Cometabolic Bioremediation

  • Terry C. Hazen
Living reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)


Cometabolic bioremediation is probably the most underappreciated bioremediation strategy currently available. Cometabolism strategies stimulate only indigenous microbes with the ability to degrade the contaminant and cosubstrate, e.g., methane, propane, toluene, and others. This highly targeted stimulation insures that only those microbes that can degrade the contaminant are targeted, thus reducing amendment costs, well and formation plugging, etc. Cometabolic bioremediation has been used on some of the most recalcitrant contaminants, e.g., PCE, TCE, MTBE, TNT, dioxane, atrazine. Methanotrophs have been demonstrated to produce methane monooxygenase, an oxidase that can degrade over 1000 compounds. Cometabolic bioremediation also has the advantage of being able to degrade contaminants to trace concentrations, since the biodegrader is not dependent on the contaminant for carbon or energy. In the Gulf of Mexico and in the Arctic Tundra, we have recently found that natural attenuation can be a cometabolic process also. Increasingly we are finding that in order to protect human health and the environment that we must remediate to lower and lower concentrations, especially for compounds like endocrine disrupters and trace organics, thus cometabolism may be the best and may be the only possibility that we have to bioremediate some contaminants.


  1. American public health association (APHA) (1992) Standard methods for examination of water and waste 18th ed. American Public health Association, Washing ton DCGoogle Scholar
  2. Anderson JE, McCarty PL (1997) Transformation yields of chlorinated ethenes by a methanotrophic mixed culture expressing particulate methane monooxygenase. Appl Environ Microbiol 63:687–693PubMedPubMedCentralGoogle Scholar
  3. Arciero DM, Vannelli T, Logan M, Hooper AB (1989) Degradation of trichloroethylene by the ammonia-oxidizing bacterium, Nitrosomonas europaea. Biochem Biophys Res Commun 159:640–643CrossRefGoogle Scholar
  4. Bouwer EJ, McCarty PL (1984) Modeling of trace organics biotransformation in the subsurface. Ground Water 22:433–440CrossRefGoogle Scholar
  5. Cappelletti M, Pinelli D, Fedi S, Zannoni D, Frascari D (2018) Aerobic co-metabolism of 1,1,2,2-tetrachloroethane by Rhodococcus aetherivorans TPA grown on propane: kinetic study and bioreactor configuration analysis. J Chem Technol Biotechnol 93:155–165CrossRefGoogle Scholar
  6. Cardy DNL, Laidler V, Salmond GPC, Murrell JC (1991) Molecular analysis of the methane monooxygenase (MMO) gene cluster of Methylosinus trichosporium OB3b. Mol Microbiol 5:1261–1264CrossRefGoogle Scholar
  7. Chan SI, Chen KHC, Yu SSF, Chen CL, Kuo SSJ (2004) Toward delineating the structure and function of the particulate methane monooxygenase from methanotrophic bacteria. Biochemistry 43:4421–4430CrossRefGoogle Scholar
  8. Chaudhry GR, Chapalamadugu S (1991) Biodegradation of halogenated organic-compounds. Microbiol Rev 55:59–79PubMedPubMedCentralGoogle Scholar
  9. Chen KF, Kao CM, Chen TY, Weng CH, Tsai CT (2006) Intrinsic bioremediation of MTBE-contaminated groundwater at a petroleum-hydrocarbon spill site. Environ Geol 50:439–445CrossRefGoogle Scholar
  10. Dubinsky EA, Conrad ME, Chakraborty R, Bill M, Borglin SE, Hollibaugh JT, Mason OU, Piceno YM, Reid FC, Stringfellow WT, Tom LM, Hazen TC, Andersen GL (2013) Succession of hydrocarbon-degrading bacteria in the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico. Environ Sci Technol 47:10860–10867CrossRefGoogle Scholar
