Anaerobic benzene biodegradation--a new era

Identification of critical members in a sulfidogenic benzene-degrading consortium by DNA stable isotope probing

Stable isotope probing (SIP) was used to identify the active members in a benzene-degrading sulfidogenic consortium. SIP-terminal restriction fragment length polymorphism analysis indicated that a 270-bp peak incorporated the majority of the (13)C label and is a sequence closely related to that of clone SB-21 (GenBank accession no. AF029045). This target may be an important biomarker for anaerobic benzene degradation in the field.

Anaerobic degradation of benzene by a marine sulfate-reducing enrichment culture, and cell hybridization of the dominant phylotype

The anaerobic biodegradation of benzene, a common constituent of petroleum and one of the least reactive aromatic hydrocarbons, is insufficiently understood with respect to the involved microorganisms and their metabolism. To study these aspects, sulfate-reducing bacteria were enriched with benzene as sole organic substrate using marine sediment as inoculum. Repeated subcultivation yielded a sediment-free enrichment culture constituted of mostly oval-shaped cells and showing benzene-dependent sulfate reduction and growth under strictly anoxic conditions. Amplification and sequencing of 16S rRNA genes from progressively diluted culture samples revealed an abundant phylotype; this was closely related to a clade of Deltaproteobacteria that includes sulfate-reducing bacteria able to degrade naphthalene or other aromatic hydrocarbons. Cell hybridization with two specifically designed 16S rRNA-targeted fluorescent oligonucleotide probes showed that the retrieved phylotype accounted for more than 85% of the cells detectable via DAPI staining (general cell staining) in the enrichment culture. The result suggests that the detected dominant phylotype is the 'candidate species' responsible for the anaerobic degradation of benzene. Quantitative growth experiments revealed complete oxidation of benzene with stoichiometric coupling to the reduction of sulfate to sulfide. Suspensions of benzene-grown cells did not show metabolic activity towards phenol or toluene. This observation suggests that benzene degradation by the enriched sulfate-reducing bacteria does not proceed via anaerobic hydroxylation (mediated through dehydrogenation) to free phenol or methylation to toluene, respectively, which are formerly proposed alternative mechanisms for benzene activation.

Monoaromatics removal from polluted water through bioreactors-a review

Water contaminated by oil products is becoming a major problem in water supplies as these organic compounds cause hazards for human health. Different types of aerobic and anaerobic bioreactors have been widely used for water cleanup from organic pollutants such as petroleum hydrocarbons. Many studies report that aerobic biofilm processes are a very efficient method for monoaromatic hydrocarbons removal from contaminated water as they are able to reduce up to 99% of the pollutants from water, but generally these works do not discuss possible pollutant loss through gas stripping. On the other hand, some research is related to the ability of anaerobic bioreactors for monoaromatics treatment and results have shown that anaerobic immobilized reactors are able to remove monoaromatic compounds from water with maximal efficiencies between 95-99%. But here again, no data are found about the amount of volatile organic compounds that can be found in the biogas. Also, the data generated when a solid biomass support (activated carbon, polyurethane, etc.) is present in the medium do not take care about possible solute sorption phenomena. This paper reviews various properties of monoaromatic compounds including benzene, toluene, ethylbenzene and mixture of xylenes. The sources of pollutants, various analytical methods suitable for identification and quantitative measurement of monoaromatics, and knowledge gained on the true removal rates by aerobic and anaerobic bioreactors are reviewed and discussed in this study.

