Chapter 14 : Biodegradation of Hydrocarbons Under Anoxic Conditions

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Biodegradation of Hydrocarbons Under Anoxic Conditions, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817589/9781555813277_Chap14-1.gif /docserver/preview/fulltext/10.1128/9781555817589/9781555813277_Chap14-2.gif


This chapter provides an update on the current knowledge about anaerobically hydrocarbon-degrading microorganisms, the reactions involved, and recent insights into the underlying genetics and regulatory mechanisms, and it describes the suitability of growth studies with crude oil as model systems. However, anoxic conditions prevail in many natural environments, such as soils, groundwater aquifers, freshwater and marine sediments, and oil reservoirs. Early reports of the anaerobic oxidation of alkylbenzenes in microcosms and enrichment cultures and in situ biodegradation of crude oil in anoxic reservoirs provided evidence that anaerobic hydrocarbon oxidation indeed occurred. Anaerobic hydrocarbon oxidation can also be coupled to phototrophic energy conservation, as was demonstrated with the toluene-degrading ToP1. During anaerobic growth with crude oil, strain HxN1 formed succinate derivatives of C to C n-alkanes and alicyclic hydrocarbons. Identification of cyclopentylpropionate suggests further degradation of cyclopentylsuccinate via C-skeleton rearrangement and decarboxylation and thereby the possibility that the “n-alkane degradation pathway” could in principle also be applicable for anaerobic degradation of alicyclic hydrocarbons. Several other types of reactions such as carboxylation, methylation, hydration, methanogenesis are currently discussed for anaerobic initial activation of various hydrocarbons.

Citation: Rabus R. 2005. Biodegradation of Hydrocarbons Under Anoxic Conditions, p 277-300. In Ollivier B, Magot M (ed), Petroleum Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555817589.ch14
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Generalized scheme for radical-driven formation of arylsuccinates or alkylsuccinates during the initial activation of alkylbenzenes and -alkanes. An activating enzyme generates the primary radical by reducing -adenosylmethionine in a one-electron step. After transfer, the radical is stored at a glycyl residue in the polypeptide chain of the hydrocarbon-activating enzyme. Analogous to PFL ( ), binding of the hydrocarbon substrate may trigger further transfer of the radical to a cysteine residue in exchange for a hydrogen atom, whereby the catalytically active thiyl radical is formed. The latter abstracts a hydrogen atom from the hydrocarbon substrate, yielding the hydrocarbon radical, which attacks the double bond of fumarate. Recombination of the substituted succinyl radical with the enzyme-bound hydrogen results in the aryl- or alkylsuccinate and regeneration of the catalytic thiyl radical. Further degradation of the aryl- or alkylsuccinates follows different routes, depending on the nature of the hydrocarbon substrate. R, alkyl or aryl; R, H or CH.

Citation: Rabus R. 2005. Biodegradation of Hydrocarbons Under Anoxic Conditions, p 277-300. In Ollivier B, Magot M (ed), Petroleum Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555817589.ch14
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

Pathways of anaerobic hydrocarbon degradation. (A) Ethylbenzene in denitrifying strain EbN1 ( ) and EB1 ( ). (B) Toluene in denitrifying K172 ( ), T1 ( ), strain T ( ), strain EbN1 ( ), sulfate-reducing Tol2 ( ), strain PRTOL1 ( ), and phototrophic ToP1 ( ). (C) Ethylbenzene in sulfate-reducing strain EbS7 ( ). Further degradation of the common intermediate benzoyl-CoA involves reductive dearomatization and hydrolytic ring cleavage ( ). (D) -Hexane in denitrifying strain HxN1 ( ). Compound names: 1, ethylbenzene; 2, (S )-1-phenylethanol; 3, acetophenone; 4, benzoylacetate; 5, benzoylacetyl-CoA; 6, benzoyl-CoA; 7, toluene; 8, (R)-benzylsuccinate; 9, benzylsuccinyl-CoA; 10, phenylitaconyl-CoA; 11, benzoylsuccinyl-CoA; 12, (1-phenylethyl)succinate; 13, (1-phenylethyl)succinyl-CoA; 14, (2-phenylpropyl)malonyl-CoA; 15, 4-phenylpentanoyl-CoA; 16, -hexane; 17, (1-methylpentyl)succinate; 18, (1-methylpentyl)succinyl-CoA; 19, (2-methylhexyl) malonyl-CoA; 20, 4-methyloctanoyl-CoA; 21, 2-methylhexanoyl-CoA. *, chiral carbon atoms in products of initial reactions.

Citation: Rabus R. 2005. Biodegradation of Hydrocarbons Under Anoxic Conditions, p 277-300. In Ollivier B, Magot M (ed), Petroleum Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555817589.ch14
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3

Gene regulation in anaerobic alkylbenzene degradation of denitrifying strain EbN1. (A) The TdiSR two-component system recognizes toluene and mediates coordinative regulation of (encoding BSS) and (encoding β-oxidation enzymes) operons of anaerobic toluene oxidation to benzoyl-CoA. (B) The Tcs2/Tcr2 and Tcs1/Tcr1 two-component systems recognize ethylbenzene and acetophenone, respectively, and mediate sequential regulation of [encoding ethylbenzene and ()-1-phenylethanol dehydrogenases] and (encoding acetophenone carboxylase and benzoylacetate-CoA ligase) operons, respectively, of anaerobic ethylbenzene oxidation to benzoyl-CoA. The numbers designating chemical compounds are the same as those used in Fig. 2 .

