–1190

    Article  CAS  Google Scholar 

  • McGuinness MC, Mazurkiewicz V, Brennan E, Dowling DN (2007) Dechlorination of pesticides by a specific bacterial glutathione S-transferase, BphKLB400: potential for bioremediation. Eng Life Sci 7:611–615

    Article  CAS  Google Scholar 

  • McLeod MP, Warren RL, Hsiao WW, Araki Myhre NM, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh Hara MH, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD (2006) The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci USA 103:15582–15587

    Article  Google Scholar 

  • Megharaj M, Ramakrishnan B, Venkateswarlu K, Sethunathan N, Naidu R (2011) Bioremediation approaches for organic pollutants: a critical perspective. Environ Int 37:1362–1375

    Article  CAS  Google Scholar 

  • Meier MJ (2014) Metagenomic analysis of contaminated soils. Doctoral dissertation, Carleton University Ottawa

    Google Scholar 

  • Merlin C, Devers M, Crouzet O, Heraud C, Steinberg C, Mougin C, Martin-Laurent F (2014) Characterization of chlordecone-tolerant fungal populations isolated from long-term polluted tropical volcanic soil in the French West Indies. Environ Sci Pollut Res 21:4914–4927

    Article  CAS  Google Scholar 

  • Miyauchi K, Sukda P, Nishida T, Ito E, Matsumoto Y, Masai E, Fukuda M (2008) Isolation of dibenzofuran-degrading bacterium, Nocardioides sp. DF412, and characterization of its dibenzofuran degradation genes. J Biosci Bioeng 105:628–635

    Article  CAS  Google Scholar 

  • Mohn WW, Tiedje JM (1992) Microbial reductive dehalogenation. Microbiol Rev 56:482–507

    CAS  Google Scholar 

  • Molin S, Nielsen TT (2003) Gene transfer occurs with enhanced efficiency in biofilms and induces stabilization of the biofilm structure. Curr Opin Biotechnol 14:255–261

    Article  CAS  Google Scholar 

  • More RP, Mitra S, Raju SC, Kapley A, Purohit HJ (2014) Mining and assessment of catabolic pathways in the metagenome of a common effluent treatment plant to induce the degradative capacity of biomass. Bioresour Technol 153:137–146

    Article  CAS  Google Scholar 

  • Morgante V, López-López A, Flores C, González M, González B, Vásquez M, Seeger M (2010) Bioaugmentation with Pseudomonas sp. strain MHP41 promotes simazine attenuation and bacterial community changes in agricultural soils. FEMS Microbiol Ecol 71:114–126

    Article  CAS  Google Scholar 

  • Mougin C, Pericaud C, Malosse C, Laugero C, Ashter M (1999) Biotransformation of the insecticide lindane by the white-rot basidiomycete Phanerochaete chrysosporium. Pestic Sci 41:1–59

    Google Scholar 

  • Mrozik A, Piotrowska-Seget Z, Labuzek S (2003) Bacterial degradation and bioremediation of polycyclic aromatic hydrocarbons. Pol J Environ Stud 12(1)

  • Mwangi K, Boga HI, Muigai AW, Kiiyuikia C, Tsanuo MK (2010) Degradation of dichlorodiphenyltrichloroethane (DDT) by bacterial isolates from cultivated and uncultivated soil. Afr J Microbiol Res 4:185–196

    CAS  Google Scholar 

  • Nadeau LJ, Menn FM, Breen A, Sayler GS (1994) Aerobic degradation of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) by Alcaligenes eutrophus A5. Appl Environ Microbiol 60:51–55

    CAS  Google Scholar 

  • Nagao T (1998) Health effects of endocrine disruptors. JPN J Tox Environ Health 44:151–167

    Article  CAS  Google Scholar 

  • Nakatsu C, Ng J, Singh R, Straus N, Wyndham C (1991) Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences. Pro Nat Acad Sci 88:8312–8316

    Article  CAS  Google Scholar 

  • Niedle EL, Harnett C, Bonitz S, Ornston LN (1988) DNA sequence of Acinetobacter calcoaceticus catechol 1, 2-dioxygenase-I structural gene catA: evidence for evolutionary divergence of intradiol dioxygenases by acquisition of DNA sequence repetitions. J Bacteriol 170:4874–4880

