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.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

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

Key Concept Ranking

Bacteria and Archaea
Methyl Coenzyme M Reductase
Aromatic Hydrocarbons
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. 183:67636770.
2. Aeckersberg, F.,, F. Bak,, and F. Widdel. 1991. Anaerobic oxidation of saturated hydrocarbons to CO2 by a new type of sulfate-reducing bacterium. Arch. Microbiol. 156:514.
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. 170:361369.
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. 45:327333.
5. Anderson, R. T.,, and D. R. Lovley. 2000. Hexadecane decay by methanogenesis. Nature 404: 722723.
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: 53295333.
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. 68:852858.
8. Atlas, R. M. 1995. Petroleum biodegradation and oil spill bioremediation. Mar. Pollut. Bull. 31:178182.
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: 57555761.
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. 6:969975.
11. Beller, H. R. 2000. Metabolic indicators for detecting in situ anaerobic alkylbenzene degradation. Biodegradation 11:125139.
12. Beller, H. R.,, and E. A. Edwards. 2000. Anaerobic toluene activation by benzylsuccinate synthase in a highly enriched methanogenic culture. Appl. Environ. Microbiol. 66:55035505.
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. 63:37293731.
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. 179:670676.
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: 54545457.
16. Beller, H. R.,, and A. M. Spormann. 1999. Substrate range of benzylsuccinate synthase from Azoarcus sp. strain T. FEMS Microbiol. Lett. 178:147153.
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. 36:39773984.
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. 58:31923195.
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. 62:11181196.
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. 238:661668.
21. Birch, L. D.,, and R. Bachofen,. 1988. Microbial production of hydrocarbons, p. 7199. 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 407:623626.
23. Boll, M.,, G. Fuchs,, and J. Heider. 2002. Anaerobic oxidation of aromatic compounds and hydrocarbons. Curr. Opin. Chem. Biol. 6:604611.
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 10:201217.
25. Chakraborty, R.,, and J. D. Coates. 2004. Anaerobic degradation of monoaromatic hydrocarbons. Appl. Microbiol. Biotechnol. 64:437446.
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. 1:157164.
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. 51:581588.
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 411:10391043.
29. Coates, J. D.,, R. Chakraborty,, and M. J. McInerney. 2002. Anaerobic benzene biodegradation— a new era. Res. Microbiol. 153:621628.
30. Connan, J., 1984. Biodegradation of crude oils in reservoirs, p. 299335. 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): 97106.
32. Coschigano, P. W. 2000. Transcriptional analysis of the tutE tutFDGH gene cluster from Thauera aromatica strain T1. Appl. Environ. Microbiol. 66: 11471152.
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. 231:261266.
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. 63:652660.
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. 64:16501656.
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. 54:7783.
37. Dean, B. J. 1985. Recent findings on the genetic toxicology of benzene, toluene, xylenes and phenols. Mutat. Res. 154:153181.
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. 154:336341.
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. 125:3839.
40. Ehrenreich, P.,, A. Behrends,, J. Harder,, and F. Widdel. 2000. Anaerobic oxidation of alkanes by newly isolated denitrifying bacteria. Arch. Microbiol. 173:5864.
41. Eklund, H.,, and M. Fontecave. 1999. Glycyl radical enzymes: a conservative structural basis for radicals. Structure 7:R257R262.
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. 35:682689.
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. 57:11391145.
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. 58:496501.
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: 183188.
46. Fishbein, L. 1985. An overview of environmental and toxicological aspects of aromatic hydrocarbons. II. Toluene. Sci. Total Environ. 42:267288.
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. 1:415420.
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:233245.
49. Gibson, D. T.,, and V. Subramanian,. 1984. Microbial degradation of aromatic hydrocarbons, p. 181252. 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. 11:236243.
51. Grbić-Galić , D.,, and T. M. Vogel. 1987. Transformation of toluene and benzene by mixed methanogenic cultures. Appl. Environ. Microbiol. 53:254260.
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. 69:54835491.
53. Harayama, S.,, M. Kok,, and E. L. Neidle. 1992. Functional and evolutionary relationships among diverse oxygenases. Annu.Rev.Microbiol. 46:565601.
54. Harder, J.,, and S. Foss. 1999. Anaerobic formation of the aromatic hydrocarbon p-cymene from monoterpenes by methanogenic enrichment cultures. Geomicrobiol. J. 16:295306.
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. 172:303312.
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. 65:9991004.
57. Harwood, C.,, G. Burchhardt,, H. Herrmann,, and G. Fuchs. 1998. Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway. FEMS Microbiol. Rev. 22:439458.
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 426:344352.
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: 120131.
60. Heider, J.,, A. M. Spormann,, H. R. Beller,, and F. Widdel. 1999. Anaerobic bacterial metabolism of hydrocarbons. FEMS Microbiol. Rev. 22:459473.
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. 177:132138.
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. 63:21362141.
63. Himo, T. 2002. Catalytic mechanisms of benzylsuccinate synthase, a theoretical study. J. Phys. Chem. B 106:76887692.
64. Hylemon, P. B.,, and J. Harder. 1999. Biotransformation of monoterpenes, bile acids, and other isoprenoids in anaerobic ecosystems. FEMS Microbiol. Rev. 22:475488.
65. Johnson, H. A.,, and A.M. Spormann. 1999. In vitro studies on the initial reactions of anaerobic ethylbenzene mineralization. J. Bacteriol. 181:56625668.
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. 183:45364542.
67. Jordan, A.,, and P. Reichard. 1998. Ribonucleotide reductases. Annu. Rev. Biochem. 67:7198.
68. Jørgensen, B. B. 1982. Mineralization of organic matter in the sea bed—the role of sulphate reduction. Nature 296:643645.
69. Jüttner, F.,, and J. J. Henatsch. 1986. Anoxic hypolimnion is a significant source of biogenic toluene. Nature 323:797798.
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 13:149154.
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 81:13321335.
72. Kniemeyer, O.,, and J. Heider. 2001a. Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme. J. Biol. Chem. 276:2138121386.
