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Biodegredation of Toxic Chemicals

The following sources are recommended by a professor whose research specialty is the biodegredation of toxic chemicals.


Six Superlative Sources

· Leadbetter, ER, and Foster, JW (1959) Incorporation of molecular oxygen in bacterial cells utilizing hydrocarbons for growth. Nature 184:1428-30.

· Swisher, RD (1963) The chemistry of surfactant biodegradation. J. Am. Oil Chem. Soc. 40:648-56.

· Beam, HW, and Perry, JJ (1973) Co-metabolism as a factor in microbial degradation of cycloparaffinic hydrocarbons. Arch. Microbiol. 91:87-90.

· Chakrabarty, AM (1972) Genetic basis of the biodegradation of salicylate in Pseudomonas. J. Bacteriol. 112:815-23.

· Bryant, MP, Wolin, EA, Wolin, MJ, and Wolfe, RS (1967) Methanobacillus omelianskii, a symbiotic association of two species of bacteria. Arch. Microbiol. 59:20-31.

· Shelton, DR, and Tiedje, RM (1984) Isolation and partial characterization of bacteria in an anaerobic consortium that mineralizes 3-chlorobenzoic acid. Appl. Environ. Microbiol. 48:840-48.

Other Excellent Sources

-- NOTE: An extensive list of other excellent sources is displayed after the following annotation.--

The enrichment culture, devised by Martinus Beijerinck during the end of the 19th century, has been the basis for isolation of microorganisms able to grow on specific chemicals as their sole source of carbon and energy. However, many chemicals that cannot be utilized for growth are oxidized by microorganisms, which would not be isolated by this method. Although this was understood for some time, Leadbetter and Foster (Leadbetter and Foster 1959) demonstrated the first recognition of this limitation. They observed that many hydrocarbons, which were not utilized as growth substrates, could be oxidized to terminal products, while growing on structurally related compounds. They used the word "co-oxidation" to define this phenomenon. Jensen (Jensen 1963) later recognized that similar non-growth supporting reactions occurred, which did not involve oxygen. He broadened the concept by calling it "cometabolism," which is now recognized as a very important mechanism in biodegradation of recalcitrant chemicals. Cometabolism is metabolism of a substrate that is not utilized for growth as a sole carbon source (Horvath 1972). Further studies eventually demonstrated that the most persistent chemicals, such as DDT, PCBs (polychlorinated biphenyls), and other organochlorine compounds (chlorinated solvents) are metabolized by cells grown on non-chlorinated, structurally-related substrates. See:
(Horvath and Alexander 1970)
(Focht and Alexander 1970)
(Ahmed and Focht 1973)
(Pfaender and Alexander 1972)
(Furukawa et al. 1978)
(Bedard et al. 1986)
(Bedard et al. 1987)
(Hay and Focht 1998)
(Alvarez-Cohen and McCarty 1991)
(Nadeau et al. 1994)

The replacement of soaps by the synthetic alkylbenzenesulfonate detergents, in the early 1950s, eventually led to pollution of rivers and aquifers by these compounds. So severe was the problem, that many sewage treatment plants had to be shut down because of foam being blown away and into nearby residential communities. R.D. Swisher, a chemist from Monsanto Chemical Corporation, determined that the most important characteristic determining resistance to biodegradation was the configuration of the alkyl side chain (Swisher 1963). He correctly surmised that branched-chain hydrocarbons were not as readily attacked by microbial enzymes as the linear, unbranched chains. The results of his studies eventually led to the replacement of tetrapropylbenzene sulfonate (branched chain) with a linear dodecyl chain in commercial detergents. A complete synopsis of the alkylbenzene sulfonate story can be found in a much later reference (Swisher 1987). Branched-chain hydrocarbons were likewise found to be more persistant by McKenna and Kallio (McKenna and Kallio 1964). They also noted that the species diversity able to metabolize these compounds was much more restricted than those able to metabolize linear hydrocarbons. The greater difference in microbial degradation rates between branched-chain and linear-chain hydrocarbons was used to assess the effects of bioremediation during the clean-up of the Exxon-Valdez oil spill on the beaches (Pritchard and Costa 1991). Because of the extreme variability of oil contamination throughout the beach, the authors normalized this spatial variability problem by measuring the differences between the ratio of octadecane (18 carbon linear chain) to phytane (18 carbon branched chain) with time. The ratios remained the same in control plots, while decreasing dramatically in the treated plots.