Physiological and phylogenetic characterization of a stable benzene-degrading, chlorate-reducing microbial community

A stable anoxic enrichment culture was obtained that degraded benzene with chlorate as an electron acceptor. The benzene degradation rate was 1.65 mM benzene per day, which is similar to reported aerobic benzene degradation rates but 20-1650 times higher than reported for anaerobic benzene degradation. Denaturing gradient gel electrophoresis of part of the 16S rRNA gene, cloning and sequencing showed that the culture had a stable composition after the seventh transfer. Five bacterial clones were further analyzed. Two clones corresponded to bacteria closely related to Alicycliphilus denitrificans K601. The three other clones corresponded to bacteria closely related to Zoogloea resiniphila PIV-3A2w, Mesorhizobium sp. WG and Stenotrophomonas acidaminiphila. DGGE analysis of cultures grown with different electron donors and acceptors indicated that the bacterium related to Alicycliphilus denitrificans K601 is able to degrade benzene coupled to chlorate reduction. The role of the other bacteria could not be conclusively determined. The bacterium related to Mesorhizobium sp. WG can be enriched with benzene and oxygen, but not with acetate and chlorate, while the bacterium related to Stenotrophomonas acidaminophila grows with acetate and chlorate, but not with benzene and oxygen. As oxygen is produced during chlorate reduction, an aerobic pathway of benzene degradation is most likely.

Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker

Benzylsuccinate synthase (Bss) is the key enzyme of anaerobic toluene degradation and has been found in all anaerobic toluene degrading bacterial isolates tested. However, only a few pure cultures capable of anaerobic toluene oxidation are available to date, and it is important to understand the relevance of these model organisms for in situ bioremediation of hydrocarbon-contaminated aquifers. Due to their phylogenetic dispersal, it is not possible to specifically target anaerobic toluene degraders using marker rRNA genes. We therefore established an assay targeting a approximately 794 bp fragment within the Bss alpha-subunit (bssA) gene, which allows for the specific detection and affiliation of both known and unknown anaerobic degraders. Three distinct tar-oil-contaminated aquifer sites were screened for intrinsic bssA gene pools in order to identify and compare the diversity of hydrocarbon degraders present at these selected sites. We were able to show that local diversity patterns of degraders were entirely distinct, apparently highly specialized and well-adapted to local biogeochemical settings. Discovered at one of the sites were bssA genes closely related to that of Geobacter spp., which provides evidence for an importance of iron reduction for toluene degradation in these sediments. Retrieved from the other two sites, dominated by sulfate reduction, were previously unidentified bssA genes and also deeply branching putative bssA homologues. We provide evidence for a previously unrecognized diversity of anaerobic toluene degraders and also of other hydrocarbon degraders using fumarate-adding key reactions in contaminated aquifers. These findings enhance our current understanding of intrinsic hydrocarbon-degrading microbial communities in perturbed aquifers and may have potential for the future assessment and prediction of natural attenuation based on degradation genes.

Anaerobic biodegradation of benzene series compounds by mixed cultures based on optional electronic acceptors

A series of batch experiments were performed using mixed bacterial consortia to investigate biodegradation performance of benzene, toluene, ethylbenzene and three xylene isomers (BTEX) under nitrate, sulfate and ferric iron reducing conditions. The results showed that toluene, ethylbenzene, m-xylene and o-xylene could be degraded independently by the mixed cultures coupled to nitrate, sulfate and ferric iron reduction. Under ferric iron reducing conditions the biodegradation of benzene and p-xylene could be occurred only in the presence of other alkylbenzenes. Alkylbenzenes can serve as the primary substrates to stimulate the transformation of benzene and p-xylene under anaerobic conditions. Benzene and p-xylene are more toxic than toluene and ethylbenzene, under the three terminal electron acceptors conditions, the degradation rates decreased with toluene > ethylbenzene > m-xylene > o-xylene > benzene > p-xylene. Nitrate was a more favorable electron acceptor compared to sulfate and ferric iron. The ratio between sulfate consumed and the loss of benzene, toluene, ethylbenzene, o-xylene, m-xylene, p-xylene was 4.44, 4.51, 4.42, 4.32, 4.37 and 4.23, respectively; the ratio between nitrate consumed and the loss of these substrates was 7.53, 6.24, 6.49, 7.28, 7.81, 7.61, respectively; the ratio between the consumption of ferric iron and the loss of toluene, ethylbenzene, o-xylene, m-xylene was 17.99, 18.04, 18.07, 17.97, respectively.

