Genomic and biotechnological potential of a novel oil-degrading strain Enterobacter kobei DH7 isolated from petroleum-contaminated soil

In this study, a novel oil-degrading strain Enterobacter kobei DH7 was isolated from petroleum-contaminated soil samples from the industrial park in Taolin Town, Lianyungang, China. The whole genome of the strain was sequenced and analyzed to reveal its genomic potential. The oil degradation and growth conditions including nitrogen, and phosphorus sources, degradation cycle, biological dosing, pH, and oil concentration were optimized to exploit its commercial application. The genome of the DH7 strain contains 4,705,032 bp with GC content of 54.95% and 4653 genes. The genome analysis revealed that there are several metabolic pathways and enzyme-encoding genes related to oil degradation in the DH7 genome, such as the paa gene cluster which is involved in the phenylacetic acid degradation pathway, and complete degradation pathways for fatty acid and benzoate, genes related to chlorinated alkanes and olefins degradation pathway including adhP, frmA, and adhE, etc. The strain DH7 under the optimized conditions has demonstrated a maximum degradation efficiency of 84.6% after 14 days of treatment using synthetic oil, which comparatively displays a higher oil degradation efficiency than any Enterobacter species known to date. To the best of our knowledge, this study presents the first-ever genomic studies related to the oil degradation potential of any Enterobacter species. As Enterobacter kobei DH7 has demonstrated significant oil degradation potential, it is one of the good candidates for application in the bioremediation of oil-contaminated environments.

Characterization of pumilacidin, a lipopeptide biosurfactant produced from Bacillus pumilus NITDID1 and its prospect in bioremediation of hazardous pollutants

Highly hydrophobic compounds like petroleum and their byproducts, once released into the environment, can persist indefinitely by virtue of their ability to resist microbial degradation, ultimately paving the path to severe environmental pollution. Likewise, the accumulation of toxic heavy metals like lead, cadmium, chromium, etc., in the surroundings poses an alarming threat to various living organisms. To remediate the matter in question, the applicability of a biosurfactant produced from the mangrove bacterium Bacillus pumilus NITDID1 (Accession No. KY678446.1) is reported here. The structural characterization of the produced biosurfactant revealed it to be a lipopeptide and has been identified as pumilacidin through FTIR, NMR, and MALDI-TOF MS. The critical micelle concentration of pumilacidin was 120 mg/L, and it showed a wide range of stability in surface tension reduction experiments under various environmental conditions and exhibited a high emulsification index of as much as 90%. In a simulated setup of engine oil-contaminated sand, considerable oil recovery (39.78%) by this biosurfactant was observed, and upon being added to a microbial consortium, there was an appreciable enhancement in the degradation of the used engine oil. As far as the heavy metal removal potential of biosurfactant is concerned, as much as 100% and 82% removal was observed for lead and cadmium, respectively. Thus, in a nutshell, the pumilacidin produced from Bacillus pumilus NITDID1 holds promise for multifaceted applications in the field of environmental remediation.

Chemical conversions of free phytosterols during the bleaching of corn oil

Phytosterols have health benefits; however, they are partially removed during the bleaching of corn oil. We evaluated the chemical conversion of free phytosterols (FPs) during bleaching. FP degradation accelerated with increased time and temperature, following a first-order kinetic model. In the n-heptane system, air and activated clay promoted the chemical conversion of the FPs. Sterenes formation was analysed under different conditions using a zero-order kinetic model. The apparent activation energies revealed sterene formation decreasing in the following order: campesta-3,5-diene ≈ stigmasta-3,5,22-triene > stigmasta-3,5-diene. Isomers of the above were not detected, indicating that these sterenes were the only primary products of FPs. The desorption test indicated that the FP loss from corn oil was not only due to FPs being adsorbed the activated clay, but also FPs adsorbed at acidic activated sites being degraded. This study presents a vital scientific foundation for retaining FPs to develop healthier and more nutritious oils.

