Study on bioadsorption and biodegradation of petroleum hydrocarbons by a microbial consortium

Efficient Bioremediation of Petroleum-Contaminated Soil by Immobilized Bacterial Agent of Gordonia alkanivorans W33

In this article, we report a method for preparing an immobilized bacterial agent of petroleum-degrading bacteria Gordonia alkanivorans W33 by combining high-density fermentation and bacterial immobilization technology and testing its bioremediation effect on petroleum-contaminated soil. After determining the optimal combination of MgCl₂, CaCl₂ concentration, and culture time in the fermentation conditions by conducting a response surface analysis, the cell concentration reached 7.48 × 10⁹ CFU/mL by 5 L fed-batch fermentation. The W33-vermiculite-powder-immobilized bacterial agent mixed with sophorolipids and rhamnolipids in a weight ratio of 9:10 was used for the bioremediation of petroleum-contaminated soil. After 45 days of microbial degradation, 56.3% of the petroleum in the soil with 20,000 mg/kg petroleum content was degraded, and the average degradation rate reached 250.2 mg/kg/d.

Genomics for the characterization of the mechanisms of microbial strains in degrading petroleum pollutants

Four petroleum-tolerant bacteria, namely, Pseudomonas hibiscicola, Enterobacter hormaechei, Rhizobium pusense and Pseudomonas japonica were isolated. These strains showed excellent performance in the remediation of petroleum contamination with degradation percentages of 26.13%, 26.47%, 32.27%, and 18.74% for petroleum hydrocarbons, 29.63%, 70.11%, 88.38%, and 67.03% for n-docosane, and 61.00%, 96.36%, 98.00%, and 67.01% for fluorene. Accordingly, the strain of Rhizobium pusense was used to further study its underlying degradation mechanism. N-docosane could be metabolised through the pathway of subterminal oxidation by Rhizobium pusense, while the main pathway for fluorene metabolism is the meta-cleavage. R. pusense contains 10 genes that are involved in the synthetic of biosurfactants and 71 genes that are involved in the metabolism of petroleum hydrocarbons and organic pollutants, such as hydrocarbons, toluene, xylene, ethylbenzene and naphthalene. This study was the first to determine that concerning the metabolism ability and metabolic genes of R. pusense for petroleum pollutant degradation, which is important for understanding the bioremediation mechanism of petroleum pollution.

Bioremediation of heavy oily sludge: a microcosms study

Oily sludge is a residue from the petroleum industry composed of a mixture of sand, water, metals, and high content of hydrocarbons (HCs). The heavy oily sludge used in this study originated from Colombian crude oil with high density and low American Petroleum Institute (API) gravity. The residual waste from heavy oil processing was subject to thermal and centrifugal extraction, resulting in heavy oily sludge with very high density and viscosity. Biodegradation of the total petroleum hydrocarbons (TPH) was tested in microcosms using several bioremediation approaches, including: biostimulation with bulking agents and nutrients, the surfactant Tween 80, and bioaugmentation. Select HC degrading bacteria were isolated based on their ability to grow and produce clear zones on different HCs. Degradation of TPH in the microcosms was monitored gravimetrically and with gas chromatography (GC). The TPH removal in all treatments ranged between 2 and 67%, regardless of the addition of microbial consortiums, amendments, or surfactants within the tested parameters. The results of this study demonstrated that bioremediation of heavy oily sludge presents greater challenges to achieve regulatory requirements. Additional physicochemical treatments analysis to remediate this recalcitrant material may be required to achieve a desirable degradation rate.

Degradation characteristics of crude oil by a consortium of bacteria in the existence of chlorophenol

In order to enhance the degradation effect of microorganisms on crude oil in the existence of chlorophenol compounds, oil-degrading bacteria C4 (Alcaligenes faecails), C5 (Bacillus sp.) and 2,4-dichlorophenol (2,4-DCP) degrading bacteria L3 (Bacillus marisflavi), L4 (Bacillus aquimaris) were isolated to construct a highly efficient consortium named (C4C5 + L3L4). When the compound bacteria agent combination by V_C4: V_C5: V_L3: V_L4 = 1:2:2:1, the crude oil degradation efficiency of 7 days was stable at 50.63% ~ 55.43% under different conditions. Degradation mechanism was analyzed by FTIR, GC-MS and IC technology and the following conclusions showed that in the system of adding consortium (C4C5 + L3L4), the heavy components were converted into saturated and unsaturated components. The bacterial consortium could first degrade medium and long chain alkanes into short chain hydrocarbons and then further degrade. And the dechlorination efficiency of 2,4-DCP in the degradation system reached 73.83%. The results suggested that the potential applicability and effectiveness of the selected bacteria consortium for the remediation of oil-contaminated water or soil with the existence of chlorophenol compound.

Effects of chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB

Many microorganisms have been reported to degrade organic pollutants in the environment and plants, however, the specific information about the effect of organic pollutants on the metabolism of microorganisms is poorly investigated. In the present study, the effect of the pesticide chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB was investigated using metabolomics. Our data show that chlorpyrifos acting as an energy source was readily concentrated in the strain RRB from the culture medium. During early cultivation, the shift in energy sources from tryptic soy broth to chlorpyrifos may temporarily cause the strain RRB to enter the starvation stage, where some synthesis-related amino acids and intermediates in the pathways of TCA cycle and pyridoxine metabolism were decreased. The increase of nucleotides and lysine may help the strain RRB cope with the starvation stage. During later cultivation, many metabolites including organic acids, nucleosides and sugar phosphates were gradually accumulated, which indicates that chlorpyrifos could be utilized by the stain RRB to generate metabolites bacteria needed. In addition, arginine acting as a nitrogen-storage amino acid was gradually decreased with later cultivation, suggesting that chlorpyrifos could not provide enough nitrogen for bacteria.

