The Metabolic Pathways of Biodegradation

  • Lawrence P. Wackett

Abstract

Biodegradation is the study of metabolic breakdown of chemicals, both natural and anthropogenic. Globlly, biodegradation is principally carried out by microorganisms. Microbes carry out diverse metabolic reactions and this gives them the ability to break down many synthetic chemicals that have been made for commercial purposes. The University of Minnesota Biocatalysis/Biodegradation Database [UM-BBD] (http://umbbd.ethz.ch) has captured information on diverse biodegradation reactions and shows metabolic pathways degrading natural and synthetic chemicals. A software tool is available on the database to predict the biodegradation of any organic chemical entered by the user.

Keywords

Enrichment Culture Methyl Chloride Biodegradation Pathway BTEX Compound Arene Oxide 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

I thank the many talented colleagues with whom I have collaborated on metabolic pathways of biodegradation. Special thanks go to Professor Lynda Ellis for her meticulous work on the University of Minnesota Biocatalysis/Biodegradation Database, making it a resource that has been worth accessing millions of times by researchers around the world.

References

  1. Barker HA (1940) Studies on the methane fermentation. IV: the isolation and culture of Methanobacterium omelianskii. Antonie Van Leeuwenhoek 6:201–220CrossRefGoogle Scholar
  2. Beijerinck MW (1901) Enrichment culture studies with urea bacteria. Cen Bakteriol 7(II):33–61Google Scholar
  3. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453–1474PubMedCrossRefGoogle Scholar
  4. Bouquard C, Ouazzani J, Prome JC, Michel-Briand Y, Plesiat P (1997) Dechlorination of atrazine by a Rhizobium sp. isolate. Appl Environ Microbiol 63:862–866PubMedGoogle Scholar
  5. Bulbulyan MA, Figgs LW, Zahm SH, Savitskaya T, Goldfarb A, Astashevsky S, Zaridze D (1995) Cancer incidence and mortality among beta-naphthylamine and benzidine dye workers in Moscow. Int J Epidemiol 24:266–275PubMedCrossRefGoogle Scholar
  6. Bull AT, Slater JH (1982) In: Bull AT, Slater JH (eds) Microbial interactions and communities. Academic, New YorkGoogle Scholar
  7. Cerniglia CE, Hebert RL, Szaniszlo PJ, Gibson DT (1978) Fungal transformation of naphthalene. Arch Microbiol 117:135–143PubMedCrossRefGoogle Scholar
  8. Christiansen N, Ahring BK, Wohlfarth G, Diekert G (1998) Purification and characterization of the 3-chloro-4-hydroxy-phenylacetate reductive dehalogenase of Desulfitobacterium hafniense. FEBS Lett 436:159–162PubMedCrossRefGoogle Scholar
  9. Clarke PH (1985) The scientific study of bacteria, 1780–1980. In: Leadbetter ER, Poindexter JS (eds) Bacteria in nature, vol I. Plenum, New York, pp 1–37CrossRefGoogle Scholar
  10. de Souza ML, Newcombe D, Alvey S, Crowley DE, Hay A, Sadowsky MJ, Wackett LP (1998a) Molecular basis of a bacterial consortium: interspecies catabolism of atrazine. Appl Environ Microbiol 64:178–184PubMedGoogle Scholar
  11. de Souza ML, Seffernick J, Martinez B, Sadowsky SJ, Wackett LP (1998b) The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol 180:1951–1954PubMedGoogle Scholar
  12. Dettori G, Grillo R, Cattani P, Calderaro A, Chezzi C, Milner J, Truelove K, Sellwood R (1995) Comparative study of the enzyme activities of Borrelia burgdorferi and other non-intestinal and intestinal spirochaetes. New Microbiol 18:13–26PubMedGoogle Scholar
  13. Dojka MA, Hugenholtz P, Haack SK, Pace NR (1998) Microbial diversity in a hydrocarbon-and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877PubMedGoogle Scholar
  14. Ellis LBM, Hershberger CD, Wackett LP (2000) The University of Minnesota biocatalysis/biodegradation database: microorganisms, genomics and prediction. Nucleic Acids Res 28:377–379PubMedCrossRefGoogle Scholar
  15. Goto S, Nishioka T, Kanehisa M (2000) LIGAND: chemical database of enzyme reactions. Nucleic Acids Res 28:380–382PubMedCrossRefGoogle Scholar
  16. Harkness MR, McDermott JB, Abramowicz DA, Salvo JJ, Flanagan WP, Stephens ML, Mondello FJ, May RJ, Lobos JH, Carroll KM, Brennan MJ, Bracco AA, Fish KM, Warner GL, Wilson PR, Dietrich DK, Lin DT, Morgan CB, Gately WL (1993) In situ stimulation of aerobic PCB biodegradation in Hudson River sediments. Science 259:503–507PubMedCrossRefGoogle Scholar
  17. Hungate RE (1985) Anaerobic fermentations. In: Poindexter JS, Leadbetter ER (eds) Bacteria in nature, vol 1. Plenum, New York, pp 39–95CrossRefGoogle Scholar