Biodegradation research in its early development was focused mostly on pure cultures, even after the discovery of co-oxidation. One of the most peculiar phenomenon observed in many soils was the rapid degradation of cyclohexane, a common industrial chemical, with the accompanying inability to isolate pure cultures able to utilize it as a growth substrate. Beam and Perry (Beam and Perry 1973) correctly surmised that more than one organism was involved in the complete metabolism of cyclohexane. They isolated organisms able to grow on propane and other hydrocarbons that were able to cometabolize cyclohexane to cyclohexanol. These bacteria, however, could not further metabolize cyclohexanol. However, many bacteria that could metabolize cyclohexanol were readily isolated from soil. When the two types of cultures were mixed together, cyclohexane was mineralized (degraded completely to carbon dioxide and water). These studies were the first to demonstrate the nature of cometabolic-commensalistic catabolism: the organism carrying out the first reaction requires a co-substrate (e.g. propane) for its growth, but gets no benefit from cometabolism of cyclohexane, in contrast to the commensal, which utilizes the product (cyclohexanol) as its growth substrate. Similar studies on this specific phenomenon and chemical added further support to the concept. See:
(Beam and Perry 1973)
(Beam and Perry 1974)
(deKlerk and van der Linden 1974)
Additional studies demonstrated the importance of microbial consortia (communities of more than one member) in the biodegradation of synthetic and persistent chemicals, including PCBs (polychlorinated biphenyls). In some cases, this may have involved coupled reactions between aerobic and anaerobic bacteria (last two references below). See:
(Senior et al. 1976)
(Slater and Lovatt 1984)
(Focht and Brunner 1985)
(Flanagan and May 1993)
(Gerritse and Gottschal 1992)
(Gerritse et al. 1992)
(Mandelbaum et al. 1993)

One of the major reasons why chlorinated aromatic hydrocarbons are not utilized for growth substrates is because bacteria produce toxic metabolites from cometabolism of them. Reineke and Knackmuss (Reineke and Knackmuss 1979) showed that the formation of acyl halides from the oxidative cleavage of a benzene ring at carbon bearing a chlorine atom would cause immediate denaturation of the enzyme, and thus halt further activity. This study pointed the way to the genetic construction of catabolic pathways by combining complementary genes, which encoded enzymes that rerouted the hybrid pathway through non-suicidal productive routes. The last reference below brings yet another new development to this topic, by its clever title, in demonstrating a different type of suicidal inactivation, and hence a different mechanism for antibiotic therapy. See:
(Reineke et al. 1982)
(Reineke and Knackmuss 1980)
(Kröckel and Focht 1987)
(McCullar et al. 1994)
(Haigler et al. 1992)
(Pettigrew et al. 1991)
(Koh et al. 1996)
(Blasco et al. 1995)

The first realization that certain biodegradative enzymes were encoded on plasmids (extrachromosomal genes) was with salicylate metabolism in Pseudomonas by Chakrabarty (Chakrabarty 1972). The smaller nature of plasmids, particularly transmissible ones, greatly facilitated genetic engineering of catabolic pathways. Further studies by Chakrabarty and other workers shortly thereafter led to similar findings about the importance of plasmids. The loss or "curing" of plasmids has frequently been observed when cultures are grown on other substrates, whose degradation is encoded by chromosomal genes. The paradigm concerning biodegradative plasmids is that they permit greater flexibility and diversion of energy, because they are not synthesized in the absence of substrate. See:
(Chakrabarty et al. 1973)
(Dunn and Gunsalus 1973)
(Williams and Murray 1974)
(Don et al. 1985)
(Timmis et al. 1985)
(Zeyer et al. 1985)
(Furukawa and Chakrabarty 1982)
(Carney and Leary 1989)
(Brenner et al. 1993)

