Skip to main content
SpringerLink
Log in

The Metabolic Pathways of Biodegradation

  • Reference work entry
The Prokaryotes

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.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 599.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 549.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Barker HA (1940) Studies on the methane fermentation. IV: the isolation and culture of Methanobacterium omelianskii. Antonie Van Leeuwenhoek 6:201–220

    Article  Google Scholar 

  • Beijerinck MW (1901) Enrichment culture studies with urea bacteria. Cen Bakteriol 7(II):33–61

    Google Scholar 

  • 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 277:1453–1474

    Article  PubMed  CAS  Google Scholar 

  • Bouquard C, Ouazzani J, Prome JC, Michel-Briand Y, Plesiat P (1997) Dechlorination of atrazine by a Rhizobium sp. isolate. Appl Environ Microbiol 63:862–866

    PubMed  CAS  Google Scholar 

  • 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 24:266–275

    Article  PubMed  CAS  Google Scholar 

  • Bull AT, Slater JH (1982) In: Bull AT, Slater JH (eds) Microbial interactions and communities. Academic, New York

    Google Scholar 

  • Cerniglia CE, Hebert RL, Szaniszlo PJ, Gibson DT (1978) Fungal transformation of naphthalene. Arch Microbiol 117:135–143

    Article  PubMed  CAS  Google Scholar 

  • 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 436:159–162

    Article  PubMed  CAS  Google Scholar 

  • 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 1–37

    Chapter  Google Scholar 

  • 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 64:178–184

    PubMed  Google Scholar 

  • de Souza ML, Seffernick J, Martinez B, Sadowsky SJ, Wackett LP (1998b) The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol 180:1951–1954

    PubMed  Google Scholar 

  • 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 18:13–26

    PubMed  CAS  Google Scholar 

  • 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 64:3869–3877

    PubMed  CAS  Google Scholar 

  • Ellis LBM, Hershberger CD, Wackett LP (2000) The University of Minnesota biocatalysis/biodegradation database: microorganisms, genomics and prediction. Nucleic Acids Res 28:377–379

    Article  PubMed  CAS  Google Scholar 

  • Goto S, Nishioka T, Kanehisa M (2000) LIGAND: chemical database of enzyme reactions. Nucleic Acids Res 28:380–382

    Article  PubMed  CAS  Google Scholar 

  • 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 259:503–507

    Article  PubMed  CAS  Google Scholar 

  • Hungate RE (1985) Anaerobic fermentations. In: Poindexter JS, Leadbetter ER (eds) Bacteria in nature, vol 1. Plenum, New York, pp 39–95

    Chapter  Google Scholar 

  • 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 90:6525–6527

    Article  PubMed  CAS  Google Scholar 

  • 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 57:65–68

    Article  PubMed  CAS  Google Scholar 

  • 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 28:615–628

    Article  PubMed  CAS  Google Scholar 

  • Lipscomb JD (1994) Biochemistry of the soluble methane monooxygenase. Annu Rev Microbiol 48:371–399

    Article  PubMed  CAS  Google Scholar 

  • Maltoni C, Cotti G (1988) Carcinogenicity of vinyl chloride in Sprague–Dawley rats after prenatal and postnatal exposure. Ann N Y Acad Sci 534:145–159

    Article  PubMed  CAS  Google Scholar 

  • Mandelbaum RT, Allan DA, Wackett LP (1995) Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine. Appl Environ Microbiol 61:1451–1457

    PubMed  CAS  Google Scholar 

  • Nelson KE, Paulsen IT, Heidelberg JF, Fraser CM (2000) Status of genome projects for nonpathogenic bacteria and archaea. Nat Biotechnol 18:1049–1054

    Article  PubMed  CAS  Google Scholar 

  • 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 57:3367–3370

    PubMed  CAS  Google Scholar 

  • Radosevich M, Traina SJ, Hao Y, Tuovinen OH (1995) Degradation and mineralization of atrazine by a soil bacterial isolate. Appl Environ Microbiol 61:297–302

    PubMed  CAS  Google Scholar 

  • 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 39–40:781–789

    Article  PubMed  Google Scholar 

  • 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 181:5701–5710

    PubMed  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  PubMed  CAS  Google Scholar 

  • 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 181:6679–6688

    PubMed  CAS  Google Scholar 

  • 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 2:91–98

    Article  PubMed  CAS  Google Scholar 

  • 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 64:3368–3375

    PubMed  CAS  Google Scholar 

  • 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 274:20287–20292

    Article  PubMed  Google Scholar 

  • Vogel TM, McCarty PL (1985) Biotransformation of tetrachloroethylene to trichloroethylene, dichloroethylene, vinyl chloride, and carbon dioxide under methanogenic conditions. Appl Environ Microbiol 49:1080–1083

    PubMed  CAS  Google Scholar 

  • 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 34:4628–4634

    Article  Google Scholar 

  • Wiegel J, Zhang X, Wu Q (1999) Anaerobic dehalogenation of hydroxylated polychlorinated biphenyls by Desulfitobacterium dehalogenans. Appl Environ Microbiol 65:2217–2221

    PubMed  CAS  Google Scholar 

  • Winogradsky S (1890) Sur les organismes de la nitrification. C R Acad Sci 110:1013–1016

    Google Scholar 

  • Zengler K, Richnow HH, Rossello-Mora R, Michaelis W, Widdel F (1999) Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401:266–269

    Article  PubMed  CAS  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

  1. Department of Biochemistry, Molecular Biology and Biophysics, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA

    Lawrence P. Wackett

Authors
  1. Lawrence P. Wackett
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel

    Eugene Rosenberg

  2. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Edward F. DeLong

  3. Department of Microbiology and Immunology, Harvard Medical School, Boston, MA, USA

    Stephen Lory

  4. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany

    Erko Stackebrandt

  5. Laboratory of Microbiology, Institute of Biology, Center for Health Sciences, Federal University of Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil

    Fabiano Thompson

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this entry

Cite this entry

Wackett, L.P. (2013). The Metabolic Pathways of Biodegradation. In: Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., Thompson, F. (eds) The Prokaryotes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31331-8_76

Download citation

Publish with us

Policies and ethics

Search

Navigation