Recent advances in petroleum microbiology

Escravos light crude oil degrading potentials of axenic and mixed bacterial cultures

We assessed the relationship between growth profile and the extent of biodegradation of Escravos light crude oil by axenic and mixed bacteria cultures in a shake flask. Eleven petroleum-degrading bacteria were isolated by enrichment from oil-contaminated soils including, Pseudomonas effusa, Pseudomonas fluorescens, Pseudomonas cruciviae, Arthrobacter tumescens, Pseudomonas species, Pseudomonas tralucida, Alcaligenes metacaligenes, Micrococcus colpogenes, Bacillus badius, Nocardia paraffinae and Bacillus species. Specific growth rates of axenic cultures of the bacteria during degradation of Escravos light crude oil ranged between 0.0037 and 0.0505 h(-1), while that of the mixed cultures varied from 0.0144 to 0.1301 h(-1). The crude oil was biodegraded by between 28.71% and 99.01% for single cultures and between 12.38% and 91.58% for the mixed cultures. Although specific growth rate and biomass were important at the initial stages of biodegradation, there was no significant correlation between growth rate and biomass and the extent of biodegradation of Escravos light crude oil.

Biocatalytic desulfurization (BDS) of petrodiesel fuels

Oil refineries are facing many challenges, including heavier crude oils, increased fuel quality standards, and a need to reduce air pollution emissions. Global society is stepping on the road to zero-sulfur fuel, with only differences in the starting point of sulfur level and rate reduction of sulfur content between different countries. Hydrodesulfurization (HDS) is the most common technology used by refineries to remove sulfur from intermediate streams. However, HDS has several disadvantages, in that it is energy intensive, costly to install and to operate, and does not work well on refractory organosulfur compounds. Recent research has therefore focused on improving HDS catalysts and processes and also on the development of alternative technologies. Among the new technologies one possible approach is biocatalytic desulfurization (BDS). The advantage of BDS is that it can be operated in conditions that require less energy and hydrogen. BDS operates at ambient temperature and pressure with high selectivity, resulting in decreased energy costs, low emission, and no generation of undesirable side products. Over the last two decades several research groups have attempted to isolate bacteria capable of efficient desulfurization of oil fractions. This review examines the developments in our knowledge of the application of bacteria in BDS processes, assesses the technical viability of this technology and examines its future challenges.

Disentangling oil weathering at a marine seep using GC x GC: broad metabolic specificity accompanies subsurface petroleum biodegradation

Natural seeps contribute nearly half of the oil entering the coastal ocean. However, environmental fate studies generally monitor fewer than 5% of these petroleum compounds. Hence, the rates and relevance of physical, chemical, and biological weathering processes are unknown for the large majority of hydrocarbons, both released from natural seeps and also from human activities. To investigate the specific compositional changes occurring in petroleum during subsurface degradation and submarine seepage, we studied the natural oil seeps offshore Santa Barbara, California with comprehensive, two-dimensional gas chromatography (GC x GC). With this technique, we quantified changes in the molecular diversity and abundance of hydrocarbons between subsurface reservoirs, a proximal sea floor seep, and the sea surface overlying the seep. We also developed methods to apportion hydrocarbon mass losses due to biodegradation, dissolution, and evaporation, for hundreds of tracked compounds that ascended from the subsurface to the sea floor to the sea surface. The results provide the first quantitative evidence of broad metabolic specificity for anaerobic hydrocarbon degradation in the subsurface and reveal new trends of rapid hydrocarbon evaporation at the sea surface. This study establishes GC x GC as a powerful technique for differentiating biological and physical weathering processes of complex mixtures at a molecular level.

Human Health Risk Assessment Approach for Urban Park Development

A Human Health Risk Assessment (HHRA) was undertaken for a proposed park development "River Landing", to be constructed along the north bank of the South Saskatchewan River in the City of Saskatoon, Saskatchewan, Canada. The purpose of the HHRA was to determine whether chemical constituents identified at the site, including polycyclic aromatic hydrocarbons (PAHs), petroleum hydrocarbons (PHCs), and toxic and heavy metals, would adversely affect the health of construction workers and potential park users. Although more traditional remediation options were considered, the risk assessment approach was chosen since it represented the best available technology. The HHRA was undertaken using protocols and methodologies proposed and readily accepted by the Canadian Council of Ministers of the Environment (CCME), Health Canada, and the United States Environmental Protection Agency (US EPA). Results of the risk assessment revealed that the magnitude and distribution of the chemicals at the site were such that extensive remediation was not required, and that the site could be developed without any significant restrictions on the proposed use. The assessment revealed that potential exposure to soil constituents would not result in adverse health risk to construction workers involved in park development or future park users.

Bacterial diversity characterization in petroleum samples from Brazilian reservoirs

This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments.

In situ bioremediation of monoaromatic pollutants in groundwater: a review

Monoaromatic pollutants such as benzene, toluene, ethylbenzene and mixture of xylenes are now considered as widespread contaminants of groundwater. In situ bioremediation under natural attenuation or enhanced remediation has been successfully used for removal of organic pollutants, including monoaromatic compounds, from groundwater. Results published indicate that in some sites, intrinsic bioremediation can reduce the monoaromatic compounds content of contaminated water to reach standard levels of potable water. However, engineering bioremediation is faster and more efficient. Also, studies have shown that enhanced anaerobic bioremediation can be applied for many BTEX contaminated groundwaters, as it is simple, applicable and economical. This paper reviews microbiology and metabolism of monoaromatic biodegradation and in situ bioremediation for BTEX removal from groundwater under aerobic and anaerobic conditions. It also discusses the factors affecting and limiting bioremediation processes and interactions between monoaromatic pollutants and other compounds during the remediation processes.

