research paper on bioremediation of oil spills

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• Published: 08 June 2020

Bioremediation of oil contaminated soil using agricultural wastes via microbial consortium

• Chao Zhang 1 , 2 ,
• Daoji Wu 1 , 2 &
• Huixue Ren 1 , 2  

Scientific Reports volume  10 , Article number:  9188 ( 2020 ) Cite this article

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• Environmental biotechnology
• Soil microbiology

Agricultural wastes, such as wheat bran and swine wastewater, were used for bioremediation of oil-contaminated soil. Two optimised strains that could degrade oil efficiently were selected. The result showed that the best ratio of strain A to strain B was 7:3. Swine wastewater could be a replacement for nitrogen source and process water for bioremediation. Next, the Box-Behnken design was used to optimise the culture medium, and the optimal medium was as follows: microbial dosage of 97 mL/kg, wheat bran of 158 g/kg and swine wastewater of 232 mL/kg. Under the optimal medium, the oil degradation rate reached 68.27 ± 0.71% after 40 d. The urease, catalase, and dehydrogenase activities in oil-contaminated soil all increased, and the microbe quantity increased significantly with manual composting. These investigations might lay a foundation for reducing the pollution of agricultural wastes, exploring a late model for bioremediation of oil-contaminated soil.

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Introduction.

A large number of oil pollutants are produced during the production, processing, transportation, and utilisation of oil 1 , 2 . This has caused serious soil pollution. Therefore, it is urgent to repair the oil-contaminated soil. Compared with physical repair and chemical repair, bioremediation has been widely used because of its advantages of good effect, easy operation, low cost, rapid degradation rate, and lack of secondary pollution 3 , 4 .

Bioremediation is divided into two types of remediation: in-situ and ex-situ . In-situ remediation techniques include land tillage, microorganism addition, bio-culture, and bio-ventilation. Ex-situ remediation technologies include prefabricated bed and bioreactor 5 , 6 . For example, Besalatpour et al 7 . used land tillage to remediate 500 kg of oil-contaminated soil in farmland. After four months, total petroleum hydrocarbons decreased by 50%. The essence of bioremediation technology is the degradation of pollutants through microbial metabolic activities. A majority of the microorganisms used in the process of remediation are indigenous microorganisms 8 . In order to improve the repair effect, domesticated high-efficiency oil-degrading bacteria were introduced. Wu et al 9 . repaired the contaminated soil with 82,533 mg/kg petroleum hydrocarbon content by adding mixed degrading bacteria. After 13 weeks, the content of petroleum hydrocarbon decreased to 47,600 mg/kg, and the removal rate of petroleum hydrocarbon reached 42.3%. Although there are many scholars engaged in this field, there remains a lack of low-cost and positive-effect technology. Existing investigations reported that the expensive refined supplements were still necessary for bioremediation, such as refined carbon source, refined nitrogen source, process water, or surface active agent. Therefore, the high cost is the bottleneck of bioremediation.

Swine wastewater mainly includes pig urine, partial pig manure, and piggery flushing water. These types of wastewater include high concentrations of organic matter (biochemical oxygen demand 4.5-8.0 g/L), ammonia nitrogen (1.3-1.5 g/L), and total nitrogen (1.6-2.2 g/L) 10 . It is a kind of organic wastewater which is difficult to treat. If discharged directly into local bodies of water, it will cause enormous environmental pollution. Dealing with the discharge according to standards is very difficult and costly. If the wastewater can be used as a medium for remediation of contaminated soil, not only can the cost of remediation be greatly reduced but also the wastewater can be recycled, and the pollution to the environment can be reduced.

Two strains ( Bacillus subtilis CICC 21312 and Candida bombicola ATCC 22214) had good oil decomposing ability. Accordingly, they were used for bioremediation of simulated oil-contaminated soil in the present study. Swine wastewater was used instead of a nitrogen source and process water for bioremediation. The optimal ratio of strains and the optimal medium for mixed strains were determined. In addition, the soil changes after bioremediation were studied to understand physicochemical properties, enzyme activities, and microbial population, which provided technical reference and theoretical support for the field application of bioremediation in DongYing oil-contaminated soil.

Comparison of oil degradation rates among different strains and indigenous microorganisms

The main component of petroleum pollutants in soil is polycyclic aromatic hydrocarbons (PAHs), yet the solubility of PAHs in soil aqueous solution is very low, and PAHs can be adsorbed on soil particles, resulting in poor bioavailability. This retards the biodegradation rate of PAHs at the solid-liquid interface of soil 11 . Surfactant is a kind of macromolecule with both hydrophilic and hydrophobic groups. It can increase the contact area between PAHs and soil microorganisms, improving the availability and degradation rate by curling, solubilisation, and elution 12 . However, exogenous surfactants increase the cost of soil remediation. Therefore, a strain producing sophorolipid(strain B) was selected as the soil remediation strain in this study. At the same time, sophorolipid is degradable and does not easily cause secondary pollution.