Heterogeneous aerobic benzene-degrading communities in oxygen-depleted groundwaters

A sandstone aquifer beneath a petrochemicals plant (SIReN site, UK) is heterogeneously contaminated with benzene and oxygen-depleted. Despite low redox potentials in three of the most contaminated groundwaters (benzene concentrations from 17.8 to 294 mg L(-1)), we observed aerobic benzene degradation in microcosms, indicating the presence in situ of a latent community of obligate aerobic microorganisms or an active community of facultative aerobes responding rapidly to oxygen ingress. Moreover, benzene degradation occurred at the ambient pH of 8.9 and 9.4, considerably more alkaline conditions than previously reported. 16S rRNA analyses showed that the groundwater microcosm communities were distinct from each other, despite sharing the function of aerobic benzene degradation. From DNA fingerprinting, one consortium was dominated by Acidovorax spp., another by Pseudomonas spp.; these benzene-degrading consortia were similar to the in situ communities, perhaps indicating that these organisms are active in situ and degrading benzene microaerophilically or by denitrification. Conversely, in the third sample, benzene degradation occurred only after the community changed from a Rhodoferax-dominated community to a mix of Rhodococcus and Hydrogenophaga spp. Four of the main benzene-degrading strains were brought into culture: Hydrogenophaga and Pseudomonas spp., and two strains of Rhodococcus erythropolis, a ubiquitous and metabolically versatile organism.

Rapid intrinsic biodegradation of benzene, toluene, and xylenes at the boundary of a gasoline-contaminated plume under natural attenuation

A groundwater plume contaminated with gasoline constituents [mainly benzene, toluene, and xylenes (BTX)] had been treated by pumping and aeration for approximately 10 years, and the treatment strategy was recently changed to monitored natural attenuation (MNA). To gain information on the feasibility of using MNA to control the spread of BTX, chemical and microbiological parameters in groundwater samples obtained inside and outside the contaminated plume were measured over the course of 73 weeks. The depletion of electron acceptors (i.e., dissolved oxygen, nitrate, and sulfate) and increase of soluble iron were observed in the contaminated zone. Laboratory incubation tests revealed that groundwater obtained immediately outside the contaminated zone (the boundary zone) exhibited much higher potential for BTX degradation than those in the contaminated zone and in uncontaminated background zones. The boundary zone was a former contaminated area where BTX were no longer detected. Denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR)-amplified bacterial 16S rRNA gene fragments revealed that DGGE profiles for groundwater samples obtained from the contaminated zone were clustered together and distinct from those from uncontaminated zones. In addition, unique bacterial rRNA types were observed in the boundary zone. These results indicate that the boundary zone in the contaminant plumes served as a natural barrier for preventing the BTX contamination from spreading out.

Methylation is the initial reaction in anaerobic naphthalene degradation by a sulfate-reducing enrichment culture

The sulfate-reducing culture N47 can utilize naphthalene or 2-methylnaphthalene as the sole carbon source and electron donor. Here we show that the initial reaction in the naphthalene degradation pathway is a methylation to 2-methylnaphthalene which then undergoes the subsequent oxidation to the central metabolite 2-naphthoic acid, ring reduction and cleavage. Specific metabolites occurring exclusively during anaerobic degradation of 2-methylnaphthalene were detected during growth on naphthalene, i.e. naphthyl-2-methyl-succinate and naphthyl-2-methylene-succinate. Additionally, all three enzymes involved in anaerobic degradation of 2-methylnaphthalene to 2-naphthoic acid that could be measured in vitro so far, i.e. naphthyl-2-methyl-succinate synthase, succinyl-CoA:naphthyl-2-methyl-succinate CoA-transferase and naphthyl-2-methyl-succinyl-CoA dehydrogenase were also detected in naphthalene-grown cells with similar activities. Induction experiments were performed to study the growth behaviour of the cell when transferred from naphthalene to 2-methylnaphthalene or vice versa. When the cells were transferred from naphthalene to 2-methylnaphthalene they grew immediately, indicating that no new enzymes had to be induced. On the contrary, the transfer of cells from 2-methylnaphthalene to naphthalene caused a lag-phase of almost 100 days demonstrating that an additional catabolic enzyme has to be activated in this case. We propose the methylation as a novel general mechanism of activation reactions in anaerobic degradation of unsubstituted aromatic hydrocarbons.