Biodiversity and degradation potential of oil-degrading bacteria isolated from sediments of hydrothermal and non-hydrothermal areas of the Southwest Mid-Indian Ocean Ridge

In this study, sediments from eight sites were collected from hydrothermal areas (e.g., the Tiancheng, Tianzuo, and Longqi hydrothermal areas) and non-hydrothermal area on the Southwest Mid-Indian Ocean Ridge. Using crude oil as the only carbon and energy source, 162 strains of culturable oil-degrading bacteria were isolated and obtained. The rate of oil degradation of the consortia was 39.48-46.00% in hydrothermal and non-hydrothermal areas. High-throughput sequencing found that the alpha diversity indices (e.g., Shannon and Simpson) of the communities in hydrothermal areas were higher than those in non-hydrothermal area. The species diversities of the oil-degrading bacteria were different among different hydrothermal areas. The composition of the oil-degrading bacterial species in the Tianzuo hydrothermal area tended to be more similar to that in the non-hydrothermal area. This similarity is attributed to the changes in the bacterial community that followed the cessation of hydrothermal vent eruptions at this site. The Alphaproteobacteria abundance of the oil-degrading bacteria was significantly different in oil-degrading bacteria between the hydrothermal and non-hydrothermal areas.

Oil degradation and variation of microbial communities in contaminated soils induced by different bacterivorous nematodes species

Oil pollution poses a great threat to environments and makes the remediation of oil-contaminated soils an urgent task. Microorganisms are the main biological factor for oil removal in the environment but microbial remediation is greatly affected by environmental factors. For our research, we inoculated three species of bacterivorous nematodes into oil-contaminated soil to explore how bacterivorous nematodes affect soil microbial activities and community structure in contaminated soil, as well as how efficiently different nematodes remove oil pollution from the soil. Six treatments were set in this experiment: sterilized oil-contaminated soil (SOC); nematode-free soil (S); oil-contaminated soil (OC); oil-contaminated soil + Caenorhabditis elegans (OCN1); oil-contaminated soil + Cephalobus persegnis (OCN2); oil-contaminated soil + Rhabditis marina (OCN3) for a 168-day incubation experiment. After the experiment was done, the oil contents in SOC, OC, OCN1, OCN2, and OCN3 were reduced by 6.5%, 32.3%, 38.2%, 42.8%, and 40.2%, respectively, compared with the beginning of the experiment. The amount of phospholipid fatty acids (PLFAs) of Gram-negative bacteria in OC, OCN1, OCN2, and OCN3 was increased by 50.9%, 43.4%, 37.7%, and 47.9%, respectively, compared with that of S. During the 168-day incubation period, the maximum growth of the number of nematodes in OCN1, OCN2, and OCN3 compared with the initial number of the nematodes were 2.25-, 1.52-, and 1.65-fold, respectively. The amount of oil residue in the contaminated soil negatively correlated with the populations of nematodes, total microorganisms, Gram-negative bacteria, actinomycetes, and eukaryotes. Thus, oil pollution increased the number of Gram-negative bacteria, decreased the ratio of Gram-positive bacteria/Gram-negative bacteria and Fungi/Bacteria significantly, and altered the community structure of soil microorganisms. Each species of bacterivorous nematodes has got its unique effect on the microbial activity and community structure in oil contaminated soils, but those tested can promote oil degradation and thus improve the environment of oil contaminated soils.

An innovative method to reduce oil waste using a sensor made of recycled material to evaluate engine oil life in automotive workshops

In this work, a capacitive sensor made of recycled material is proposed to monitor oil quality in automotive workshops in order to reduce the waste of useful lubricant oil caused by shorter periods of use than those established by the manufacturers. The sensor was fabricated from a recycled aluminum heat sink and used to measure the permittivity of oil samples. The proposed method was compared with Fourier-transform infrared spectroscopy analysis to evaluate degradation parameters, as described in standard practice ASTM E-2412. The obtained results showed good agreement between both techniques, validating the use of the proposed sensor to evaluate oil condition. The use of permittivity measurements could be used to evaluate oil quality in an easier, faster, and economical way compared with other laboratory tests.

