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Chapter 14 : Biodegradation of Hydrocarbons Under Anoxic Conditions

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Abstract:

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

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Bacteria and Archaea
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Methyl Coenzyme M Reductase
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Aromatic Hydrocarbons
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Image of FIGURE 1
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
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Image of FIGURE 2
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
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Image of FIGURE 3
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
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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
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Tables

Generic image for table
TABLE 1

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

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