Citation: Rabus R. 2005. Biodegradation of Hydrocarbons Under Anoxic Conditions, p 277-300. In Ollivier B, Magot M (ed), Petroleum Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555817589.ch14
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4

Anaerobic growth of strain EbN1 with crude oil as the sole source of organic carbon under nitrate-reducing conditions. (A) Control with inoculum but without nitrate. (B) Growth culture reaching an optical density at 600 nm of approximately 0.3 after 120 h of incubation and consumption of 10mM nitrate ( ).

Citation: Rabus R. 2005. Biodegradation of Hydrocarbons Under Anoxic Conditions, p 277-300. In Ollivier B, Magot M (ed), Petroleum Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555817589.ch14
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Achong, G. R.,, A. M. Rodriguez,, and A. M. Spormann. 2001. Benzylsuccinate synthase of Azoarcus sp. strain T: cloning, sequencing, transcriptional organization, and its role in anaerobic toluene and m-xylene mineralization. J. Bacteriol. 183: 6763 6770.
2. Aeckersberg, F.,, F. Bak,, and F. Widdel. 1991. Anaerobic oxidation of saturated hydrocarbons to CO 2 by a new type of sulfate-reducing bacterium. Arch. Microbiol. 156: 5 14.
3. Aeckersberg, F.,, F. A. Rainey,, and F. Widdel. 1998. Growth, natural relationships, cellular fatty acids and metabolic adaptation of sulfate-reducing bacteria that utilize long-chain alkanes under anoxic conditions. Arch. Microbiol. 170: 361 369.
4. Anders, H.-J.,, A. Kaetzke,, P. Ka¨mpfer,, W. Ludwig,, and G. Fuchs. 1995. Taxonomic position of aromatic-degrading denitrifying pseudomonad strainsK172 andKB740 and their description as new members of the genera Thauera, as Thauera aromatica sp. nov., and Azoarcus, as Azoarcus evansii sp. nov., respectively, members of the beta subclass of the Proteobacteria. Int. J. Syst. Bacteriol. 45: 327 333.
5. Anderson, R. T.,, and D. R. Lovley. 2000. Hexadecane decay by methanogenesis. Nature 404: 722 723.
6. Annweiler, E.,, A. Materna,, M. Safinowski,, A. Kappler,, H. H. Richnow,, W. Michaelis,, and R. U. Meckenstock. 2000. Anaerobic degradation of 2-methylnaphthalene by a sulfate-reducing enrichment culture. Appl. Environ. Microbiol. 66: 5329 5333.
7. Annweiler, E.,, W. Michaelis,, and R. U. Meckenstock. 2002. Identical ring cleavage products during anaerobic degradation of naphthalene, 2- methylnaphthalene, and tetralin indicate a new metabolic pathway. Appl. Environ. Microbiol. 68: 852 858.
8. Atlas, R. M. 1995. Petroleum biodegradation and oil spill bioremediation. Mar. Pollut. Bull. 31: 178 182.
9. Ball, H. A.,, H. A. Johnson,, M. Reinhard,, and A. M. Spormann. 1996. Initial reactions in anaerobic ethylbenzene oxidation by a denitrifying bacterium, strain EB1. J. Bacteriol. 178: 5755 5761.
10. Becker, A.,, K. Fritz-Wolf,, W. Kabsch,, J. Knappe,, S. Schultz,, and A. F. V. Wagner. 1999. Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase. Nat. Struct. Biol. 6: 969 975.
11. Beller, H. R. 2000. Metabolic indicators for detecting in situ anaerobic alkylbenzene degradation. Biodegradation 11: 125 139.
12. Beller, H. R.,, and E. A. Edwards. 2000. Anaerobic toluene activation by benzylsuccinate synthase in a highly enriched methanogenic culture. Appl. Environ. Microbiol. 66: 5503 5505.
13. Beller, H. R.,, and A. M. Spormann. 1997a. Benzylsuccinate formation as a means of anaerobic toluene activation by sulfate-reducing strain PRTOL1. Appl. Environ. Microbiol. 63: 3729 3731.
14. Beller, H. R.,, and A. M. Spormann. 1997b. Anaerobic activation of toluene and o-xylene by addition to fumarate in denitrifying strain T. J. Bacteriol. 179: 670 676.
15. Beller, H. R.,, and A. M. Spormann. 1998. Analysis of the novel benzylsuccinate synthase reaction for anaerobic toluene activation based on structural studies of the product. J. Bacteriol. 180: 5454 5457.
16. Beller, H. R.,, and A. M. Spormann. 1999. Substrate range of benzylsuccinate synthase from Azoarcus sp. strain T. FEMS Microbiol. Lett. 178: 147 153.
17. Beller, H. R.,, S. R. Kane,, T. C. Legler,, and P. J. Alvarez. 2002. A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon- degrading bacteria based on a catabolic gene. Environ. Sci. Technol. 36: 3977 3984.
18. Beller, H. R.,, M. Reinhard,, and D. Grbić-Galić . 1992. Metabolic by-products of anaerobic toluene degradation by sulfate-reducing enrichment cultures. Appl. Environ. Microbiol. 58: 3192 3195.
19. Beller, H. R.,, A. M. Spormann,, P. K. Sharma,, J. R. Cole,, and M. Reinhard. 1996. Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium. Appl. Environ. Microbiol. 62: 1118 1196.
20. Biegert, T.,, G. Fuchs,, and J. Heider. 1996. Evidence that anaerobic oxidation of toluene in the denitrifying bacterium Thauera aromatica is initiated by formation of benzylsuccinate fromtoluene and fumarate. Eur. J. Biochem. 238: 661 668.
21. Birch, L. D.,, and R. Bachofen,. 1988. Microbial production of hydrocarbons, p. 71 99. In H. J. Rehm, and G. Reed (ed.), Biotechnology: Special Microbial Processes, vol. 6b. VCH Verlagsgesellschaft, Weinheim, Germany.
