Bacterial Hydrocarbon Degradation Research Articles

Bacterial Degradation of Petroleum Hydrocarbons in Saudi Arabia.

The Kingdom of Saudi Arabia (KSA) is the leading oil-exploring and -exploiting country in the world. As a result, contamination of the environment by petroleum products (mainly hydrocarbons) is common, necessitating strategies for their removal from the environment. Much work has been conducted on bacterial degradation of hydrocarbons in the KSA. This review comprehensively analyzed 43 research investigation articles on bacterial hydrocarbon degradation, mainly polyaromatic hydrocarbons (PAHs) within the KSA. More than 30 different bacterial genera were identified that were capable of degrading simple and complex PAHs, including benzo[a]pyrene and coronene. Different strategies for selecting and isolating these bacterial strains and their advantages and disadvantages were highlighted. The review also discussed the origins of sample inocula and the contributions of various research groups to this field. PAH metabolites produced by these bacteria were presented, and biochemical pathways of PAH degradation were proposed. More importantly, research gaps that could enrich our understanding of petroleum product biodegradation mechanisms were highlighted. Overall, the information presented in this paper will serve as a baseline for further research on optimizing bioremediation strategies in all petroleum-contaminated environments.

Recent Advances in Bacterial Degradation of Hydrocarbons

Hydrocarbons occur in fossil fuels such as crude oil and consist mainly of hydrogen and carbon. Although they are natural chemicals, crude oil refining results in commercial products with new physico-chemical properties, which can increase their complexity and toxicity, and hamper their degradation. The presence of biodiverse natural microbial communities is a prerequisite for an effective homeostatic response to the various hydrocarbons, that contaminate ecosystems. However, their removal depends on the compartment contaminated (water, sediment, soil), their molecular weight, and their toxicity not hampering microbial activity. This paper reports different bacterial species involved in the biodegradation of aliphatic and aromatic hydrocarbons. Hydrocarbon contamination is generally due to the co-presence of a mixture of these chemicals, and their removal from the environment cannot rely on only a single species but generally requires bacterial consortia. Versatile bacterial metabolism relies on specific genes encoding the key enzymes involved in the peripheral metabolic and central metabolic pathways for degrading aliphatic and polycyclic aromatic hydrocarbons. Although microbial metabolism can have the potential for natural attenuation of these contaminants, hydrocarbon bioremediation, through biostimulation (e.g., use of surfactants, plants, earthworms, and nanoparticles) and bioaugmentation, can be a valid tool for removing them from actually contaminated soil, freshwater, groundwater, and seawater.

Bioaugmentation-Enhanced Remediation of Crude Oil Polluted Water in Pilot-Scale Floating Treatment Wetlands

Floating treatment wetlands (FTWs) are cost-effective systems for the remediation of polluted water. In FTWs, the metabolic activity of microorganisms associated with plants is fundamental to treatment efficiency. Bioaugmentation, the addition of microorganisms with pollutant-degrading capabilities, appears to be a promising means to enhance the treatment efficiency of FTWs. Here, we quantified the effect of bioaugmentation with a four-membered bacterial consortium on the remediation of water contaminated with crude oil in pilot-scale FTWs planted with Phragmites australis or Typha domingensis. The bacteria had been isolated from the endosphere and rhizosphere of various plants and carry the alkane hydroxylase gene, alkB, involved in aerobic hydrocarbon degradation. During a treatment period of 36 days, FTWs planted with P. australis achieved a reduction in hydrocarbon concentration from 300 mg/L to 16 mg/L with and 56 mg/L without bioaugmentation. In the FTWs planted with T. domingensis, respective hydrocarbon concentrations were 46 mg/L and 84 mg/L. The inoculated bacteria proliferated in the rhizoplane and in the plant interior. Copy numbers of the alkB gene and its mRNA increased over time in plant-associated samples, suggesting increased bacterial hydrocarbon degradation. The results show that bioaugmentation improved the treatment of oil-contaminated water in FTWs by at least a factor of two, indicating that the performance of full-scale systems can be improved at only small costs.

Effects of a Simulated Acute Oil Spillage on Bacterial Communities from Arctic and Antarctic Marine Sediments.

