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Applied and Environmental Microbiology, September 2005, p. 5427-5432, Vol. 71, No. 9
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.9.5427-5432.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Hydroxylation and CarboxylationTwo Crucial Steps of Anaerobic Benzene Degradation by Dechloromonas Strain RCB
Romy Chakraborty and
John D. Coates*
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
Received 19 January 2005/
Accepted 1 April 2005

ABSTRACT
Benzene is a highly toxic industrial compound that is essential
to the production of various chemicals, drugs, and fuel oils.
Due to its toxicity and carcinogenicity, much recent attention
has been focused on benzene biodegradation, especially in the
absence of molecular oxygen. However, the mechanism by which
anaerobic benzene biodegradation occurs is still unclear. This
is because until the recent isolation of
Dechloromonas strains
JJ and RCB no organism that anaerobically degraded benzene was
available with which to elucidate the pathway. Although many
microorganisms use an initial fumarate addition reaction for
hydrocarbon biodegradation, the large activation energy required
argues against this mechanism for benzene. Other possible mechanisms
include hydroxylation, carboxylation, biomethylation, or reduction
of the benzene ring, but previous studies performed with undefined
benzene-degrading cultures were unable to clearly distinguish
which, if any, of these alternatives is used. Here we demonstrate
that anaerobic nitrate-dependent benzene degradation by
Dechloromonas strain RCB involves an initial hydroxylation, subsequent carboxylation,
and loss of the hydroxyl group to form benzoate. These studies
provide the first pure-culture evidence of the pathway of anaerobic
benzene degradation. The outcome of these studies also suggests
that all anaerobic benzene-degrading microorganisms, regardless
of their terminal electron acceptor, may use this pathway.

INTRODUCTION
Benzene has a broad range of industrial uses and is one of the
top 20 production volume chemicals in the United States, with
an annual production of almost 9 million metric tons (
16). In
addition to its presence in petroleum-based fuels, benzene is
often used as a raw material for the manufacture of other chemicals,
rubbers, lubricants, dyes, detergents, drugs, and pesticides.
Other sources, including volcanoes, forest fires, and cigarette
smoke, also contribute to the benzene in the environment. Benzene
is among the most prevalent organic contaminants in groundwater
and is a major concern due to its toxicity and relatively high
solubility (
16). It is currently ranked sixth on the U.S. National
Priorities List, and has been found in at least 813 of the 1,430
current or former National Priorities List sites (
http://www.atsdr.cdc.gov/cxcx3.html).
Benzene is biodegradable (
16,
26), especially in the presence
of oxygen; however, when soils and sediments are contaminated
with benzene, extensive anaerobic zones frequently develop due
to stimulation of the indigenous aerobic microbial population,
resulting in rapid depletion of the dissolved oxygen content
of the groundwater (
2,
11,
12,
27). As a result, a lot of attention
has been focused on anaerobic benzene degradation over the past
two decades, and anaerobic benzene degradation has been demonstrated
under nitrate-reducing (
9), Fe(III)-reducing (
29,
30), sulfate-reducing
(
14,
18,
28), and methanogenic (
21,
37) conditions. However,
until recently, no organism existed in pure culture that was
capable of this metabolism (
16,
26). Microbial community analysis
of benzene-degrading sediments and enrichment cultures using
molecular techniques has suggested that a functional role in
anaerobic benzene degradation is played by members of the family
Geobacteraceae under Fe(III)-reducing conditions (
33) and by
members of the family
Desulfobacteriaceae under both sulfate-reducing
and methanogenic conditions (
31,
35). However, there is no direct
evidence which shows that members of either of these families
of organisms are capable of benzene degradation. Recently,
Dechloromonas strains RCB and JJ, the first two organisms capable of anaerobic
benzene degradation, were isolated from completely different
environments and described (
15). Strains RCB and JJ belong to
the beta subclass of the
Proteobacteria, exhibit 98.1% 16S rRNA
gene sequence similarity, and metabolize benzene aerobically
or anaerobically with nitrate as the sole electron acceptor
(
15). Anaerobically,
Dechloromonas strain RCB completely degrades
benzene to CO
2, and concentrations as high as 160 µM are
removed within 5 days (
15).
