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Biomineralization of 3-nitrotoluene by Diaphorobacter species

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Abstract

Three bacterial strains utilizing 3-nitrotoluene (3-NT) as a sole source of carbon, nitrogen and energy were isolated from an industrial wastewater treatment plant. Biochemical tests and 16S rDNA sequence analysis revealed that the isolated strains belonged to Diaphorobacter sp. Detailed studies were carried out with Diaphorobacter sp. strain DS2. Degradation of 3-NT by Diaphorobacter sp. strain DS2 was accompanied by the release of nitrite in the culture broth with increase in biomass. Total organic carbon analysis confirmed the extensive mineralization of 3-NT. The strain could degrade 3-methylcatechol, 4-methylcatechol and catechol easily suggesting that the degradation pathway could involve these as possible intermediates. Successful PCR amplification of the oxygenase large subunit and the presence of high activity for catechol 2,3-dioxygenase in the crude cell lysate further confirmed that the degradation of 3-NT occurred through (methyl)catechol intermediates in strain DS2. The strain DS2 was found to degrade other isomers of mononitrotoluene (2-NT and 4-NT) and nitrobenzene as well.

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References

  • Ali-Sadat S, Mohan KS, Walia SK (1995) A novel pathway for the biodegradation of 3-nitrotoluene in Pseudomonas putida. FEMS Microbiol Ecol 17:169–176

    Article  CAS  Google Scholar 

  • An D, Gibson DT, Spain JC (1994) Oxidative release of nitrite from 2-nitrotoluene by a three-component enzyme system from Pseudomonas sp. strain JS42. J Bacteriol 176:7462–7467

    PubMed  CAS  Google Scholar 

  • Arora PK, Sasikala C, Ramana CV (2012) Degradation of chlorinated nitroaromatic compounds. Appl Microbiol Biotechnol 93:2265–2277

    Article  PubMed  CAS  Google Scholar 

  • Autschul SF, Gish W, Miller W, Myers EM, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Google Scholar 

  • Bhattacharya D, Sarma PM, Krishnan S, Mishra S, Lal B (2003) Evaluation of genetic diversity among Pseudomonas citronellolis strains isolated from oily sludge contaminated sites. Appl Environ Microbiol 69:1435–1441

    Article  PubMed  CAS  Google Scholar 

  • Booth G (2007) Nitro compounds, aromatic. In: Ullmann’s encyclopedia of industrial chemistry. Wiley, New York, pp 1–47. doi:10.1002/14356007.a17_411

  • Bradford MM (1976) A rapid and sensitive method for the quantization of microgram quantities of protein utilizing the principle of protein–dye binding. Anal Biochem 72:248–254

    Article  PubMed  CAS  Google Scholar 

  • Cappuccino GJ, Sherman N (1999) Microbiology: a laboratory manual, 4th edn. Addison Wesley, San Francisco

    Google Scholar 

  • Cerdan P, Wasserfallen A, Rekik M, Timmis KN, Harayama S (1994) Substrate specificity of catechol 2,3-dioxygenase encoded by TOL plasmid pWW0 of Pseudomonas putida and its relationship to cell growth. J Bacteriol 176(19):6074–6081

    PubMed  CAS  Google Scholar 

  • Cl Kado, Liu ST (1981) Rapid procedure for detection and isolation of large and small plasmids. J Bacteriol 145:1365–1373

    Google Scholar 

  • Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarell DM, Garrity GM, Tiedje JM (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 1:33

    Google Scholar 

  • Copley SD (2009) Evolution of efficient pathways for degradation of anthropogenic chemicals. Nat Chem Biol 5:559–566

    Article  PubMed  CAS  Google Scholar 

  • Dalpozzo R, Bartoli G (2005) Bartoli indole synthesis. Curr Org Chem 9:163–178

    Article  CAS  Google Scholar 

  • Delgado A, Wubbolts MG, Abril MA, Ramos JL (1992) Nitroaromatics are substrates for the TOL plasmid upper-pathway enzymes. Appl Environ Microbiol 58:415–417

    PubMed  CAS  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the boot strap. Evolution 39:783–791

    Article  Google Scholar 

  • Ferraro DJ, Gakhar L, Ramaswamy S (2005) Rieske business: structure-function of Rieske non-heme oxygenase. Biochem Biophys Res Commun 338:175–190

    Article  PubMed  CAS  Google Scholar 

  • Haigler BE, Spain JC (1993) Biodegradation of 4-nitrotoluene by Pseudomonas sp. strain 4NT. Appl Environ Microbiol 59:2239–2243