Background: The bacterial community responses to oil spill events are key elements to predict the fate of hydrocarbon pollution in receiving aquatic environments. In polar systems, cold temperatures and low irradiance levels can limit the effectiveness of contamination removal processes. In this study, the effects of a simulated acute oil spillage on bacterial communities from polar sediments were investigated, by assessing the role of hydrocarbon mixture, incubation time and source bacterial community in selecting oil-degrading bacterial phylotypes. Methods: The bacterial hydrocarbon degradation was evaluated by gas chromatography. Flow cytometric and fingerprinting profiles were used to assess the bacterial community dynamics over the experimental incubation time. Results: Direct responses to the simulated oil spill event were found from both Arctic and Antarctic settings, with recurrent bacterial community traits and diversity profiles, especially in crude oil enrichment. Along with the dominance of Pseudomonas spp., members of the well-known hydrocarbon degraders Granulosicoccus spp. and Cycloclasticus spp. were retrieved from both sediments. Conclusions: Our findings indicated that polar bacterial populations are able to respond to the detrimental effects of simulated hydrocarbon pollution, by developing into a more specialized active oil degrading community.

Hydrophobicity-responsive engineered mesoporous silica nanoparticles: application in the delivery of essential nutrients to bacteria combating oil spills.

Facile chemical modification of mesoporous silica particles allows the production of gated reservoir systems capable of hydrophobicity-triggered release. Applied to the delivery of nutrients specifically to an oil phase, the systems developed have been shown to reliably assist the bacterial degradation of hydrocarbons. The gated system developed, made of C18 hydrocarbon chains, is demonstrated to be in a closed collapsed state in an aqueous environment, yet opens up through solvation by lipophilic alkanes and releases its content on contact with the oil phase.

Nontronite-enhanced biodegradation of Deepwater Horizon crude oil by Alcanivorax borkumensis

Abstract Laboratory experiments demonstrate that adding clay to crude oil pollution generally has a positive effect on the bacterial degradation of hydrocarbons, largely by maintaining nutrient supply. The objective of this investigation was to constrain the influence of nontronite (Fe-smectite) based clay flakes on the biodegradation of Mississippi Canyon (MC 252) crude oil from the Deepwater Horizon spill in the presence of Alcanivorax borkumensis: a dominant alkane degrader of oil pollution. Containing large amounts of Fe, dioctahedral nontronite is of particular interest as a potential source for this nutrient. Based on 37 day (888 h) long agitated batch experiments containing oil-polluted nutrient-poor seawater, the addition of nontronite clay increased the bacteria population by a factor of up to 5, reduced alkane compounds by 57.7% compared to the 45.3% reduction achieved without clay additives and stimulated the breakdown of C13-C28 molecules by oxygenase reactions. With the exception of naphthalene compounds, which were depleted largely by evaporation, a reduction in alkylated polycyclic aromatic hydrocarbons was also observed suggestive of additional biodegradation reactions. In contrast, the non-alkylated polycyclic aromatic hydrocarbons were little influenced by the presence of the clay. Although control experiments indicate that Fe2+ did not act as a limiting nutrient under the oxygenated conditions of experimentation, our results confirm that nontronite clay represents a useful amendment for enhancing the biodegradation and acts in a similar way to other smectites by sustaining nutrient supply.

Experimental study of clay-hydrocarbon interactions relevant to the biodegradation of the Deepwater Horizon oil from the Gulf of Mexico

Adding clay to marine oil pollution represents a promising approach to enhance bacterial hydrocarbon degradation in nutrient poor waters. In this study, three types of regionally available clays (Ca-bentonite, Fuller's Earth and kaolin) were tested to stimulate the biodegradation of source and weathered oil collected from the Deepwater Horizon spill. The weathered oil showed little biodegradation prior to experimentation and was extensively degraded by bacteria in the laboratory in a similar way as the alkane-rich source oil. For both oils, the addition of natural clay-flakes showed minor enhancement of oil biodegradation compared to the non-clay bearing control, but the clay-oil films did limit evaporation. Only alkanes of a molecular weight (MW) > 420 showed significant reduction by enhanced biodegradation following natural clay treatment. In contrast, all fertilized clay flakes showed major bacterial degradation of the oil, with a 6–10 times reduction in alkane content, and an up to 8 fold increase in the rate of O2 consumption. Compared to the control, such treatment showed particular reduction of longer chained alkanes (MW > 226). The application of natural and fertilized clay flakes also showed selective reduction of PAHs, mainly in the MW range of 200–300, but without significant change in the toxicity indices measured. These results imply that a large variety of clays may be used to boost oil biodegradation by aiding attachment of fertilizing nutrients to the oil.