Anaerobic degradation of benzene, toluene, ethylbenzene, and xylene compounds by Dechloromonas strain RCB

Dechloromonas strain RCB has been shown to be capable of anaerobic degradation of benzene coupled to nitrate reduction. As a continuation of these studies, the metabolic versatility and hydrocarbon biodegradative capability of this organism were investigated. The results of these revealed that in addition to nitrate, strain RCB could alternatively degrade benzene both aerobically and anaerobically with perchlorate or chlorate [(per)chlorate] as a suitable electron acceptor. Furthermore, with nitrate as the electron acceptor, strain RCB could also utilize toluene, ethylbenzene, and all three isomers of xylene (ortho-, meta-, and para-) as electron donors. While toluene and ethylbenzene were completely mineralized to CO2, strain RCB did not completely mineralize para-xylene but rather transformed it to some as-yet-unidentified metabolite. Interestingly, with nitrate as the electron acceptor, strain RCB degraded benzene and toluene concurrently when the hydrocarbons were added as a mixture and almost 92 microM total hydrocarbons were oxidized within 15 days. The results of these studies emphasize the unique metabolic versatility of this organism, highlighting its potential applicability to bioremediative technologies.

Benzene Degradation Coupled with Chlorate Reduction in a Soil Column Study

Perchlorate and chlorate are electron acceptors that during reduction result in the formation of molecular oxygen. The produced oxygen can be used for activation of anaerobic persistent pollutants, like benzene. In this study chlorate was tested as potential electron acceptor to stimulate benzene degradation in anoxic polluted soil column. A chlorate amended benzene polluted soil column was operated over a period of 500 days. Benzene was immediately degraded in the column after start up, and benzene removal recovered completely after omission of chlorate or a too high influent chlorate concentration (22 mM). Mass balance calculations showed that per mole of benzene five mole of chlorate were reduced. At the end of the experiment higher loading rates were applied to measure the maximal benzene degradation rate in this system; a breakthrough of benzene was not observed. The average benzene degradation rate over this period was 31 micromol l(-1) h(-1) with a maximal of 78 micromol l(-1) h(-1). The high degradation rate and the necessity of chlorate indicate that oxygen produced during chlorate reduction indeed is used for the activation of benzene. This is the first column study where benzene biodegradation at a high rate coupled with anaerobic chlorate reduction is observed.

Treatment of gasoline-contaminated waters by advanced oxidation processes

In this study, the efficiency of advanced oxidative processes (AOPs) was investigated toward the degradation of aqueous solutions containing benzene, toluene and xylenes (BTX) and gasoline-contaminated waters. The results indicated that BTX can be effectively oxidized by near UV-assisted photo-Fenton process. The treatment permits almost total degradation of BTX and removal of more than 80% of the phenolic intermediates at reaction times of about 30 min. Preliminary investigations using water contaminated by gasoline suggest a good potentiality of the process for the treatment of large volumes of aqueous samples containing these polluting species. Heterogeneous photocatalysis and H2O2/UV system show lower degradation efficiency, probably due to the heterogeneous character of the TiO2-mediated system and lost of photonic efficiency of the H2O2/UV system in the presence of highly colored intermediated.