Comparative mesocosm study of biostimulation efficiency in two different oil-amended sub-antarctic soils

Biological treatment has become increasingly popular as a remediation method for soils and groundwater contaminated with petroleum hydrocarbon, chlorinated solvents, and pesticides. Bioremediation has been considered for application in cold regions such as Arctic and sub-Arctic climates and Antarctica. Studies to date suggest that indigenous microbes suitable for bioremediation exist in soils in these regions. This paper reports on two case studies at the sub-Antarctic Kerguelen Island in which indigenous bacteria were found that were capable of mineralizing petroleum hydrocarbons in soil contaminated with crude oil and diesel fuel. All results demonstrate a serious influence of the soil properties on the biostimulation efficiency. Both temperature elevation and fertilizer addition have a more significant impact on the microbial assemblages in the mineral soil than in the organic one. Analysis of the hydrocarbons remaining at the end of the experiments confirmed the bacterial observations. Optimum temperature seems to be around 10 degrees C in organic soil, whereas it was higher in mineral soil. The benefit of adding nutrients was much stronger in mineral than in the organic soil. Overall, this study suggests that biostimulation treatments were driven by soil properties and that ex situ bioremediation for treatment of cold contaminated soils will allow greater control over soil temperature, a limiting factor in cold climates.

Arbuscular mycorrhiza and petroleum-degrading microorganisms enhance phytoremediation of petroleum-contaminated soil

While plants can phytoremediate soils that are contaminated with petroleum hydrocarbons, adding microbes to remediate contaminated sites with petroleum-degrading microorganisms and arbuscular mycorrhizal fungi (AMF) is not well understood. The phytoremediation of Arabian medium crude oil (ACO) was done with a Lolium multiflorum system inoculated with an AMF (Glomus intraradices) and a mixture of petroleum-degrading microorganisms--the bacterium, Sphingomonas paucimobilis (Sp) and the filamentous fungus, Cunninghamella echinulata (Ce, SpCe)--or with a combination of microorganisms (AMF + SpCe). Based on an earlier study on screening plants for phytoremediation of ACO, L. multiflorum (Italian ryegrass) was selected for its tolerance and rapid growth response (Alarcón, 2006). The plants were exposed to ACO-contaminated soil (6000 mg kg(-1)) for 80 d under greenhouse conditions. A modified Long Ashton Nutrient Solution (LANS) was supplied to all treatments at 30 microg P mL(-1), except for a second, higher P, control treatment at 44 microg P mL(-1). Inoculation with AMF, SpCe, or AMF + SpCe resulted in significantly increased leaf area as well as leaf and pseudostem dry mass as compared to controls at 30 microg P mL(-1). Populations of bacteria grown on a nitrogen-free medium and filamentous fungi increased with AMF + SpCe and SpCe treatments. The average total colonization and arbuscule formation of AMF-inoculated plants in ACO-contaminated soil were 25% and 8%, respectively. No adverse effects were caused by SpCe on AMF colonization. Most importantly, ACO degradation was significantly enhanced by the addition of petroleum-degrading microorganisms and higher fertility controls, as compared to plants at 30 microg P mL(-1). The highest ACO degradation (59%) was observed with AMF + SpCe. The phytoremediation of ACO was also enhanced by single inoculation of AMF or SpCe. The effect of AMF and petroleum-degrading microorganisms on plant growth and ACOdegradation was not attributable to differences in proline, total phenolics, nitrate reductase levels, or variation in plant-gas exchange.

Biodegradation pattern of hydrocarbons from a fuel oil-type complex residue by an emulsifier-producing microbial consortium

The biodegradation of a hazardous waste (bilge waste), a fuel oil-type complex residue from normal ship operations, was studied in a batch bioreactor using a microbial consortium in seawater medium. Experiments with initial concentrations of 0.18 and 0.53% (v/v) of bilge waste were carried out. In order to study the biodegradation kinetics, the mass of n-alkanes, resolved hydrocarbons and unresolved complex mixture (UCM) hydrocarbons were assessed by gas chromatography (GC). Emulsification was detected in both experiments, possibly linked to the n-alkanes depletion, with differences in emulsification start times and extents according to the initial hydrocarbon concentration. Both facts influenced the hydrocarbon biodegradation kinetics. A sequential biodegradation of n-alkanes and UMC was found for the higher hydrocarbon content. Being the former growth associated, while UCM biodegradation was a non-growing process showing enzymatic-type biodegradation kinetics. For the lower hydrocarbon concentration, simultaneous biodegradation of n-alkanes and UMC were found before emulsification. Nevertheless, certain UCM biodegradation was observed after the medium emulsification. According to the observed kinetics, three main types of hydrocarbons (n-alkanes, biodegradable UCM and recalcitrant UCM) were found adequate to represent the multicomponent substrate (bilge waste) for future modelling of the biodegradation process.