22. Boetius, A.,, K. Ravenschlag,, C. J. Schubert,, D. Rickert,, F. Widdel,, A. Gieseke,, R. Amann,, B. B. Jørgensen,, U. Witte,, and O. Pfannkuche. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623 626.
23. Boll, M.,, G. Fuchs,, and J. Heider. 2002. Anaerobic oxidation of aromatic compounds and hydrocarbons. Curr. Opin. Chem. Biol. 6: 604 611.
24. Bolliger, C.,, P. Hö hener,, D. Hunkeler,, K. Häberli,, and J. Zeyer. 1999. Intrinsic bioremediation of a petroleum hydrocarbon-contaminated aquifer and assessment of mineralization based on stable carbon isotopes. Biodegradation 10: 201 217.
25. Chakraborty, R.,, and J. D. Coates. 2004. Anaerobic degradation of monoaromatic hydrocarbons. Appl. Microbiol. Biotechnol. 64: 437 446.
26. Champion, K. M.,, K. Zengler,, and R. Rabus. 1999. Anaerobic degradation of ethylbenzene and toluene in denitrifying strain EbN1 proceeds via independent substrate-induced pathways. J. Mol. Microbiol. Biotechnol. 1: 157 164.
27. Coates, J. D.,, V. K. Bhupathiraju,, L. A. Achenbach,, M. J. McInerney,, and D. R. Lovley. 2001a. Geobacter hydrogenophilus, Geobacter chapellei, and Geobacter grbiciae—three new strictly anaerobic dissimilatory Fe(III)-reducers. Int. J. Syst. Evol. Microbiol. 51: 581 588.
28. Coates, J. D.,, R. Chakraborty,, J. G. Lack,, S. M. O’Connor,, K. A. Cole,, K. S. Bender,, and L. A. Achenbach. 2001b. Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411: 1039 1043.
29. Coates, J. D.,, R. Chakraborty,, and M. J. McInerney. 2002. Anaerobic benzene biodegradation— a new era. Res. Microbiol. 153: 621 628.
30. Connan, J., 1984. Biodegradation of crude oils in reservoirs, p. 299 335. In J. Brooks, and D. H. Welte (ed.), Advances in Petroleum Geochemistry. Academic Press, London, United Kingdom.
31. Cord-Ruwisch, R.,, W. Kleinitz,, and F. Widdel. 1987. Sulfate-reducing bacteria and their activity in oil production. J. Petrol. Technol. 1987( January): 97 106.
32. Coschigano, P. W. 2000. Transcriptional analysis of the tutE tutFDGH gene cluster from Thauera aromatica strain T1. Appl. Environ. Microbiol. 66: 1147 1152.
33. Coschigano, P. W.,, and B. J. Bishop. 2004. Role of benzylsuccinate in the induction of the tutE tutFDGH gene complex of T. aromatica strain T1. FEMS Microbiol. Lett. 231: 261 266.
34. Coschigano, P. W.,, and L. Y. Young. 1997. Identification and sequence analysis of two regulatory genes involved in anaerobic toluene metabolism by strain T1. Appl. Environ. Microbiol. 63: 652 660.
35. Coschigano, P. W.,, T. S. Wehrmann,, and L. Y. Young. 1998. Identification and analysis of genes involved in anaerobic toluene metabolism by strain T1: Putative role of a glycine free radical. Appl. Environ. Microbiol. 64: 1650 1656.
36. Cravo-Laureau, C.,, R. Matheron,, J.-L. Cayol,, C. Joulian,, and A. Hirschler-Re´a. 2004. Desulfatibacillum aliphaticivorans gen. nov., sp. nov., an n-alkane- and n-alkene-degrading, sulfate-reducing bacterium. Int. J. Syst. Evol. Microbiol. 54: 77 83.
37. Dean, B. J. 1985. Recent findings on the genetic toxicology of benzene, toluene, xylenes and phenols. Mutat. Res. 154: 153 181.
38. Dolfing, J.,, J. Zeyer,, P. Binder-Eicher,, and R. P. Schwarzenbach. 1990. Isolation and characterization of a bacterium that mineralizes toluene in the absence of molecular oxygen. Arch. Microbiol. 154: 336 341.
39. Duboc-Toia, C.,, A. K. Hassan,, E. Mulliez,, S. Ollagnier-de Choudens,, M. Fontecave,, C. Leutwein,, and J. Heider. 2003. Very high-field EPR study of glycyl radical enzymes. J. Am. Chem. Soc. 125: 38 39.
40. Ehrenreich, P.,, A. Behrends,, J. Harder,, and F. Widdel. 2000. Anaerobic oxidation of alkanes by newly isolated denitrifying bacteria. Arch. Microbiol. 173: 58 64.
41. Eklund, H.,, and M. Fontecave. 1999. Glycyl radical enzymes: a conservative structural basis for radicals. Structure 7: R257 R262.
42. Elshahed, M. S.,, L. M. Gieg,, M. J. McInerney,, and J. M. Suflita. 2001. Signature metabolites attesting to the in situ attenuation of alkylbenzenes in anaerobic environments. Environ. Sci.Technol. 35: 682 689.
43. Evans, P. J.,, D. T. Mang,, K. S. Kim,, and L. Y. Young. 1991. Anaerobic degradation of toluene by a denitrifying bacterium. Appl. Environ. Microbiol. 57: 1139 1145.
44. Evans, P. J.,, W. Ling,, B. Goldschmidt,, E. R. Ritter,, and L. Y. Young. 1992. Metabolites formed during anaerobic transformation of toluene and o-xylene and their proposed relationship to the initial steps of toluene mineralization. Appl. Environ. Microbiol. 58: 496 501.