    PubMed  CAS  Google Scholar 

  • Haigler BE, Wallace WH, Spain JC (1994) Biodegradation of 2-nitrotoluene by Pseudomonas sp. strain JS 42. Appl Environ Microbiol 60:3466–3469

    PubMed  CAS  Google Scholar 

  • Harayama S, Rekik M (1990) The meta cleavage operon of TOL degradative plasmid pWW0 comprises 13 genes. Mol Gen Genet 221:113–120

    Article  PubMed  CAS  Google Scholar 

  • He Z, Spain JC (1991) Comparison of downstream pathways for degradation of nitrobenzene by Pseudomonas pseudoalcaligenes JS45 (2-aminophenol pathway) and by Comamonas sp. JS765 (catechol pathway). Arch Microbiol 171:309–316

    Article  Google Scholar 

  • Johnson GR, Jain RK, Spain JC (2002) Origins of the 2,4-dinitrotoluene pathway. J Bacteriol 184:4219–4232

    Article  PubMed  CAS  Google Scholar 

  • Ju KS, Parales RE (2010) Nitroaromatic compounds: from synthesis to biodegradation. Microbiol Mol Biol Rev 74:250–272

    Article  PubMed  CAS  Google Scholar 

  • Ju KS, Parales RE (2011) Evolution of a new bacterial pathway for 4-nitrotoluene degradation. Mol Microbiol 82(2):355–364

    Article  PubMed  CAS  Google Scholar 

  • Kanekar P, Doudpure P, Sarnaik S (2003) Biodegradation of nitroexplosives. Indian J Exp Biol 41:991–1001

    PubMed  CAS  Google Scholar 

  • Kivissar M (2009) Degaradation of nitroaromatic compounds: a model to study evolution of metabolic pathways. Mol Microbiol 74:777–781

    Article  Google Scholar 

  • Kivissar M (2011) Evolution of catabolic pathways and their regulatory systems in synthetic nitroaromatic compounds degrading bacteria. Mol Microbiol 82(2):265–268

    Article  Google Scholar 

  • Klecka GM, Gibson DT (1981) Inhibition of catechol 2,3-dioxygenase from Pseudomonas putida by 3-chlorocatechol. Appl Environ Microbiol 41:1159–1165

    PubMed  CAS  Google Scholar 

  • Kulkarni M, Chaudhari A (2007) Microbial remediation of nitro-aromatic compounds: an overview. J Environ Manag 85:496–512

    Article  CAS  Google Scholar 

  • Lague D (2005) China blames oil company for benzene spill in river. The New York Times, New York

    Google Scholar 

  • Lee KS, Parales JV, Friemann R, Parales RE (2005) Active site residues controlling substrate specificity in 2-nitrotoluene dioxygenase from Acdovorax sp. strain JS42. J Ind Microbiol Biotechnol 32:465–473

    Article  PubMed  CAS  Google Scholar 

  • Lessner DJ, Johnson GR, Parales RE, Spain JC, Gibson DT (2002) Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765. Appl Environ Microbiol 68:634–641

    Article  PubMed  CAS  Google Scholar 

  • Liu H, Wang SJ, Zhang JJ, Dai H, Tang H, Zhou NY (2011) Patchwork assembly of nag-like nitroarene dioxygenase genes and the 3-chlorocatechol degradation cluster for evolution of the 2-chloronitrobenzene catabolism pathway in Pseudomonas stutzeri ZWLR2-1. Appl Environ Microbiol 77:4547–4552

    Article  PubMed  CAS  Google Scholar 

  • Mulla SI, Hoskeri RS, Shouche YS, Ninnekar HZ (2010) Biodegradation of 2-nitrotoluene by Micrococcus sp. strain SMN-1. Biodegradation 22:95–102

    Article  PubMed  Google Scholar 

  • Nishino SF, Spain JC (1995) Oxidative pathway for the biodegradation of nitrobenzene by Comamonas sp. strain JS765. Appl Environ Microbiol 61:2308–2313

    PubMed  CAS  Google Scholar 

  • Nishino SF, Spain JC (2004) Catabolism of nitroaromatic compounds. In: Rams JL (ed) Pseudomonas, vol 3. Kluwer Academic/Plenum Publishers, New York, pp 575–608

    Chapter  Google Scholar 

  • Nishino N, Atkinson R, Arey J (2008) Formation of nitro products from the gas-phase OH radical-initiated reactions of toluene, naphthalene and biphenyl: effect of NO2 concentration. Environ Sci Technol 42:9203–9209