Variation of Microbial Diversity in Catastrophic Oil Spill Area in Marine Ecosystem and Hydrocarbon Degradation of UCMs (Unresolved Complex Mixtures) by Marine Indigenous Bacteria

The study targeted an assessment of microbial diversity during oil spill in the marine ecosystem (Kaohsiung port, Taiwan) and screened dominant indigenous bacteria for oil degradation, as well as UCM weathering. DO was detected lower and TDS/conductivity was observed higher in oil-spilled area, compared to the control, where a significant correlation (R² = 1; P < 0.0001) was noticed between DO and TDS. The relative abundance (RA) of microbial taxa and diversities (> 90% similarity by NGS) were found higher in the boundary region of spilled-oily-water (site B) compared to the control (site C) and center of the oil spill area (site A) (B_RA/diversity > C_RA/diversity > A_RA/diversity). The isolated indigenous bacteria, such as Staphylococcus saprophyticus (CYCTW1), Staphylococcus saprophyticus (CYCTW2), and Bacillus megaterium (CYCTW3) degraded the C₁₀-C₃₀ including UCM of oil, where Bacillus sp. are exhibited more efficient, which are applicable for environmental cleanup of the oil spill area. Thus, the marine microbial diversity changes due to oil spill and the marine microbial community play an important role to biodegrade the oil, besides restoring the catastrophic disorders through changing their diversity by ecological selection and adaptation process.

Characterisation of Streptomyces violascens OC125-8 lipase for oily wastewater treatment

In this study, the lipase-producing bacterium Streptomyces violascens (GenBank number MF621564) was identified, and the extracellular S. violascens OC125-8 lipase produced by this strain was characterised for use in wastewater treatment. The lipase was partially purified by ammonium sulphate precipitation at a final yield of 3.28-fold purification and a recovery of 56%. The S. violascens OC125-8 lipase exhibited optimum catalytic activity at 40 °C and pH 8.0; it was stable at 30-40 °C with more than 86% residual activity after 1 h; it was also stable over a relatively broad pH range of pH 7.0-11.0, retaining 83.3-100% activity. V _max and K _m values were calculated as 0.61 µmol/min/mg and 0.259 mM, respectively. Enzyme activity significantly increased in the presence of Fe²⁺ ion but was inhibited by Ca²⁺, Mn²⁺, Cu²⁺ and Mg²⁺. The addition of a serine protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), strongly inhibited enzyme activity while ethylenediaminetetraacetic acid (EDTA), a metal chelating agent, had no inhibitory effect. The enzyme was fairly stable in the presence of surfactants as well as sodium perborate. Examination of commercial detergent tolerance revealed that the lipase was strongly stable in Tursil (88%), Pril (97%) and Fairy (98.5%), while the lipase was activated in Omo (113.4%) and Ariel (128.3%). Moreover, the lipase showed highest activity towards olive oil (100%), sunflower oil (90%) and burned sunflower oil (55%), while corn oil (44%) and burned olive oil (15%) were less hydrolysed by the enzyme. These properties demonstrate that S. violascens OC125-8 lipase is an ideal choice for oily wastewater management.

Effects of bacterial-feeding nematodes and organic matter on microbial activity and oil degradation in contaminated soil

Increasing rates of oil exploitation and utilization are associated with increasing rates of oil pollution in soil. Nematodes are abundant in soils with or without oil contamination, among which bacterial-feeding nematodes are the dominant group. However, their function in oil-contaminated soil is unclear. This study explores the effects of bacterial-feeding nematode and organic matter addition on microbial activity and oil degradation in contaminated soil. Experiments were conducted using six treatments of oil-contaminated soil: sterilized (Control), nematode-free (OC), nematode addition (OCN), nematode + wheat straw addition (OCNW), nematode + rapeseed cake addition (OCNR), and nematode + biochar addition (OCNB). At the end of a 168-day incubation experiment, the oil concentration of OCN soil was 26.77% lower than that of OC soil, and those of OCNW, OCNR, and OCNB were 12.83%, 27.81%, and 4.77% lower, respectively, than that of OCN soil. Over the experiment, soil microbial biomass carbon, fluorescein diacetate hydrolysis activity, and dehydrogenase activity increased by 4.35-382.30%, 1.75-302.22%, and - 2.73-224.55%, respectively, in oil-contaminated soils, with or without nematode and organic matter addition. These results suggest that the addition of organic matter and bacterial-feeding nematodes to oil-contaminated soil can promote the growth and activity of microorganisms that break down oil.