45. Fischer-Romero, C.,, B. J. Tindall,, and F. Jüttner. 1996. Tolumonas auensis gen. nov., sp. nov., a toluene-producing bacterium from anoxic sediment of a freshwater lake. Int. J. Syst. Bacteriol. 46: 183 188.
46. Fishbein, L. 1985. An overview of environmental and toxicological aspects of aromatic hydrocarbons. II. Toluene. Sci. Total Environ. 42: 267 288.
47. Galushko, A.,, D. Minz,, B. Schink,, and F. Widdel. 1999. Anaerobic degradation of naphthalene by a pure culture of a novel type of marine sulphate-reducing bacterium. Environ. Microbiol. 1: 415 420.
48. Gersberg, R. M.,, W. J. Dawsey,, and M. D. Bradley. 1993. Nitrate enhancement of in situ bioremediation of monoaromatic compounds in groundwater. Remediation Spring: 233 245.
49. Gibson, D. T.,, and V. Subramanian,. 1984. Microbial degradation of aromatic hydrocarbons, p. 181 252. In D. T. Gibson (ed.), Microbial Degradation of Organic Compounds. Marcel Dekker, Inc., New York, N.Y.
50. Gibson, D. T.,, and R. E. Parales. 2000. Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr. Opin. Biotechnol. 11: 236 243.
51. Grbić-Galić , D.,, and T. M. Vogel. 1987. Transformation of toluene and benzene by mixed methanogenic cultures. Appl. Environ. Microbiol. 53: 254 260.
52. Hallam, S. J.,, P. R. Girguis,, C. M. Preston,, P. M. Richardson,, and E. F. DeLong. 2003. Identification of methyl coenzyme M reductase A ( mcrA) genes associated with methane-oxidizing archaea. Appl. Environ. Microbiol. 69: 5483 5491.
53. Harayama, S.,, M. Kok,, and E. L. Neidle. 1992. Functional and evolutionary relationships among diverse oxygenases. Annu.Rev.Microbiol. 46: 565 601.
54. Harder, J.,, and S. Foss. 1999. Anaerobic formation of the aromatic hydrocarbon p-cymene from monoterpenes by methanogenic enrichment cultures. Geomicrobiol. J. 16: 295 306.
55. Harms, G.,, R. Rabus,, and F. Widdel. 1999a. Anaerobic oxidation of the aromatic plant hydrocarbon p-cymene by newly isolated denitrifying bacteria. Arch. Microbiol. 172: 303 312.
56. Harms, G.,, K. Zengler,, R. Rabus,, F. Aeckersberg,, D. Minz,, R. Rosselló-Mora,, and F. Widdel. 1999b. Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria. Appl. Environ. Microbiol. 65: 999 1004.
57. Harwood, C.,, G. Burchhardt,, H. Herrmann,, and G. Fuchs. 1998. Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway. FEMS Microbiol. Rev. 22: 439 458.
58. Head, I. M.,, D. M. Jones,, and S. R. Larter. 2003. Biological activity in the deep subsurface and the origin of heavy oil. Nature 426: 344 352.
59. Heider, J.,, M. Boll,, K. Breese,, S. Breinig,, C. Ebenau-Jehle,, U. Feil,, N. Gad’on,, D. Laempe,, B. Leuthner,, M. E.-S. Mohamed,, S. Schneider,, G. Burchhardt,, and G. Fuchs. 1998. Differential induction of enzymes involved in anaerobic metabolism of aromatic compounds in the denitrifying bacterium Thauera aromatica. Arch. Microbiol. 170: 120 131.
60. Heider, J.,, A. M. Spormann,, H. R. Beller,, and F. Widdel. 1999. Anaerobic bacterial metabolism of hydrocarbons. FEMS Microbiol. Rev. 22: 459 473.
61. Hermuth, K.,, B. Leuthner,, and J. Heider. 2002. Operon structure and expression of the genes for benzylsuccinate synthase in Thauera aromatica strain K172. Arch. Microbiol. 177: 132 138.
62. Hess, A.,, B. Zarda,, D. Hahn,, A. Ha¨ner,, D. Stax,, P. Höhener,, and J. Zeyer. 1997. In situ analysis of denitrifying toluene- and m-xylene-degrading bacteria in a diesel fuel-contaminated laboratory aquifer column. Appl. Environ. Microbiol. 63: 2136 2141.
63. Himo, T. 2002. Catalytic mechanisms of benzylsuccinate synthase, a theoretical study. J. Phys. Chem. B 106: 7688 7692.
64. Hylemon, P. B.,, and J. Harder. 1999. Biotransformation of monoterpenes, bile acids, and other isoprenoids in anaerobic ecosystems. FEMS Microbiol. Rev. 22: 475 488.
65. Johnson, H. A.,, and A.M. Spormann. 1999. In vitro studies on the initial reactions of anaerobic ethylbenzene mineralization. J. Bacteriol. 181: 5662 5668.
66. Johnson, H. A.,, D. A. Pelletier,, and A. M. Spormann. 2001. Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J. Bacteriol. 183: 4536 4542.
67. Jordan, A.,, and P. Reichard. 1998. Ribonucleotide reductases. Annu. Rev. Biochem. 67: 71 98.
68. Jørgensen, B. B. 1982. Mineralization of organic matter in the sea bed—the role of sulphate reduction. Nature 296: 643 645.
69. Jüttner, F.,, and J. J. Henatsch. 1986. Anoxic hypolimnion is a significant source of biogenic toluene. Nature 323: 797 798.