The biochemical pathway of anaerobic benzene degradation by any organism is currently unknown, but several possibilities exist (16). These include initial carboxylation, hydroxylation, and methylation with subsequent transformation to the central aromatic intermediate benzoate or to its coenzyme A (CoA) thioester form, benzoyl-CoA (16). This compound then undergoes further enzymatic ring reduction and ring cleavage, which forms 3-acetyl-CoA and CO2. Previous studies of methanogenic benzene-degrading enrichments have indicated that phenol, cyclohexanone, propionate, and acetate are possible metabolites (21, 36, 37). Furthermore, phenol and benzoate were both detected as intermediates of benzene degradation with sulfate-reducing and Fe(III)-reducing enrichments (10, 32). However, all of these studies were performed with undefined sediments or enrichment cultures, and whether the compounds were formed directly from benzene catabolism by a single organism or were formed as a result of several sequential metabolic steps involving several different organisms is unknown.
As part of our ongoing studies on the anaerobic degradation of benzene by Dechloromonas strain RCB, we investigated the metabolic intermediates formed with nitrate as the electron acceptor. The results of these studies provide the first documentation of the mechanism of anaerobic nitrate-dependent metabolism of benzene in pure culture and also provide significant insight into the initial process of oxidation of this compound in the absence of oxygen.

MATERIALS AND METHODS
Media and stock preparation.
All media and solutions were prepared using strictly anaerobic
techniques, as previously described (
8,
15). All anaerobic culturing
was performed in sealed serum bottles under an N
2-CO
2 (80:20,
vol/vol) headspace. Unless otherwise stated, all chemicals were
acquired from Sigma Chemicals, Missouri. Anoxic aqueous stock
solutions of propyl iodide (100 mM), sodium iodide (100 mM),
5,5-dimethyl-1-pyrroline-
N-oxide (1 M), mannitol (1 M), sodium
dithionite (100 mM), sodium nitrate (1 M), phenol (10 mM), benzoic
acid (10 mM), and benzene (3.5 mM) were prepared under an N
2 headspace. Amendments were made anaerobically as needed into
experimental bottles from these anoxic stock solutions. Strain
RCB was routinely cultured on anoxic minimal media (
8) using
10 mM acetate and 16 mM nitrate as the electron donor and acceptor,
respectively, in 1-liter bottles sealed with thick butyl rubber
stoppers under an N
2-CO
2 (80:20, vol/vol) headspace. Small amounts
of benzene (10 µM) were added to the culture media during
growth and incubation of the cells to ensure induction of the
appropriate biochemical pathway.
Sample preparation for analysis of benzene and its metabolites.
Samples (15 to 20 ml) of culture broth for analysis of volatile metabolites of benzene were collected at regular time intervals from active benzene-degrading cultures and extracted with diethyl ether (5 ml) by vigorous shaking for 90 s. The ether layer was then collected in Supelco screw-top clear vials with polytetrafluoroethylene/Neoprene-lined caps and dried over anhydrous sodium sulfate to remove any traces of water prior to injection using a Hamilton gas-tight syringe into a gas chromatograph-mass spectrometer (GC-MS) for analysis.
Samples (25 to 30 ml) of culture broth for analysis of water-soluble nonvolatile metabolites were first alkalized using 1 M NaOH to pH 12 for 30 min to cleave thioesters. This was followed by acidification of the samples for 30 min using concentrated HCl to approximately pH 2. Acidified samples were then extracted twice using 10 to 15 ml ethyl acetate each time. The ethyl acetate extracts were combined and filtered over anhydrous sodium sulfate prior to concentration to approximately 1 ml by rotary evaporation at 80°C. The concentrated ethyl acetate extracts were subsequently evaporated to dryness under a steady stream of nitrogen gas and then redissolved using 0.5 ml of ethyl acetate before derivatization with 0.1 ml/sample of N,O-bis[trimethylsilyl]trifluoroacetamide and 1% trimethylchlorosilane (Pierce Chemicals, Rockford, Ill.) according to the manufacturer's instructions.
