Thermophilic biodegradation of BTEX by two consortia of anaerobic bacteria

A review on anaerobic microorganisms isolated from oil reservoirs

The Role of microorganisms in the petroleum industry is wide-ranging. To understand the role of microorganisms in hydrocarbon transformation, identification of such microorganisms is vital, especially the ones capable of in situ degradation. Microorganisms play a pivotal role in the degradation of hydrocarbons and remediation of heavy metals. Anaerobic microorganisms such as Sulphate Reducing Bacteria (SRB), responsible for the production of hydrogen sulphide (H₂S) within the reservoir, reduces the oil quality by causing reservoir souring and reduction in oil viscosity. This paper reviews the diversity of SRB, methanogens, Nitrogen Reducing Bacteria (NRB), and fermentative bacteria present in oil reservoirs. It also reviews the extensive diversity of these microorganisms, their applications in petroleum industries, characteristics and adaptability to survive in different conditions, the potential to alter the petroleum hydrocarbons properties, the propensity to petroleum hydrocarbon degradation, and remediation of metals.

Aerobic and anaerobic enrichment cultures highlight the pivotal role of facultative anaerobes in soil hydrocarbon degradation

Aliphatic and aromatic hydrocarbons are ubiquitous in the environment due to natural and anthropogenic processes. Under aerobic conditions hydrocarbons can be rapidly biodegraded but oxygenated environments often quickly become anaerobic when microbial respiration is coupled to contaminant oxidation. Most studies in literature usually focus on the initial microbial diversity of the hydrocarbon impacted environment and examine either aerobic or anaerobic conditions for enrichment. Hence, the aim of the present study was to enrich bacterial consortiums from two diesel impacted soil samples under both these conditions to assess the enrichment diversities and hydrocarbon degradation potentials. This would shed light upon how an environmental population shift would correlate to oxygen intrusion and depletion and still continue hydrocarbon degradation. Analysis of the 16S rRNA gene sequences showcases the different microbial populations that could emerge as the environmental factors change, resulting in different populations that are still capable of hydrocarbon degradation. Microbial diversity analysis also highlights the role of facultative anaerobic bacteria like Pseudomonas spp. and Citrobacter spp. in maintaining hydrocarbon degradation. This study shows that microorganisms capable of surviving under both oxic and anoxic (aerobic and anaerobic) conditions are the most crucial to the long term degradation of hydrocarbons in the environment.

Life in the slow lane; biogeochemistry of biodegraded petroleum containing reservoirs and implications for energy recovery and carbon management

Our understanding of the processes underlying the formation of heavy oil has been transformed in the last decade. The process was once thought to be driven by oxygen delivered to deep petroleum reservoirs by meteoric water. This paradigm has been replaced by a view that the process is anaerobic and frequently associated with methanogenic hydrocarbon degradation. The thermal history of a reservoir exerts a fundamental control on the occurrence of biodegraded petroleum, and microbial activity is focused at the base of the oil column in the oil water transition zone, that represents a hotspot in the petroleum reservoir biome. Here we present a synthesis of new and existing microbiological, geochemical, and biogeochemical data that expands our view of the processes that regulate deep life in petroleum reservoir ecosystems and highlights interactions of a range of biotic and abiotic factors that determine whether petroleum is likely to be biodegraded in situ, with important consequences for oil exploration and production. Specifically we propose that the salinity of reservoir formation waters exerts a key control on the occurrence of biodegraded heavy oil reservoirs and introduce the concept of palaeopickling. We also evaluate the interaction between temperature and salinity to explain the occurrence of non-degraded oil in reservoirs where the temperature has not reached the 80-90°C required for palaeopasteurization. In addition we evaluate several hypotheses that might explain the occurrence of organisms conventionally considered to be aerobic, in nominally anoxic petroleum reservoir habitats. Finally we discuss the role of microbial processes for energy recovery as we make the transition from fossil fuel reliance, and how these fit within the broader socioeconomic landscape of energy futures.

Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus

The thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain VC-16 (DSM 4304), which is known to oxidize fatty acids and n-alkenes, was shown to oxidize saturated hydrocarbons (n-alkanes in the range C10-C21) with thiosulfate or sulfate as a terminal electron acceptor. The amount of n-hexadecane degradation observed was in stoichiometric agreement with the theoretically expected amount of thiosulfate reduction. One of the pathways used by anaerobic microorganisms to activate alkanes is addition to fumarate that involves alkylsuccinate synthase as a key enzyme. A search for genes encoding homologous enzymes in A. fulgidus identified the pflD gene (locus-tag AF1449) that was previously annotated as a pyruvate formate lyase. A phylogenetic analysis revealed that this gene is of bacterial origin and was likely acquired by A. fulgidus from a bacterial donor through a horizontal gene transfer. Based on three-dimensional modeling of the corresponding protein and molecular dynamic simulations, we hypothesize an alkylsuccinate synthase activity for this gene product. The pflD gene expression was upregulated during the growth of A. fulgidus on an n-alkane (C16) compared with growth on a fatty acid. Our results suggest that anaerobic alkane degradation in A. fulgidus may involve the gene pflD in alkane activation through addition to fumarate. These findings highlight the possible importance of hydrocarbon oxidation at high temperatures by A. fulgidus in hydrothermal vents and the deep biosphere.

Effect of external voltage on Pseudomonas putida F1 in a bio electrochemical cell using toluene as sole carbon and energy source

A bio electrochemical cell (BEC) was constructed as a typical two-chamber microbial fuel cell (MFC), except that it was operated under external voltage instead of constant resistance as in an MFC. The anode chamber contained a pure culture of Pseudomonas putida F1 grown in a minimal medium containing toluene as the sole carbon and energy source. Operating the BEC under external voltages of 75, 125, 175, 250 and 500 mV (versus an Ag/AgCl reference electrode) led to increased bacterial cell growth to an OD(600) of 0.62-0.75, while the control BEC, which was not connected to external voltage, reached an OD(600) of only 0.3. Examination of the current generated under external voltages of 75, 125, 175, 250 and 500 mV showed that the maximal currents were 11, 23, 28, 54 and 94 mA m(-2), respectively. Cyclic voltammetry experiments demonstrated an anodic peak at 270 mV, which may imply oxidation of a vital molecule. The average residual toluene concentration after 147 h in the BEC operated under external voltage was 22 %, whereas in the control BEC it was 81 %. Proteome analysis of bacterial cells grown in the BEC (125 mV) revealed two groups of proteins, which are ascribed to charge transfer in the bacterial cells and from the cell to the electrode. In conclusion, operating the BEC at 75-500 mV enabled growth of a pure culture of P. putida F1 and toluene degradation even in an oxygen-limited environment.

Anaerobic oxidation of benzene by the hyperthermophilic archaeon Ferroglobus placidus

Anaerobic benzene oxidation coupled to the reduction of Fe(III) was studied in Ferroglobus placidus in order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions. F. placidus conserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor. The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [(14)C]benzene to [(14)C]carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III). Benzoate, but not phenol or toluene, accumulated at low levels during benzene metabolism, and [(14)C]benzoate was produced from [(14)C]benzene. Analysis of gene transcript levels revealed increased expression of genes encoding enzymes for anaerobic benzoate degradation during growth on benzene versus growth on acetate, but genes involved in phenol degradation were not upregulated during growth on benzene. A gene for a putative carboxylase that was more highly expressed in benzene- than in benzoate-grown cells was identified. These results suggest that benzene is carboxylated to benzoate and that phenol is not an important intermediate in the benzene metabolism of F. placidus. This is the first demonstration of a microorganism in pure culture that can grow on benzene under strict anaerobic conditions and for which there is strong evidence for degradation of benzene via clearly defined anaerobic metabolic pathways. Thus, F. placidus provides a much-needed pure culture model for further studies on the anaerobic activation of benzene in microorganisms.

Biochemistry, physiology and biotechnology of sulfate-reducing bacteria

Chemolithotrophic bacteria that use sulfate as terminal electron acceptor (sulfate-reducing bacteria) constitute a unique physiological group of microorganisms that couple anaerobic electron transport to ATP synthesis. These bacteria (220 species of 60 genera) can use a large variety of compounds as electron donors and to mediate electron flow they have a vast array of proteins with redox active metal groups. This chapter deals with the distribution in the environment and the major physiological and metabolic characteristics of sulfate-reducing bacteria (SRB). This chapter presents our current knowledge of soluble electron transfer proteins and transmembrane redox complexes that are playing an essential role in the dissimilatory sulfate reduction pathway of SRB of the genus Desulfovibrio. Environmentally important activities displayed by SRB are a consequence of the unique electron transport components or the production of high levels of H(2)S. The capability of SRB to utilize hydrocarbons in pure cultures and consortia has resulted in using these bacteria for bioremediation of BTEX (benzene, toluene, ethylbenzene and xylene) compounds in contaminated soils. Specific strains of SRB are capable of reducing 3-chlorobenzoate, chloroethenes, or nitroaromatic compounds and this has resulted in proposals to use SRB for bioremediation of environments containing trinitrotoluene and polychloroethenes. Since SRB have displayed dissimilatory reduction of U(VI) and Cr(VI), several biotechnology procedures have been proposed for using SRB in bioremediation of toxic metals. Additional non-specific metal reductase activity has resulted in using SRB for recovery of precious metals (e.g. platinum, palladium and gold) from waste streams. Since bacterially produced sulfide contributes to the souring of oil fields, corrosion of concrete, and discoloration of stonework is a serious problem, there is considerable interest in controlling the sulfidogenic activity of the SRB. The production of biosulfide by SRB has led to immobilization of toxic metals and reduction of textile dyes, although the process remains unresolved, SRB play a role in anaerobic methane oxidation which not only contributes to carbon cycle activities but also depletes an important industrial energy reserve.