    Google Scholar 

  • Nojiri H, Omori T (2002) Molecular bases of aerobic bacterial degradation of dioxins: involvement of angular dioxygenation. Biosci Biotechnol Biochem 66:2001–2016

    Article  CAS  Google Scholar 

  • Nzila A (2013) Update on the cometabolism of organic pollutants by bacteria. Environ Pollut 178:474–482

    Article  CAS  Google Scholar 

  • Omura T (1999) Forty years of cytochrome P450. Biochem Biophys Res Comm 266:690–698

    Article  CAS  Google Scholar 

  • Othsubo Y, Nagata Y, Kimbara K, Takagi M, Ohta A (2000) Expression of the bph genes involved in biphenyl/PCB degradation in Pseudomonas sp. KKS102 induced by the biphenyl degradation intermediate, 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoic acid. Gene 256:223–228

    Article  Google Scholar 

  • Pal R, Bala S, Dadhwal M, Kumar M, Dhingra G, Prakash O, Lal R (2005) Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. Nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov. Int J Syst Evol Microbiol 55:1965–1972

    Article  CAS  Google Scholar 

  • Parales RE, Lee K, Resnick SM, Jiang H, Lessner DJ, Gibson DT (2000) Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme. J Bacteriol 182:1641–1649

    Article  CAS  Google Scholar 

  • Parsons JR, Storms MCM (1989) Biodegradation of chlorinated dibenzo-para-dioxins in batch and continuous cultures of strain JB1. Chemosphere 19:1297–1308

    Article  CAS  Google Scholar 

  • Patil KC, Matsumura F, Boush GM (1970) Degradation of Endrin, Aldrin, and DDT by soil microorganisms. J Appl Microbiol 19:879–881

    CAS  Google Scholar 

  • Pemberton JM, Schmidt R (2001) Catabolic plasmids. Encyclopaedia Life Science, University of Queensland, Australia

    Book  Google Scholar 

  • Pieper DH, Reineke W (2000) Engineering bacteria for bioremediation. Curr Opin Biotechnol 11:262–27

    Article  CAS  Google Scholar 

  • Pieper DH (2005) Aerobic degradation of polychlorinated biphenyls. Appl Microbiol Biotechnol 67:170–191

    Article  CAS  Google Scholar 

  • Qi Y, Zhao L, Olusheyi OZ, Tan X (2007) Isolation and preliminary characterization of a 3-chlorobenzoate degrading bacteria. J Environ Sci (China) 19:332–7

    Article  CAS  Google Scholar 

  • Quensen JF, Mueller SA, Jain MK, Tiedje JM (1998) Reductive dechlorination of DDE to DDMU in marine sediment microcosms. Science 280:722–724

    Article  CAS  Google Scholar 

  • Rabausch U, Juergensen J, Ilmberger N, Böhnke S, Fischer S, Schubach B, Streit WR (2013) Functional screening of metagenome and genome libraries for detection of novel flavonoid-modifying enzymes. Appl Environ Microbiol 79:4551–4563

    Article  CAS  Google Scholar 

  • Ramesh C, Atur K, Ajay S, Owen P (2004) Bioremediation of pesticide contaminated soils, Applied Bioremediation and Phytoremediation. Springer-verlag Berlin Heidelberg pp. 35–55

  • Ray MB (2000) Photodegradation of the volatile organic compounds in the gas phase: a review. Dev Chem Eng Min Proc 8:405–439

    Article  Google Scholar 

  • Rappe C (1991) Sources of and human exposure to PCDDs and PCDFs. In: Gallo MA et al (eds) Biological basis for risk assessment of dioxins and related compounds. Cold Spring Harbor, New York, pp 121–129

    Google Scholar 

  • Rayssiguier C, Thaler D, Radman M (1989) The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch repair mutants. Nature 342:396–401

    Article  CAS  Google Scholar 

  • Rentz JA, Alvarez PJ, Schnoor JL (2008) Benzo[a]pyrene degradation by Sphingomonas yanoikuyae JAR02. Environ Pollut 151:669–677

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Richardson AR, Stojiljkovic I (2001) Mismatch repair and the regulation of phase variation in Neisseria meningitidis. Mol Microbiol 40:645–655