Effects of illuminance and nutrients on bacterial photo-physiology of hydrocarbon degradation

Bacterial photophysiology was previously limited to photoautotrophs. The discovery of bacteriophytochromes in non-photoautotrophs raised a question whether these non-photoautotrophs are affected by the presence or absence of light? In this research work for the first time, bacterial hydrocarbon degradation and biomass production was studied under the influence of nutrients, illuminance (light flux) and time. An experimental model was designed, with six isolated bacterial strains (Pseudomonas poae BA1, Pseudomonas rhizosphaerae BP3, Bacillus thuringiensis BG3, Acinetobacter bouvetii BP18, Pseudomonas proteolytica BG31 and Stenotrophomonas rhizophila BG32) under four different conditions of nutrient media and illuminance at three time intervals of 15, 30, and 45days without shaking. All strains showed statistically higher hydrocarbon degradation under nutrient rich, dark conditions. Highest biodegradation (80.8, 79.4, and 78.7mg) was observed in BG31, BG17 and BG3 respectively. Nutrient rich media along with dark conditions improved the biomass production, and when media was nutrient deprived, higher biomass was produced in the presence of light. This work proved that light and nutrients significantly affect bacterial populations and hydrocarbon degradation. The optimal use of these parameters could facilitate to achieve the goal of remediation of hydrocarbon contaminated sites.

Bioremediation of Petroleum Sludge

Bioremediation, or the use of micro-organisms to decontaminate soil or groundwater, is being increasingly seen as an effective, environmentfriendly treatment for oilcontaminated sites. Many reports indicated that, large quantities of organic and inorganic compounds are released into the environments every year as results of human activities causing serious environmental problems. Among those problems are oil contamination of soil and water from industrial sources and other activity, which create a great environmental hazard [1]. Petroleum hydrocarbon continues to be used as principle source of energy and hence a large global environmental pollutant. Petroleum is a complex mixture of non-aqueous and hydrophobic components. Many of these components are toxic, mutagenic and carcinogenic [2]. Therefore, the release to the environment is strictly controlled and they classified as priority environmental pollutant by US Environmental Protection Agency, due to their adverse impaction human health and environment [3]. Various physiochemical treatments techniques have been developed to clean up contaminated soil such as incineration, thermal desorption, chemical oxidation, immobilization and solvent extraction [4]. In general such treatments are more expensive, energy intensive and not sustainable with respect to their environmental impact which includes damage to the soil structure and toxicity issue associated with chemical additives [5]. Many of these techniques simply dilute or sequester the contaminants and do not eliminate the problem [6]. In general such treatments are more expensive, energy intensive and not sustainable with respect to their environmental impact which includes damage to the soil structure and toxicity issue associated with chemical additives. Traditionally, petroleum hydrocarbon contaminated soils have been dealt with by excavation and disposal to landfill. However, as landfills have become scarcer and more cost prohibition, this method has become less feasible [7]. These limitations have been the basis of search for more economical and environmentally sound approaches to remediate contaminated soil. Biological treatment of organic pollutants is a promising field of research, which gives reliable, simple and cheap technologies over chemical and physical process [8]. Bioremediation has become a major method employed in the restoration of oil polluted environments, and attempts to accelerate the natural hydrocarbon degradation rates by overcoming factors that limit bacterial hydrocarbon degradation activities [8,9]. Microorganisms, namely heterotrophic bacteria and fungi have evolved a tremendous ability to metabolize simple and complex hydrocarbon contaminants [10]. By harnessing their metabolic ability, it is possible to remediate contaminated environments, a technique referred to as bioremediation [11].