Treatment of groundwater contaminated with PAHs, gasoline hydrocarbons, and methyl tert-butyl ether in a laboratory biomass-retaining bioreactor

In this study, we investigated the treatability of co-mingled groundwater contaminated with polycyclic aromatic hydrocarbons (PAHs), gasoline hydrocarbons, and methyl tert-butyl ether (MtBE) using an ex-situ aerobic biotreatment system. The PAHs of interest were naphthalene, methyl-naphthalene, acenaphthene, acenaphthylene, and carbazole. The gasoline hydrocarbons included benzene, toluene, ethyl benzene, and p-xylene (BTEX). Two porous pot reactors were operated for a period of 10 months under the same influent contaminant concentrations. The contaminated groundwater was introduced into the reactors at a flow rate of 4 and 9 l/day, resulting in a hydraulic retention time (HRT) of 32 and 15 h, respectively. In both reactors, high removal efficiencies were achieved for the PAHs (>99%), BTEX and MtBE (>99.7%). All the PAHs of interest and the four BTEX compounds were detected at concentrations less than 1 mug/l throughout the study duration. Effluent MtBE from both reactors was observed at higher levels; nevertheless, its concentration was lower than the 5 mug/l Drinking Water Advisory for MtBE implemented in California.

Recent advances in petroleum microbiology

Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times (<60 s) are being used effectively. Microbes are being injected into partially spent petroleum reservoirs to enhance oil recovery. However, these microbial processes have not exhibited consistent and effective performance, primarily because of our inability to control conditions in the subsurface environment. Microbes may be exploited to break stable oilfield emulsions to produce pipeline quality oil. There is interest in replacing physical oil desulfurization processes with biodesulfurization methods through promotion of selective sulfur removal without degradation of associated carbon moieties. However, since microbes require an environment containing some water, a two-phase oil-water system must be established to optimize contact between the microbes and the hydrocarbon, and such an emulsion is not easily created with viscous crude oil. This challenge may be circumvented by application of the technology to more refined gasoline and diesel substrates, where aqueous-hydrocarbon emulsions are more easily generated. Molecular approaches are being used to broaden the substrate specificity and increase the rates and extents of desulfurization. Bacterial processes are being commercialized for removal of H(2)S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.

Determination of benzylsuccinic acid in gasoline-contaminated groundwater by solid-phase extraction coupled with gas chromatography-mass spectrometry

Benzylsuccinic acid (BSA) and methylbenzylsuccinic acid (methyl-BSA) are unambiguous biotransformation products resulting from anaerobic toluene and xylene biodegradation, respectively. A solid-phase extraction method based on polystyrene-divinylbenzene sorbent was developed for the quantitative BSA determination in groundwater samples as an alternative to liquid-liquid extraction. Gas chromatography coupled with mass spectrometry was used for separation and detection. The recovery from spiked 11 groundwater samples was 88 to 100%. The precision of the method, indicated by the relative standard deviation, was +/- 4% and the method detection limit was 0.2 microg/l. The concentration of BSA and methyl-BSA in groundwater samples from anaerobic BTEX (benzene, toluene, ethylbenzene and xylenes)-contaminated sites ranged from below the detection limit (3 microg/l) to 155 microg/l.

Use of stable isotopes to identify benzoate as a metabolite of benzene degradation in a sulphidogenic consortium

An enriched sulphidogenic consortium capable of mineralizing benzene was used to study the metabolic pathway of anaerobic benzene degradation. Benzoate was detected in active cultures and benzene was confirmed to be the source of this benzoate by the addition of deuterated benzene (D6) and subsequent detection of deuterated benzoate (D5) in active cultures but not in autoclaved controls. Benzoate was utilized by this culture at 1/12 the rate of benzene, while its presence did not inhibit benzene utilization. The benzene utilization rate was reduced, however, in the presence of 2-fluorobenzoate. When the culture was supplemented with [(13)C]-bicarbonate, the carboxyl group on benzoate was not labelled with [(13)C]-carbon, suggesting that this transformation relies on a more complex set of reactions than simple addition of carbonate.