RNA-seq analysis reveals the significant effects of different light conditions on oil degradation by marine Chlorella vulgaris

Marine Chlorella vulgaris, an efficient hydrocarbon-degrading organism, is easily affected by light. In this study, we investigated the direct effects of different light conditions on crude oil degradation by C. vulgaris and its crude enzyme. Under 12 h illumination, the crude enzyme improved hydrocarbon removal by 39.36%, whereas the addition of the enzyme and C. vulgaris increased the degradation rate by 121.73%. Conversely, the addition of enzyme under heterotrophic condition was negatively related to oil degradation by C. vulgaris, and the degradation rate decreased from 74.32% to 48.65% and further reduced by 34.54%. The results of RNA sequencing analysis suggested that hydrocarbons removal was attributed to C. vulgaris metabolism in heterotrophic physiological state. While enhanced removal efficiency of hydrocarbons was achieved in mixotrophic physiological state due to the coupling of C. vulgaris metabolism with photocatalytic oxidation. Functional enzymes played key roles in photocatalysis and biodegradation processes.

Analysis of fatty acid profiles of free fatty acids generated in deep-frying process

During the deep fat food frying process, the frying media, oil, continuously degenerates when exposed to high temperature, oxygen and moisture. This leads to physical and chemical changes including the formation of hydrolysis products such as free fatty acids (FFAs) which are associated with undesirable darkening in colour, off-flavouring and a lowering of the smoke point. This study was aiming to develop a method capable of identifying and quantifying individual free fatty acids within oil using a small sample size (100 mg of oil). We used liquid/liquid extraction technique to separate FFAs from the rest of the oil followed by esterification using boron trifluoride (BF3) and then gas chromatography analysis. Various extraction conditions were tested. A mixture of 0.02 M phosphate buffer at pH 12 and acetonitrile at solvent: buffer ratio larger than 2:1 showed the highest efficiency in extraction of FFAs. The method was capable of producing accurate fatty acid profiles of FFAs and showed good precision on medium rancidity oil samples. It also captured the differences induced by adding free fatty acids to samples. An interesting discrepancy was found between the new method and the traditional titration method in terms of overall FFA content, which suggests further optimisation and investigation are required.

Soybean plant-based toxicity assessment and phytoremediation of soils contaminated by vegetable and mineral oils used in power electrical transformers

In this work, deleterious effects in soils due to the presence of dielectric fluids were investigated. For this purpose, vegetable (Envirotemp® FR3) and mineral (Lubrax AV 66 IN) oils were used for simulating a set of soils contaminated in different oil contents (0.5, 1.0, 2.0, 2.5, 5.0, 7.5 and 10%) in which three 120-days soybean crop periods (SCP) were carried out using the species Glycine max (L.) Merr. Both soil and soybean plant samples were analysed on following the changes on chemical attributes, content of oils and greases (COG) in soils and phytotechnical characteristics of soybean plant. No significant changes on soil chemical attributes were found. For a 0.5% vegetable oil fraction, COG removals of 35, 60 and 90% were observed after the 1st, 2nd, and 3rd SCPs, respectively, whereas removals of 25, 40 and 70% were observed for 0.5% mineral oil fraction after the 1st, 2nd, and 3rd SCPs, respectively. There was an effectively accumulated removal on all tested oil fractions as being proportional to the integrated 120-days SCPs, suggesting a lesser number of crops for a complete abatement of oil fraction in soil. A 100% recovery on the seedlings emergence fractions was also evidenced, revealing that at least a number of 7 and 9 SCPs should be applied continuously in soils contaminated by vegetable and mineral oils, respectively, in order to no longer jeopardize soybean plant growth. Finally, an empirical prediction of the number of SCPs necessary for the complete removal of oil from the soil was proposed.