70. Kane, S. R.,, H. R. Beller,, T. C. Legler,, and R. T. Anderson. 2002. Biochemical and genetic evidence of benzylsuccinate synthase in toluene-degrading, ferric iron-reducing Geobacter metallireducens. Biodegradation 13: 149 154.
71. Knappe, J.,, F. A. Neugebauer,, H.P. Blaschkowski,, And M. Gänzler. 1984. Post-translational activation introduces a free radical into pyruvate formate-lyase. Proc. Natl. Acad. Sci. USA 81: 1332 1335.
72. Kniemeyer, O.,, and J. Heider. 2001a. Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme. J. Biol. Chem. 276: 21381 21386.
73. Kniemeyer, O.,, and J. Heider. 2001b. (S )-1- Phenylethanol dehydrogenase of Azoarcus sp. strain EbN1, an enzyme of anaerobic ethylbenzene catabolism. Arch. Microbiol. 176: 129 135.
74. Kniemeyer, O.,, T. Fischer,, H. Wilkes,, F. O. Glöckner,, and F. Widdel. 2003. Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium. Appl. Environ. Microbiol. 69: 760 768.
75. Koch, R.,, and B. O. Wagner. 1989. Umweltchemikalien: Physikalisch-Chemische Daten, Toxizitäten, Grenz- und Richtwerte, Umweltverhalten. VCH Verlagsgesellschaft, Weinheim, Germany.
76. Krieger, C. J.,, H. R. Beller,, M. Reinhard,, and A. M. Spormann. 1999. Initial reactions in anaerobic oxidation of m-xylene by the denitrifying bacterium Azoarcus sp. strain T. J. Bacteriol. 181: 6403 6410.
77. Krieger, C. J.,, W. Roseboom,, S. P. J. Albracht,, and A. M. Spormann. 2001. A stable organic free radical in anaerobic benzylsuccinate synthase from Azoarcus sp. strain T. J. Biol. Chem. 276: 12924 12927.
78. Kropp, K. G.,, I. A. Davidova,, and J. M. Suflita. 2000. Anaerobic oxidation of n-dodecane by an addition reaction in a sulfate-reducing bacterial enrichment culture. Appl. Environ. Microbiol. 66: 5393 5398.
79. Krüger, M.,, A. Meyerdierks,, F. O. Glöckner,, R. Amann,, F. Widdel,, M. Kube,, R. Reinhardt,, J. Kahnt,, R. Böcher,, R. K. Thauer,, and S. Shima. 2003. A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426: 878 881.
80. Kube, M.,, J. Heider,, J. Amann,, P. Hufnagel,, S. Kühner,, A. Beck,, R. Reinhardt,, and R. Rabus. 2004. Genes involved in the anaerobic degradation of toluene in a denitrifying bacterium, strain EbN1. Arch. Microbiol. 181: 182 194.
81. Kuhn, E. P.,, P. J. Colberg,, J. L. Schnoor,, O. Wanner,, A. J. B. Zehnder,, and R. P. Schwarzenbach. 1985. Microbial transformation of substituted benzenes during infiltration of river water to groundwater: laboratory column studies. Environ. Sci. Technol. 19: 961 968.
82. Kühner, S.,, L. Wöhlbrand,, I. Fritz,, W. Wruck,, C. Hultschig,, P. Hufnagel,, M. Kube,, R. Reinhardt,, and R. Rabus. 2005. Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J. Bacteriol. 187: 1493 1503.
83. Langenhoff, A. A. M.,, I. Nijenhuis,, N. C. G. Tan,, M. Briglia,, A. J. B. Zehnder,, and G. Schraa. 1997. Characterisation of a manganese-reducing, toluene-degrading enrichment culture. FEMS Microbiol. Ecol. 24: 113 125.
84. Leuthner, B.,, and J. Heider. 1998. A two-component system involved in regulation of anaerobic toluene metabolism in Thauera aromatica. FEMS Microbiol. Lett. 166: 35 41.
85. Leuthner, B.,, and J. Heider. 2000. Anaerobic toluene catabolism of Thauera aromatica: the bbs operon codes for enzymes of β-oxidation of the intermediate benzylsuccinate. J. Bacteriol. 182: 272 277.
86. Leuthner, B.,, C. Leutwein,, H. Schulz,, P. Hörth,, W. Haehnel,, E. Schiltz,, H. Schaegger,, and J. Heider. 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.
87. Leutwein, C.,, and J. Heider. 1999. Anaerobic toluene-catabolic pathway in denitrifying Thauera aromatica: activation and beta-oxidation of the first intermediate, ( R)-(+)-benzylsuccinate. Microbiology 145: 3265 3271.
88. Leutwein, C.,, and J. Heider. 2001. Succinyl- CoA:( R)-benzylsuccinate CoA-transferase: an enzyme of the anaerobic toluene catabolic pathway in denitrifying bacteria. J. Bacteriol. 183: 4288 4295.
89. Leutwein, C.,, and J. Heider. 2002. ( R)-Benzylsuccinyl- CoA dehydrogenase of Thauera aromatica, an enzyme of the anaerobic toluene catabolic pathway. Arch. Microbiol. 178: 517 524.
90. Lovley, D. R.,, M. J. Baedecker,, D. J. Lonergan,, I. M. Cozzarelli,, E. J. P. Phillips,, and O. I. Siegel. 1989. Oxidation of aromatic contaminants coupled to microbial iron reduction. Nature 339: 297 300.
91. Lovley, D. R.,, S. J. Giovannoni,, D. C. White,, J. E. Champine,, E. J. Phillips,, Y. A. Gorby,, and S. Goodwin. 1993. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron or other metals. Arch. Microbiol. 159: 336 344.