  11. EPA (2004) How to Evaluate Alternative Cleanup Technologies for Underground Storage Tank Sites: A Guide for Corrective action plan reviewers. United States Environmental Protection Agency, Agency USEP, Washington, DCGoogle Scholar
  12. Ensign SA, Hyman MR, Arp DJ (1992) Cometabolic degradation of chlorinated alkenes by alkene monooxygenase in a propylene-grown Xanthobacter strain. Appl Environ Microbiol 58:3038–3046PubMedPubMedCentralGoogle Scholar
  13. Ensley BD (1991) Biochemical diversity of trichloroethylene metabolism. Annu Rev Microbiol 45:283–299CrossRefGoogle Scholar
  14. Enzien MV, Picardal F, Hazen TC, Arnold RG, Fliermans CB (1994) Reductive dechlorination of trichloroethylene and tetrachloroethylene under aerobic conditions in a sediment column. Appl Environ Microbiol 60:2200–2205PubMedPubMedCentralGoogle Scholar
  15. Fliermans CB, Bohlool BB, Schmidt EL (1974) Detection of Nitrobacter in natural habitats using fluorescent antibodies. Appl Microbiol 27:124–129PubMedPubMedCentralGoogle Scholar
  16. Fliermans CB, Dougherty JM, Franck MM, McKinsey PC, Hazen TC (1994) Immunological techniques as tools to characterize the subsurface microbial community at a trichloroethylene contaminated site. In: Hinchee RE et al (eds) Applied biotechnology for site remediation. Lewis Publishers, Boca Raton, pp 186–203Google Scholar
  17. Fogel MM, Taddeo AR, Fogel S (1986) Biodegradation of chlorinated ethenes by a methane-utilizing mixed culture. Appl Environ Microbiol 51(4):720–724PubMedPubMedCentralGoogle Scholar
  18. Gauthier H, Yargeau V, Cooper DG (2010) Biodegradation of pharmaceuticals by Rhodococcus rhodochrous and Aspergillus niger by co-metabolism. Sci Total Environ 408:1701–1706CrossRefGoogle Scholar
  19. Ghosh PK, Philip L (2004) Atrazine degradation in anaerobic environment by a mixed microbial consortium. Water Res 38:2277–2284CrossRefGoogle Scholar
  20. Gu C, Wang J, Liu SS, Liu GF, Lu H, Jin RF (2016) Biogenic Fenton-like reaction involvement in cometabolic degradation of tetrabromobisphenol A by Pseudomonas sp fz. Environ Sci Technol 50:9981–9989CrossRefGoogle Scholar
  21. Hazen TC (1997) Bioremediation. In: Amy P, Haldeman D (eds) Microbiology of the terrestrial subsurface. CRC Press, Boca Raton, pp 247–266Google Scholar
  22. Hazen TC, Sayler GS (2016) Environmental systems microbiology of contaminated environments. In: Yates M, Nakatsu C, Miller R, Pillai S (eds) Manual of environmental microbiology, 4th edn. ASM Press, Washington, DC, pp 5.1.6-1–5.1.6-10Google Scholar
  23. Hazen TC, Lombard KH, Looney BB, Enzien MV, Dougherty JM, Fliermans CB, Wear J, Eddy-Dilek CA (1994) Summary of in situ bioremediation demonstration (methane biostimulation) via horizontal wells at the Savannah River Site Integrated Demonstration Project. In: Gee GW, Wing NR (eds) Proceedings of thirty-third Hanford symposium on health and the environment: in-situ remediation: scientific basis for current and future technologies. Battelle, Columbus, pp 135–150Google Scholar
  24. Hazen TC, Chakraborty R, Fleming J, Gregory IR, Bowman JP, Jimenez L, Zhang D, Pfiffner SM, Brockman FJ, Sayler GS (2009) Use of gene probes to assess the impact and effectiveness of aerobic in situ bioremediation of TCE. Arch Microbiol 191:221–232CrossRefGoogle Scholar
  25. Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D’Haeseleer P, Holman HYN, Osman S, Lu ZM, Van Nostrand JD, Deng Y, Zhou JZ, Mason OU (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330:204–208CrossRefGoogle Scholar