PAHs biodegradation in soil washing effluent by native mixed bacteria embedded in polyvinyl alcohol-sodium alginate-nano alumina gel beads

In this study, the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil washing solution containing Tween 80 was conducted using native mixed bacteria (Pseudomonas sp. Z1, Sphingobacterium sp. Z2, and Klebsiella sp. K) embedded in polyvinyl alcohol-sodium alginate-nano alumina (PVA-SA-ALNPs) gel beads. The optimal dosage of immobilized beads and embedded biomass for the biodegradation of phenanthrene (PHE), fluoranthene (FLU), and pyrene (PYR) were 10 % (v/v) and 20 % (v/v), respectively. SEM analysis showed that the porous structure of the immobilized beads was a cross-linked network with abundant pores that provided many potential adhesion sites for microorganisms. The beads with the immobilized mixed bacteria maintained a high activity during batch experiments and could even be reused for 3 cycles (90 d). Compared with the beads containing individual immobilized strain, the immobilized mixed bacteria showed a more efficient biodegradation of PHE (91.67 %), FLU (88.6 %), and PYR (88.5 %) in synthetic soil washing effluent within 30 d. The first-order kinetic model suitably described the degradation process of the three target PAHs. By adding Tween 80 to the synthetic eluent, the degradation of PHE, FLU, and PYR increased by 16.39 %, 22.25 %, and 21.29 %, respectively, indicating that Tween 80 promoted PAHs biodegradation, even though it was also rapidly degraded during the reaction cycle. These findings suggest that the developed mixed bacteria embedded in PVA-SA-ALNPs gel beads has great potential for PAHs remediation.

Mycoremediation potential of Aspergillus ochraceus NRRL 3174

Mycoremediation is an important process that targets the removal of petroleum hydrocarbons by fungi. Fungi have advantages with their extensive enzymatic systems, rapid adaptation to toxic organic pollutants, and to adverse environmental conditions. In this study, the colorimetric method was used for the preliminary investigation of petroleum degradation with ten fungal strains. Petroleum degradation ability of spore suspension, live biomass (fungal pellet and disc) and cell-free culture supernatant of the potent A. ochraceus strain were investigated by gravimetric analysis. It was found that the fungal disc (94%) was more successful than the spore suspension (87%) in petroleum degradation under physiological conditions determined as pH:5.0, 1% of petroleum concentration, 5% (v/v) of inoculum concentration (with spore suspension) and 1 g/100 mL of inoculum amount (with fungal disc) and 7 days of the incubation period. The degradation rate constant and half-life period of spore suspension were calculated as 0.291 day^-1 and t_1/2 = 0.340 and of the fungal disc were 0.401 day^-1 and t_1/2 = 0.247. Although, 7.5% and 10% (v/v) concentration of cell-free culture supernatant achieved more than 80% petroleum removal, it was not as effective as a fungal disc. According to gas chromatography/mass spectrometry analysis, the fungal disc of A. ochraceus strain degraded long-chain n-alkanes such as C₃₅ and C₃₆ more effectively than n-alkanes in the range of C₂₂-C₃₄. The fact that the A. ochraceus NRRL 3174 strain has a high petroleum degradation capacity as well as being a potent biosurfactant producer will provide a different perspective to advanced mycoremediation studies.

Mitigation of petroleum-hydrocarbon-contaminated hazardous soils using organic amendments: A review

The term "Total petroleum hydrocarbons" (TPH) is used to describe a complex mixture of petroleum-based hydrocarbons primarily derived from crude oil. Those compounds are considered as persistent organic pollutants in the terrestrial environment. A wide array of organic amendments is increasingly used for the remediation of TPH-contaminated soils. Organic amendments not only supply a source of carbon and nutrients but also add exogenous beneficial microorganisms to enhance the TPH degradation rate, thereby improving the soil health. Two fundamental approaches can be contemplated within the context of remediation of TPH-contaminated soils using organic amendments: (i) enhanced TPH sorption to the exogenous organic matter (immobilization) as it reduces the bioavailability of the contaminants, and (ii) increasing the solubility of the contaminants by supplying desorbing agents (mobilization) for enhancing the subsequent biodegradation. Net immobilization and mobilization of TPH have both been observed following the application of organic amendments to contaminated soils. This review examines the mechanisms for the enhanced remediation of TPH-contaminated soils by organic amendments and discusses the influencing factors in relation to sequestration, bioavailability, and subsequent biodegradation of TPH in soils. The uncertainty of mechanisms for various organic amendments in TPH remediation processes remains a critical area of future research.

Rapid capturing of oil-degrading bacteria by engineered attapulgite and their synergistic remediation for oil spill

HYPOTHESIS

High-efficiency dispersion and enhanced biodegradation play important roles in the treatment of oily wastewater. Due to the flaws of chemical surfactants, it is necessary to study the alternative dispersants that are eco-friendly and sustainable. Therefore, applying natural attapulgite (ATP) to coat Brevibacillus parabrevis for dispersion and biodegradation was studied.

EXPERIMENTS

To capture negatively charged bacteria in water, ATP was modified by positively charged Poly (allylamine hydrochloride) (PAH). The capturing capability of Poly (allylamine hydrochloride)-attapulgite (PAH-ATP) particles for bacterial cells, emulsification of PAH-ATP particles and bacteria on oil, toxicity of PAH-ATP to bacteria, biodegradation of oil, etc., were comprehensively investigated.