Analytical methods.
14CO2 production in the headspace of active cultures amended with [14C]acetate (1 µCi) or [14C]benzene (1 µCi) was determined with a gas chromatograph equipped with gas proportional counting detection, as previously described (15). Both [14C]acetate (43 mCi/mmol) and [UL-14C]benzene (55mCi/mmol) were purchased from Sigma.
Chemicals.
Analysis of ether extracts for benzene and phenol detection was performed using a gas chromatograph equipped with a mass spectrometry detector (Shimadzu GCMS-QP2010) with electron ionization. The injector port temperature was set at 110°C with a 1:20 split ratio, and the carrier gas used was helium flowing through the column at a rate of 1.48 ml · min1. Chromatography of each sample was performed using an XTI-5 column (Restek Corp., Pennsylvania). The column temperature was initially set at 40°C for 1 min and was subsequently ramped at a rate of 4°C min1 to a final temperature of 125°C.
Analysis of aqueous-phase extracts for metabolite detection was performed similarly by GC-MS of 3-µl sample extracts. The injection port temperature was set at 110°C with a 1:50 split ratio, and helium was used as the carrier gas at a flow rate of 1.46 ml · min1. Chromatography of each sample was performed using an XTI-5 column which was temperature ramped at a rate of 4°C · min1 to a final temperature of 230°C after an initial 2-min hold at 80°C. The hold time at the final temperature was 5 min. In all cases, mass spectra data were characterized by comparison with the standard National Institute of Standards and Technology (NIST) library, and compound identification was confirmed by comparison with chemical standards freshly prepared and derivatized using the sample preparation protocols outlined above.
Iodide determinations were performed by ion chromatography by using a DX 500 ion chromatograph with suppressed conductivity detection and an IonPac AS16 anion-exchange column (Dionex Corp., Sunnyvale, CA). A mobile phase of 35 mM NaOH was used at a flow rate of 1 ml · min1.
Optical density at 600 nm was determined using a Cary 50 Bio UV-visible spectrophotometer manufactured by Varian Analytical Instruments, Palo Alto, CA.

RESULTS AND DISCUSSION
Phenol as a metabolite of benzene degradation.
GC-MS of ether extracts of an active benzene-degrading anaerobic
culture revealed the presence of a single peak in addition to
benzene with a mass spectrum identical to that of phenol (data
not shown). The peak identification was confirmed by comparison
of mass spectra data with data from the NIST library and freshly
prepared chemical standards. The phenol peak appeared in samples
collected shortly after the onset of benzene degradation amended
with 5 mM nitrate as the electron acceptor (Fig.
1). No benzene
degradation or phenol formation was observed in the absence
of the electron acceptor. The phenol concentration peaked at
almost 2 µM within 30 h of inoculation, at which point
almost 19 µM benzene had been utilized by the active culture
(Fig.
1). Once benzene was completely depleted, the phenol concentration
rapidly dropped to levels below detection (Fig.
1). When the
culture was refed with 35 µM benzene, rapid benzene degradation
with concomitant phenol formation was again observed (Fig.
1).
Benzoate as a metabolite of benzene degradation.
In order to investigate the production of nonvolatile water-soluble
intermediates formed during anaerobic nitrate-dependent benzene
catabolism by strain RCB, samples were collected and extracted
with ethyl acetate prior to derivatization by silylation for
chromatographic analysis. GC-MS analysis revealed the presence
of a monoaromatic compound which was identified as benzoate
by comparison of the mass spectra with data from the NIST library
and authentic benzoate standards (data not shown). Benzoate
accumulated gradually to a concentration of almost 1.5 µM
after 70 h of incubation (Fig.
2). As observed with phenol,
benzoate was formed concomitant with benzene degradation. The
transient nature of benzoate observed correlated well with the
transient formation and removal of phenol (Fig.
2). Benzoate
formation was not observed in cultures that were not amended
with the electron acceptor nitrate.
Sequence of catabolite production.