Anaerobic degradation of aromatic compounds coupled to Fe(III) reduction by Ferroglobus placidus

Aromatic compounds are an important component of the organic matter in some of the anaerobic environments that hyperthermophilic microorganisms inhabit, but the potential for hyperthermophilic microorganisms to metabolize aromatic compounds has not been described previously. In this study, aromatic metabolism was investigated in the hyperthermophile Ferroglobus placidus. F. placidus grew at 85 degrees C in anaerobic medium with a variety of aromatic compounds as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. Growth coincided with Fe(III) reduction. Aromatic compounds supporting growth included benzoate, phenol, 4-hydroxybenzoate, benzaldehyde, p-hydroxybenzaldehyde and t-cinnamic acid (3-phenyl-2-propenoic acid). These aromatic compounds did not support growth when nitrate was provided as the electron acceptor, even though nitrate supports the growth of this organism with Fe(II) or H2 as the electron donor. The stoichiometry of benzoate and phenol uptake and Fe(III) reduction indicated that F. placidus completely oxidized these aromatic compounds to carbon dioxide, with Fe(III) serving as the sole electron acceptor. This is the first example of an Archaea that can anaerobically oxidize an aromatic compound. These results also demonstrate for the first time that hyperthermophilic microorganisms can anaerobically oxidize aromatic compounds and suggest that hyperthermophiles may metabolize aromatic compounds in hot environments such as the deep hot subsurface and in marine and terrestrial hydrothermal zones in which Fe(III) is available as an electron acceptor.

Signature metabolites attesting to the in situ attenuation of alkylbenzenes in anaerobic environments

Accurate assessment of the fate of hydrocarbons spilt in aquifers is essential for gauging associated health and ecological risks. Regulatory pressure to actively remediate such contaminated ecosystems can be substantially diminished if solid evidence for in situ microbial destruction of pollutants is obtained. In laboratory incubations, sediment-associated microorganisms from a gas condensate-contaminated aquifer anaerobically biodegraded toluene, ethylbenzene, xylene, and toluic acid isomers with stoichiometric amounts of sulfate consumed or methane produced. The activation of the alkylated aromatic contaminants involved conversion to their corresponding benzylsuccinic acid derivatives, a reaction known to occur for toluene and m-xylene decay, but one previously unrecognized for ethylbenzene, o- and p-xylene, and m-toluate metabolism. Benzylsuccinates were further biodegraded to toluates, phthalates, and benzoate. In laboratory incubations, these metabolites were transiently produced. Several of the metabolites were also detected in groundwater samples from an aquifer where alkylbenzene concentrations decreased over time, suggesting that anaerobic microbial metabolism of these contaminants also occurs in situ. Our studies confirm the utility of the aforementioned compounds as signature metabolites attesting to the natural attenuation of aromatic hydrocarbons in anaerobic environments.

Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria

Various alkylbenzenes were depleted during growth of an anaerobic, sulfate-reducing enrichment culture with crude oil as the only source of organic substrates. From this culture, two new types of mesophilic, rod-shaped sulfate-reducing bacteria, strains oXyS1 and mXyS1, were isolated with o-xylene and m-xylene, respectively, as organic substrates. Sequence analyses of 16S rRNA genes revealed that the isolates affiliated with known completely oxidizing sulfate-reducing bacteria of the delta subclass of the class Proteobacteria. Strain oXyS1 showed the highest similarities to Desulfobacterium cetonicum and Desulfosarcina variabilis (similarity values, 98.4 and 98.7%, respectively). Strain mXyS1 was less closely related to known species, the closest relative being Desulfococcus multivorans (similarity value, 86.9%). Complete mineralization of o-xylene and m-xylene was demonstrated in quantitative growth experiments. Strain oXyS1 was able to utilize toluene, o-ethyltoluene, benzoate, and o-methylbenzoate in addition to o-xylene. Strain mXyS1 oxidized toluene, m-ethyltoluene, m-isoproyltoluene, benzoate, and m-methylbenzoate in addition to m-xylene. Strain oXyS1 did not utilize m-alkyltoluenes, whereas strain mXyS1 did not utilize o-alkyltoluenes. Like the enrichment culture, both isolates grew anaerobically on crude oil with concomitant reduction of sulfate to sulfide.