Bacterial metabolism of polycyclic aromatic hydrocarbons: strategies for bioremediation

Polycyclic aromatic hydrocarbons (PAHs) are compounds of intense public concern due to their persistence in the environment and potentially deleterious effects on human, environmental and ecological health. The clean up of such contaminants using invasive technologies has proven to be expensive and more importantly often damaging to the natural resource properties of the soil, sediment or aquifer. Bioremediation, which exploits the metabolic potential of microbes for the clean-up of recalcitrant xenobiotic compounds, has come up as a promising alternative. Several approaches such as improvement in PAH solubilization and entry into the cell, pathway and enzyme engineering and control of enzyme expression etc. are in development but far from complete. Successful application of the microorganisms for the bioremediation of PAH-contaminated sites therefore requires a deeper understanding of the physiology, biochemistry and molecular genetics of potential catabolic pathways. In this review, we briefly summarize important strategies adopted for PAH bioremediation and discuss the potential for their improvement.

Dimethyl sulfoxide (DMSO) as the sulfur source for the production of desulfurizing resting cells of Gordonia alkanivorans RIPI90A

The sulfate repression of desulfurization (Dsz) phenotype represents a major barrier to the mass production of desulfurizing resting cells. This repression can be avoided by replacing sulfate with dibenzothiophene (DBT) as the main substrate for the 4S pathway. However, mass production of biocatalyst using DBT is impractical because of its high price, low water solubility, and growth inhibition by 2-hydroxybiphenyl (2-HBP), which is the end product of the 4S pathway. In this work, the results showed that readily bioavailable sulfur compounds led to repression of the desulfurization activity of Gordonia alkanivorans RIPI90A. However, the Dsz phenotype was expressed through the 4S pathway in the presence of DMSO as the sulfur source for growth. Resting cells grown on DMSO were more active than the resting cells grown on DBT. The growth rate of strain RIPI90A on DMSO was higher than when DBT was used as the sole sulfur source. DMSO concentration significantly influenced the growth pattern of the strain, and the highest growth rate was observed at a concentration of 200 microg ml(-1). Above this concentration, the growth rate gradually decreased. DBT was found to induce the Dsz phenotype, with no observed lag period, in cells grown on DMSO as the sole sulfur source. Prior to induction, the specific activity was detected as 1.4 micromol 2-HBP (g dry cell weight)(-1) h(-1), and following incubation (5 h) the highest specific activity was observed as 5.11 micromol 2-HBP (g dry cell weight)(-1 )h(-1). This study identified that resting cells can be prepared in a two-step process. First, resting cells can be produced using DMSO as the sulfur source for growth; in the second step, improvements to their desulfurizing activity can be made using DBT as an inducer. DMSO is recommended as an appropriate sulfur source for the mass production of G. alkanivorans RIPI90A.

Isolation and characterization of phenanthrene-degrading strains Sphingomonas sp. ZP1 and Tistrella sp. ZP5

Two bacteria strains Sphingomonas sp. strain ZP1 and Tistrella sp. strain ZP5 were identified as phenanthrene-degrading ones, based on Gram staining, oxydase reaction, biochemical tests, FAME analysis, G+C content and 16S rDNA gene sequence analysis. We isolated these two bacteria strains Sphingomonas sp. ZP1 and Tistrella sp. ZP5 from soil samples contaminated with polycyclic aromatic hydrocarbon (PAH)-containing waste from oil refinery field in Shanghai, China. Strain Sphingomonas sp. ZP1 was able to degrade naphthalene, phenanthrene, toluene, methanol and ethanol, salicylic acid and Tween 80. Moreover, it can remove nearly all the phenanthrene at 0.025% concentration in 8 days. Strain Tistrella sp. ZP5 cannot degrade phenanthrene individually but it can increase the speed of phenanthrene degradation together with ZP1. The growth conditions of strain Sphingomonas sp. ZP1 were optimized. The result also indicated that the degradation rate of phenanthrene ranged from 250 to 1000 ppm with strain ZP1 remained nearly the same, i.e., a high concentration of phenanthrene did not inhibit both the growth of microbial strains and the phenanthrene-degradation ability. Besides, the effect of non-ionic surfactants such as Brij 30, Triton X-100 and Tween 80 on the phenanthrene degradation was determined. Such two strains may be useful for bioremediation applications.

Microcosm experiments of oil degradation by microbial mats. II. The changes in microbial species

The influence of microbial mats on the degradation of two crude oils (Casablanca and Maya) and the effect of oil pollution on the mat structure were assessed using model ecosystems, prepared under laboratory conditions subject to tidal movements, from pristine Ebro Delta microbial-mat ecosystems. Both selected oils are examples of those currently used for commercial purposes. Casablanca crude oil is aliphatic with a low viscosity; Maya represents a sulphur-rich heavy crude oil that is predominantly aromatic. In the unpolluted microcosms, Microcoleus chthonoplastes-, Phormidium- and Oscillatoria-like were the dominant filamentous cyanobacterial morphotypes, whilst Synechoccocus-, Synechocystis- and Gloeocapsa-like were the most abundant unicellular cyanobacteria. After oil contamination, no significant changes of chlorophyll a and protein concentrations were observed, though cyanobacterial diversity shifts were monitored. Among filamentous cyanobacteria, M. chthonoplastes-like morphotype was the most resistant for both oils, unlike the other cyanobacteria, which tolerated Casablanca but not Maya. Unicellular cyanobacteria seemed to be resistant to pollution with both essayed oils, with the exception of the morphotype resembling Gloeocapsa, which was sensitive to both oils. The crude-oil addition also had a significant effect on certain components of the heterotrophic microbial community. Casablanca oil induced an increase in anaerobic heterotrophic bacteria, whereas the opposite effect was observed in those heterotrophs when polluted with Maya oil. The overall results, microbiological and crude-oil transformation analysis, indicate that the indigenous community has a considerable potential to degrade oil components by means of the metabolic cooperation of phototrophic and heterotrophic populations.