  26. Hyman MR, Murton IB, Arp DJ (1988) Interactions of ammonia monoxygenase from Nitrosomonas europaea with alkanes, alkenes and alkynes. Appl Environ Microbiol 54:3187–3190PubMedPubMedCentralGoogle Scholar
  27. ITRC (2008) Use of Risk assessment in management of contaminated sites. The Interstate Technoogy &Regulatory Council, Council TITR, Washington, DCGoogle Scholar
  28. Karim ME, Dhar K, Hossain MT (2017) Co-metabolic decolorization of a textile reactive dye by Aspergillus fumigatus. Int J Environ Sci Technol 14:177–186CrossRefGoogle Scholar
  29. Keener WK, Arp DJ (1993) Kinetic-studies of ammonia monooxygenase inhibition in Nitrosomonas europaea by hydrocarbons and halogenated hydrocarbons in an optimized whole-cell assay. Appl Environ Microbiol 59:2501–2510PubMedPubMedCentralGoogle Scholar
  30. Koh S-C, Bowman JP, Sayler GS (1993) Soluble methane monooxygenase production and trichloroethylene degradation by a type I methanotroph, Methlomonas methanica 68-1. Appl Environ Microbiol 59:960–967PubMedPubMedCentralGoogle Scholar
  31. Lajoie CA, Layton AC, Sayler GS (1994) Cometabolic oxidation of polychlorinated-biphenyls in soil with a surfactant-based field application vector. Appl Environ Microbiol 60:2826–2833PubMedPubMedCentralGoogle Scholar
  32. Li YC, Zhou J, Gong BZ, Wang YM, He Q (2016) Cometabolic degradation of lincomycin in a Sequencing Batch Biofilm Reactor (SBBR) and its microbial community. Bioresour Technol 214:589–595CrossRefGoogle Scholar
  33. Little CD, Palumbo AV, Herbes SE, Lidstrom ME, Tyndall RL, Gilmer PL (1988) Trichloroethylene biodegradation by a methane-oxidizing bacterium. Appl Environ Microbiol 54:951–956PubMedPubMedCentralGoogle Scholar
  34. Liu L, Binning PJ, Smets BF (2015) Evaluating alternate biokinetic models for trace pollutant cometabolism. Environ Sci Technol 49:2230–2236CrossRefGoogle Scholar
  35. Mahendra S, Petzold CJ, Baidoo EE, Keasling JD, Alvarez-Cohen L (2007) Identification of the intermediates of in vivo oxidation of 1,4-dioxane by monooxygenase-containing bacteria. Environ Sci Technol 41:7330–7336CrossRefGoogle Scholar
  36. McCarty PL (1987) Bioengineering issues related to in situ remediation of contaminated soils and groundwater. In: Omenn GS (ed) Environmental biotechnology. Plenum, New York, pp 143–162Google Scholar
  37. Murrell JC (1992) The genetics and molecular biology of obligate methane-oxidizing bacteria. In: Murrell JC, Dalton H (eds) Methane and methanol utilizers. Plenum, New York, pp 115–148CrossRefGoogle Scholar
  38. Nelson MJK, Montgomery SO, Prichard PH (1988) Trichloroethylene metabolism by microorganisms that degrade aromatic compounds. Appl Environ Microbiol 54:604–606PubMedPubMedCentralGoogle Scholar
  39. Newman LM, Wackett LP (1991) Fate of 2,2,2-trichloroacetaldehyde (chloral hydrate) produced during trichloroethylene oxidation by methanotrophs. Appl Environ Microbiol 57:2399–2402PubMedPubMedCentralGoogle Scholar
  40. Nguyen HHT, Elliott SJ, Yip JHK, Chan SI (1998) The particulate methane monooxygenase from Methylococcus capsulatus (Bath) is a novel copper-containing three-subunit enzyme – isolation and characterization. J Biol Chem 273:7957–7966CrossRefGoogle Scholar
  41. Oremland RS, Culbertson CW (1992) Importance of methane-oxidizing bacteria in the methane budget as revealed by the use of a specific inhibitor. Nature 356:421–423CrossRefGoogle Scholar
  42. Paulsen KE, Liu Y, Fox BG, Lipscomb JD, Munck E, Stankovich MT (1994) Oxidation-reduction potentials of the methane monooxygenase hydroxylase component from Methylosinus trichosporium OB3b. Biochemistry 33:713–722CrossRefGoogle Scholar