Groundwater contamination by chlorinated naphthalenes and related substances caused by activities of a former military base

Water samples derived from two different aquifer layers of six sampling sites were analysed by GC/MS in order to characterize a groundwater contamination caused by chemicals used for wood impregnation. Mono- and dichlorinated naphthalenes, chlorobenzo(b)thiophene, 1-chloro-4-naphthol, 1-chloronaphthoic acid, acenaphthene and methyled naphthalenes were identified as the main pollutants and quantified. 1-Chloro-4-naphthol and 1-chloronaphthoic acid are discussed as possible indicators for anaerobic degradation processes. Results of inorganic and compound specific stable carbon isotope analyses revealed only a minor degree of microbiological transformation. Thus, sorption was characterized as the main attenuation process within the aquifer affecting the contamination described.

Hydroxylation and carboxylation--two crucial steps of anaerobic benzene degradation by Dechloromonas strain RCB

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.

Anaerobic degradation of hexachlorocyclohexane isomers in liquid and soil slurry systems

Gamma-hexachlorocyclohexane (gamma-HCH or lindane), one of the most commonly used insecticides, has been mainly used in agriculture. Organochloride compounds are known to be highly toxic and persistent, causing serious water and soil pollution. The objective of the present study is the evaluation of the anaerobic degradation of alpha-, beta-, gamma-, delta-HCH in liquid and slurry cultures. The slurry system with anaerobic sludge appears as an effective alternative in the detoxification of polluted soils with HCH, as total degradation of the four isomers was attained. While alpha- and gamma-HCH disappeared after 20-40d, the most recalcitrant isomers: beta- and delta-HCH were only degraded after 102d. Intermediate metabolites of HCH degradation as pentachlorocyclohexane (PCCH), tetrachlorocyclohexene (TCCH), tri-, di- and mono-chlorobenzenes were observed during degradation time.

Metabolites detected during biodegradation of 13C6-benzene in nitrate-reducing and methanogenic enrichment cultures

The mechanism for anaerobic metabolism of benzene remains unknown. To date, there have been only a few studies reporting metabolites of anaerobic benzene biodegradation, in part because anaerobic benzene-degrading enrichment cultures are not very common and only two isolates have been characterized to date. Phenol and benzoate, metabolites consistent with benzene hydroxylation or benzene carboxylation, have been identified previously in mixed cultures, and more recently benzene methylation to toluene has been proposed as another possible mechanism for anaerobic benzene degradation. In this study, 13C6-benzene was added to nitrate-reducing and methanogenic enrichment cultures and specific 13C-labeled metabolites were monitored over time. The putative metabolites were detected by gas chromatography/mass spectrometry in ether extracts of 100-mL samples of culture taken at each time point. This method of analysis provided the sensitivity required to accurately quantify low concentrations of these compounds. In addition, benzoate trapping was used in an attemptto increase concentrations of upstream metabolites. In both cultures, in the presence and absence of unlabeled benzoate (trap), [ring-13C]-toluene and [ring-13C]benzoate were detected transiently during degradation. The data strongly support initial methylation of benzene to toluene, followed bytransformation to benzoate. Although benzene methylation has been proposed previously, this is the first direct evidence to supportthis pathway. In the methanogenic culture only, 13C6-phenol was also detected. The transient appearance of phenol, which appeared to be further transformed to benzoate, suggests that a pathway involving hydroxylation to phenol, as proposed in other studies, was also operative.

In situ assessment of biodegradation potential using biotraps amended with 13C-labeled benzene or toluene