To determine the sequence of phenol and benzoate formation during
benzene catabolism by strain RCB, anaerobic active cultures
were grown with 45 µM phenol as the sole electron donor
and 5 mM nitrate as the electron acceptor. At regular intervals
throughout the incubation, samples were collected and analyzed
by GC-MS. Analysis revealed that benzoate was transiently formed
by strain RCB concomitant with phenol degradation (Fig.
3).
No benzoate was formed in cultures that were not amended with
either phenol or nitrate. After 24 h of incubation, almost 1.5
µM benzoate was detected in the culture broth.
In contrast, no phenol formation occurred in similar experiments
performed with active cultures of strain RCB growing anaerobically
on 50 µM benzoate with nitrate as the electron acceptor.
These results indicate that phenol formation precedes formation
of benzoate as an intermediate of anaerobic nitrate-dependent
benzene oxidation by strain RCB.
Location of intermediate formation.
In order to determine if the intermediates were formed extracellularly or were extracted from the intracellular cytoplasmic pools of whole cells of strain RCB during sample preparation, subsamples from active benzene-oxidizing culture broths were prefiltered through 0.2-µm-pore-size filters to remove the cells prior to extraction and analysis. GC-MS analysis indicated that the phenol levels in extracts of filtered and unfiltered culture broths were identical throughout the incubation (Fig. 4), suggesting that the hydroxylation reaction occurs on the outer membrane or in the periplasm of the cell, from which the phenol readily diffuses into the culture milieu. Like the phenol levels, the benzoate levels were identical in extracts of both the filtered (0.2-µm-pore-size filters) and unfiltered culture broths throughout the incubation (data not shown), implying that benzoate formation also occurs on the outer membrane or in the periplasm of strain RCB.
Role of molecular oxygen.
Hydroxylation of benzene to phenol is the accepted primary route
of benzene metabolism by mammalian systems (
25). However, this
reaction is catalyzed by a monooxygenase P450 cytochrome isozyme
and is dependent on the availability of molecular oxygen. To
ensure that the benzene degradation in the active cultures of
strain RCB was not due to a similar mechanism involving molecular
oxygen, experiments were performed in anoxic culture media amended
with 0.5 mM sodium dithionite or 0.1 mM sodium ascorbate as
an alternative chemical reductant to remove any traces of dissolved
O
2 (Fig.
5). In spite of the presence of the chemical reductants
at the concentrations tested, [
14C]benzene was rapidly oxidized
to
14CO
2 in these experiments only in the presence of nitrate
(5 mM) (Fig.
5), discounting any possible role for molecular
oxygen in the metabolism. GC-MS analysis revealed the formation
of phenol concomitant with benzene degradation in culture broths
amended with sodium dithionite (data not shown). In addition,
no phenol was detected in benzene-degrading cultures of strain
RCB incubated with oxygen as the electron acceptor (data not
shown). This result is consistent with previous reports of studies
on the metabolites of aerobic microbial benzene degradation,
in which phenol was not detected as an intermediate (
19).
It is interesting that although the metabolism was not inhibited,
addition of dithionite as a reducing agent (0.5 mM) retarded
the rate of benzene degradation and the subsequent phenol formation
compared to unamended controls. At elevated concentrations (>1
mM) sodium dithionite completely inhibited benzene degradation.
However, even at a dithionite concentration of 0.5 mM, the phenol
degradation rates remained unaffected compared to those of unamended
controls (data not shown). These results suggest that dithionite
played an inhibitory role in the initial hydroxylation step
of benzene degradation rather than the subsequent oxidation
of phenol to CO
2 by strain RCB.
H2O as a potential source of the hydroxyl group.