    Article  PubMed  CAS  Google Scholar 

  • Padda RS, Wang C, Hughes JB, Kutty R, Bennett GN (2003) Mutagenicity of nitroaromatic degradation compounds. Environ Toxicol Chem 22:2293–2297

    Article  PubMed  CAS  Google Scholar 

  • Parales JV, Kumar A, Parales RE, Gibson DT (1996) Cloning and sequencing of the genes encoding 2-nitrotoluene dioxygenase from Pseudomonas sp. JS42. Gene 181:57–61

    Article  PubMed  CAS  Google Scholar 

  • Park H-S, Kim H-S (2000) Identification and characterization of the nitrobenzene catabolic plasmids pNB1 and pNB2 in Pseudomonas putida HS12. J Bacteriol 182:573–580

    Article  PubMed  CAS  Google Scholar 

  • Robertson JB, Spain JC, Haddock JD, Gibson DT (1992) Oxidation of nitrotoluenes by toluene dioxygenase: evidence for a monooxygenase reaction. Appl Environ Microbiol 58:2643–2648

    PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Sambrook J, Rusell DW (2001) Molecular cloning, vol 1, 3rd edn. CSHL Press, New York

    Google Scholar 

  • Schmidt M, Teitge M, Castillo ME, Brandt T, Dobner B, Langner A (2008) Synthesis and biochemical characterization of new phenothiazines and related drugs as MDR reversal agents. Arch Pharm Chem Life Sci 341:624–638

    Article  CAS  Google Scholar 

  • Shields MS, Montgomery SO, Chapman PJ, Cuskey SM, Pritchard PH (1989) Novel pathway of toluene catabolism in the trichloroethylene-degrading bacterium G4. Appl Environ Microbiol 55:1624–1629

    PubMed  CAS  Google Scholar 

  • Shin KA, Spain JC (2009) Pathway and evolutionary implications of diphenylamine biodegradation by Burkholderia sp. strain JS667. Appl Environ Microbiol 75:2694–2704

    Article  PubMed  CAS  Google Scholar 

  • Spiess T, Desiere F, Fischer P, Spain JC, Knackmuss HJ, Lenke H (1998) A new 4-nitrotoluene degradation pathway in a Mycobacterium strain. Appl Environ Microbiol 64:446–452

    PubMed  CAS  Google Scholar 

  • Struijs J, Stoltenkamp J (1986) Ultimate biodegradation of 2-, 3-, and 4-nitrotoluene. Sci Total Environ 57:161–170

    Article  PubMed  CAS  Google Scholar 

  • Swaroop S, Sughosh P, Ramanathan G (2009) Biomineralization of N,N-dimethylformamide by Paracoccus sp. strain DMF. J Hazard Mater 171:268–272

    Article  PubMed  CAS  Google Scholar 

  • Talmage SS, Opresco DM, Maxevel CZ, Welsh CJE, Cretella EM, Keno PH, Daniel FB (1999) Nitroaromatic munition compounds: environmental effects and screening values. Rev Environ Contam Toxicol 161:1–156

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Walia SK, Ali-Sadat S, Chaudhry GR (2003) Influence of nitro group on biotransformation of nitrotoluenes in Pseudomonas putida strain OU83. Pestic Biochem Physiol 76:73–81

    Article  CAS  Google Scholar 

  • Williams WR, Taylor SC, Williams PA (1993) A novel pathway for the catabolism of 4-nitrotoluene by Pseudomonas. J Gen Microbiol 139:1967–1972

    Article  PubMed  Google Scholar 

  • Winkler R, Hertweck C (2007) Biosynthesis of nitro compounds. ChemBioChem 8:973–977

    Article  PubMed  CAS  Google Scholar 

  • Ye J, Singh A, Ward OP (2004) Biodegradation of nitroaromatics and other nitrogen containing xenobiotics. World J Microbiol Biotechnol 20:117–135

    Article  CAS  Google Scholar 

  • Yen JH, Lin KH, Wang YS (2002) Acute lethal toxicity of environmental pollutants to aquatic organisms. Ecotoxicol Environ Saf 52:113–116

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

Deepak Singh thanks IIT Kanpur for a research fellowship. The department of biotechnology (DBT), India is gratefully acknowledged for partial funding of this project. We are thankful to Hindustan Organic Chemicals Limited for providing sludge from their waste water treatment plant.

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Correspondence to Gurunath Ramanathan.

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Singh, D., Ramanathan, G. Biomineralization of 3-nitrotoluene by Diaphorobacter species. Biodegradation 24, 645–655 (2013). https://doi.org/10.1007/s10532-012-9612-3

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