Biocatalytic transformation of petroporphyrins by chemical modified cytochrome C

Biodegradation of asphaltenes by an indigenous bioemulsifier-producing Pseudomonas stutzeri YWX-1 from shale oil in the Ordos Basin: Biochemical characterization and complete genome analysis

Crude oil pollution is environmentally ubiquitous and has become a global public concern about its impact on human health. Asphaltenes are the key components of heavy crude oil (HCO) that are underutilized due to their high viscosity and density, and yet, the associated information about biodegradation is extremely limited in the literature. In the present study, an indigenous bacterium with effective asphaltene-degrading activity was isolated from oil shale and identified as Pseudomonas stutzeri by a polyphasic taxonomic approach, named YWX-1. Supplemented with 75 g L^-1 heavy crude oil as the sole carbon source for growth in basic mineral salts liquid medium (MSM), strain YWX-1 was able to remove 49% of asphaletene fractions within 14 days, when it was cultivated with an initial inoculation size of 1%. During the degradation process, the bioemulsifier produced by strain YWX-1 could emulsify HCO obviously into particles, as well as it had the ability to solubilize asphaletenes. The bioemulsifier was identified to be a mixture of polysaccharide and protein through Fourier transform infrared spectroscopy (FT-IR). The genome of strain YWX-1 contains one circular chromosome of 4488441 bp with 63.98% GC content and 4145 protein coding genes without any plasmid. Further genome annotation indicated that strain YWX-1 possesses a serial of genes involved in bio-emulsification and asphaltenes biodegradation. This work suggested that P. stutzeri YWX-1 could be a promising species for bioremediation of HCO and its genome analysis provided insight into the molecular basis of asphaltene biodegradation and bioemulsifier production.

Lysine-PEGylated Cytochrome C with Enhanced Shelf-Life Stability

Cytochrome c (Cyt-c), a small mitochondrial electron transport heme protein, has been employed in bioelectrochemical and therapeutic applications. However, its potential as both a biosensor and anticancer drug is significantly impaired due to poor long-term and thermal stability. To overcome these drawbacks, we developed a site-specific PEGylation protocol for Cyt-c. The PEG derivative used was a 5 kDa mPEG-NHS, and a site-directed PEGylation at the lysine amino-acids was performed. The effects of the pH of the reaction media, molar ratio (Cyt-c:mPEG-NHS) and reaction time were evaluated. The best conditions were defined as pH 7, 1:25 Cyt-c:mPEG-NHS and 15 min reaction time, resulting in PEGylation yield of 45% for Cyt-c-PEG-4 and 34% for Cyt-c-PEG-8 (PEGylated cytochrome c with 4 and 8 PEG molecules, respectively). Circular dichroism spectra demonstrated that PEGylation did not cause significant changes to the secondary and tertiary structures of the Cyt-c. The long-term stability of native and PEGylated Cyt-c forms was also investigated in terms of peroxidative activity. The results demonstrated that both Cyt-c-PEG-4 and Cyt-c-PEG-8 were more stable, presenting higher half-life than unPEGylated protein. In particular, Cyt-c-PEG-8 presented great potential for biomedical applications, since it retained 30-40% more residual activity than Cyt-c over 60-days of storage, at both studied temperatures of 4 °C and 25 °C.

Sedimentary Cobalt Protoporphyrin as a Potential Precursor of Prosthetic Heme Group for Bacteria Inhabiting Fossil Organic Matter-Rich Shale Rock

This study hypothesizes that bacteria inhabiting shale rock affect the content of the sedimentary cobalt protoporphyrin present in it and can use it as a precursor for heme synthesis. To verify this hypothesis, we conducted qualitative and quantitative comparative analyses of cobalt protoporphyrin as well as heme, and heme iron in shale rock that were (i) inhabited by bacteria in the field, (ii) treated with bacteria in the laboratory, and with (iii) bacterial culture on synthetic cobalt protoporphyrin. Additionally, we examined the above-mentioned samples for the presence of enzymes involved in the heme biosynthesis and uptake as well as hemoproteins. We found depletion of cobalt protoporphyrin and a much higher heme concentration in the shale rock inhabited by bacteria in the field as well as the shale rock treated with bacteria in the laboratory. Similarly, we observed the accumulation of protoporphyrin in bacterial cells grown on synthetic cobalt protoporphyrin. We detected numerous hemoproteins in metaproteome of bacteria inhabited shale rock in the field and in proteomes of bacteria inhabited shale rock and synthetic cobalt protoporhyrin in the laboratory, but none of them had all the enzymes involved in the heme biosynthesis. However, proteins responsible for heme uptake, ferrochelatase and sirohydrochlorin cobaltochelatase/sirohydrochlorin cobalt-lyase were detected in all studied samples.