  43. Rasche ME, Hicks RE, Hyman MR, Arp DJ (1990) Oxidation of monohalogenated ethanes and n-chlorinated alkanes by whole cells of Nitosomonas europaea. J Bacteriol 172:5368–5373CrossRefGoogle Scholar
  44. Reddy CM, Arey JS, Seewald JS, Sylva SP, Lemkau KL, Nelson RK, Carmichael CA, McIntyre CP, Fenwick J, Ventura GT, Van BAS M, Camilli R (2012) Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill. Proc Natl Acad Sci U S A 109:20229–20234CrossRefGoogle Scholar
  45. Redmond MC, Valentine DL (2012) Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proc Natl Acad Sci U S A 109:20292–20297CrossRefGoogle Scholar
  46. Rosenzweig AC, Frederick CA, Lippard SJ, Nordlund P (1993) Crystal-structure of a bacterial nonheme iron hydroxylase that catalyzes the biological oxidation of methane. Nature 366:537–543CrossRefGoogle Scholar
  47. Sayler GS, Layton A, Lajoie C, Bowman J, Tschantz M, Fleming JT (1995) Molecular site assessment and process monitoring in bioremediation and natural attenuation. Appl Biochem Biotechnol 54:277–290CrossRefGoogle Scholar
  48. Shi SN, Zhang XW, Ma F, Sun TH, Li A, Zhou JT, Qu YY (2013) Cometabolic degradation of dibenzofuran by Comamonas sp MQ. Process Biochem 48:1553–1558CrossRefGoogle Scholar
  49. Shi SN, Qu YY, Zhou H, Ma Q, Ma F (2015) Characterization of a novel cometabolic degradation carbazole pathway by a phenol-cultivated Arthrobacter sp W1. Bioresour Technol 193:281–287CrossRefGoogle Scholar
  50. Stackhouse B, Lau MCY, Vishnivetskaya T, Burton N, Wang R, Southworth A, Whyte L, Onstott TC (2017) Atmospheric CH4 oxidation by Arctic permafrost and mineral cryosols as a function of water saturation and temperature. Geobiology 15:94–111CrossRefGoogle Scholar
  51. Stanley SH, Prior SD, Leak DJ, Dalton H (1983) Copper stress underlies the fundamental change in intracellular location of methane mono-oxygenase in methane-oxidizing organisms – studies in batch and continuous cultures. Biotechnol Lett 5:487–492CrossRefGoogle Scholar
  52. Tsien HC, Brusseau GA, Hanson RS, Wackett LP (1989) Biodegradation of trichloroethylene by Methylosinus trichosporium OB3b. Appl Environ Microbiol 55:3155–3161PubMedPubMedCentralGoogle Scholar
  53. Vannelli T, Logan M, Arciero D, Hooper AB (1990) Degradation of halogenated aliphatics by the ammonia-oxidizing bacterium Nitrosomonas europaea. Appl Environ Microbiol 56:1169–1171PubMedPubMedCentralGoogle Scholar
  54. Wilson JT, Wilson BH (1985) Biotransformation of trichloroethylene in soil. Appl Environ Microbiol 29:242–243Google Scholar
  55. Wood PM (1986) Nitrification as a bacterial energy source. In: Prosser JI (ed) Nitrification. Society for General Microbiology (IRL Press), Washington, DC, pp 39–62Google Scholar
  56. Yang L, Chang YF, Chou MS (1999) Feasibility of bioremediation of trichloroethylene contaminated sites by nitrifying bacteria through cometabolism with ammonia. J Hazard Mater 69:111–126CrossRefGoogle Scholar
  57. Yasin M, Shah AA, Hameed A, Ahmed S, Hasan F (2008) Use of microorganisms for the treatment of trinitrotoluene (TNT) containing effluents. J Chem Soc Pak 30:442–448Google Scholar
  58. Zahn JA, Arciero DM, Hooper AB, DiSpirito AA (1996) Cytochrome c′ of Methylococcus capsulatus Bath. Eur J Biochem 240:684–691CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Civil & Environmental Engineering, Microbiology, Earth & Planetary Sciences & Institute for Secure and Sustainable EnvironmentsUniversity of TennesseeKnoxvilleUSA
  2. 2.Oak Ridge National LaboratoryKnoxvilleUSA

Personalised recommendations