Previous studies performed using an undefined benzene-degrading methanogenic enrichment culture also showed that phenol is a metabolite of benzene degradation (36). In these studies, the undefined culture was incubated in media amended with 9% H218O, and a small fraction (2.5%) of the observed phenol pool contained the 18O label, suggesting that the hydroxyl group originated from H2O (36). When a similar experiment was performed by incubating strain RCB for 24 h in anaerobic medium prepared using 25% H218O, GC-MS analysis of the ether extracts indicated that there was an increase of only 1.40% [18O]phenol in the phenol pool compared to an unlabeled control culture. A similar increase (1.13% [18O]phenol) was observed in the phenol pool if the experiment was repeated using medium prepared with 50% H218O. The low level of incorporation of the 18O label into the hydroxyl group of phenol produced from benzene under the conditions tested and the lack of a correlation with the initial H218O content suggest that H2O is not the source of the hydroxyl group during benzene catabolism by strain RCB. This suggestion is supported by the fact that an increase of 1.40% [18O]phenol in the phenol pool was observed in sterile culture medium containing 50% H218O and 1.5 µM unlabeled phenol after 24 h of incubation, demonstrating that the 18O atom of H218O could interchange to a small extent with the more abundant 16O atom of phenol. This may more likely account for the [18O]phenol produced in the biologically active samples. This result is unexpected and leaves the source of the hydroxyl group unknown. Final elucidation of the details of the mechanism involved in the initial hydroxylation process may shed further light on this.
Mechanism of hydroxylation.
In other known microbial hydroxylation reactions involving substrates such as enoyl-CoA or fumarate, the double bond is generally adjacent to a carbonyl group that plays a critical role by delocalizing the negative charge of the reaction intermediate, making the reaction favorable (5). This cannot occur with benzene due to its molecular symmetry and lack of functional side groups. Thus, hydroxyl group addition for benzene under standard conditions is an endogonic reaction (
Go' = 25.8 kJ/mol) (16). One possible mechanism for overcoming the unfavorable thermodynamics of benzene hydroxylation is through the formation of highly reactive hydroxyl free radicals (HO·), which subsequently attack the aromatic ring (1, 16, 38). When benzene-degrading cultures of strain RCB with nitrate as the electron acceptor were incubated in the presence of the hydroxyl free radical scavenger sodium iodide (0.5 mM), benzene degradation and subsequent phenol formation were inhibited compared to controls not amended with sodium iodide (Table 1). After 24 h of incubation, almost 19 µM of the initial benzene concentration (35 µM) was degraded by active cultures of strain RCB using nitrate as the electron acceptor, while only 1.75 µM of the initial benzene was degraded in the samples that were amended with sodium iodide (Table 1). In contrast, sodium iodide addition had no effect either on phenol degradation by strain RCB under nitrate-reducing conditions or on the growth of strain RCB on acetate and nitrate, demonstrating that the iodide was not generally toxic to the cell (Fig. 6). Phenol degradation by strain RCB proceeded at the same rate regardless of the presence of 0.5 mM sodium iodide, and almost 50% of the substrate was degraded within 24 h both in the presence and in the absence of sodium iodide (Fig. 6A). Ion chromatography analysis demonstrated that iodide concentrations remained constant throughout the incubation, indicating that the iodide was not used (oxidized to iodate) in place of benzene as an alternative, more favorable electron donor by strain RCB (data not shown).
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TABLE 1. Degradation of benzene by strain RCB in the presence and absence of various hydroxyl free radical scavengers
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Similar inhibition of anaerobic benzene degradation and phenol
formation by strain RCB with nitrate as the terminal electron
acceptor was also observed in the presence of other hydroxyl
free radical scavengers, such as 10 mM 5,5-dimethyl-1-pyrroline-
N-oxide
or 10 mM mannitol, which inhibited benzene degradation to different
extents (Table
1). Phenol degradation and acetate oxidation
under nitrate-reducing conditions by strain RCB remained unaffected
in the presence of these scavengers after 24 to 48 h of incubation
(data not shown). Although the results described above are not
direct evidence, they strongly support the hypothesis that benzene
ring hydroxylation is mediated through hydroxyl free radical
attack.
Mechanism of benzoate formation from phenol.