FINDINGS

PAH-ATP modified bacteria show a highly effective emulsification for oil due to the synergism of PAH-ATP and bacteria. The emulsion stabilized by (PAH-ATP)@bacteria presents small and stable oil droplets in one month, which is benefit for the following biodegradation. Compared with bare bacteria and PAH-ATP, PAH-ATP can capture bacteria to the surface of the oil droplets which can greatly improve the degradation of oil pollution. Importantly, the presence of PAH-ATP does not inhibit the reproduction and activity of bacteria. Treatment of oily wastewater by combining natural nanoparticles and oil-degrading bacteria has the advantages of economy, environmental protection, and sustainability.

Use of biomass-derived adsorbents for the removal of petroleum pollutants from water: a mini-review

Over the past decades, a large amount of petroleum pollutants has been released into the environment resulting from various activities related to petrochemicals. The discharge of wastewater with petrochemicals can pose considerable risk of harm to the human health and the environment. The use of adsorbents has received much consideration across the environmental field as an effective approach for organic pollutant removal. There is a particular interest in the use of biomass adsorbent as a promising environmentally-friendly and low-cost option for removing pollutants. In this article, we present a review of biomass-derived adsorbents for the removal of petroleum pollutants from water. The features of different adsorbents such as algae, fungi, and bacteria biomasses are summarized, as is the process of removing oil and PAHs using biomass-derived adsorbents. Finally, recommendations for future study are proposed.

Treatment of petroleum refinery sludge by petroleum degrading bacterium Stenotrophomonas pavanii IRB19 as an efficient novel technology

Petroleum hydrocarbons (PHCs) in petroleum refinery sludge (PRS) are the most adverse components because of their toxic nature, which are harmful to human health and the aquatic ecosystem. This study aimed to identify and characterize an indigenous bacterium isolated from PRS of Indian oil corporation ltd. (IOCL), Haldia, India, and evaluate its performance for biodegradation of total petroleum hydrocarbon (TPH) of PRS. The bacterium molecularly characterized as Stenotrophomonas sp. IRB19 by 16S rRNA sequencing and phylogenetic analysis. The strain IRB19 showed a significant ability to utilize four different oils (kerosene, diesel, petrol and hexadecane) in-vitro. IRB19 could able to degrade up to 65 ± 2.4% of TPH in 28 d of incubation. Solvent extraction study showed that PRS contain 180.57 ± 3.44 g kg^-1 of TPH and maltene fraction composed of aliphatic, aromatics and polar components of 52 ± 4, 39 ± 2 and 9 ± 1%, respectively. The TPH degradation best fitted for the Gompertz model and followed the first-order kinetics having the rate constant (k) and half-life period (t _1/2) of 0.036 d^-1 and 19 d, respectively. Results of this study verified the suitability of the novel strain IRB19 for the biodegradation of PHCs.

Coupled photocatalytic-bacterial degradation of pyrene: Removal enhancement and bacterial community responses

Polycyclic aromatic hydrocarbons (PAHs) are a class of pollutants that ubiquitously present in environment and hard to be degraded by microorganisms. Herein, we reported a novel photocatalytic-bacterial coupled removal system to treat PAH-polluted water. Using pyrene as the model pollutant, we demonstrated that the removal percentage of different groups was in order: 63.89% ± 1.03% (Vis-Biological) > 61.27% ± 1.08% (UV-Biological) > 59.58% ± 1.15% (UV) > 57.41% ± 1.13% (Vis) > 6.65% ± 0.72% (Biological) > 1.70% ± 0.34% (Control), showing the coupled system significantly improved the removal percentage of pyrene. Additionally, we observed that the coupled system driven by visible light showed higher removal percentage than UV light, exhibiting a good potential for future application. Sequencing analysis of 16S rRNA genes showed that alpha diversity (richness, evenness and diversity) got promoted and data of the relative abundance showed that Pseudomonadaceae was substituted as the dominant bacteria for Planococcaceae, with some other functional bacteria quickly acclimatizing in the bacterial community. Difference analysis indicated that over half of top fifteen genera were generally different significantly (p < 0.001) among two different samples, and UV light altered structure and composition of bacterial community more than visible light. Functional features' change suggested that the bacterial community not only protected itself but also participated in degrading pyrene. Overall, our study offered a new method for PAH degradation and contributed to further understanding of coupled catalytic-bacterial degradation processes.

Biodegradation of hydrolyzed polyacrylamide by a Bacillus megaterium strain SZK-5: Functional enzymes and antioxidant defense mechanism

Hydrolyzed polyacrylamide (HPAM) is the most widely used water-soluble linear polymer with high molecular weight in polymer flooding. Microbiological degradation is an environment-friendly and effective method of treating HPAM-containing oilfield produced water. In this study, a strain SZK-5 that could degrade HPAM was isolated from soil contaminated by oilfield produced water. Based on morphological, biochemical characteristics and 16S rDNA sequence homology analysis, the strain was identified as Bacillus megaterium. The biodegradation capability of strain SZK-5 was determined by incubation in a mineral salt medium (MSM) containing HPAM under different environmental conditions, showing 55.93% of the HPAM removed after 7 d of incubation under the optimum conditions ((NH₄)₂SO₄ = 1667.9 mg L^-1, temperature = 24.05 °C and pH = 8.19). Cytochrome P450 (CYP) and urease (URE) played significant roles in biological carbon and nitrogen removal, respectively. The strain SZK-5 could resist the damages caused by oxidative stress given by crude oil and HPAM. To our knowledge, this is the first report about the biodegradation of HPAM by B. megaterium. These results suggest that strain SZK-5 might be a new auxiliary microbiological resource for the biodegradation of HPAM residue in wastewater and soil.