Electro-biocatalytic treatment of petroleum refinery wastewater using microbial fuel cell (MFC) in continuous mode operation

Refinery wastewater (RW) treatment in microbial fuel cell (MFC) was studied in batch mode operation followed by continuous mode operation with 8h and 16h hydraulic retention time (HRT). The MFC performance was evaluated in terms of power density, organics removal, specific contaminants (oil & grease, phenol and sulfide) removal and energy conversion efficiency with respect to operation mode. Higher power density of 225±1.4mW/m² was observed during continuous mode operation with 16h HRT along with a substrate degradation of 84.4±0.8% including the 95±0.6 of oil content. The columbic efficiency during this operation was about 2±0.8% and the projected power yield was 340±20kWh/kg COD_R/day. Batch mode operation also showed good substrate degradation (81±1.8%) but took longer HRT which resulted in significantly low substrate degradation rate (0.036±0.002kgCOD_R/m³-day) over continuous mode operation (1.05±0.01kgCOD_R/m³-day). Overall, current study depicted the possibility of utilizing RW as substrate in MFC for power generation along with its treatment.

Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill

The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we present a preliminary set of physiological features of strain O3.65 and a description and annotation of its draft genome sequence. Based on our data we suggest potential ecological roles of the isolate in the degradation of crude oil within the network of the oil-enriched microbial community. The draft genome comprises 4,852,484 bp with 4,591 protein-coding genes and 63 RNA genes. Strain O3.65 utilizes pentoses, hexoses, disaccharides and amino acids as carbon and energy source and is able to grow on several hydroxylated and substituted aromatic compounds. Based on 16S rRNA gene comparison the closest described and validated strain is Phaeobacter inhibens DSM 17395, however, strain O3.65 is lacking several phenotypic and genomic characteristics specific for the genus Phaeobacter. Phylogenomic analyses based on the whole genome support extensive genetic exchange of strain O3.65 with members of the genus Ruegeria, potentially by using the secretion system type IV. Our physiological observations are consistent with the genomic and phylogenomic analyses and support that strain O3.65 is a novel species of a new genus within the Rhodobacteraceae.

Isolation and characterization of a crude oil degrading bacteria from formation water: comparative genomic analysis of environmental Ochrobactrum intermedium isolate versus clinical strains

In this study, we isolated an environmental clone of Ochrobactrum intermedium, strain 2745-2, from the formation water of Changqing oilfield in Shanxi, China, which can degrade crude oil. Strain 2745-2 is aerobic and rod-shaped with optimum growth at 42 °C and pH 5.5. We sequenced the genome and found a single chromosome of 4 800 175 bp, with a G+C content of 57.63%. Sixty RNAs and 4737 protein-coding genes were identified: many of the genes are responsible for the degradation, emulsification, and metabolizing of crude oil. A comparative genomic analysis with related clinical strains (M86, 229E, and LMG3301(T)) showed that genes involved in virulence, disease, defense, phages, prophages, transposable elements, plasmids, and antibiotic resistance are also present in strain 2745-2.

Perennial crop growth in oil-contaminated soil in a boreal climate

Soil contamination by petroleum hydrocarbons is a global problem. Phytoremediation by plants and their associated microorganisms is a cost-effective strategy to degrade soil contaminants. In boreal regions the cool climate limits the efficiency of phytoremediation. The planting of oil-tolerant perennial crops, especially legumes, in oil-contaminated soil holds promise for great economic benefits for bioenergy and bio-fertilizer production while accelerating the oil degradation process. We established a multi-year field experiment to study the ecological and agronomic feasibility of phytoremediation by a legume (fodder galega) and a grass (smooth brome) in a boreal climate. In 40 months, soil oil content decreased by 73%-92%, depending on the crop type. The oil degradation followed first-order kinetics with the reduction rates decreasing as follows: bare fallow > galega-brome grass mixture > brome grass > galega. Surprisingly, the presence of oil enhanced crop dry matter and nitrogen yield, particularly in the fourth year. The unfertilized galega-brome grass mixture out-yielded the N-fertilized pure grass swards over years by an average of 33%. Thus, a perennial legume-grass mixture is both ecologically and agronomically sustainable as a cropping system to alleviate soil contamination in the boreal zone, with considerable potential for bioenergy and bio-fertilizer production.