    Article  CAS  Google Scholar 

  • Richardson SD, Ternes TA (2011) Water analysis: emerging contaminants and current issues. Anal Chem 83:4614–4648

    Article  CAS  Google Scholar 

  • Romero ML, Terrazas E, Van Bavel B, Mattiasson B (2006) Degradation of toxaphene by Bjerkandera sp. strain BOL13 using waste biomass as a cosubstrate. Appl Microbiol Biotechnol 71(4):549–554

    Article  CAS  Google Scholar 

  • Ron EZ, Rosenberg E (2002) Biosurfactants and oil bioremediation. Curr Opin Biotechnol 13:249–252

    Article  CAS  Google Scholar 

  • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547

    Article  CAS  Google Scholar 

  • Rossjohn J, Polekhina G, Feil SC, Allocati N, Masulli M, Di Ilio C, Parker MW (1998) A mixed disulfide bond in bacterial glutathione transferase: functional and evolutionary implications. Structure 6:721–734

    Article  CAS  Google Scholar 

  • Rout P, Jiwal S, Sasikala C, Mohandass R (2012) Biodegradation of Benzo[a]pyrene by the mixed culture of Bacillus cereus and Bacillus vireti isolated from the petrochemical industry. J Environ Biol 33:985–989

    Google Scholar 

  • Roy DR, Parthasarathi R, Subramanian V, Chattaraj PK (2006) An electrophilicity based analysis of toxicity of aromatic compounds towards Tetrahymena pyriformis. QSAR Comb Sci 25:114–122

    Article  CAS  Google Scholar 

  • Rylott EL, Jackson RG, Edwards J, Womack GL, Seth-Smith HM, Rathbone DA, Bruce NC (2006) An explosive-degrading cytochrome P450 activity and its targeted application for the phytoremediation of RDX. Nature Biotechnol 24:216–219

    Article  CAS  Google Scholar 

  • Sadowsky D, McNeill K, Cramer CJ (2014) Dehalogenation of aromatics by nucleophilic aromatic substitution. Environ Sci Technol 48:10904–10911

    Article  CAS  Google Scholar 

  • Sahu SK, Patnaik KK, Sethunathan N (1992) Dehydrochlorination of δ-isomer of hexachlorocyclohexane by a soil bacterium, Pseudomonas sp. Bull Environ Contam Toxicol 48:265–268

    Article  CAS  Google Scholar 

  • Sakakibara F, Takagi K, Kataoka R, Kiyota H, Sato Y, Okada S (2011) Isolation and identification of dieldrin-degrading Pseudonocardia sp. strain KSF27 using a soil-charcoal perfusion method with aldrin trans-diol as a structural analog of dieldrin. Biochem Biophys Res Commun 411:76–81

    Article  CAS  Google Scholar 

  • Samardjieva K, Tavares F, Pissarra J (2015) Histological and ultrastructural evidence for zinc sequestration in Solanum nigrum L. Protoplasma 252:345–357

    Article  CAS  Google Scholar 

  • Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N, Kaur J, Lal R (2012) Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels. PLoS One 7:e46219

    Article  CAS  Google Scholar 

  • Sangwan N, Verma H, Kumar R, Negi V, Lax S, Khurana P, Lal R (2014) Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data. ISME J 8:398–408

    Article  CAS  Google Scholar 

  • Sato A, Watanabe T, Watanabe Y, Harazono K, Fukatsu T (2002) Screening for basidiomycetous fungi capable of degrading 2, 7-dichlorodibenzo-p-dioxin. FEMS Microbiol Lett 213:213–217

    Article  CAS  Google Scholar 

  • Saylor GS, Layton AC (1990) Environmental application of nucleic acid. Annu Rev Microbiol 44:625–648

    Article  Google Scholar 

  • Scheller U, Zimmer T, Becher D, Schauer F, Schunck WH (1998) Oxygenation cascade in conversion of n-alkanes to α, ω-dioic acids catalyzed by cytochrome P450 52A3. J Biol Chem 273:32528–32534

    Article  CAS  Google Scholar 

  • Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303–310

    Article  CAS  Google Scholar 

  • Schlüter A, Szczepanowski R, Pühler A, Top EM (2007) Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol Rev 31:449–477