Characterization of Biofilm Formed by Phenanthrene-Degrading Bacteria on Rice Root Surfaces for Reduction of PAH Contamination in Rice

One effective method in to reduce the uptake of organic contaminants by plants is the development of a root barrier. In this study, the characterization of biofilm structure and function by phenanthrene-degrading Pseudomonas sp. JM2-gfp on rice root surfaces were carried out. Our results showed that root surfaces from three rice species, namely Liaojing401, Koshihikari, and Zhenzhuhong all present hydrophobicity and a high initial adhesion of strain JM2-gfp. Matured robust biofilm formation occurred at 48 h on the root surfaces. The biofilm exhibited cell dense aggregates and biomass embedded in the extracellular polymeric substance (EPS) matrix. EPS composition results showed that the proteins, carbohydrates, lipids and nucleic acids are produced in the biofilm, while the content varied with rice species. Under the initial concentration of phenanthrene 50 mg·L-1, the residual phenanthrene in plant roots from 'Zhengzhuhong', 'Koshihikari' and 'Liaojing401' with biofilm mediated were significantly decreased by 71.9%, 69.3% and 58.7%, respectively, compared to those without biofilm groups after 10 days of exposure. Thus, the biofilm colonized on roots plays an important role of degradation in order to reduce the level of phenanthrene uptake of plants. Thereby, the present work provides significant new insights into lowering the environmental risks of polycyclic aromatic hydrocarbons (PAHs) in crop products from contaminated agriculture soils.

Great correlation: Biodegradation and chemotactic adsorption of Pseudomonas synxantha LSH-7' for oil contaminated seawater bioremediation

Oil Contaminated Seawaters is treated by biological processes of sorption or degradation. Considering the chemotaxis of bacteria, they migrate towards a better way to survive. However, the information concerning the chemotactic biosorption of microorganism is severely limited thus far. Therefore, chemotactic biosorption a novel way of sorption was put forward. The equation was defined as: A _{chemotactic biosorption} = A _{extracellular biosorption} - A _{passive extracellular biosorption} + E _{intracellular}. Effects of controlling parameters like pollutant, fertilizer, sediments and surfactant on bacterial chemotactic sorption capacity of tetradecane, hexadecane, phenanthrene or pyrene were described in detail. The results showed bacterial chemotactic biosorption would be promoted under the conditions of low pollutant concentration, high sediment concentration and fertilizer. However, Tween 80 would promote the sorption of pollutants onto bacterial cells depending on the concentration of surfactant. Correlational analyses were conducted with the biodegradation rate and the concentration (mg/g) of hydrocarbons measured in the biomass. We concluded there existed great correlation between them. Biodegradation rate were all linearly correlated with the concentration (mg/g) of hydrocarbons measured in the biomass in all respects with tetradecane (R² = 0.9873), hexadecane (R² = 0.9705), phenanthrene (R² = 0.9098) and pyrene (R² = 0.9424). The above idea may provide a new insight into oil spill bioremediation from sorption to degradation.

Synergistic degradation of crude oil by indigenous bacterial consortium and exogenous fungus Scedosporium boydii

The purpose of this study was to investigate the potential of defined co-culture of indigenous bacterial consortium and exogenous fungus Scedosporium boydii for biodegradation of crude oil. After 7 days of incubation, residual oil, n-alkanes and aromatic fraction were analyzed. The degradation rate of crude oil was increased from 61.06% to 81.45% by the defined co-culture according to the 3:1 inoculation ratio of bacteria to fungi. The microbial activity was enhanced markedly and the formation of biofilms was accelerated after suitable inoculation of Scedosporium boydii. High throughput analysis showed that bacterial evenness and diversity were increased and the relative abundance of Paraburkholderia tropica was increased observably from 7.67% to 56.13% in the defined co-culture. These results indicated that synergistic degradation of crude oil in the bacteria-fungi consortium may be advantageous for bioremediation of petroleum-contaminated site.

Biodegradation of pyraclostrobin by two microbial communities from Hawaiian soils and metabolic mechanism

Pyraclostrobin has been widely and long-termly applicated to agricultural fields. The removal of pyraclostrobin from ecological environment has received wide attention. In this study, using sequential enrichments with pyraclostrobin as a sole carbon source, two microbial communities (HI2 and HI6) capable of catabolizing pyraclostrobin were obtained from Hawaiian soils. The microfloras analysis indicated that only Proteobacteria and Bacteroides could survive in HI2-soil after acclimatization, whereas the number of Proteobacteria in HI6-soil accounted for more than 99%. The percentages of Pseudomonas in the HI2 and HI6 microfloras were 69.3% and 59.3%, respectively. More than 99% of pyraclostrobin (C₀ = 100 mg L^-1) was degraded by the HI2 and HI6 microorganisms within five days. A unique metabolite was identified by high performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry (HPLC-QTOF-MS/MS). A metabolic pathway involving carbamate hydrolysis was proposed. The tertiary amine group of pyraclostrobin was hydrolyzed to primary amine group with the decarboxylation, which facilitated pyraclostrobin detoxification because carboxylester was an important functional group. The metabolic mechanism suggested that Pseudomonas expressing carboxylesterase might be able to degrade carbamate chemicals. Therefore, Pseudomonas might be an ideal candidate for expression and cloning of carbamate-degrading gene in genomics studies. The current study would have important implications in detoxification and bioremediation of carbamates through the CN bond cleavage of methyl carbamate.