Identification and characterisation of oil sludge degrading bacteria isolated from compost

AbstractCompounds present in oil sludge such as polycyclic aromatic hydrocarbons (PAHs) are known to be cytotoxic, mutagenic and potentially carcinogenic. Microorganisms including bacteria and fungi have been reported to degrade oil sludge components to innocuous compounds such as carbon dioxide, water and salts. In the present study, we isolated different bacteria with PAH-degrading capabilities from compost prepared from oil sludge and animal manures. These bacteria were isolated on a mineral base medium and mineral salt agar plates. A total of 31 morphologically distinct isolates were carefully selected from 5 different compost treatments for identification using polymerase chain reaction (PCR) of the 16S rRNA gene with specific primers (universal forward 16S-P1 PCR and reverse 16S-P2 PCR). The amplicons were sequenced and sequences were compared with the known nucleotides from the GenBank. The phylogenetic analyses of the isolates showed that they belong to 3 different clades; Firmicutes, Proteobacteria and Actinobacteria. These bacteria identified were closely related to the generaBacillus, Arthrobacter, Staphylococcus, Brevibacterium, Variovorax, Paenibacillus, Ralstonia and Geobacillus.The results showed thatBacillus species were predominant in all composts. Based on the results of the degradation of the PAHs in the composts and results of previous studies on bacterial degradation of hydrocarbons in oil, the characteristics of these bacterial isolates suggests that they may be responsible for the breakdown of PAHs of different molecular weights in the composts. Thus, they may be potentially useful for bioremediation of oil sludge during compost bioremediation.

Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs

Biodegradation of crude oil in subsurface petroleum reservoirs has adversely affected the majority of the world's oil, making recovery and refining of that oil more costly. The prevalent occurrence of biodegradation in shallow subsurface petroleum reservoirs has been attributed to aerobic bacterial hydrocarbon degradation stimulated by surface recharge of oxygen-bearing meteoric waters. This hypothesis is empirically supported by the likelihood of encountering biodegraded oils at higher levels of degradation in reservoirs near the surface. More recent findings, however, suggest that anaerobic degradation processes dominate subsurface sedimentary environments, despite slow reaction kinetics and uncertainty as to the actual degradation pathways occurring in oil reservoirs. Here we use laboratory experiments in microcosms monitoring the hydrocarbon composition of degraded oils and generated gases, together with the carbon isotopic compositions of gas and oil samples taken at wellheads and a Rayleigh isotope fractionation box model, to elucidate the probable mechanisms of hydrocarbon degradation in reservoirs. We find that crude-oil hydrocarbon degradation under methanogenic conditions in the laboratory mimics the characteristic sequential removal of compound classes seen in reservoir-degraded petroleum. The initial preferential removal of n-alkanes generates close to stoichiometric amounts of methane, principally by hydrogenotrophic methanogenesis. Our data imply a common methanogenic biodegradation mechanism in subsurface degraded oil reservoirs, resulting in consistent patterns of hydrocarbon alteration, and the common association of dry gas with severely degraded oils observed worldwide. Energy recovery from oilfields in the form of methane, based on accelerating natural methanogenic biodegradation, may offer a route to economic production of difficult-to-recover energy from oilfields.

Evidence for bacterial degradation of hydrocarbons in uranium deposits

ABSTRACTThe biodegradation of free hydrocarbons migrated in reservoir faaes has often been observed in petroleum exploration. This bacterial alteration is characterized by the progressive removal of different classes of hydrocarbons. One of the most important consequences of biodegradation is the reduction of sulphate, as noted in several Pb‐Zn deposits. Biodegradation of oils spatially associated with uranium deposits has also been observed in Lodeve (France), Grand Canyon (Arizona, USA), Temple Mountain (Utah, USA) and leads to the transformation of fluid oils into solid bitumens. Within this study emphasis has been laid on the relationships between the effects of biodegradation on organic matter (oxidation or aromatization) and the nature of aqueous solutions analysed in fluid inclusions trapped in authigenic minerals. Different mechanisms are proposed to explain the transformations of organic matter during biodegradation and their possible links with ore‐forming processes.

Post-Hydrocarbon Migration Deep Burial Diagenesis of Smackover Formation, Black Creek Field, Wiggins Arch, Mississippi Salt Basin: ABSTRACT