Postdiagenetic Bacterial Transformation of Nickel and Vanadyl Sedimentary Porphyrins of Organic-Rich Shale Rock (Fore-Sudetic Monocline, Poland)

Nickel and vanadyl porphyrins belong to the so-called fossil geo- or sedimentary porphyrins. They occur in different types of organic matter-rich sediments but mostly occur in crude oils and their source rocks, oil shales, coals, and oil sands. In this study, we aimed to understand the process of bacterial transformation of geoporphyrins occurring in the subsurface shale rock (Fore-Sudetic Monocline, SW Poland). We studied these transformations in rock samples directly obtained from the field; in rock samples treated with bacterial strain isolated from shale rock (strain LM27) in the laboratory; and using synthetic nickel and vanadyl porphyrins treated with LM27. Our results demonstrate the following: (i) cleavage and/or degradation of aliphatic and aromatic substituents of porphyrins; (ii) degradation of porphyrin (tetrapyrrole) ring; (iii) formation of organic compounds containing 1, 2, or 3 pyrrole rings; (iv) formation of nickel- or vanadium-containing organic compounds; and (v) mobilization of nickel and vanadium. Our results also showed that the described bacterial processes change the composition and content of geoporphyrins, composition of extractable organic matter, as well as nickel and vanadium content in shale rock.

Asphaltene biotransformation for heavy oil upgradation

Globally, the reserves of heavy crude oil are seven times more abundant than that of light crude, and yet, they are underutilized because of their high viscosity and density, which is largely due to the presence of large amounts of asphaltenes. Biotransformation of heavy oil asphaltenes into smaller metabolites can be used for reducing their viscosity. Several microorganisms capable of asphaltene biodegradation have been reported but only few have been characterized for its biotransformation. In the present study, a 9-membered microbial consortium was isolated from an oil contaminated soil. About 72% and 75% asphaltene biotransformation was achieved by growing cells at shake flask level and in a 1.5 l bioreactor, respectively. A representative structure of asphaltene was constructed based on LC–MS, ¹H-NMR, ¹³C-NMR, FT-IR, ICPMS and elemental analysis (CHNS) of n-heptane purified asphaltene from Maya crude oil. Biotransformation of asphaltene, as analyzed by performing ¹H-NMR, FT-IR and elemental analysis, resulted in 80% decrease in S and N when compared to the control along with incorporation of oxygen in the structure of asphaltene. About 91% decrease in the viscosity of the Maya crude oil was observed after two weeks when oil: aqueous phase ratio was 1:9. The results suggest that the isolated microbial consortium can be used for biological upgradation of heavy crude oil. To our knowledge, this is the first report where a microbial consortium resulted in such high asphaltene biotransformation.

Developmental toxicity of carbon nanoparticles during embryogenesis in chicken

Nanoparticles (NPs) are very small particles present in a wide range of materials. There is a dearth of knowledge regarding their potential secondary effects on the health of living organisms and the environment. Increasing research attention, however, has been directed toward determining the effects on humans exposed to NPs in the environment. Although the majority of studies focus on adult animals or populations, embryos of various species are considered more susceptible to environmental effects and pollutants. Hence, research studies dealing mainly with the impacts of NPs on embryogenesis have emerged recently, as this has become a major concern. Chicken embryos occupy a special place among animal models used in toxicity and developmental investigations and have also contributed significantly to the fields of genetics, virology, immunology, cell biology, and cancer. Their rapid development and easy accessibility for experimental observance and manipulation are just a few of the advantages that have made them the vertebrate model of choice for more than two millennia. The early stages of chicken embryogenesis, which are characterized by rapid embryonic growth, provide a sensitive model for studying the possible toxic effects on organ development, body weight, and oxidative stress. The objective of this review was to evaluate the toxicity of various types of carbon black nanomaterials administered at the beginning of embryogenesis in a chicken embryo model. In addition, the effects of diamond and graphene NPs and carbon nanotubes are reviewed.