Improved polycyclic aromatic hydrocarbon degradation in a crude oil by individual and a consortium of bacteria

In this study, we report the ability of Stenotrophomonas maltophilia, Ochrobactrum anthropi, Pseudomonas mendocina, Microbacterium esteraromaticum and Pseudomonas aeruginosa to degrade multiple polycyclic aromatic hydrocarbons (PAHs) present in crude oil. The PAHs in the crude oil sample obtained from Digboi oil refinery, India were estimated to be naphthalene (10.0 mg L^-1), fluorene (1.9 mg L^-1), phenanthrene (3.5 mg L^-1) and benzo(b)fluoranthene (6.5 mg L^-1). Exposure of individual bacteria to crude oil showed high rate of biodegradation of specific PAHs by M. esteraromaticum, 81.4%-naphthalene; P. aeruginosa, 67.1%-phenanthrene and 61.0%-benzo(b)fluoranthene; S. maltophilia, 47.9%-fluorene in 45 days. However, consortium of these bacteria showed enhanced biodegradation of 89.1%-naphthalene, 63.8%-fluorene, 81% of phenanthrene and 72.8% benzo(b)fluoranthene in the crude oil. The degradation was further improved up to 10% by consortium on addition of 40 μg mL^-1 rhamnolipid JBR-425 biosurfactant. These results suggest that the developed bacterial consortium has significant potential in PAH remediation.

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site

The study of microbial communities involved in soil bioremediation is important to identify the specific microbial characteristics that determine improved decontamination rates. Here, we characterized bacterial, archaeal, and fungal communities in terms of (i) abundance (using quantitative PCR) and (ii) taxonomic diversity and structure (using Illumina amplicon sequencing) during the bioremediation of long-term hydrocarbon-contaminated soil from an Alpine former military site during 15 weeks comparing biostimulation (inorganic NPK fertilization) vs. natural attenuation and considering the effect of temperature (10 vs. 20 °C). Although a considerable amount of total petroleum hydrocarbon (TPH) loss could be attributed to natural attenuation, significantly higher TPH removal rates were obtained with NPK fertilization and at increased temperature, which were related to the stimulation of the activities of indigenous soil microorganisms. Changing structures of bacterial and fungal communities significantly explained shifts in TPH contents in both natural attenuation and biostimulation treatments at 10 and 20 °C. However, archaeal communities, in general, and changing abundances and diversities in bacterial and fungal communities did not play a decisive role on the effectiveness of soil bioremediation. Gammaproteobacteria and Bacteroidia classes, within bacterial community, and undescribed/novel groups, within fungal community, proved to be actively involved in TPH removal in natural attenuation and biostimulation at both temperatures.

Removal and biodegradation of different petroleum hydrocarbons using the filamentous fungus Aspergillus sp. RFC-1

Petroleum pollution inevitably occurs at any stage of oil production and exerts a negative impact on the environment. Some microorganisms can degrade petroleum hydrocarbons (PHs). Polluted sludge of Rumaila oil field was use to isolate the highly efficient hydrocarbon‐degrading fungal strain. Aspergillus sp. RFC‐1 was obtained and its degradation ability for petroleum hydrocarbons was evaluated through surface adsorption, cell uptake, hydrophobicity, surface tension, biosurfactant production, and emulsification activity. In addition, the degradation mechanism was investigated. The results indicated the strain RFC‐1 showed high removal activity for PHs, including biodegradation, adsorption, and emulsifiability. On the day 7 of incubation, the removal efficiencies of crude oil, naphthalene (NAP), phenanthrene (PHE), and pyrene (PYR) reached 60.3%, 97.4%, 84.9%, and 90.7%, respectively. Biodegradation efficiencies of crude oil, NAP, PHE, and PYR were 51.8%, 84.6%, 50.3%, and 55.1%, respectively. Surface adsorption and cell absorption by live mycelial pellets followed a decreasing order: PYR ≥ PHE > NAP > crude oil. Adsorption by heat‐killed mycelial pellets increased within 40 and 10 min for crude oil and PAHs, respectively, and remained constant thereafter. Effects of cell surface hydrophobicity, surface tension, and emulsification index were discussed. Intra‐ and extracellular enzymes of strain RFC‐1 played important roles in PHs degradation. The strain RFC‐1 is a prospective strain for removing PHs from aqueous environments.

Individually immobilized and surface-modified hydrocarbon-degrading bacteria for oil emulsification and biodegradation

Effective emulsification plays an important role in the treatment of marine oil spills. The negative effects of chemical surfactants have necessitated a search for alternative dispersant that are sustainable and environmentally-friendly. To identify alternate dispersants, oil-in-seawater emulsions stabilized by hydrocarbon-degrading bacteria were investigated. After individual immobilization and surface-modification, the hydrocarbon-degrading bacteria, Bacillus cereus S-1, was found to produce a stable oil-in-seawater Pickering emulsion, which was similar to particle emulsifiers. The individual immobilization and surface-modification process improved the surface hydrophobicity and wettability of the bacterial cells, which was responsible for their effective adsorption at the oil-water interface. Through effective emulsification, the biodegradation of oil was remarkably facilitated by these treated bacteria, because of the increased interfacial area. By combining the emulsification and biodegradation, the results of this reported work demonstrated a novel approach for developing environmentally-friendly bioremediation technology in the field of oil treatment.

Microbial communities in pyrene amended soil-compost mixture and fertilized soil

Polycyclic aromatic hydrocarbons are distributed ubiquitously in the environment and form metabolites toxic to most organisms. Organic amendment of PAH contaminated soil with compost and farmyard manure has proven to be efficient for PAH bioremediation mediated by native microorganisms, even though information on the identity of PAH degraders in organic-amended soil is still scarce. Here we provide molecular insight into the bacterial communities in soil amended with compost or farmyard manure for which the degradation mass balances of ¹³C-labeled pyrene have been recently published and assess the relevant bacterial genera capable of degrading pyrene as a model PAH. We performed statistical analyses of bacterial genera abundance data based on total DNA and RNA (for comparison) extracted from the soil samples. The results revealed complex pyrene degrading communities with low abundance of individual degraders instead of a limited number of abundant key players. The bacterial degrader communities of the soil-compost mixture and soil fertilized with farmyard manure differed considerably in composition albeit showing similar degradation kinetics. Additional analyses were carried out on enrichment cultures and enabled the reconstruction of several nearly complete genomes, thus allowing to link microcosm and enrichment experiments. However, pyrene mineralizing bacteria enriched from the compost or unfertilized soil-compost samples did not dominate pyrene degradation in the soils. Based on the present findings, evaluations of PAH degrading microorganisms in complex soil mixtures with high organic matter content should not target abundant key degrading species, since the specific degraders may be highly diverse, of low abundance, and masked by high bacterial background.