Interspecies H2 transfer refers to obligate symbiosis of two organisms, one of which supplies reducing power (syntroph), indirectly via liberation of H2, and the other which oxidizes H2 by reducing CO2 to methane (methanogen) or sulfate to sulfide (sulfidogen). The phenomenon was discovered from a culture of Methanobacillus omelianskii, which had been subcultured for more than 60 years and was thought to be a pure culture. Bryant et al (Bryant et al. 1967) found that it was not a pure culture but a consortium consisting of two bacteria growing on ethanol. The syntroph oxidized ethanol to acetic acid and H2, while the methanogen oxidized H2 by reduction of CO2. Syntrophs have since been shown to grow on a variety of unsaturated fatty acids by themselves. Interspecies H2 transfer was later demonstrated to be an important coupled reaction between syntrophs and sulfate-reducing bacteria. In fact, sulfidogens and methanogens are now recognized to be the ultimate consumers of organic compounds under anaerobic conditions. As sulfate reduction is more thermodynamically favorable than CO2 formation, the former generally prevails in high sulfate concentrations (e.g., marine environments) and the latter in low sulfate concentrations (e.g., fresh water sediments). See:
(Inerney 1992)
(Jackson et al. 1999)
(Suflita et al. 1992)
(Cozzarelli et al. 2000)

Although it had been known for some time that DDT and other organochlorine compounds were subjected to limited dehalogenation by bacteria, it was never known if energy was obtained or how many organisms were involved. Shelton and Tiedje (Shelton and Tiedje 1984) discovered the first defined consortia of obligate anaerobic bacteria that grew on 3-chlorobenzoate as a sole carbon source. Neither of the three isolates would grow alone on this substrate. The organism involved in the dehalogenations reaction was an unusual bacterium having a collar structure. It was later found that this bacterium was a sulfidogen and would grow by itself on 3-chlorobenzoate when sulfate was supplied as the electron acceptor (Stevens et al. 1988). This bacterium was eventually named Desulfomonile tiedje (DeWeerd et al. 1990). As a result of this discovery, there has been a considerable expansion into anaerobic biodegradation. Many compounds, particularly the extensively cholorinated and persistent PCBs and dioxanes, have been shown to be recalcitrant to aerobic attack, yet amenable to reductive dehalogenation. The lesser chlorinated products can be degraded anaerobically. Thus, a conceptual model exists for the complete destruction of compounds that were once thought to be non-biodegradable. The current challenge is to understand the extent to which these coupled aerobic/anaerobic consortia function in the environment (natural attenuation) and to devise strategies to enhance the process. See:
(Fathepure et al. 1988)
(Quensen III et al. 1988)
(Quensen et al. 1990)
(Griffith et al. 1992)
(Mohn and Tiedje 1992)
(Quensen III et al. 2001)
(Bedard and VanDort 1998)
(Brown et al. 1987)
(Bedard et al. 1997)
(Wiegel and Wu 2000)

· Ahmed, M, and Focht, DD (1973) Degradation of polychlorinated biphenyls by two species of Achromobacter. Can. J. Microbiol. 19:47-52.

· Alvarez-Cohen, L, and McCarty, PL (1991) Effects of toxicity, aeration, and reductant supply on trichloroethylene transformation by a mixed methanotrophic culture. Appl. Environ. Microbiol. 57:228-35.

· Beam, HW, and Perry, JJ (1974) Microbial degradation of cycloparaffinic hydrocarbons via co-metabolism and commensalism. J. Gen. Microbiol. 82:163-69.