Potential applications of microbial enhanced oil recovery to heavy oil

Heavy oil accounts for around one-third of total global oil and gas resources. The progressive depletion of conventional energy reserves has led to an increased emphasis on the efficient exploitation of heavy oil and bitumen reserves in order to meet energy demand. Therefore, it is imperative to develop new technologies for heavy oil upgrading and recovery. Biologically-based technology that involves using microorganisms or their metabolites to mobilize heavy oil trapped in reservoir rocks can make a significant contribution to the recovery of heavy oils. Here, the results of laboratory experiments and field trials applying microbial enhanced oil recovery (MEOR) technologies are summarized. This review provides an overview of the basic concepts, mechanisms, advantages, problems, and trends in MEOR, and demonstrates the credibility of MEOR methods for applications in enhanced heavy oil recovery and the petroleum refining processes. This technology is cost-effective and environmentally-friendly. The feasibility of MEOR technologies for heavier oil has not yet been fully realized due to the perceived process complexity and a lack of sufficient laboratory research and field test data. However, novel developments such as enzyme-enhanced oil recovery continues to improve MEOR methods.HighlightsHeavy oil represents the largest known potentially-recoverable petroleum energy resource.Novel biotechnological processes are needed to recover or upgrade heavy oil.Microbial technologies have great potential for heavy oil recovery.Microorganisms can produce metabolic byproducts to mobilize oil trapped in reservoirs.More technological research is needed to develop microbial enhanced oil recovery.

Effect of Various Isolated Microbial Consortiums on the Biodegradation Process of Precipitated Asphaltenes from Crude Oil

One of the serious problems in the oil industry is precipitation and deposition of asphaltenes in the different oil production stages including formation, wellbore, production tubing, flow lines, and separation units. This phenomenon causes a dramatic increase in the cost of oil production, processing, and transferring. Thus, it seems to be very necessary to use the removing methods for precipitated asphaltenes in different crude oil production and transferring stages. In this study, the ability of microorganisms for biodegradation of precipitated asphaltenes was investigated. For this purpose, four bacterial consortiums were isolated from oil-contaminated soil, crude oil, reservoir water, and oil sludge samples of an oil field located in the southwest of Iran. Based on the results of the designed experiments, by using response surface methodology (RSM) and central composite design, the bacterial consortiums were cultured in the flasks. Three levels of temperatures, salinity, pH, and initial asphaltene concentration as the substrate were considered as the parameters of culture medium and incubated growth mediums for 60 days. The maximum asphaltene biodegradation was 46.41% caused by the crude oil consortium including Staphylococcus saprophyticus sp. and Bacillus cereus sp. at 45 °C, salinity 160 g·L^-1, pH 6.5, and 25 g·L^-1 initial asphaltene concentration. Also, it was observed that the negative or positive impacts of culture media conditions such as temperature and salinity on asphaltene degradation depended on the type of the available bacterial consortium. The carbon-hydrogen-nitrogen-sulfur analysis showed that carbon, hydrogen, nitrogen, and in some cases, the sulfur in biodegraded samples are less than in control samples. Moreover, Fourier transform infrared analysis indicated that the alkyne groups were less resistant to biodegradation and were eliminated thoroughly after 2 months of incubation. In addition, alkane components were partially removed in treated asphaltene fraction. The parameters of culture medium were optimized by RSM, and besides, their effects on the performance of bacteria in the asphaltene biodegradation process were discussed. The validity of some available kinetic models to describe the behavior of the studied bacteria consortium was investigated, and it was observed that Tessier, Moser, and Contois models accurately predict the values of asphaltenes and biomass concentration at 30, 45, and 60 °C, respectively.

PEGylation as an efficient tool to enhance cytochrome c thermostability: a kinetic and thermodynamic study

PEGylation of cytochrome-c preserves activity and increases thermal stability, favoring the protein application as a biosensor.

Simultaneous valorization and biocatalytic upgrading of heavy vacuum gas oil by the biosurfactant-producing Pseudomonas aeruginosa AK6U

Heavy vacuum gas oil (HVGO) is a complex and viscous hydrocarbon stream that is produced as the bottom side product from the vacuum distillation units in petroleum refineries. HVGO is conventionally treated with thermochemical process, which is costly and environmentally polluting. Here, we investigate two petroleum biotechnology applications, namely valorization and bioupgrading, as green approaches for valorization and upgrading of HVGO. The Pseudomonas aeruginosa AK6U strain grew on 20% v/v of HVGO as a sole carbon and sulfur source. It produced rhamnolipid biosurfactants in a growth-associated mode with a maximum crude biosurfactants yield of 10.1 g l-1 , which reduced the surface tension of the cell-free culture supernatant to 30.6 mN m-1 within 1 week of incubation. The rarely occurring dirhamnolipid Rha-Rha-C12 -C12 dominated the congeners' profile of the biosurfactants produced from HVGO. Heavy vacuum gas oil was recovered from the cultures and abiotic controls and the maltene fraction was extracted for further analysis. Fractional distillation (SimDist) of the biotreated maltene fraction showed a relative decrease in the high-boiling heavy fuel fraction (BP 426-565 °C) concomitant with increase in the lighter distillate diesel fraction (BP 315-426 °C). Analysis of the maltene fraction revealed compositional changes. The number-average (Mn) and weight-average (Mw) molecular weights, as well as the absolute number of hydrocarbons and sulfur heterocycles were higher in the biotreated maltene fraction of HVGO. These findings suggest that HVGO can be potentially exploited as a carbon-rich substrate for production of the high-value biosurfactants by P. aeruginosa AK6U and to concomitantly improve/upgrade its chemical composition.