Multilevel samplers as microcosms to assess microbial response to biostimulation

Passive multilevel samplers (MLS) containing a solid matrix for microbial colonization were used as in situ microcosms in conjunction with a push-pull biostimulation experiment designed to promote biological U(VI) and Tc(VII) reduction. MLS were deployed at 24 elevations in the injection well and two downgradient wells to investigate the spatial variability in microbial community composition and growth prior to and following biostimulation. The microbial community was characterized by real-time quantitative polymerase chain reaction (Q-PCR) quantification of bacteria, NO(3)(-)-reducing bacteria (nirS and nirK), delta-proteobacteria, Geobacter sp., and methanogens (mcrA). Pretest cell densities were low overall but varied substantially with significantly greater bacterial populations detected at circumneutral pH (t-test, alpha= 0.05), suggesting carbon substrate and low pH limitations of microbial activity. Although pretest cell densities were low, denitrifying bacteria were dominant members of the microbial community. Biostimulation with an ethanol-amended ground water resulted in concurrent NO(3)(-) and Tc(VII) reduction, followed by U(VI) reduction. Q-PCR analysis of MLS revealed significant (1 to 2 orders of magnitude, Mann-Whitney U-test, alpha= 0.05) increases in cell densities of bacteria, denitrifiers, delta-proteobacteria, Geobacter sp., and methanogens in response to biostimulation. Traditionally, characterization of sediment samples has been used to investigate the microbial community response to biostimulation; however, collection of sediment samples is expensive and not conducive to deep aquifers or temporal studies. The results presented demonstrate that push-pull tests with passive MLS provide an inexpensive approach to determine the effect of biostimulation on contaminant concentrations, geochemical conditions, and the microbial community composition and function.

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.

Biodegradation of petroleum compounds in soil by a solid-phase circulating bioreactor with poultry manure amendments

Petroleum compounds account for the vast majority of contaminants in soils. Bioremediation is a widely accepted strategy in degrading these contaminants. This study demonstrates the effectiveness of nitrogenous nutrient (nitrogen) amendments in enhancing biodegradation of petroleum contaminants in soil by using a solid-phase circulating bioreactor (SCB). In a bench-scale SCB, total petroleum hydrocarbon (TPH) concentration (~5000 mg kg(-1)) in soil decreased 92% within 15 days. In a scaled-up SCB system containing approximately 120 kg petroleum-contaminated soil (TPH at approximately 125,000 mg kg(-1)), a degradation rate of 635 mg kg(-1)d(-1) was obtained from the poultry manure-amended treatment during a 200-day period of operation. Treatments with the same amount of nitrogen (as ammonium nitrate) attained a TPH degradation rate of 469 mg kg(-1)d(-1) during the same period. Control SCB unit, which was maintained under the same aerobic conditions but not amended with nitrogen, had a TPH degradation rate of 273 mg kg(-1)d(-1). Results from this study indicate that SCB can achieve significantly higher degradative rates than conventional landfarming (reported rates < 150 mg kg(-1)d(-1)) and poultry manure appears to be a preferred nitrogen amendment that can further enhance the biodegradation of petroleum contaminants in soils.

The use of molecular techniques to characterize the microbial communities in contaminated soil and water

Traditionally, the identification and characterization of microbial communities in contaminated soil and water has previously been limited to those microorganisms that are culturable. The application of molecular techniques to study microbial populations at contaminated sites without the need for culturing has led to the discovery of unique and previously unrecognized microorganisms as well as complex microbial diversity in contaminated soil and water which shows an exciting opportunity for bioremediation strategies. Nucleic acid extraction from contaminated sites and their subsequent amplification by polymerase chain reaction (PCR) has proved extremely useful in assessing the changes in microbial community structure by several microbial community profiling techniques. This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water. Techniques that identify and quantify microbial population and catabolic genes involved in biodegradation are examined. In addition, methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies are discussed.

Potential of hexadecane-utilizing soil-microorganisms for growth on hexadecanol, hexadecanal and hexadecanoic acid as sole sources of carbon and energy

Bacteria and fungi in pristine and oily desert soil samples were counted on inorganic medium aliquots containing 0.5% hexadecane, hexadecanol, hexadecanal or hexadecanoic acid, as sole sources of carbon and energy. It was found that the carbon and energy source most commonly utilized by soil bacteria was the alkane n-hexadecane, and by soil fungi hexadecanoic acid. Representative microorganisms were isolated and identified. The most predominant bacteria in all soil samples belonged to the genera Micrococcus and Pseudomonas; less dominant bacteria belonged to the group of nocardioforms. The most frequent fungal genera were Aspergillus and Penicillium, while Microsporium and Ulocladium were minor fungi. Irrespective of the substrate on which the microbial strains had initially been isolated, the majority of the isolated microorganisms could grow, albeit to a varying degree, on an inorganic medium containing any of the remaining three substrates as sole carbon and energy sources. Bacterial strains preferred the alkane as a carbon and energy source over any of its oxidation products, while fungal strains preferred to grow mainly on the fatty acids. Quantitative analysis by gas liquid chromatography revealed that the predominant bacterial and fungal isolates had a potential for the attenuation of the alkane and its immediate oxidation products in the medium. In view of the continuous release of hydrocarbon oxidation products by oil-utilizing microorganisms in oily environments, it is interesting that the indigenous microflora contribute to the uptake and utilization of all such intermediate compounds, thus, having a potential for efficient self-cleaning and bioremediation of oily soils.