· Bedard, DL, Unterman, R, Bopp, LH, Brennan, MJ, Haberl, ML, and Johnson, C (1986) Rapid assay for screening and characterizing microorganisms for the ability to degrade polychlorinated biphenyls. Appl. Environ. Microbiol. 51:761-68.

· Bedard, DL, Van Dort, HM, May, RJ, and Smullen, KA (1997) Enrichment of microorganisms that sequentially meta-, para-dechlorinate the residue of Aroclor 1260 in Housatonic River sediment. Environ. Sci. Technol. 31:3308-13.

· Bedard, DL, and VanDort, HM (1998) Complete reductive dehalogenation of brominated biphenyls by anaerobic microorganisms in sediment. Appl. Environ. Microbiol. 64:940-47.

· Bedard, DL, Wagner, RE, Brennan, MJ, Haberl, ML, and Brown, JF (1987) Extensive degradation of Aroclors and environmentally transformed polychlorinated biphenyls by Alcaligenes eutrophus H850. Appl. Environ. Microbiol. 53:1094-102.

· Blasco, R, Wittich, RM, Mallavarapu, M, Timmis, KN, and Pieper, DH (1995) From xenobiotic to antibiotic, formation of protoanemonin from 4-chlorocatechol by enzymes of the 3-oxoadipate pathway. J. Biol. Chem. 270:29229-35.

· Brenner, V, Hernandez, BS, and Focht, DD (1993) Variation in chlorobenzoate catabolism by Pseudomonas putida P111 as a consequence of genetic alterations. Appl. Environ. Microbiol. 59:2790-94.

· Brown, JFJ, Wagner, RE, Feng, H, Bedard, DL, Brennan, MJ, Carnahan, JC, and May, RJ (1987) Environmental dechlorination of PCBs. Environ. Toxicol. Chem. 6:579-93.

· Carney, BF, and Leary, JV (1989) Novel alterations in plasmid DNA associated with aromatic hydrocarbon utilization by Pseudomonas putida strain R5-3. Appl. Environ. Microbiol. 55:1523-30.

· Chakrabarty, AM, Chou, G, and Gunsalus, IC (1973) Genetic regulation of octane dissimilation plasmid in Pseudomonas. Proc. Nat. Acad. Sci. U.S.A. 70:1137-40.

· Cozzarelli, IM, Suflita, JM, Ulrich, GA, Harris, SH, Scholl, MA, Schlottmann, JL, and Christenson, S (2000) Geochemical and microbiological methods for evaluating anaerobic processes in an aquifer contaminated by landfill leachate. Environ. Sci. Technol. 34:4025-33.

· deKlerk, H, and van der Linden, AC (1974) Bacterial degradation of cyclohexane: Participation of a co-oxidation reaction. Antonie van Leeuwenhoek 40:7-15.

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

· Don, RH, Weightman, AJ, Knackmuss, H-J, and Timmis, KN (1985) Transposon mutagenesis and cloning analysis of the pathways for degradation of 2,4-dichlorophenoxyacetic acid and 3-chlorobenzoate in Alcaligenes eutrophus JMP134 (pJP4). J. Bacteriol. 161:85-90.

· Dunn, NW, and Gunsalus, IC (1973) Transmissible plasmid coding early enzymes of naphthalene oxidation in Pseudomonas. J. Bacteriol. 114:974-79.

· Fathepure, BZ, Tiedje, JM, and Boyd, SA (1988) Reductive dechlorination of hexachlorobenzene to tri- and dichlorobenzenes in anaerobic sewage sludge. Appl. Environ. Microbiol. 54:327-30.

· Flanagan, WP, and May, RJ (1993) Metabolite detection as evidence for naturally occurring aerobic PCB biodegradation in Hudson River sediments. Environ. Sci. Technol. 27:2207-12.

· Focht, DD, and Alexander, M (1970) DDT metabolites and analogs: ring fission by Hydrogenomonas. Science 170:91-92.