Potential role of oxidative exoenzymes of the extremophilic fungus Pestalotiopsis palmarum BM-04 in biotransformation of extra-heavy crude oil

Large amount of drilling waste associated with the expansion of the Orinoco Oil Belt (OOB), the biggest proven reserve of extra-heavy crude oil (EHCO) worldwide, is usually impregnated with EHCO and highly salinized water-based drilling fluids. Oxidative exoenzymes (OE) of the lignin-degrading enzyme system (LDS) of fungi catalyse the oxidation of a wide range of toxic pollutants. However, very little evidences on fungal degradation or biotransformation of EHCO have been reported, which contain high amounts of asphaltenes and its biodegradation rate is very limited. The aims of this work were to study the ability of Pestalotiopsis palmarum BM-04 to synthesize OE, its potential to biotransform EHCO and to survive in extreme environmental conditions. Enzymatic studies of the LDS showed the ability of this fungus to overproduce high amounts of laccase (LACp) in presence of wheat bran or lignin peroxidase (LIPp) with EHCO as sole carbon and energy source (1300 U mgP(-1) in both cases). FT-IR spectroscopy with Attenuated Total Reflectance (ATR) analysis showed the enzymatic oxidation of carbon and sulfur atoms in both maltenes and asphaltenes fractions of biotreated EHCO catalysed by cell-free laccase-enriched OE using wheat bran as inducer. UV-visible spectrophotometry analysis revealed the oxidation of the petroporphyrins in the asphaltenes fraction of biotreated EHCO. Tolerance assays showed the ability of this fungus to grow up to 50,000 p.p.m. of EHCO and 2000 mM of NaCl. These results suggest that P. palmarum BM-04 is a hopeful alternative to be used in remediation processes in extreme environmental conditions of salinity and EHCO contamination, such as the drilling waste from the OOB.

First evidence of mineralization of petroleum asphaltenes by a strain of Neosartorya fischeri

A fungal strain isolated from a microbial consortium growing in a natural asphalt lake is able to grow in purified asphaltenes as the only source of carbon and energy. The asphaltenes were rigorously purified in order to avoid contamination from other petroleum fractions. In addition, most of petroporphyrins were removed. The 18S rRNA and β-tubulin genomic sequences, as well as some morphologic characteristics, indicate that the isolate is Neosartorya fischeri. After 11 weeks of growth, the fungus is able to metabolize 15.5% of the asphaltenic carbon, including 13.2% transformed to CO(2) . In a medium containing asphaltenes as the sole source of carbon and energy, the fungal isolate produces extracellular laccase activity, which is not detected when the fungus grow in a rich medium. The results obtained in this work clearly demonstrate that there are microorganisms able to metabolize and mineralize asphaltenes, which is considered the most recalcitrant petroleum fraction.

Microbial biocatalyst developments to upgrade fossil fuels

Steady increases in the average sulfur content of petroleum and stricter environmental regulations concerning the sulfur content have promoted studies of bioprocessing to upgrade fossil fuels. Bioprocesses can potentially provide a solution to the need for improved and expanded fuel upgrading worldwide, because bioprocesses for fuel upgrading do not require hydrogen and produce far less carbon dioxide than thermochemical processes. Recent advances have demonstrated that biodesulfurization is capable of removing sulfur from hydrotreated diesel to yield a product with an ultra-low sulfur concentration that meets current environmental regulations. However, the technology has not yet progressed beyond laboratory-scale testing, as more efficient biocatalysts are needed. Genetic studies to obtain improved biocatalysts for the selective removal of sulfur and nitrogen from petroleum provide the focus of current research efforts.

Use and improvement of microbial redox enzymes for environmental purposes

Industrial development may result in the increase of environmental risks. The enzymatic transformation of polluting compounds to less toxic or even innocuous products is an alternative to their complete removal. In this regard, a number of different redox enzymes are able to transform a wide variety of toxic pollutants, such as polynuclear aromatic hydrocarbons, phenols, azo dyes, heavy metals, etc. Here, novel information on chromate reductases, enzymes that carry out the reduction of highly toxic Cr(VI) to the less toxic insoluble Cr(III), is discussed. In addition, the properties and application of bacterial and eukaryotic proteins (lignin-modifying enzymes, peroxidases and cytochromes) useful in environmental enzymology is also discussed.