A new perspective of particle adsorption: Dispersed oil and granular materials interactions in simulated coastal environment

This study, adsorption behaviors of dispersed oil in seawaters by granular materials were explored in simulation environment. We quantitatively demonstrated the dispersed oil adsorbed by granular materials were both dissolved petroleum hydrocarbons (DPHs) and oil droplets. Furthermore, DPHs were accounted for 42.5%, 63.4%, and 85.2% (35.5% was emulsion adsorption) in the adsorption of dispersed oil by coastal rocks, sediments, and bacterial strain particles respectively. Effects of controlling parameters, such as temperature, particle size and concentration on adsorption of petroleum hydrocarbons were described in detail. Most strikingly, adsorption concentration was followed a decreasing order of bacterial strain (0.5-2μm)>sediments (0.005-0.625mm)>coastal rocks (0.2-1cm). With particle concentration or temperature increased, adsorption concentration increased for coastal rocks particle but decreased for sediments particle. Besides, particle adsorption rate of petroleum hydrocarbons (n-alkanes and PAHs) was different among granular materials during 60 days.

Phylogeny and polycyclic aromatic hydrocarbons degradation potential of bacteria isolated from crude oil-contaminated site

This study employed the use of 16S rRNA gene sequence analysis to identify three of four native bacterial strains isolated from crude oil-contaminated site in Poza Rica, Veracruz, Mexico. The identified bacteria were Ochrobactrum intermedium, Pandoraea pnomenusa and Ochrobactrum sp., but SA2-09 strain was not identified. The ability of the isolates to degrade polycyclic aromatic hydrocarbons (PAHs) was evaluated at 31.61 and 54.52 mg/kg PAHs in soil, when used as crude oil in soil microcosm during 80 days of incubation at 30°C. The results demonstrated that O. intermedium biodegraded many PAHs, including the high molecular weight (HMW) PAHs fluoranthene (100% equivalent 0.24 mg/kg), benzo [b] fluoranthene (81.8% equal 0.18 mg/kg), Benzo[a]pyrene (87.0%, 0.20 mg/kg) and Benzo[g,h,i]perylene (52.7%, 0.39 mg/kg). P. pnomenusa had a degradation profile of HMW PAHs, which was similar to O. intermedium, while Ochrobactrum sp. and the strain SA-09 exhibited lower degradation rates of HMW.

Bioremoval of priority polycyclic aromatic hydrocarbons by a microbial community with high sorption ability

The treatment of large volumes of wastewater during oil refining is presently a challenge. Bioremediation has been considered an eco-friendly approach for the removal of polycyclic aromatic hydrocarbons (PAHs), which are one of the most hazardous groups of organic micropollutants. However, it is crucial to identify native PAH-removing microorganisms for the development of an effective bioremediation process. This study reports the high potential of an anaerobic microbial consortium enriched from a petrochemical refinery wastewater to remove two priority PAHs-acenaphthene and phenanthrene. Seventy-seven percent of acenaphthene was removed within 17 h, whereas phenanthrene was no longer detected after 15 h. Bioremoval rates were extremely high (0.086 and 0.156 h^-1 for acenaphthene and phenanthrene, respectively). The characterization of the microbial communities by next-generation sequencing and fluorescence in situ hybridization showed that the PAH-removing consortium was mainly composed by bacteria affiliated to Diaphorobacter and Paracoccus genera, independently of the PAH tested. Moreover, besides biodegradation, biosorption was a relevant mechanism involved in the removal of both PAHs, which is an important finding since biosorption is less expensive than biodegradation and can be carried out with dead biomass. Although biodegradation is the most commonly reported biological mechanism for PAH removal, this study demonstrated that biosorption by this microbial community may be extremely efficient for their removal. Given the outstanding ability of this microbial consortium to quickly remove the compounds addressed, it could be further applied for the bioremediation of PAHs in refinery wastewaters and other contaminated environments.

Metabolic pathway for a new strain Pseudomonas synxantha LSH-7': from chemotaxis to uptake of n-hexadecane

Bacteria can use n-hexadecane as a carbon source, but it remains incompletely understood whether n-hexadecane is transformed into metabolic intermediates prior to cellular uptake or not. We newly isolated a strain identified as Pseudomonas synxantha LSH-7' and conducted chemotaxis experiment of this bacterial strain towards n-hexadecane, hexadecanol and hexadecanoic acid with qualitative assays respectively. Furthermore, we described the identification of extracellular alkane hydroxylase and alcohol dehydrogenase activity; acidification of the culture medium; identification of hexadecanoic acid in the culture medium by the GC-MS analysis; and variation concentration of intracellular n-hexadecane and hexadecanoic acid. A detailed analysis of the experimental data revealed the chemotaxis of this bacterial strain towards n-hexadecane instead of its metabolic intermediates. Our results further suggested that only a fraction of total n-hexadecane followed this path, and alkane hydrolase and hexadecanol dehydrogenase were constitutively expressed when grown in the medium of n-hexadecane. Most strikingly, we quantitatively investigated the concentration of n-hexadecane adsorbed by bacterial chemotaxis. Our findings provided an original insight n-hexadecane might be converted to hexadecanoic acid extracellularly before it was taken up across the cell membrane.