· Focht, DD, and Brunner, W (1985) Kinetics of biphenyl and polychlorinated biphenyl metabolism in soil. Appl. Environ. Microbiol. 50:1058-63.

· Furukawa, K, and Chakrabarty, AM (1982) Involvement of plasmids in total degradation of chlorinated biphenyls. Appl. Environ. Microbiol. 44:619-26.

· Furukawa, K, Tonomura, K, and Kamibayashi, A (1978) Effect of chlorine substitution of the biodegradability of polychlorinated biphenyls. Appl. Environ. Microbiol. 35:223-27.

· Gerritse, J, and Gottschal, JC (1992) Mineralization of the herbicide 2,3,6-trichlorobenzoic acid by a co-culture of anaerobic and aerobic bacteria. FEMS Microbiol. Ecol. 101:89-98.

· Gerritse, J, Schut, F, and Gottschal, JC (1992) Modelling of mixed chemostat cultures of an aerobic bacterium, Comamonas testosteroni, and an anaerobic bacterium, Veillonella alcalescens: comparison with experimental data. Appl. Environ. Microbiol. 58:1466-76.

· Griffith, GD, Cole, JR, Quensen, JFI, and Tiedje, JM (1992) Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O. Appl. Environ. Microbiol. 58:409-11.

· Haigler, BE, Pettigrew, CA, and Spain, JC (1992) Biodegradation of mixtures of substituted benzenes by Pseudomonas sp. strain JS150. Appl. Environ. Microbiol. 58:2237-44.

· Hay, AG, and Focht, DD (1998) Cometabolism of 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene by Pseudomonas acidovorans M3GY grown on biphenyl. Appl. Environ. Microbiol. 54:2141-46.

· Horvath, RS (1972) Microbial cometabolism and the degradation of organic compounds in nature. Bacteriol. Rev. 36:146-55.

· Horvath, RS, and Alexander, M (1970) Cometabolism of m-chlorobenzoate by an Arthrobacter. Appl. Microbiol. 20:254-58.

· Inerney, M (1992) The genus Syntrophus, and other syntrophic bacteria, pp. 2048-57. In: Balow, A, Truper, HG, Dworkin, M, Harder, W, and Schliefer, KH (eds.), The procaryotes, a handbook of the biology of bacteria; ecophysiology, isolation, identification, and applications. Springer.

· Jackson, BE, Bhupathiraju, VK, Tanner, RS, Woese, CR, and McInerney, MJ (1999) Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms. Arch. Microbiol. 171:107-14.

· Jensen, HL (1963) Carbon nutrition of some microorganisms decomposing halogen-substituted aliphatic acids. Acta Agricultura Scandinavica 13:404-12.

· Koh, S-C, McCullar, MV, and Focht, DD (1996) Biodegradation of 2,4-dichlorophenol through a productive meta ring cleavage pathway. Abstracts of the General Meetings of the American Society for Microbiology. American Society for Microbiology.

· Kröckel, L, and Focht, DD (1987) Construction of chlorobenzene-utilizing recombinants by progenitive manifestation of a rare event. Appl. Environ. Microbiol. 53:2470-75.

· Mandelbaum, RT, Wackett, LP, and Allan, DL (1993) Mineralization of the s-triazine ring of atrazine by stable bacterial mixed cultures. Appl. Environ. Microbiol. 59:1695-701.

· McCullar, MV, Brenner, V, Adams, RH, and Focht, DD (1994) Construction of a novel polychlorinated biphenyl-degrading bacterium: utilization of 3,4'-dichlorobiphenyl by Pseudomonas acidovorans M3GY. Appl. Environ. Microbiol. 60:3833-39.

· McKenna, EJ, and Kallio, RE (1964) Hydrocarbon sturcture: its effects on bacterial utilization of alkanes, pp. 1-14. In: Heukelekian, H, and Dondero, NC (eds.), Principles and applications in aquatic microbiology. John Wiley and Sons.