In order to select better oil degrading bacteria, four strains were selected for comparison. The comparison of oil degradation rates among different strains and indigenous microorganisms is shown in Fig.  1 . The results shows that A and B have high oil degradation rate. The oil degradation rate of C and D is relatively low, so no further study is required. Because the effects of A and B are high, the synergistic effect of A and B is also investigated. The sequence of oil degradation rate of strains is A + B > A (30.08 ± 1.08%)> B (21.19 ± 1.30%), which are higher than indigenous microorganisms. After 40 d culture of strain A + B, the oil degradation rate was 41.12 ± 1.50%, while the oil degradation rate of indigenous microorganisms after 40 d was only 5.02 ± 0.15%. The main reason for the treatment effect of the mixed bacteria being better than that of the single bacterium was that strain B was a sophorolipid-producing bacteria, which could degrade PAHs well. Moreover, there was no competition between strain B and strain A, which could be mixed cultured. Strain A degraded alkane, and strain B degraded PAHs. They played a complementary role, so the degradation rate reached the optimal value.

Comparison of oil degradation rates among different strains and indigenous microorganisms (▲: A; ▼ : Indigenous microorganisms; ● : A + B; ■: B; ♦: C; ★ : D); ( a ) Oil degradation rate (%); ( b ) Total petroleum hydrocarbons (mg/kg).

Construction of dominant flora and determination of the optimal ratio

The effect of mixed proportions (A:B) on oil degradation rate were investigated; the results are shown in Fig.  2 .

Effect of mixed proportion (A,B) on the oil degradation rate.

As can be seen, the proportion of strains affected the oil degradation rate. A ratio that was too low or too high reduced the oil degradation rate. The maximum oil degradation rate was 55.31 ± 1.32% at 7:3.

Box-Behnken design and response surface analysis

The best level of the three factors (inoculation amount of mixed strains, the amount of wheat bran and the amount of swine wastewater) was determined by BBD. The factor levels used in the BBD are shown in Table  1 , and results are in Table  2 . Variance for the quadratic design is in Table  3 .

Values of “Prob> F” less than 0.0500 indicate model terms are significant. In this case F, F 2 , and G 2 are significant model terms. The final coding factor formula is as follows:

Oil degradation rate = 65.19 – 1.79 × E + 3.98 × F + 1.04 × G – 0.078 × E × F + 1.68 × E × G + 0.56 × F × G – 2.45×E 2 – 5.14 × F 2 – 4.44 × G 2 (1) where Y is oil degradation rate, E is the inoculation amount, F is the amount of wheat bran, and G is the amount of swine wastewater.

F test was used to judge the significance of each variable in the regression equation to the response value. The smaller the probability of P, the higher the corresponding variable. The first order term F (P < 0.05) of model (1) was significant, while E and G (P > 0.05) had no significant effects. The effects of secondary order item F 2 , G 2 (P < 0.05) was significant, and E 2 (P > 0.05) had no significant effects. There was no significant difference between EF, EG, and FG (P > 0.05).

These results clearly showed that experimental values had a linear distribution and a good correlation (R 2  = 0.9912). Therefore, the model could be used to predict the degradation rate of crude oil in the variable range. The maximum oil degradation rate of 68.22% was obtained at 96.53 mL/kg inoculation, 157.85 g/kg wheat bran and 232.29 mL/kg swine wastewater. To validate this prediction, three independent experiments were carried out, and an oil degradation rate of 68.27 ± 0.71% was obtained via 97 mL/kg inoculation, 158 g/kg wheat bran and 232 mL/kg swine wastewater.

The effects of the inoculation amount of mixed strains, amount of wheat bran and amount of swine wastewater on oil degradation rate were analysed by RSM. As shown in Fig.  3 , three-dimensional response surface plots and contour plots were generated. This allows for studying the interaction of any two variables on the response. From the observation of the response surface graph of the interaction between the two factors, there was a strong interaction among the factors, and it was found that the steeper the curve trend, the more significant the influence. The smoother the curve trend, the smaller the influence. The shape of the contour plot represents the strength of interaction. The contour plot was round, indicating that the interaction between the two factors was weak. Moreoeer, the contour plot was oval, indicating that the interaction between the two factors was strong. Comparing the highest points and contours of the response surface in Fig.  3 , there were extreme values in the selected range.

Surface and contour plots of mutual-influence. (1) effect of inoculation amount ( E ) and wheat bran ( F ); (2) effect of inoculation amount ( E ) and swine wastewater ( G ); and (3) effect of wheat bran ( F ) and swine wastewater ( G ).