Bioremediation of Heavy Crude Oil Contamination

Crude oil contamination is one of the major environmental concerns and it has drawn interest from researchers and industries. Heavy oils contain 24-64% saturates and aromatics, 14-39% resins and 11-45% asphaltene. Resins and asphaltenes mainly consist of naphthenic aromatic hydrocarbons with alicyclic chains which are the hardest to degrade. Crude oil biodegradation process, with its minimal energy need and environmentally friendly approach, presents an opportunity for bioremediation and as well for enhanced oil recovery to utilize heavy oil resources in an efficient manner. Biodegradation entails crude oil utilization as a carbon source for microorganisms that in turn change the physical properties of heavy crude oil by oxidizing aromatic rings, chelating metals and severing internal bonds/chains between molecules. Biodegradation does not necessarily lower quality of crude oil as there are cases where quality was improved. This paper provides information on heavy crude oil chemistry, bioremediation concept, biodegradation enzymes, cases of Microbial Enhanced heavy crude Oil Recovery (MEOR) and screening criteria towards a better understanding of the biodegradation application. Through the utilization of single microorganisms and consortia, researchers were able to biodegrade single pure hydrocarbon components, transform heavy crude oil fractions to lighter fractions, remove heavy metals and reduce viscosity of crude oil.

Biodegradation of engine oil by fungi from mangrove habitat

The pollution of land and water by petroleum compounds is a matter of growing concern necessitating the development of methodologies, including microbial biodegradation, to minimize the impending impacts. It has been extensively reported that fungi from polluted habitats have the potential to degrade pollutants, including petroleum compounds. The Red Sea is used extensively for the transport of oil and is substantially polluted, due to leaks, spills, and occasional accidents. Tidal water, floating debris, and soil sediment were collected from mangrove stands on three polluted sites along the Red Sea coast of Saudi Arabia and forty-five fungal isolates belonging to 13 genera were recovered from these samples. The isolates were identified on the basis of a sequence analysis of the 18S rRNA gene fragment. Nine of these isolates were found to be able to grow in association with engine oil, as the sole carbon source, under in vitro conditions. These selected isolates and their consortium accumulated greater biomass, liberated more CO2, and produced higher levels of extracellular enzymes, during cultivation with engine oil as compared with the controls. These observations were authenticated by gas chromatography-mass spectrophotometry (GC-MS) analysis, which indicated that many high mass compounds present in the oil before treatment either disappeared or showed diminished levels.

Aerobic degradation of BDE-209 by Enterococcus casseliflavus: Isolation, identification and cell changes during degradation process

Decabromodiphenyl ether (BDE-209) is one of the most commonly used brominated flame retardants that have contaminated the environment worldwide. Microbial bioremediation has been considered as an effective technique to remove these sorts of persistent organic pollutants. Enterococcus casseliflavus, a gram-positive bacterium capable of aerobically transforming BDE-209, was isolated by our team from sediments in Guiyu, an e-waste dismantling area in Guangdong Province, China. To promote microbial bioremediation of BDE-209 and elucidate the mechanism behind its aerobic degradation, the effects of BDE-209 on the cell changes of E. casseliflavus were examined in this study. The experimental results demonstrated that the high cell surface hydrophobicity (CSH) of E. casseliflavus made the bacteria absorb hydrophobic BDE-209 more easily. E. casseliflavus responded to BDE-209 stress, resulting in an increase in cell membrane permeability and accumulation of BDE-209 inside the cell. The differential expression of intracellular protein was analyzed through two-dimensional gel electrophoresis (2-DE). More than 50 differentially expressed protein spots were reproducibly detected, including 25 up, and 25 down regulated after a 4 days exposure. Moreover, the apoptotic-like cell changes were observed during E. casseliflavus mediated degradation of BDE-209 by means of flow cytometry.

Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach

This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed.

Metabolic biotransformation of copper-benzo[a]pyrene combined pollutant on the cellular interface of Stenotrophomonas maltophilia

Previous studies have confirmed that Stenotrophomonas maltophilia can bind an appreciable amount of Cu(II) and degrade BaP. However, the removal mechanisms of Cu(II) coexisted with BaP by S. maltophilia are still unclear. In this study, the micro-interaction of contaminants on the cellular surface was investigated. The results indicated that carboxyl groups played an important role in the binding of copper to the thallus and that the cell walls were the main adsorption sites. Nevertheless, these reactive groups had no obvious effect on the uptake of BaP. Instead, the disruption and modification of cell walls accelerated transportation of BaP across the membrane into cells. The observation of SEM-EDS confirmed that Cu(II) would be adsorbed and precipitated onto the cell surface but would also be removed by extracellular precipitation when BaP coexisted. And the XPS analysis reflected that part of Cu(II) bound onto biosorbents changed into Cu(I) and Cu.