92. Macy, J. M.,, S. Rech,, G. Auling,, M. Dorsch,, E. Stackebrandt,, and L. I. Sly. 1993. Thauera selenatis gen. nov., sp. nov., a member of the beta subclass of Proteobacteria with a novel type of anaerobic respiration. Int. J. Syst. Bacteriol. 43: 135 142.
93. Magot, M.,, P. Caumette,, J. M. Desperrier,, R. Matheron,, C. Dauga,, F. Grimont,, and L. Carreau. 1992. Desulfovibrio longus sp. nov., a sulfate-reducing bacterium isolated from an oil-producing well. Int. J. Syst. Bacteriol. 42: 398 403.
94. Magot, M.,, B. Ollivier,, and B. K. C. Patel. 2000. Microbiology of petroleum reservoirs. Antonie Leeuwenhoek 77: 103 116.
95. Meckenstock, R. U. 1999. Fermentative toluene degradation in anaerobic defined syntrophic cocultures. FEMS Microbiol. Lett. 177: 67 73.
96. Meckenstock, R. U.,, E. Annweiler,, W. Michaelis,, H. H. Richnow,, and B. Schink. 2000. Anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Appl. Environ. Microbiol. 66: 2743 2747.
97. Meckenstock, R. U.,, R. Krieger,, S. Ensign,, P. M. H. Kroneck,, and B. Schink. 1999. Acetylene hydratase of Pelobacter acetylenicus. Molecular and spectroscopic properties of the tungsten iron-sulfur enzyme. Eur. J. Biochem. 264: 176 182.
98. Meckenstock, R. U.,, M. Safinowski,, and C. Griebler. 2004. Anaerobic degradation of polycyclic aromatic hydrocarbons. FEMS Microbiol. Ecol. 49: 27 36.
99. Migaud, M. E.,, J. C. Chee-Sanford,, J. M. Tiedje,, and J. W. Frost. 1996. Benzylfumaric, benzylmaleic, and Z- and E-phenylitaconic acids: synthesis, characterization, and correlation with a metabolite generated by Azoarcus tolulyticus Tol-4 during anaerobic toluene degradation. Appl. Environ. Microbiol. 62: 974 978.
100. Morasch, B.,, H.H. Richnow,, A. Vieth,, B. Schink,, and R. U. Meckenstock. 2004a. Stable isotope fractionation caused by glycyl radical enzymes during bacterial degradation of aromatic compounds. Appl. Environ. Microbiol. 70: 2935 2940.
101. Morasch, B.,, B. Schink,, C. C. Tebbe,, and R. U. Meckenstock. 2004b. Degradation of o-xylene and m-xylene by a novel sulfate-reducer belonging to the genus Desulfotomaculum. Arch. Microbiol. 181: 407 417.
102. Nazina, T. N.,, A. E. Ivanova,, O. V. Golubeva,, R. R. Ibatullin,, S. S. Belyaev, andM.V. Ivanov. 1995. Occurrence of sulfate- and iron-reducing bacteria in stratal waters of the Romashkinskoe oil field. Microbiology (New York) 64: 203 208.
103. Nazina, T. N.,, E. P. Rozanova,, and S. I. Kuznetsov. 1985. Microbial oil transformation processes accompanied by methane and hydrogen-sulfide formation. Geomicrobiol. J. 4: 103 130.
104. Neretin, L. N.,, A. Schippers,, A. Pernthaler,, K. Hamann,, R. Amann,, and B. B. Jørgensen. 2003. Quantification of dissimilatory (bi)sulphite reductase gene expression in Desulfobacterium autotrophicum using real-time RT-PCR. Environ. Microbiol. 5: 660 671.
105. Nielsen, H.,, J. Pilot,, L. N. Grinenko,, V. A. Grinenko,, A. Y. Lein,, J. W. Smith,, and R. G. Pankina,. 1991. Lithospheric sources of sulfur, p. 65 132. In H. R. Krouse, and V. A. Grinenko (ed.), Stable Isotopes: Natural and Anthropogenic Sulphur in the Environment, vol. 43. John Wiley & Sons, New York, N.Y.
106. Odom, J. M., 1993. Industrial and environmental activities of sulfate-reducing bacteria, p. 189 210. In J. M. Odom, and R. Singleton, Jr. (ed.), The Sulfate-Reducing Bacteria: Contemporary Perspectives. Springer-Verlag, New York, N.Y.
107. Plamer, S. E., 1993. Effect of biodegradation and water washing on crude oil composition, p. 511 533. In M. H. Engel, and S. A. Macko (ed.), Organic Geochemistry. Plenum Press, New York, N.Y.
108. Rabus, R.,, and J. Heider. 1998. Initial reactions of anaerobic metabolism of alkylbenzenes in denitrifying and sulfate-reducing bacteria. Arch. Microbiol. 170: 377 384.
109. Rabus, R.,, and F. Widdel. 1995a. Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch. Microbiol. 163: 96 103.
110. Rabus, R.,, and F. Widdel. 1995b. Conversion studies with substrate analogues of toluene in a sulfate-reducing bacterium, strain Tol2. Arch. Microbiol. 164: 448 451.
111. Rabus, R.,, and F. Widdel. 1996. Utilization of alkylbenzenes during anaerobic growth of pure cultures of denitrifying bacteria on crude oil. Appl. Environ. Microbiol. 62: 1238 1241.
112. Rabus, R.,, M. Fukui,, H. Wilkes,, and F. Widdel. 1996. Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Appl. Environ.Microbiol. 62: 3605 3613.
113. Rabus, R.,, T. Hansen,, and F. Widdel,. 2000. Dissimilatory sulfate- and sulfur-reducing prokaryotes. In M. Dworkin (ed.), The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community, 3rd ed., release 3.3. Springer-Verlag, New York, N.Y. [Online.] http://springerlink. metapress.com.