    Article  CAS  Google Scholar 

  • Seeger M, Saavedra JM, Acevedo Gonzalez FM (2009) Mineralization of PCBs by the genetically modified strain Cupriavidus necator JMS34 and its application for bioremediation of PCBs in soil. Appl Environ Microbiol 87:1543–1554

    Google Scholar 

  • Seeger M, Hernández M, Méndez V, Ponce B, Córdova M, González M (2010) Bacterial degradation and bioremediation of chlorinated herbicides and biphenyls. J Soil Sci Plant Nut 10:320–332

    Google Scholar 

  • Seo JS, Keum YS, Li QX (2009) Bacterial degradation of aromatic compounds. Int J Environ Res Pub Health 6:278–309

    Article  CAS  Google Scholar 

  • Sharma SK, Sadasivam KV, Dave JM (1987) DDT degradation by bacteria from activated sludge. Environ Int 13:183–190

    Article  CAS  Google Scholar 

  • Shields MS, Hooper SW, Sayler GS (1985) Plasmid-mediated mineralization of 4-chlorobiphenyl. J Bacteriol 163:882–889

    CAS  Google Scholar 

  • Sierra-García IN, Alvarez JC, de Vasconcellos SP, de Souza AP, de Oliveira VM, de Oliveira VM (2014) New hydrocarbon degradation pathways in the microbial metagenome from Brazilian petroleum reservoirs. PloS One 9:e90087

    Article  CAS  Google Scholar 

  • Singh BK, Kuhad RC (1999) Biodegradation of lindane (γ-hexachlorocyclohexane) by the white-rot fungus Trametes hirsutus. Lett Appl Microbiol 28:238–241

    Article  CAS  Google Scholar 

  • Singh BK, Kuhad RC (2000) Degradation of the insecticide lindane (γ-HCH) by white-rot fungi Cyathus bulleri and Phanerochaete sordida. Pest Manage Sci 56:142–146

    Article  CAS  Google Scholar 

  • Sinha S, Chattopadhyay P, Pan I, Chatterjee S, Chanda P, Bandyopadhyay D, Sen SK (2009) Microbial transformation of xenobiotics for environmental bioremediation. Afr J Biotechnol 8:6016–6027

    Article  CAS  Google Scholar 

  • Sinha S, Chattopadhyay P, Pan I, Chatterjee S, Chanda P, Bandyopadhyay D, Sen SK (2011) Microbial transformation of xenobiotics for environmental bioremediation. Afr J Biotechnol 8:22

    Google Scholar 

  • Sørensen SJ, Bailey M, Hansen LH, Kroer N, Wuertz S (2005) Studying plasmid horizontal transfer in situ: a critical review. Nat Rev Microbiol 3:700–710

    Article  CAS  Google Scholar 

  • Stockholm Convention (2001) Persistent Organic Pollutants and the Stockholm Convention: A Resource Guide Prepared by Resource Futures International for the World Bank and CIDA

  • Stockholm Convention (2009) Stockholm convention on persistent organic pollutants (POPs). Secretariat of the Stockholm Convention on Persistent Organic Pollutants, United Nations Environment Programme (UNEP), United Nations Treaty, Stockholm

    Google Scholar 

  • Stockholm Convention (2010) The new POPs under the Stockholm Convention. http://chm.pops.int/Implementation/NewPOPs/TheNewPOPs/tabid/672/Default.aspx. C.N.681.2015.TREATIES-XXVII. Accessed 15 Dec 2015

  • Suenaga H, Nishi A, Watanabe T, Sakai M, Furukawa K (1999) Engineering a hybrid Pseudomonad to acquire 3,4-dioxygenase activity for polychlorinated biphenyls. J Biosci Bioeng 87:430–435

    Article  CAS  Google Scholar 

  • Suenaga H, Goto M, Furukawa K (2001) Emergence of multifunctional oxygenase activities by random priming recombination. J Biol Chem 276:22500–22506

    Article  CAS  Google Scholar 

  • Suenaga H, Watanabe T, Sato M, Furukawa KN (2002) Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering. J Bacteriol 184:3682–8

    Article  CAS  Google Scholar 

  • Sulistyaningdyah WT, Ogawa J, Li QS, Shinkyo R, Sakaki T, Nouye K, Schmid RD, Shimizu S (2004) Metabolism of polychlorinated dibenzo-p-dioxins by cytochrome P450BM-3 and its mutant. Biotechnol Lett 26:1857–1860