Biodegradation, Biosorption of Phenanthrene and Its Trans-Membrane Transport by Massilia sp. WF1 and Phanerochaete chrysosporium

Reducing phenanthrene (PHE) in the environment is critical to ecosystem and human health. Biodegradation, biosorption, and the trans-membrane transport mechanism of PHE by a novel strain, Massilia sp. WF1, and an extensively researched model fungus, Phanerochaete chrysosporium were investigated in aqueous solutions. Results showed that the PHE residual concentration decreased with incubation time and the data fitted well to a first-order kinetic equation, and the t_1/2 of PHE degradation by WF1, spores, and mycelial pellets of P. chrysosporium were about 2 h, 87 days, and 87 days, respectively. The biosorbed PHE was higher in P. Chrysosporium than that in WF1, and it increased after microorganisms were inactivated and inhibited, especially in mycelial pellets. The detected intracellular auto-fluorescence of PHE by two-photon excitation microscopy also proved that PHE indeed entered into the cells. Based on regression, the intracellular (K_din) and extracellular (K_dout) dissipation rate constants of PHE by WF1 were higher than those by spores and mycelial pellets. In addition, the transport rate constant of PHE from outside solution into cells (K_inS/V_out) for WF1 were higher than the efflux rate constant of PHE from cells to outside solution (K_outS/V_in), while the opposite phenomena were observed for spores and mycelial pellets. The amount of PHE that transported from outside solution into cells was attributed to the rapid degradation and active PHE efflux in the cells of WF1 and P. Chrysosporium, respectively. Besides, the results under the inhibition treatments of 4°C, and the presence of sodium azide, colchicine, and cytochalasin B demonstrated that a passive trans-membrane transport mechanism was involved in PHE entering into the cells of WF1 and P. Chrysosporium.

Biodegradation of different petroleum hydrocarbons by free and immobilized microbial consortia

The efficiencies of free and immobilized microbial consortia in the degradation of different types of petroleum hydrocarbons were investigated. In this study, the biodegradation rates of naphthalene, phenanthrene, pyrene and crude oil reached about 80%, 30%, 56% and 48% under the optimum environmental conditions of free microbial consortia after 7 d. We evaluated five unique co-metabolic substances with petroleum hydrocarbons, α-lactose was the best co-metabolic substance among glucose, α-lactose, soluble starch, yeast powder and urea. The orthogonal biodegradation analysis results showed that semi-coke was the best immobilized carrier followed by walnut shell and activated carbon. Meanwhile, the significance of various factors that contribute to the biodegradation of semi-coke immobilized microbial consortia followed the order of: α-lactose > semi-coke > sodium alginate > CaCl2. Moreover, the degradation rate of the immobilized microbial consortium (47%) was higher than that of a free microbial consortium (26%) under environmental conditions such as the crude oil concentration of 3 g L(-1), NaCl concentration of 20 g L(-1), pH at 7.2-7.4 and temperature of 25 °C after 5 d. SEM and FTIR analyses revealed that the structure of semi-coke became more porous and easily adhered to the microbial consortium; the functional groups (e.g., hydroxy and phosphate) were identified in the microbial consortium and were changed by immobilization. This study demonstrated that the ability of microbial adaptation to the environment can be improved by immobilization which expands the application fields of microbial remediation.

Bioremediation of PAHs and VOCs: Advances in clay mineral-microbial interaction

Bioremediation is an effective strategy for cleaning up organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs). Advanced bioremediation implies that biotic agents are more efficient in degrading the contaminants completely. Bioremediation by microbial degradation is often employed and to make this process efficient, natural and cost-effective materials can serve as supportive matrices. Clay/modified clay minerals are effective adsorbents of PAHs/VOCs, and readily available substrate and habitat for microorganisms in the natural soil and sediment. However, the mechanism underpinning clay-mediated biodegradation of organic compounds is often unclear, and this requires critical investigation. This review describes the role of clay/modified clay minerals in hydrocarbon bioremediation through interaction with microbial agents in specific scenarios. The vision is on a faster, more efficient and cost-effective bioremediation technique using clay-based products. This review also proposes future research directions in the field of clay modulated microbial degradation of hydrocarbons.

Petroleum hydrocarbon degrading bacteria associated with chitosan as effective particle-stabilizers for oil emulsification

Bacteria act as an effective oil emulsifier with chitosan in sea water, together with its dramatically enhanced biodegradation.

Combined hydrolysis acidification and bio-contact oxidation system with air-lift tubes and activated carbon bioreactor for oilfield wastewater treatment

This paper investigated the enhancement of the COD reduction of an oilfield wastewater treatment process by installing air-lift tubes and adding an activated carbon bioreactor (ACB) to form a combined hydrolysis acidification and bio-contact oxidation system with air-lift tubes (HA/air-lift BCO) and an ACB. Three heat-resistant bacterial strains were cultivated and subsequently applied in above pilot plant test. Installing air-lift tubes in aerobic tanks reduced the necessary air to water ratio from 20 to 5. Continuous operation of the HA/air-lift BCO system for 2 months with a hydraulic retention time of 36 h, a volumetric load of 0.14 kg COD/(m(3)d) (hydrolysis-acidification or anaerobic tank), and 0.06 kg COD/(m(3)d) (aerobic tanks) achieved an average reduction of COD by 60%, oil and grease by 62%, total suspended solids by 75%, and sulfides by 77%. With a COD load of 0.56 kg/(m(3)d), the average COD in the ACB effluent was 58 mg/L.

Influence of co-existed benzo[a]pyrene and copper on the cellular characteristics of Stenotrophomonas maltophilia during biodegradation and transformation

Microbial remediation has been proposed as a promising technique to remove pollutions, however, its application has been hindered by the lack of understanding the mechanisms involved in contaminants conversion and the influence of pollutants on cellular characteristics. To address this problem, biodegradation and transformation of BaP-Cu(II) by Stenotrophomonas maltophilia, along with interactions of these pollutants with microbial cells through FCM assay were investigated. The results indicated that BaP and Cu(II) were rapidly removed by S. maltophilia on the 1st d, but only less than 10% BaP was broken down due to temporary store in cells, instead of being decomposed immediately. The key ATP enzymes in cells were then activated by BaP to promote bacteria to further decompose BaP. Stimulation of co-existed contaminants strengthened cell membrane permeability and altered cell structure, but a higher esterase activity and DNA in cells of S. maltophilia were still retained.