Reports on anaerobic phenol degradation by the monoaromatic hydrocarbon degrader Thauera aromatica have demonstrated that phenol is initially phosphorylated in an ATP-dependent mechanism to form phenylphosphate, which is then carboxylated by phenylphosphate carboxylase, forming 4-hydroxybenzoate (34). The 4-hydroxybenzoate is further activated by a specific CoA ligase, and the hydroxyl group is reductively removed (22). Molybdenum-containing iron-sulfur proteins have been shown to catalyze the dehydroxylation of hydroxy-benzoyl-CoA thioesters (6, 7, 20, 23). Whether a similar mechanism is involved during benzene metabolism by strain RCB is currently unknown. Phenylphosphate or 4-hydroxybenzoate was not detected in culture extracts of strain RCB analyzed during nitrate-dependent benzene degradation. Furthermore, recent reports have demonstrated that 0.1 mM dithionite inhibits carboxylation of phenylphosphate to form 4-hydroxybenzoate (34). Whether this is a reversible reaction is not known. In our experiments, while the addition of 0.1 mM dithionite to active benzene-degrading cultures decreased the rate of degradation of benzene and the subsequent formation of phenol (data not shown), it did not completely inhibit the process and had no significant effect on phenol catabolism by strain RCB.
Conclusion.
The results presented here provide the first elucidation of the initial steps involved in the anaerobic metabolic pathway for benzene degradation in pure culture (Fig. 7). These studies demonstrated that phenol is a metabolic intermediate of anaerobic benzene degradation by Dechloromonas strain RCB growing with nitrate as the terminal electron acceptor. Contrary to previous reports on methanogenic benzene degradation in which the source of the hydroxyl group of phenol was suggested to be water (36), in strain RCB under nitrate-reducing conditions, phenol formation appears to be mediated through reaction with a hydroxyl free radical that does not originate from H2O but is formed on the outer membrane or in the periplasm of the organism. Initial hydroxylation has been suggested to be the first step in degradation of other hydrocarbons, such as naphthalene under sulfate-reducing conditions (3) and recently ethylbenzene under nitrate-reducing conditions (24). The recently purified Mo-containing iron-sulfur protein that adds a hydroxyl group to ethylbenzene to form (S)-()-1-phenylethanol may provide a model for hydroxylation of benzene (24). The phenol formed from benzene by strain RCB is further carboxylated and dehydroxylated to form benzoate or its CoA ester, benzoyl-CoA. Both phenol and benzoate are formed outside the cytoplasm, and it appears that benzoate is transported into the cell for subsequent catabolism to CO2. The environmental implications of such extracellular processing of benzene to more readily degradable substrates and the availability of these substrates to other organisms in the natural environment are currently unknown. Although the concentrations of phenol and benzoate detected in our studies are very low, they are in agreement with previous reports on intermediates formed during anaerobic benzene and toluene degradation (4, 10). Prior studies detected phenol, cyclohexanone, and propionate as potential intermediates in undefined methanogenic enrichments incubated with benzene (21, 37). Similarly, phenol, benzoate, and acetate were also detected in benzene-degrading iron-reducing and sulfate-reducing sediments (10). As Dechloromonas species are not known to grow by Fe(III) reduction, by sulfate reduction, or through syntrophic interactions with methanogenic bacteria (13, 17), it is unlikely that organisms closely related to strain RCB or JJ are involved in the benzene metabolism observed in the previous studies. This, combined with the fact that both phenol and benzoate have now been identified during anaerobic benzene degradation in each of these disparate terminal electron-accepting processes, suggests that a single universal biochemical pathway may exist for anaerobic benzene degradation and that it is similar to that shown here for Dechloromonas strain RCB. In this regard, strain RCB serves as an ideal model organism to study the biochemistry and genetic regulation of anaerobic benzene oxidation in pure culture.

ACKNOWLEDGMENTS
Studies on
Dechloromonas aromatica strain RCB were supported
by independent grants to J.D.C. from the U.S. Department of
Energy NABIR program (DE-FG02-98-ER-62689) and the U.S. Department
of Defense (DACA72-00-C-0016).
We acknowledge K. V. Kellaris for iodide analysis in this project.

FOOTNOTES
* Corresponding author. Mailing address: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720. Phone: (510) 643-8455. Fax: (510) 642-4995. E-mail:
jcoates{at}nature.berkeley.edu.


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Applied and Environmental Microbiology, September 2005, p. 5427-5432, Vol. 71, No. 9
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.9.5427-5432.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
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