73. Kniemeyer, O.,, and J. Heider. 2001b. (S )-1- Phenylethanol dehydrogenase of Azoarcus sp. strain EbN1, an enzyme of anaerobic ethylbenzene catabolism. Arch. Microbiol. 176:129135.
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. 69:760768.
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: 64036410.
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. 276:1292412927.
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: 53935398.
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 426:878881.
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. 181:182194.
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. 19:961968.
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. 187:14931503.
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. 24:113125.
84. Leuthner, B.,, and J. Heider. 1998. A two-component system involved in regulation of anaerobic toluene metabolism in Thauera aromatica. FEMS Microbiol. Lett. 166:3541.
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. 182:272277.
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. 28:615628.
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 145:32653271.
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. 183:42884295.
89. Leutwein, C.,, and J. Heider. 2002. (R)-Benzylsuccinyl- CoA dehydrogenase of Thauera aromatica, an enzyme of the anaerobic toluene catabolic pathway. Arch. Microbiol. 178:517524.
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 339:297300.
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. 159:336344.
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. 43:135142.
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. 42:398403.
94. Magot, M.,, B. Ollivier,, and B. K. C. Patel. 2000. Microbiology of petroleum reservoirs. Antonie Leeuwenhoek 77:103116.
95. Meckenstock, R. U. 1999. Fermentative toluene degradation in anaerobic defined syntrophic cocultures. FEMS Microbiol. Lett. 177:6773.
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. 66:27432747.
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. 264:176182.
98. Meckenstock, R. U.,, M. Safinowski,, and C. Griebler. 2004. Anaerobic degradation of polycyclic aromatic hydrocarbons. FEMS Microbiol. Ecol. 49:2736.
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. 62:974978.
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. 70:29352940.
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: 407417.
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) 64:203208.
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. 4:103130.
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. 5:660671.
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. 65132. 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. 189210. 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. 511533. 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. 170:377384.
109. Rabus, R.,, and F. Widdel. 1995a. Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch. Microbiol. 163:96103.
110. Rabus, R.,, and F. Widdel. 1995b. Conversion studies with substrate analogues of toluene in a sulfate-reducing bacterium, strain Tol2. Arch. Microbiol. 164:448451.
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. 62:12381241.
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: 36053613.
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. 178:506516.
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. 183:2736.
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: 14441451.
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. 183:17071715.
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: 145157.
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. 50:649659.
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. 36:41274134.
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. 69:434443.
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. 177:153158.
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. 65:30563063.
124. Rosner, B. M.,, and B. Schink. 1995. Purification and characterization of acetylene hydratase of Pelobacter acetylenicus, a tungsten iron-sulfur protein. J. Bacteriol. 177:57675772.
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 372:455458.
126. Schink, B. 1985. Fermentation of acetylene by an obligate anaerobe, Pelobacter acetylenicus sp. nov. Arch. Microbiol. 142:295301.
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. 378:283300.
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. 70:13851392.
129. Simoneit, B. R. T.,, and P. F. Lonsdale. 1982. Hydrothermal petroleum in mineralized mounds at the seabed of Guaymas Basin. Nature 295:198202.
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. 184:29692977.
131. So, C. M.,, and L. Y. Young. 1999a. Isolation and characterization of a sulfate-reducing bacterium that anaerobically degrades alkanes. Appl. Environ. Microbiol. 65:29692976.
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: 55325540.
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. 69:38923900.
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. 48:889894.
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. 49:11291140.
136. Spormann, A. M.,, and F. Widdel. 2000. Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria. Biodegradation 11: 85105.
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 365:743745.
138. Swannell, R. P. J.,, K. Lee,, and M. McDonagh. 1996. Field evaluations of marine oil spill bioremediation. Microbiol. Rev. 60:342365.
139. Taylor, B. L.,, and I. B. Zhulin. 1999. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 63:479506.
140. Thode, H. G.,, K. K. Wanless,, and R. Wallough. 1954. The origin of native sulfur deposits from isotopic fractionation studies. Geochim. Cosmochim. Acta 5:286298.
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. 37:52135218.
143. Tschech, A.,, and G. Fuchs. 1987. Anaerobic degradation of phenol by pure cultures of newly isolated denitrifying pseudomonads. Arch. Microbiol. 148:213217.
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. 67:503549.
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. 181:155162.
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. 62:16231629.
148. Widdel, F.,, and R. Rabus. 2001. Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr. Opin. Biotechnol. 12:259276.
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. 31:101115.
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. 34:13131323.
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. 177:235243.
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. 172:204212.
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 401:266269.
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: 944947.
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. 63:47594764.
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. 45:500506.
158. Zwolinski, M. D.,, R. F. Harris,, and W. J. Hickey. 2000. Microbial consortia involved in the anaerobic degradation of hydrocarbons. Biodegradation 11:141158.


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