114. Rabus, R.,, M. Kube,, A. Beck,, F. Widdel,, and R. Reinhardt. 2002. Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1. Arch. Microbiol. 178: 506 516.
115. Rabus, R.,, M. Kube,, J. Heider,, A. Beck,, K. Heitmann,, F. Widdel,, and R. Reinhardt. 2005. The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch. Microbiol. 183: 27 36.
116. Rabus, R.,, R. Nordhaus,, W. Ludwig,, and F. Widdel. 1993. Complete oxidation of toluene under strictly anoxic conditions by a new sulfate-reducing bacterium. Appl. Environ. Microbiol. 59: 1444 1451.
117. Rabus, R.,, H. Wilkes,, A. Behrends,, A. Armstroff,, T. Fischer,, A. J. Pierik,, and F. Widdel. 2001. Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: Evidence for (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism. J. Bacteriol. 183: 1707 1715.
118. Rabus, R.,, H. Wilkes,, A. Schramm,, G. Harms,, A. Behrends,, R. Amann,, and F. Widdel. 1999. Anaerobic utilization of alkylbenzenes and nalkanes from crude oil in an enrichment culture of denitrifying bacteria affiliating with the β-subclass of Proteobacteria. Environ. Microbiol. 1: 145 157.
119. Reinhold-Hurek, B.,, and T. Hurek. 2000. Reassessment of the taxonomic structure of the diazotrophic genus Azoarcus sensu lato and description of three new genera and new species, Azovibrio restrictus gen. nov., sp. nov., Azospira oryzae gen. nov., sp. nov. and Azonexus fungiphilus gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 50: 649 659.
120. Reusser, D. E.,, J. D. Istok,, H. R. Beller,, and J. A. Field. 2002. In situ transformation of deuterated toluene and xylene to benzylsuccinic acid analogues in BTEX-contaminated aquifers. Environ. Sci. Technol. 36: 4127 4134.
121. Rios-Hernandez, L. A.,, L. M. Gieg,, and J. M. Suflita. 2003. Biodegradation of an alicyclic hydrocarbon by a sulfate-reducing enrichment from a gas condensate-contaminated aquifer. Appl. Environ. Microbiol. 69: 434 443.
122. Rödel, W.,, W. Plaga,, R. Frank,, and J. Knappe. 1988. Primary structure of Escherichia coli pyruvate formate-lyase and pyruvate-formate-lyase-activating enzyme deduced from DNA nucleotide sequences. Eur. J. Biochem. 177: 153 158.
123. Rooney-Varga, J. N.,, R. T. Anderson,, J. L. Fraga,, D. Ringelberg,, and D. R. Lovley. 1999. Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl. Environ. Microbiol. 65: 3056 3063.
124. Rosner, B. M.,, and B. Schink. 1995. Purification and characterization of acetylene hydratase of Pelobacter acetylenicus, a tungsten iron-sulfur protein. J. Bacteriol. 177: 5767 5772.
125. Rueter, P.,, R. Rabus,, H. Wilkes,, F. Aeckersberg,, F. A. Rainey,, H. W. Jannasch,, and F. Widdel. 1994. Anaerobic oxidation of hydrocarbons in crude oil by new types of sulphate-reducing bacteria. Nature 372: 455 458.
126. Schink, B. 1985. Fermentation of acetylene by an obligate anaerobe, Pelobacter acetylenicus sp. nov. Arch. Microbiol. 142: 295 301.
127. Schmidt, T. C.,, L. Zwank,, M. Elsner,, M. Berg,, R. U. Meckenstock,, and S. B. Haderlein. 2004. Compound-specific stable isotope analysis of organic contaminants in natural environments: a critical review of the state of the art, prospects, and future challenges. Anal. Bioanal. Chem. 378: 283 300.
128. Shinoda, Y.,, Y. Sakai,, H. Uenishi,, Y. Uchihashi,, A. Hiraishi,, H. Yukawa,, H. Yurimoto,, and N. Kato. 2004. Aerobic and anaerobic toluene degradation by a newly isolated denitrifying bacterium, Thauera sp. strain DNT-1. Appl. Environ. Microbiol. 70: 1385 1392.
129. Simoneit, B. R. T.,, and P. F. Lonsdale. 1982. Hydrothermal petroleum in mineralized mounds at the seabed of Guaymas Basin. Nature 295: 198 202.
130. Sluis, M. K.,, R. A. Larsen,, J. G. Krum,, R. Anderson,, W. W. Metcalf,, and S. A. Ensign. 2002. Biochemical, molecular and genetic analysis of the acetone carboxylases from Xanthobacter autotrophicus strain Py2 and Rhodobacter capsulatus strain B10. J. Bacteriol. 184: 2969 2977.
131. So, C. M.,, and L. Y. Young. 1999a. Isolation and characterization of a sulfate-reducing bacterium that anaerobically degrades alkanes. Appl. Environ. Microbiol. 65: 2969 2976.
132. So, C. M.,, and L. Y. Young. 1999b. Initial reactions in anaerobic alkane degradation by a sulfate reducer, strain AK-01. Appl. Environ. Microbiol. 65: 5532 5540.
133. So, C. M.,, C. D. Phelps,, and L. Y. Young. 2003. Anaerobic transformation of alkanes to fatty acids by a sulfate-reducing bacterium, strain Hxd3. Appl. Environ. Microbiol. 69: 3892 3900.
134. Song, B.,, L. Y. Young,, and N. J. Palleroni. 1998. Identification of denitrifier strain T1 as Thauera aromatica and proposal for emendation of the genus Thauera definition. Int. J. Syst. Bacteriol. 48: 889 894.