    Article  CAS  Google Scholar 

  • Syed K, Doddapaneni H, Subramanian V, Lam YW, Yadav JS (2010) Genome to function characterization of novel fungal P450 monooxygenases oxidizing polycyclic aromatic hydrocarbons (PAHs). Biochem Biophys Res Commun 399:492–497

    Article  CAS  Google Scholar 

  • Takagi K, Iwasaki A, Kamei I, Satsuma K, Yoshioka Y, Harada N (2009) Aerobic mineralization of hexachlorobenzene by newly isolated pentachloronitrobenzene-degrading Nocardioides sp. strain PD653. Appl Environ Microbiol 75:4452–4458

    Article  CAS  Google Scholar 

  • Tas N, Eekert MHA, Wagner A, Schraa G, Vos W, Smidt MD (2011) Role of “Dehalococcoides” sp. in the anaerobic transformation of hexachlorobenzene in European rivers. Appl Environ Microbiol 77:4437–4445

    Article  CAS  Google Scholar 

  • Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3:711–721

    Article  CAS  Google Scholar 

  • Thomas T, Gilbert J, Meyer F (2012) Metagenomics—a guide from sampling to data analysis. Microb Inform Exp 2:1

    Article  Google Scholar 

  • Top EM, Springael D (2003) The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol 14:262–269

    Article  CAS  Google Scholar 

  • Torres-Cruz J, van der Woude MW (2003) Slipped-strand mispairing can function as a phase variation mechanism in Escherichia coli. J Bacteriol 185:6990–6994

    Article  CAS  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43

    Article  CAS  Google Scholar 

  • Uchiyama T, Watanabe K (2007) The SIGEX scheme: high throughput screening of environmental metagenomes for the isolation of novel catabolic genes. Biotechnol Genet Eng 24:107–116

    Article  CAS  Google Scholar 

  • Uchiyama T, Abe T, Ikemura T, Watanabe K (2005) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23:88–93

    Article  CAS  Google Scholar 

  • Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB, Macek T (2013) Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 31:154–165

    Article  CAS  Google Scholar 

  • UNEP (2006) Global Programme of Action (GPA) for the Protection of the Marine Environment from Land-based Activities Ecosystem based management. United Nations Environment Programme, The Hague. ISBN 92-807-2707-9

    Google Scholar 

  • United States Environmental Protection Agency (USEPA) (2009) Persistent Organic Pollutants: A Global Issue, A Global Response. http://www.epa.gov

  • Vallaeys T, Courde L, Mc Gowan C, Wright AD, Fulthorpe RR (1999) Phylogenetic analyses indicate independent recruitment of diverse gene cassettes during assemblage of the 2, 4-D catabolic pathway. FEMS Microbiol Ecol 28:373–382

    Article  CAS  Google Scholar 

  • van Belkum A, Scherer S, van Alphen L, Verbrugh H (1998) Short sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62:275–293

    Google Scholar 

  • van der Meer JR, Zehnder AJ, de Vos WM (1991) Identification of a novel composite transposable element, Tn5280, carrying chlorobenzene dioxygenase genes of Pseudomonas sp. strain P51. J Bacteriol 173:7077–7083

    Google Scholar 

  • Van Beilen JB, Funhoff EG (2007) Alkane hydroxylases involved in microbial alkane degradation. Appl Microbiol Biotechnol 74:13–21

    Article  CAS  Google Scholar 

  • Van Hamme JD, Singh A, Ward OP (2003) Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67:503–549

    Article  CAS  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    Article  CAS  Google Scholar 

  • Verma A, Ali D, Farooq M, Pant AB, Ray RS, Hans RK (2011) Expression and inducibility of endosulfan metabolizing gene in Rhodococcus strain isolated from earthworm gut microflora for its application in bioremediation. Bioresour Technol 102:2979–2984

    Article  CAS  Google Scholar 

  • Vitali VMV, Machado KMG, Andrea MMD, Bononi VLR (2006) Screening mitosporic fungi for organochlorides degradation. Brazilian J Microbiol 37:256–261

    Article  CAS  Google Scholar 

  • Wade W (2002) Unculturable bacteria-the uncharacterized organisms that cause oral infections. J R Soc Med 95:81–83