The Smackover Formation is buried to over 6 km in Black Creek field and exhibits diagenetic phases unique to deep burial. These include replacement of sulfates by calcite, pore-fill calcite cement, silicification, and elemental sulfur as cement. The above diagenetic products are the result of thermal reduction of sulfates and thermal degradation of hydrocarbons and have formed at temperatures greater than 140/degrees/C. Calcite replaces anhydrite in two textural forms, one of which is pseudomorphic. Pore-fill calcite cement contains inclusions of pyrobitumen and heals cracks formed in the pyrobitumen due to high thermal maturity. This indicates that calcite cement postdates bitumen formation. Silicification is a major deep burial event. Micron to millimetersize crystals of quartz replace the host carbonate rock as well as other deep burial diagenetic phases. Elemental sulfur occurs as inclusions in incompletely destroyed sulfates and as pore-fill cement. In both cases it exhibits extensive bubble-shaped cavities similar to pumiceous texture found in volcanic rocks. This indicates that elemental sulfur was possibly crystallized rapidly from a liquid sulfur while the cores were being taken. Similar diagenetic products are formed by low-temperature (< 80/degrees/C) bacterial reduction of sulfates and bacterial degradation of hydrocarbons. However, carbon isotopic composition of calcite, sulfurmore » isotopic composition of elemental sulfur, and textural characteristics of elemental sulfur produced by the two diagenetic processes are significantly different.« less

The Tsesis oil spill impact on the pelagic ecosystem

On 26 October, 1977, the tanker Tsesis grounded in the Swedish archipelago, 65 km south of Stockholm (northern Baltic proper, 59°N, 18°E). The Tsesis carried 17575 t of No. 5 fuel oil. The total spill was estimated as being somewhat more than 1000 t, of which about 600–700 t were recovered, thus leaving about 300 t in the environment. The spill occurred only about 5 km east of the Askö Laboratory, a marine ecological station, which made a relatively fast sampling response possible. The effects on the pelagic ecosystem were studied for 1 month following the spill. Severe effects were recorded only in the immediate vicinity of the wreck where zooplankton biomass declined substantially during the first few days after the spill. Within 5 days the zooplankton biomass was re-established. Oil contamination of zooplankton was recorded for over 3 weeks. It is suggested that an increased phytoplankton biomass and primary production in the impacted area was due to decreased zooplankton grazing rates. Increased bacterial numbers and the oil degradation pattern indicated a rapid bacterial degradation of hydrocarbons in the water column. Sediment traps positioned in the area demonstrated the importance of sedimentation as a pathway for removal of oil from the water column. During the second week after the spill, 0.7% of sedimented material was petroleum hydrocarbons. Using sediment trap data, a total sedimentation of 30–60 t of oil was estimated in the impacted area (42 km 2). This corresponds to 10–15% of the unrecovered oil.

Microbial degradation of model petroleum at low temperatures

Two areas of Chesapeake Bay, Colgate Creek in Baltimore Harbor and Eastern Bay, are presently under study, with routine sampling of water and sediment for petroleum-degrading microorganisms (bacteria, yeasts, and fungi) by direct plating and enrichment culture. Selected physical and chemical parameters are recorded for each sampling site, and water and sediment samples are extracted for hydrocarbons. Numbers of petroleum-degrading microorganisms enumerated by direct plating were found to correlate with the concentration of benzene-extractable material and were higher for the Colgate Creek than for the Eastern Bay site. Petroleum-degrading microorganisms were isolated from water and sediment samples at environmental temperatures of 0°, 5°, and 10°C.A salts medium supplemented with nitrate and phosphate was used to provide optimum conditions for petroleum degradation, whereas Chesapeake Bay water was used to simulate natural environmental conditions. Use of a model petroleum permitted quantitative measurement of utilization of individual hydrocarbons ranging in complexity from simple alkanes to polynuclear aromatic hydrocarbons. Higher growth yields and maximum hydrocarbon degradation was observed for microorganisms in the salts medium at 0°, 5°, and 10°C, although significant quantities of hydrocarbons were utilized in some samples grown in a medium for which Chesapeake Bay water was the diluent. Bacterial hydrocarbon degradation accounted for most of the model petroleum utilization at 0° and 5°C. However, oscillations of bacterial populations, with significant growth of yeasts, was observed at 10°C. Photomicroscopy and scanning electron microscopy revealed aggregates of bacteria, yeasts, and fungi associated with oil globules. From preliminary identification and classification of the hydrocarbon-utilizing bacteria, members of the generaVibrio, Aeromonas, Pseudomonas, andAcinetobacter were present in the enrichment cultures. From results of this study, it is concluded that utilization of model petroleum at low temperatures is a function of the types and numbers of microorganisms present in an original inoculum taken from the natural environment.