Biodegradation of fuel oil hydrocarbons by a mixed bacterial consortium in sandy and loamy soils

The aerobic degradation of light fuel oil in sandy and loamy soils by an environmental bacterial consortium was investigated. Soils were spiked with 1 or 0.1% of oil per dry weight of soil. Acetone extracts of dried soils were analyzed by GC and the overall degradation was calculated by comparison with hydrocarbon recovery from uninoculated soils. In sandy soils, the sum of alkanes n-C(12) to n-C(23) was degraded to about 45% within 6 days at 20 degrees C and to 27-31% within 28 days, provided that moisture and nutrients were replenished. Degradation in loamy soil was about 12% lower. The distribution of recovered alkanes suggested a preferential degradation of shorter chain molecules (n-C(12) to n-C(16)) by the bacterial consortium. Partial 16S rDNA sequences indicated the presence of strains of Pseudomonas aeruginosa, Pseudomonas citronellolis, and Stenotrophomonas maltophilia. Toxicity tests using commercial standard procedures showed a moderate inhibition of bacterial activity. The study showed the applicability of a natural microbial community for the degradation of oil spills into soils at ambient temperatures.

Engineering bacteria for production of rhamnolipid as an agent for enhanced oil recovery

Rhamnolipid as a potent natural biosurfactant has a wide range of potential applications, including enhanced oil recovery (EOR), biodegradation, and bioremediation. Rhamnolipid is composed of rhamnose sugar molecule and beta-hydroxyalkanoic acid. The rhamnosyltransferase 1 complex (RhlAB) is the key enzyme responsible for transferring the rhamnose moiety to the beta-hydroxyalkanoic acid moiety to biosynthesize rhamnolipid. Through transposome-mediated chromosome integration, the RhlAB gene was inserted into the chromosome of the Pseudomonas aeruginosa PAO1-rhlA(-) and Escherichia coli BL21 (DE3), neither of which could produce rhamnolipid. After chromosome integration of the RhlAB gene, the constitute strains P. aeruginosa PEER02 and E. coli TnERAB did produce rhamnolipid. The HPLC/MS spectrum showed that the structure of purified rhamnolipid from P. aeruginosa PEER02 was similar to that from other P. aeruginosa strains, but with different percentage for each of the several congeners. The main congener (near 60%) of purified rhamnolipid from E. coli TnERAB was 3-(3-hydroxydecanoyloxy) decanoate (C(10)-C(10)) with mono-rhamnose. The surfactant performance of rhamnolipid was evaluated by measurement of interfacial tension (IFT) and oil recovery via sand-pack flooding tests. As expected, pH and salt concentration of the rhamnolipid solution significantly affected the IFT properties. With just 250 mg/L rhamnolipid (from P. aeruginosa PEER02 with soybean oil as substrate) in citrate-Na(2)HPO(4), pH 5, 2% NaCl, 42% of oil otherwise trapped was recovered from a sand pack. This result suggests rhamnolipid might be considered for EOR applications.

Bioremediation of kerosene I: A case study in liquid media

The ability of different local isolates in addition to some isolates from Germany to degrade kerosene in liquid medium was studied. The results showed that the percent of kerosene degradation varied among the different organisms and that 59-94% of kerosene was degraded after 21d. Two local isolates (Pseudomonas sp. AP and Pseudomonas sp. CK) and one German isolate (Gordonia sp. DM) were selected for this study. The addition of wheat bran, as co-substrate, stimulated the kerosene degradation by the two local strains, while glucose inhibited the degradation rate using the three organisms with different rates. Ammonium nitrate and urea was the best nitrogen sources. The use of superphosphate (as phosphorus source) in the presence of urea stimulates the degradation rate. It was also observed that the addition of 1% surfactants, like Triton X-100, Igepal, Tergitol, or Tween 20 and 80 enhanced the kerosene degradation. The degradation percent lied between 94% and 98%. The ability of the tested organisms to degrade kerosene concentration from 2% to 8% was evaluated. It was found that the three organisms degraded about 65-85% from 8% kerosene after 21d. The use of rice straw-immobilized cells reduced the time of degradation and enhanced the degradation ability of the organisms. The sodium dodecyl sulphate-polyacrylamide gel electrophoresis revealed the presence of a common protein band when the tested organisms were grown on kerosene.

Isolation of Gram-positive n-alkane degraders from a hydrocarbon-contaminated Mediterranean shoreline

AIMS

To investigate the petroleum hydrocarbon (HC)-degrading potential of indigenous micro-organisms in a sandy Mediterranean coast, accidentally contaminated with petroleum-derived HCs.