Stable isotope fractionation analysis of an aquifer heavily contaminated with benzene (up to 850 mg L(-1)) and toluene (up to 50 mg L(-1)) at a former hydrogenation plant in Zeitz (Saxonia, Germany) has suggested that significant biodegradation of toluene was occurring. However, clear evidence of benzene biodegradation has been lacking at this site. Determining the fate of benzene is often a determining factor in regulatory approval of a risk-based management strategy. The objective of the work described here was the demonstration of a new tool that can be used to provide proof of biodegradation of benzene or other organics by indigenous microorganisms under actual aquifer conditions. Unique in situ biotraps containing Bio-Sep beads, amended with 13C-labeled or 12C nonlabeled benzene and toluene, were deployed at the Zeitz site for 32 days in an existing groundwater monitoring well and used to collect and enrich microbial biofilms. Lipid biomarkers or remaining substrate was extracted from the beads and analyzed by mass spectrometry and molecular methods. Isotopic analysis of the remaining amounts of 13C-labeled contaminants (about 15-18% of the initial loading) showed no alteration of the 12C/13C ratio during incubation. Therefore, no measurable exchange of labeled compounds in the beads by the nonlabeled compounds in the aquifer materials occurred. Isotopic ratio analysis of microbial lipid fatty acids (as methyl ester derivatives) from labeled benzene- and toluene-amended biotraps showed 13C enrichment in several fatty acids of up to delta (13C) 13400%o, clearly verifying benzene and toluene biodegradation and the transformation of the labeled carbon into biomass by indigenous organisms under aquifer conditions. Fatty acid profiles of total lipid fatty acids and the phospholipid fatty acid fraction and their isotopic composition showed significant differences between benzene- and toluene-amended biotraps, suggesting that different microbial communities were involved in the biodegradation of the two compounds.

Biodegradation of phenol and phenol-related compounds by psychrophilic and cold-tolerant alpine yeasts

We characterized 32 cold-adapted, psychrophilic and cold-tolerant, yeast strains isolated from alpine habitats with regard to their taxonomy, growth temperature profile, and ability to degrade phenol and 18 phenol-related mono-aromatic compounds at 10 degrees C. Twenty of the strains were identified by sequencing of the ribosomal ITS region as seven species of the basidiomycota: Cryptococcus terreus (three strains), Cryptococcus terricola (one strain), Rhodosporidium lusitaniae (two strains), Rhodotorula creatinivora (10 strains), Rhodotorula ingeniosa (one strain), Mastigobasidium intermedium (one strain), and Sporobolomyces roseus (two strains). Twelve strains sharing closely related ITS sequences could not be identified to the species level; according to their ITS sequence they are included in the Microbotryomycetidae. These 12 strains were psychrophilic (no growth at temperatures above 20 degrees C); one-third of these strains did not grow above 15 degrees C. None of the 32 strains utilized any of the highly volatile mono-aromatic compounds (benzene, toluene, ethylbenzene, nitrobenzene, o-xylene, m-xylene, and p-xylene) as the sole carbon source. Non/low volatile aromatic compounds were degraded in the following order: phenol>hydroquinone>resorcinol>benzoate>catechol>salicylate>>p-cresol>m-cresol. o-Cresol, guaiacol, p-nitrophenol, or p-nitrotoluene were not utilized for growth. R. creatinivora strains degraded up to seven compounds, whereas C. terricola and S. roseus strains degraded only two compounds. The toxicity of the compounds was determined via growth inhibition in the presence of toxicants and nutrients at 10 degrees C. R. creatinivora strains were characterized by higher IC50 values than other species, S. roseus was the most sensitive species. The most toxic compounds were the xylene isomers, ethylbenzene, p-nitrophenol, and m-cresol. There was a relation between the chemical structure of the compounds and their toxicity, whereas a relation between the toxicity of the compounds and the ability of the yeasts strains to utilize these compounds for growth was only detected in some cases.

Genomic and mechanistic insights into the biodegradation of organic pollutants

Several new methodologies have enabled recent studies on the microbial biodegradation mechanisms of organic pollutants. Culture-independent techniques for analysis of the genetic and metabolic potential of natural and model microbial communities that degrade organic pollutants have identified new metabolic pathways and enzymes for aerobic and anaerobic degradation. Furthermore, structural studies of the enzymes involved have revealed the specificities and activities of key catabolic enzymes, such as dioxygenases. Genome sequencing of several biodegradation-relevant microorganisms have provided the first whole-genome insights into the genetic background of the metabolic capability and biodegradation versatility of these organisms. Systems biology approaches are still in their infancy, but are becoming increasingly helpful to unravel, predict and quantify metabolic abilities within particular organisms or microbial consortia.