135. Song, B.,, M. M. Häggblom,, J. Zhou,, J. M. Tiedje,, and N. J. Palleroni. 1999. Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp. nov. and Azoarcus toluclasticus sp. nov. Int. J. Syst. Bacteriol. 49: 1129 1140.
136. Spormann, A. M.,, and F. Widdel. 2000. Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria. Biodegradation 11: 85 105.
137. Stetter, K. O.,, R. Huber,, E. Blöchl,, M. Kurr,, R. D. Eden,, M. Fielder,, H. Cash,, and I. Vance. 1993. Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature 365: 743 745.
138. Swannell, R. P. J.,, K. Lee,, and M. McDonagh. 1996. Field evaluations of marine oil spill bioremediation. Microbiol. Rev. 60: 342 365.
139. Taylor, B. L.,, and I. B. Zhulin. 1999. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 63: 479 506.
140. Thode, H. G.,, K. K. Wanless,, and R. Wallough. 1954. The origin of native sulfur deposits from isotopic fractionation studies. Geochim. Cosmochim. Acta 5: 286 298.
141. Tissot, B. P.,, and D. H. Welte. 1984. Petroleum Formation and Occurrence, 2nd ed. Springer-Verlag, Berlin, Germany.
142. Townsend, G. T.,, R. C. Prince,, and J. M. Suflita. 2003. Anaerobic oxidation of crude oil hydrocarbons by the resident microorganisms of a contaminated anoxic aquifer. Environ. Sci. Technol. 37: 5213 5218.
143. Tschech, A.,, and G. Fuchs. 1987. Anaerobic degradation of phenol by pure cultures of newly isolated denitrifying pseudomonads. Arch. Microbiol. 148: 213 217.
144. U.S. Environmental Protection Agency. 2004. Underground Storage Tanks. [Online.] http://www. epa.gov/swerust1/index.htm.
145. Van Hamme, J. D.,, A. Singh,, and O. P. Ward. 2003. Recent advances in petroleum microbiology. Microbiol. Mol. Biol. Rev. 67: 503 549.
146. Verfürth, K.,, A. J. Pierik,, C. Leutwein,, S. Zorn,, and J. Heider. 2004. Substrate specificities and electron paramagnetic resonance properties of benzyl-succinatesynthases in anaerobic toluene and m-xylene metabolism. Arch. Microbiol. 181: 155 162.
147. Voordouw, G.,, S. M. Armstrong,, M. F. Reimer,, B. Fouts,, A. J. Telang,, Y. Shen,, and D. Gevertz. 1996. Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria. Appl. Environ. Microbiol. 62: 1623 1629.
148. Widdel, F.,, and R. Rabus. 2001. Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr. Opin. Biotechnol. 12: 259 276.
149. Widdel, F.,, A. Boetius,, and R. Rabus,. 2003. Anaerobic biodegradation of hydrocarbons including methane. In A. Balows,, H. G. Trüper,, W. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.). The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community. Springer, New York, N.Y. [Online.]http://springerlink.metapress.com.
150. Wilkes, H.,, C. Boreham,, G. Harms,, K. Zengler,, and R. Rabus. 2000. Anaerobic degradation and carbon isotopic fractionation of alkylbenzenes in crude oil by sulphate-reducing bacteria. Org. Geochem. 31: 101 115.
151. Wilkes, H.,, S. Kühner,, C. Bolm,, T. Fischer,, A. Classen,, F. Widdel,, and R. Rabus. 2003. Formation of n-alkane and cycloalkane-derived organic acids during anaerobic growth of denitrifying bacteria with crude oil. Org. Geochem. 34: 1313 1323.
152. Wilkes, H.,, R. Rabus,, T. Fischer,, A. Armstroff,, A. Behrends,, and F. Widdel. 2002. Anaerobic degradation of n-hexane in a denitrifying bacterium: further degradation of the initial intermediate (1-methylpentyl)succinate via C-skeleton rearrangement. Arch. Microbiol. 177: 235 243.
153. Zengler, K.,, J. Heider,, R. Rosselló-Mora,, and F. Widdel. 1999a. Phototrophic utilization of toluene under anoxic conditions by a new strain of Blastochloris sulfoviridis. Arch. Microbiol. 172: 204 212.
154. Zengler, K.,, H. H. Richnow,, R. Rosselló-Mora,, W. Michaelis,, and F. Widdel. 1999b. Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401: 266 269.
155. Zeyer, J.,, E. P. Kuhn,, and R. P. Schwarzenbach. 1986. Rapid microbial mineralization of toluene and 1,3-dimethylbenzene in the absence of molecular oxygen. Appl. Environ. Microbiol. 52: 944 947.
156. Zhang, X.,, and L. Y. Young. 1997. Carboxylation as an initial reaction in the anaerobic metabolism of naphthalene and phenanthrene by sulfidogenic consortia. Appl. Environ. Microbiol. 63: 4759 4764.
157. Zhou, J.,, M. R. Fries,, J. C. Chee-Sanford,, and J. M. Tiedje. 1995. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene and description of Azoarcus tolulyticus sp. nov. Int. J. Syst. Bacteriol. 45: 500 506.
158. Zwolinski, M. D.,, R. F. Harris,, and W. J. Hickey. 2000. Microbial consortia involved in the anaerobic degradation of hydrocarbons. Biodegradation 11: 141 158.


Generic image for table

Pure cultures of anaerobically hydrocarbon-degrading bacteria

Citation: Rabus R. 2005. Biodegradation of Hydrocarbons Under Anoxic Conditions, p 277-300. In Ollivier B, Magot M (ed), Petroleum Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555817589.ch14

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error