METHODS AND RESULTS

Using culturable methods, a population of Gram-positive n-alkane degraders was detected in the contaminated soil. Five isolates, identified as one Nocardia, two Rhodococcus and two Gordonia strains, were able to degrade medium- and long-chain n-alkanes up to C(36) as assessed by growth assays and gas chromatography-mass spectrometry analysis. Diverging alkane hydroxylase-encoding genes (alkB) were detected by PCR, using degenerated primers, in all the strains; multiple sequences were obtained from the Nocardia strain, while only one alkB gene was detected in the Rhodococcus and Gordonia strains. The majority of the alkB sequences were related to Rhodococcus alkB2, but none was identical to it.

CONCLUSIONS

Actinomycetes might have a key role in bioremediation of n-alkane-contaminated sites under dry, resource-limited conditions, such as those found in the Mediterranean shorelines.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this is the first study on the bioremediation potential in Mediterranean contaminated beaches.

Cosmopolitan heterotrophic microeukaryotes are active bacterial grazers in experimental oil-polluted systems

We investigated the population dynamics and prevailing 18S rDNA phylotypes of microeukaryotes (<or= 10 microm) in microcosms containing seawater from either an unpolluted oligotrophic site or a chronically oil-polluted mesotrophic site of the Aegean Sea, amended with crude oil (100 p.p.m. final concentration) and crude oil plus emulsifier (10 p.p.m. final concentration). The addition of oil alone did not result in an important increase of bacteria or their predators, while the addition of oil and emulsifiers caused an important increase in bacteria followed by nanoflagellate predator response. We observed an important shift in the microeukaryotic community structure, which was characterized by the dominance of the same heterotrophic nanoflagellates in all oil-polluted treatments. Thus, the resulting 18S rDNA phylotypes were dominated (48.1-82.4%) by Paraphysomonas foraminifera in all treatments containing crude oil and crude oil plus emulsifier. The origin of the seawater, i.e. unpolluted versus chronically oil-polluted, had no effect on the dominant eukaryote, suggesting that the ubiquitous P. foraminifera is an effective opportunist in oil-polluted aquatic systems. The next dominant phylotypes were Monosiga brevicollis (<or= 27.0%) and Pseudobodo tremulans (<or= 23.1%). However, the addition of the emulsifier increased the dominance of P. foraminifera but decreased that of M. brevicollis and P. tremulans. Our study revealed that these dominant oil-tolerant eukaryotes, which are commonly found in the marine environments, are important grazers of bacteria and as such their dynamics should be taken into account in bioremediation practices in situ.

Phylogenetic Diversity of the Archaeal Community in a Continental High-Temperature, Water-Flooded Petroleum Reservoir

The diversity of an archaeal community was analyzed in the water from a continental high-temperature, long-term water-flooded petroleum reservoir in Huabei Oilfield in China. The archaea were characterized by their 16S rRNA genes. An archaeal 16S rDNA clone library was constructed from the DNA isolated from the formation water, and 237 randomly selected positive clones were clustered in 28 phylotypes by sequencing analyses. Phylogenetic analysis of these sequences indicated that the dominant members of the archaeal phylotypes were affiliated with the order Methanomicrobiales. Totally, the archaeal community was composed of methanogens belonging to four orders: Methanobacteriales, Methanococcales, Methanomicrobiales, and Methanosarcinales. Most of the clones clustered with sequences previously described for methanogens, but there was a difference in the relative distribution of sequences detected here as compared to that of previous studies. Some thermophilic methanogens detected had been previously isolated from a number of high-temperature petroleum reservoirs worldwide; thus, they might exhibit adaptations to the environments and be the common habitants of geothermally heated subsurface environments.

Insight into heterogeneity in cell-surface hydrophobicity and ability to degrade hydrocarbons among cells of two hydrocarbon-degrading bacterial populations

The sequential bacterial adherence to hydrocarbons (BATH) of successive generations of hydrophobic fractions of Paenibacillus sp. R0032A and Burkholderia cepacia gave rise to bacterial populations of increasing cell-surface hydrophobicity. Thus, hydrophobicity of the first generation (H1) was less than that of the second generation (H2), which was less than that of the third generation (H3). Beyond H3, the hydrophobic populations became less stable and tended to lyse in hexadecane after violent (vortex) agitation, resulting in an apparent decline in BATH value. The exhaustively fractionated aqueous-phase population (L) was very hydrophilic. The overall cell-surface distribution of the population was L < parental strain < H1 < H2 < H3. The ability to degrade crude oil, hexadecane, or phenanthrene matched the degree of cell-surface hydrophobicity: L < P < H1 < H2 < H3. Thus, in natural populations of hydrocarbon-degrading Paenibacillus sp. R0032A and B. cepacia, there is a heterogeneity in the hydrophobic surface characteriistics that affects the ability of cells to use various hydrocarbon substrates.

Bacterial metabolism of long-chain n-alkanes

Degradation of alkanes is a widespread phenomenon in nature, and numerous microorganisms, both prokaryotic and eukaryotic, capable of utilizing these substrates as a carbon and energy source have been isolated and characterized. In this review, we summarize recent advances in the understanding of bacterial metabolism of long-chain n-alkanes. Bacterial strategies for accessing these highly hydrophobic substrates are presented, along with systems for their enzymatic degradation and conversion into products of potential industrial value. We further summarize the current knowledge on the regulation of bacterial long-chain n-alkane metabolism and survey progress in understanding bacterial pathways for utilization of n-alkanes under anaerobic conditions.