  18. Jerina DM, Daly JW, Witkop B, Zaltzman-Nirenberg P, Udenfriend S (1968) The role of arene oxide-oxepin systems in the metabolism of aromatic substrates. 3: formation of 1,2-naphthalene oxide from naphthalene by liver microsomes. J Am Chem Soc 90:6525–6527PubMedCrossRefGoogle Scholar
  19. Langard S, Rosenberg J, Andersen A, Heldaas SS (2000) Incidence of cancer among workers exposed to vinyl chloride in polyvinyl chloride manufacture. Occup Environ Med 57:65–68PubMedCrossRefGoogle Scholar
  20. Leuthner B, Leutwein C, Schulz H, Horth P, Haehnel W, Schiltz E, Schagger H, Heider J (1998) Biochemical and genetic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. Mol Microbiol 28:615–628PubMedCrossRefGoogle Scholar
  21. Lipscomb JD (1994) Biochemistry of the soluble methane monooxygenase. Annu Rev Microbiol 48:371–399PubMedCrossRefGoogle Scholar
  22. Maltoni C, Cotti G (1988) Carcinogenicity of vinyl chloride in Sprague–Dawley rats after prenatal and postnatal exposure. Ann N Y Acad Sci 534:145–159PubMedCrossRefGoogle Scholar
  23. Mandelbaum RT, Allan DA, Wackett LP (1995) Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine. Appl Environ Microbiol 61:1451–1457PubMedGoogle Scholar
  24. Nelson KE, Paulsen IT, Heidelberg JF, Fraser CM (2000) Status of genome projects for nonpathogenic bacteria and archaea. Nat Biotechnol 18:1049–1054PubMedCrossRefGoogle Scholar
  25. Oren A, Gurevich P, Henis Y (1991) Reduction of nitrosubstituted aromatic compounds by the halophilic anaerobic eubacteria Haloanaerobium prevalens and Sporohalobacter marismortui. Appl Environ Microbiol 57:3367–3370PubMedGoogle Scholar
  26. Radosevich M, Traina SJ, Hao Y, Tuovinen OH (1995) Degradation and mineralization of atrazine by a soil bacterial isolate. Appl Environ Microbiol 61:297–302PubMedGoogle Scholar
  27. Roberts DJ, Kaake RH, Funk SB, Crawford DL, Crawford RL (1993) Anaerobic remediation of dinoseb from contaminated soil: an on-site demonstration. Appl Biochem Biotechnol 39–40:781–789PubMedCrossRefGoogle Scholar
  28. Rocha ER, Smith CJ (1999) Role of the alkyl hydroperoxide reductase (ahpCF) gene in oxidative stress defense of the obligate anaerobe Bacteroides fragilis. J Bacteriol 181:5701–5710PubMedGoogle Scholar
  29. 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 66:2541–2547PubMedCrossRefGoogle Scholar
  30. Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE (1999) Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J Bacteriol 181:6679–6688PubMedGoogle Scholar
  31. Strong LC, McTavish H, Sadowsky MJ, Wackett LP (2000) Field-scale remediation of atrazine-contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase. Environ Microbiol 2:91–98PubMedCrossRefGoogle Scholar
  32. Struthers JK, Jayachandran K, Moorman TB (1998) Biodegradation of atrazine by Agrobacterium radiobacter J14a and use of this strain in bioremediation of contaminated soil. Appl Environ Microbiol 64:3368–3375PubMedGoogle Scholar
  33. Van de Pas BA, Smidt H, Hagen WR, van der Oost J, Schraa G, Stams AJ, de Vos W (1999) Purification and molecular characterization of ortho-chlorophenol reductive dehalogenase, a key enzyme of halorespiration in Desulfitobacterium dehalogenans. J Biol Chem 274:20287–20292PubMedCrossRefGoogle Scholar
  34. Vogel TM, McCarty PL (1985) Biotransformation of tetrachloroethylene to trichloroethylene, dichloroethylene, vinyl chloride, and carbon dioxide under methanogenic conditions. Appl Environ Microbiol 49:1080–1083PubMedGoogle Scholar
  35. Wagner-Dobler I, von Canstein H, Li Y, Timmis KN, Deckwer W-D (2000) Removal of mercury from chemical wastewater by microorganisms in technical scale. Environ Sci Technol 34:4628–4634CrossRefGoogle Scholar
  36. Wiegel J, Zhang X, Wu Q (1999) Anaerobic dehalogenation of hydroxylated polychlorinated biphenyls by Desulfitobacterium dehalogenans. Appl Environ Microbiol 65:2217–2221PubMedGoogle Scholar
  37. Winogradsky S (1890) Sur les organismes de la nitrification. C R Acad Sci 110:1013–1016Google Scholar
  38. Zengler K, Richnow HH, Rossello-Mora R, Michaelis W, Widdel F (1999) Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401:266–269PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Lawrence P. Wackett
    • 1
  1. 1.Department of Biochemistry, Molecular Biology and Biophysics, BioTechnology InstituteUniversity of MinnesotaSt. PaulUSA

Personalised recommendations