· Mohn, WW, and Tiedje, JM (1992) Microbial reductive dehalogenation. Microbiol. Rev. 56:482-507.

· Nadeau, LJ, Menn, FM, Breen, A, and 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.

· Pettigrew, CA, Haigler, BE, and Spain, JC (1991) Simultaneous biodegradation of chlorobenzene and toluene by a Pseudomonas strain. Appl. Environ. Microbiol. 57:157-62.

· Pfaender, FK, and Alexander, M (1972) Extensive microbial degradation of DDT in vitro and DDT metabolism by natural communities. J. Agric. Food Chem. 20:842-46.

· Pritchard, PH, and Costa, CF (1991) EPA's Alaska oil spill bioremediation project. Environ. Sci. Technol. 25:372-79.

· Quensen III, JF, Tiedje, JM, and Boyd, SA (1988) Reductive dechlorination of polychlorinated biphenyls by anaerobic microorganisms from sediments. Science 242:752-54.

· Quensen III, JF, Tiedje, JM, Jain, MK, and Mueller, SA (2001) Factors controlling the rate of DDE dechlorination to DDMU in Palos Verdes margin sediments under anaerobic conditions. Environ. Sci. Technol. 35:286-91.

· Quensen, JF, Boyd, SA, and Tiedje, JM (1990) Dechlorination of 4 commercial polychlorinated biphenyl mixtures (Aroclors) by anaerobic microorganisms from sediments. Appl. Environ. Microbiol. 56:2360-69.

· Reineke, W, Jeenes, DJ, Williams, PA, and Knackmuss, H-J (1982) TOL plasmid pWWO in constructed halobenzoate-degrading Pseudomonas strains: prevention of the meta pathway. J. Bacteriol. 150:195-201.

· Reineke, W, and Knackmuss, H-J (1979) Construction of haloaromatics utilising bacteria. Nature 277:385-86.

· Reineke, W, and Knackmuss, H-J (1980) Hybrid pathway of chlorobenzoate metabolism in Pseudomonas sp. B13 derivatives. J. Bacteriol. 142:467-73.

· Senior, E, Bull, AT, and Slater, JH (1976) Enzyme evolution in a microbial community growing on the herbicide Dalapon. Nature 263:476-79.

· Slater, JH, and Lovatt, D (1984) Biodegradation and the significance of microbial communities, pp. 439-85. In: Gibson, DT (ed.), Microbial degradation of organic compounds. Marcel Dekker.

· Stevens, TO, Linkfield, TG, and Tiedje, JM (1988) Physiological characterization of strain DCB-1, a unique dehalogenating sulfidogenic bacterium. Appl. Environ. Microbiol. 54:2938-43.

· Suflita, JM, Gerba, CP, Ham, RK, Palmisano, AC, Rathje, WL, and Robinson, JA (1992) The world's largest landfill--a multidisciplinary investigation. Environ. Sci. Technol. 26:1486-95.

· Swisher, RD (1987) Surfactant biodegradation. Marcel Dekker.

· Timmis, KN, Lehrbach, PR, Harayama, S, Don, RH, Mermod, N, Bas, S, Leppik, R, Weightman, AJ, Reineke, W, and Knackmuss, H-J (1985) Analysis and manipulation of plasmid-coded pathways of the catabolism of aromatic compounds by soil bacteria. Plenum Publishing.

· Wiegel, J, and Wu, QZ (2000) Microbial reductive dehalogenation of polychlorinated biphenyls. FEMS Microbiol. Ecol. 32:1-15.

· Williams, PA, and Murray, K (1974) Metabolism of benoate and methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J. Bacteriol. 120:416-23.

· Zeyer, J, Lehrbach, PR, and Timmis, KN (1985) Use of cloned genes of Pseudomonas TOL plasmid to effect biotransformation of benzoates to cis-dihydrodiols and catechols by Escherichia coli cells. Appl. Environ. Microbiol. 50:1409-13.

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