Two-phase partitioning bioreactors for treatment of volatile organic compounds

Two-phase partitioning bioreactors (TPPBs) allow the biological removal of volatile organic compounds (VOCs) from contaminated gas streams at unprecedented rates and concentrations. TPPBs are constructed by adding a non-aqueous phase (e.g. hexadecane, silicone oil) to an aqueous phase that contains the microorganisms responsible for degrading the VOCs. Presence of a water-immiscible phase improves the transfer of hydrophobic substrates (e.g. hexane, oxygen) or reduces the toxicity of inhibitory substances (e.g. benzene, toluene) to the microorganisms present in the aqueous phase. The non-aqueous phase is selected based on cost, safety, good partitioning properties towards the target pollutants, biocompatibility, and non-biodegradability. TPPBs have hitherto been designed as laboratory-scale well-mixed stirred-tank reactors or as biofilters that contain a non-aqueous phase. Scale-up and industrial use of TPPBs require elucidation and modeling of the mechanisms of substrate transfer and uptake; understanding of the mechanisms of microbial selection; identification or synthesis of new inexpensive and robust non-aqueous phases; and generation of suitable guidelines for process design and control.

Microbial diversity in natural asphalts of the Rancho La Brea Tar Pits

Bacteria commonly inhabit subsurface oil reservoirs, but almost nothing is known yet about microorganisms that live in naturally occurring terrestrial oil seeps and natural asphalts that are comprised of highly recalcitrant petroleum hydrocarbons. Here we report the first survey of microbial diversity in ca. 28,000-year-old samples of natural asphalts from the Rancho La Brea Tar Pits in Los Angeles, CA. Microbiological studies included analyses of 16S rRNA gene sequences and DNA encoding aromatic ring-hydroxylating dioxygenases from two tar pits differing in chemical composition. Our results revealed a wide range of phylogenetic groups within the Archaea and Bacteria domains, in which individual taxonomic clusters were comprised of sets of closely related species within novel genera and families. Fluorescent staining of asphalt-soil particles using phylogenetic probes for Archaea, Bacteria, and Pseudomonas showed coexistence of mixed microbial communities at high cell densities. Genes encoding dioxygenases included three novel clusters of enzymes. The discovery of life in the tar pits provides an avenue for further studies of the evolution of enzymes and catabolic pathways for bacteria that have been exposed to complex hydrocarbons for millennia. These bacteria also should have application for industrial microbiology and bioremediation.

Taxonomic identification, phenanthrene uptake activity, and membrane lipid alterations of the PAH degrading Arthrobacter sp. strain Sphe3

This report describes phenanthrene uptake as well as the effect of phenanthrene on the membrane phospholipid and fatty acid composition in a newly isolated bacterial strain, Sphe3, that we taxonomically identified as Arthrobacter sp. Strain Sphe3 is able to utilize phenanthrene as a carbon source at high rates and appears to internalize phenanthrene with two mechanisms: a passive diffusion when cells are grown on glucose, and an inducible active transport system when cells are grown on phenanthrene as a sole carbon source. Active transport followed Michaelis-Menten kinetics, and it was amenable to inhibition by 2,4-dinitrophenol and sodium azide. Evidence provided here indicates that apart from inducing an active PAH uptake, the presence of phenanthrene elicits significant changes in membrane fluidity.

Microbe-aliphatic hydrocarbon interactions in soil: implications for biodegradation and bioremediation

Aliphatic hydrocarbons make up a substantial portion of organic contamination in the terrestrial environment. However, most studies have focussed on the fate and behaviour of aromatic contaminants in soil. Despite structural differences between aromatic and aliphatic hydrocarbons, both classes of contaminants are subject to physicochemical processes, which can affect the degree of loss, sequestration and interaction with soil microflora. Given the nature of hydrocarbon contamination of soils and the importance of bioremediation strategies, understanding the fate and behaviour of aliphatic hydrocarbons is imperative, particularly microbe-contaminant interactions. Biodegradation by microbes is the key removal process of hydrocarbons in soils, which is controlled by hydrocarbon physicochemistry, environmental conditions, bioavailability and the presence of catabolically active microbes. Therefore, the aims of this review are (i) to consider the physicochemical properties of aliphatic hydrocarbons and highlight mechanisms controlling their fate and behaviour in soil; (ii) to discuss the bioavailability and bioaccessibility of aliphatic hydrocarbons in soil, with particular attention being paid to biodegradation, and (iii) to briefly consider bioremediation techniques that may be applied to remove aliphatic hydrocarbons from soil.

Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oilfield

The microbial community and its diversity in production water from a high-temperature, water-flooded petroleum reservoir of an offshore oilfield in China were characterized by 16S rRNA gene sequence analysis. The bacterial and archaeal 16S rRNA gene clone libraries were constructed from the community DNA and, using sequence analysis, 388 bacterial and 220 archaeal randomly selected clones were clustered with 60 and 28 phylotypes, respectively. The results showed that the 16S rRNA genes of bacterial clones belonged to the divisions Firmicutes, Thermotogae, Nitrospirae and Proteobacteria, whereas the archaeal library was dominated by methanogen-like rRNA genes (Methanothermobacter, Methanobacter, Methanobrevibacter and Methanococcus), with a lower percentage of clones belonging to Thermoprotei. Thermophilic microorganisms were found in the production water, as well as mesophilic microorganisms such as Pseudomonas and Acinetobacter-like clones. The thermophilic microorganisms may be common inhabitants of geothermally heated specialized subsurface environments, which have been isolated previously from a number of high-temperature petroleum reservoirs worldwide. The mesophilic microorganisms were probably introduced into the reservoir as it was being exploited. The results of this work provide further insight into the composition of microbial communities of high-temperature petroleum reservoirs at offshore oilfields.

Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms

In spite of their chemical inertness, hydrocarbons are degraded by microorganisms in the complete absence of oxygen. As all known aerobic hydrocarbon degradation pathways start with oxygen-dependent reactions, hydrocarbon catabolism in anaerobes must be initiated by novel biochemical reactions. In recent years, the enzymes catalyzing oxygen-independent activation of several hydrocarbons have been identified. Surprisingly, a variety of reactions seems to be employed to overcome the activation barrier of different hydrocarbons. This review presents the current understanding on some of these reactions and the associated degradation pathways: oxygen-independent hydroxylation as employed in ethylbenzene metabolism, fumarate addition to methyl or methylene carbons in toluene or alkane degradation, and only recently discovered reactions such as methylation of naphthalene or anaerobic methane oxidation via reverse methanogenesis.

Identification of novel genes involved in long-chain n-alkane degradation by Acinetobacter sp. strain DSM 17874

Acinetobacter sp. strain DSM 17874 is capable of utilizing n-alkanes with chain lengths ranging from that of decane (C10H22) to that of tetracontane (C40H82) as a sole carbon source. Two genes encoding AlkB-type alkane hydroxylase homologues, designated alkMa and alkMb, have been shown to be involved in the degradation of n-alkanes with chain lengths of from 10 to 20 C atoms in this strain. Here, we describe a novel high-throughput screening method and the screening of a transposon mutant library to identify genes involved in the degradation of n-alkanes with C chain lengths longer than 20, which are solid at 30 degrees C, the optimal growth temperature for Acinetobacter sp. strain DSM 17874. A library consisting of approximately 6,800 Acinetobacter sp. strain DSM 17874 transposon mutants was constructed and screened for mutants unable to grow on dotriacontane (C32H66) while simultaneously showing wild-type growth characteristics on shorter-chain n-alkanes. For 23 such mutants isolated, the genes inactivated by transposon insertion were identified. Targeted inactivation and complementation studies of one of these genes, designated almA and encoding a putative flavin-binding monooxygenase, confirmed its involvement in the strain's metabolism of long-chain n-alkanes. To our knowledge, almA represents the first cloned gene shown to be involved in the bacterial degradation of long-chain n-alkanes of 32 C's and longer. Genes encoding AlmA homologues were also identified in other long-chain n-alkane-degrading Acinetobacter strains.

Molecular analysis of bacterial diversity in kerosene-based drilling fluid from the deep ice borehole at Vostok, East Antarctica

Decontamination of ice cores is a critical issue in phylogenetic studies of glacial ice and subglacial lakes. At the Vostok drill site, a total of 3650 m of ice core have now been obtained from the East Antarctic ice sheet. The ice core surface is coated with a hard-to-remove film of impure drilling fluid comprising a mixture of aliphatic and aromatic hydrocarbons and foranes. In the present study we used 16S rRNA gene sequencing to analyze the bacterial content of the Vostok drilling fluid sampled from four depths in the borehole. Six phylotypes were identified in three of four samples studied. The two dominant phylotypes recovered from the deepest (3400 and 3600 m) and comparatively warm (-10 degrees C and -6 degrees C, respectively) borehole horizons were from within the genus Sphingomonas, a well-known degrader of polyaromatic hydrocarbons. The remaining phylotypes encountered in all samples proved to be human- or soil-associated bacteria and were presumed to be drilling fluid contaminants of rare occurrence. The results obtained indicate the persistence of bacteria in extremely cold, hydrocarbon-rich environments. They show the potential for contamination of ice and subglacial water samples during lake exploration, and the need to develop a microbiological database of drilling fluid findings.

Development of a 60-mer oligonucleotide microarray on the basis of benzene monooxygenase gene diversity

We constructed a 60-mer oligonucleotide microarray on the basis of benzene monooxygenase gene diversity to develop a new technology for simultaneous detection of the functional gene diversity in environmental samples. The diversity of the monooxygenase genes associated with benzene degradation was characterized. A new polymerase chain reaction (PCR) primer set was designed using conserved regions of benzene monooxygenase gene (BO12 primer) and used for PCR-clone library analysis along with a previously designed RDEG primer which targeted the different types of benzene monooxygenase gene. We obtained 20 types of amino acid sequences with the BO12 primer and 40 with the RDEG primer. Phylogenetic analysis of the sequences obtained suggested the large diversity of the benzene monooxygenase genes. A total of 87 60-mer probes specific for each operational taxonomical unit were designed and spotted on a microarray. When genomic DNAs of single strains were used in microarray hybridization assays, corresponding sequences were successfully detected by the microarray without any false-negative signals. Hybridization with soil DNA samples showed that the microarray was able to detect sequences that were not detected in clone libraries. Constructed microarray can be a useful tool for characterizing monooxygenase gene diversity in benzene degradation.