Isolation of phenazine 1,6-di-carboxylic acid from Pseudomonas aeruginosa strain HRW.1-S3 and its role in biofilm-mediated crude oil degradation and cytotoxicity against bacterial and cancer cells

Pseudomonas sp. has long been known for production of a wide range of secondary metabolites during late exponential and stationary phases of growth. Phenazine derivatives constitute a large group of secondary metabolites produced by microorganisms including Pseudomonas sp. Phenazine 1,6-di-carboxylic acid (PDC) is one of such metabolites and has been debated for its origin from Pseudomonas sp. The present study describes purification and characterization of PDC isolated from culture of a natural isolate of Pseudomonas sp. HRW.1-S3 while grown in presence of crude oil as sole carbon source. The isolated PDC was tested for its effect on biofilm formation by another environmental isolate of Pseudomonas sp. DSW.1-S4 which lacks the ability to produce any phenazine compound. PDC showed profound effect on both planktonic as well as biofilm mode of growth of DSW.1-S4 at concentrations between 5 and 20 μM. Interestingly, PDC showed substantial cytotoxicity against three cancer cell lines and against both Gram-positive and Gram-negative bacteria. Thus, the present study not only opens an avenue to understand interspecific cooperation between Pseudomonas species which may lead its applicability in bioremediation, but also it signifies the scope of future investigation on PDC for its therapeutic applications.

The effect of sand composition on the degradation of buried oil

The potential effects of the mineralogical composition of sediment on the degradation of oil buried on sandy beaches were investigated. Toward that purpose, a laboratory experiment was carried out with sandy sediment collected along NW Iberian Peninsula beaches, tar-balls from the Prestige oil spill (NW Spain) and seawater. The results indicate that the mineralogical composition is important for the physical appearance of the oil (tar-balls or oil coatings). This finding prompted a reassessment of the current sequence of degradation for buried oil based on compositional factors. Moreover, the halo development of the oil coatings might be enhanced by the carbonate concentration of the sand. These findings open new prospects for future monitoring and management programs for oiled sandy beaches.

Yarrowia lipolytica and pollutants: Interactions and applications

Yarrowia lipolytica is a dimorphic, non-pathogenic, ascomycetous yeast species with distinctive physiological features and biochemical characteristics that are significant in environment-related matters. Strains naturally present in soils, sea water, sediments and waste waters have inherent abilities to degrade hydrocarbons such as alkanes (short and medium chain) and aromatic compounds (biphenyl and dibenzofuran). With the application of slow release fertilizers, design of immobilization techniques and development of microbial consortia, scale-up studies and in situ applications have been possible. In general, hydrocarbon uptake in this yeast is mediated by attachment to large droplets (via hydrophobic cell surfaces) or is aided by surfactants and emulsifiers. Subsequently, the internalized hydrocarbons are degraded by relevant enzymes innately present in the yeast. Some wild-type or recombinant strains also detoxify nitroaromatic (2,4,6-trinitrotoluene), halogenated (chlorinated and brominated hydrocarbons) and organophosphate (methyl parathion) compounds. The yeast can tolerate some metals and detoxify them via different biomolecules. The biomass (unmodified, in combination with sludge, magnetically-modified and in the biofilm form) has been employed in the biosorption of hexavalent chromium ions from aqueous solutions. Yeast cells have also been applied in protocols related to nanoparticle synthesis. The treatment of oily and solid wastes with this yeast reduces chemical oxygen demand or value-added products (single cell oil, single cell protein, surfactants, organic acids and polyalcohols) are obtained. On account of all these features, the microorganism has established a place for itself and is of considerable value in environment-related applications.