    Article  Google Scholar 

  • Wagner M, Horn M, Daims H (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol 6:302–9

    Article  CAS  Google Scholar 

  • Wang GL, Bi M, Liang B, Jiang J, Li S (2011) Pseudoxanthomonas jiangsuensis sp. a DDT degrading bacterium isolated from a long-term DDT-polluted soil. Curr Microbiol 62:1760–1766

    Article  CAS  Google Scholar 

  • Wang Y, Chen Y, Zhou Q, Huang S, Ning K, Xu J, Huang WE (2012) A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. PLoS One 7:e47530

    Article  CAS  Google Scholar 

  • Weir KM, Sutherland TD, Horne I, Russell RJ, Oakeshott JG (2006) A single monooxygenase, ese, is involved in the metabolism of the organochlorides endosulfan and endosulfate in an Arthrobacter sp. Appl Environ Microbiol 72:3524–30

    Article  CAS  Google Scholar 

  • Wenzel A, Gahr A, Niessner R (1999) TOC-removal and degradation of pollutants in leachate using a thin-film photoreactor. Water Res 33:937–946

    Article  CAS  Google Scholar 

  • Xiao P, Mori T, Kamei I, Kondo R (2011) Metabolism of organochlorine pesticide heptachlor and its metabolite heptachlor epoxide by white rot fungi, belonging to genus Phlebia. FEMS Microbiol Lett 314:140–146

    Article  CAS  Google Scholar 

  • Xu D, Wei Y, Wu J, Dunaway-Mariano D, Guo H, Cui Q, Gao J (2004) QM/MM studies of the enzyme-catalyzed dechlorination of 4-chlorobenzoyl-CoA provide insight into reaction energetics. J Am Chem Soc 126:13649–13658

    Article  CAS  Google Scholar 

  • Yamazoe A, Yagi O, Oyaizu H (2004) Degradation of polycyclic aromatic hydrocarbons by a newly isolated dibenzofuran-utilizing Janibacter sp. strain YY-1. Appl Microbiol Biotechnol 65:211–8

    Article  CAS  Google Scholar 

  • Yan DZ, Liu H, Zhou NY (2006) Conversion of Sphingobium chlorophenolicum ATCC 39723 to a hexachlorobenzene degrader by metabolic engineering. Appl Environ Microbiol 72:2283–2286

    Article  CAS  Google Scholar 

  • Ying GG, Toze S, Hanna J, Yu XY, Dillon PJ, Kookana RS (2008) Decay of endocrine-disrupting chemicals in aerobic and anoxic groundwater. Water Res 42:1133–1141

    Article  CAS  Google Scholar 

  • Zhang C, Bennett GN (2005) Biodegradation of xenobiotics by anaerobic bacteria. Appl Microbiol Biotechnol 67:600–618

    Article  CAS  Google Scholar 

  • Zhang S, Xia X, Xia N, Wu S, Gao F, Zhou W (2013) Identification and biodegradation efficiency of a newly isolated 2, 2′, 4, 4′-tetrabromodiphenyl ether (BDE-47) aerobic degrading bacterial strain. Int Biodeter Biodegr 76:24–31

    Article  CAS  Google Scholar 

  • Zheng YJ, Ornstein RL (1997) Mechanism of nucleophilic aromatic substitution of 1-chloro-2, 4-dinitrobenzene by glutathione in the gas phase and in solution. Implications for the mode of action of glutathione S-transferases. J Am Chem Soc 119:648–655

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors would like to acknowledge the authorities of NIT, Rourkela, for providing facilities. J.C. gratefully acknowledges the receipt of fellowship from Ministry of Human Resource Development, Government of India from NIT, Rourkela, for doctoral research. S.D. thanks the Department of Biotechnology, Ministry of Science and Technology, Government of India, for research grants on microbial bioremediation.

Author information

Authors and Affiliations

  1. Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India

    Jaya Chakraborty & Surajit Das

Authors
  1. Jaya Chakraborty
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Surajit Das
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Surajit Das.

Additional information

Responsible editor: Robert Duran

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chakraborty, J., Das, S. Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants. Environ Sci Pollut Res 23, 16883–16903 (2016). https://doi.org/10.1007/s11356-016-6887-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11356-016-6887-7

Keywords

Search

Navigation