Comparison of soil properties before and after bioremediation

Oil-contaminated soil, oil contaminated soil treated by indigenous microbial aeration composting, and oil-contaminated soil treated by microbial consortium (optimal ratio and optimal culture conditions) were recorded as M1, M2, M3, respectively. The changes of the soil’s physical and chemical properties, enzyme activities, and microbial population before and after bioremediation were investigated. The results are shown in Table  4 .

After comparing three kinds of soil samples, M3 had the best recovery effect, and the oil degradation rate reached 68.27 ± 0.71%. The oil degradation rate of M2 was only 5.02 ± 0.27%. Large amounts of nutrients were put into the sample in the process of M3 repair, so the content of organics and total nitrogen in the soil were greatly improved, while the changes in the corresponding content in M2 were not as obvious as that in M3.

The activities of dehydrogenase and catalase in M3 were the highest. This was due to the large amount of soil microorganism reproduction during the repair process, and the microorganism participated in the degradation process of oil hydrocarbon, which improved the activity of dehydrogenase and catalase. The urease activity in M3 was the highest, indicating that the soil had a strong nitrogen conversion ability, which was beneficial to the growth of microorganisms in the soil. It also provided sufficient nutritional conditions for the microorganism to participate in the degradation of oil hydrocarbon. However, the activities of various enzymes in M2 were not as obvious as those in M3.

Bacteria counts, actinomycetes counts, and fungi counts in M3 were significantly higher than that of untreated soil sample M1 and soil sample M2 after ordinary composting, which were close to the actual microbial number in the natural world.

The remediation of crude oil contaminated soil is a worldwide problem. Although there exist many remediation methods, this technology is still a promising remediation method. The comparison of different method was shown in Table  5 . The order of oil degradation rate of different methods saw this study as better than Besalatpour et al. which was better than Wu et al. In this study, the remediation time was the shortest, and the problem of piggery wastewater pollution was solved. Moreover, it had the following advantages: (1) The treatment cost was low. In the process of treatment, all materials except strains were wastes. (2) The process could offset the disposal costs of agricultural wastes. (3) No exogenous chemical surfactants were needed during the remediation process, because strain B produced sophorolipids. (4) Swine wastewater could be a replacement for process water in bioremediation.

The main reason for the lack of consideration of the effect of aeration on microflora was as follows: although many microorganisms were aerobic, they could not be supplied with oxygen in the remediation of oil-contaminated soils. It increased the processing cost to an unaffordable level. Two highly-efficient oil-degrading strains preserved in the laboratory could improve the effect of bioremediation of oil contaminated soil. The recovery efficiency of single strain in 40 d repair process was much higher than that of indigenous microorganisms. The order of oil degradation rate of two strains was A + B > A > B. The combination of A and B had the best oil degradation rate. The best ratio (mass ratio) of the two strains was 7:3. Under this condition, the oil degradation rate of soil reached 55.31 ± 1.32%. Swine wastewater could be a replacement for nitrogen source and process water for bioremediation. The optimal medium was microbial dosage of 97 mL/kg, wheat bran of 158 g/kg and swine wastewater of 232 mL/kg. Under the optimal medium, the oil degradation rate reached 68.27 ± 0.71% after 40 d. The fertility of oil-contaminated soil, which was repaired by microbial consortium, increased significantly. In addition, the activities of dehydrogenase, peroxidase, and urease increased, and the number of microbes increased significantly. These investigations may lay a foundation for reducing the pollution of agricultural wastes, exploring a late model for bioremediation of oil-contaminated soil. In the future experiments, this microbial consortium will be studied to repair the oil-contaminated soil in other places.

Materials and Methods

Soil samples.

Crude oil was obtained from DongYing refinery, China. The characteristic parameters of the crude oil were 18.5% polycyclic aromatic hydrocarbon and 48.4% alkane. Soil samples were collected from the unpolluted shallow (5~25 cm) soil in DongYing, China. Soil samples were broken, cleaned, mixed and sieved. According to the ratio of crude oil to soil mass ratio (1:20), the oil contaminated soil was made ready for use. Next, soil was sealed in the sterilised kraft paper bag, maintained in cold storage 13 .

Swine wastewater

The swine wastewater used in this study was effluent coming from ZhengBang pig farm in DongYing, China. The characteristic parameters of the swine wastewater were as follows: 15.4 ± 0.2 g/L chemical oxygen demand (COD Cr ), 6.5 ± 0.2 g/L biochemical oxygen demand (BOD 5 ), 883 ± 12 mg/L suspended solid (SS), 1.1 ± 0.1 g/L ammonia nitrogen (NH 3 -N), 1.8 ± 0.1 g/L total nitrogen, 40.5 ± 0.5 mg/L total phosphorus, and pH of 7.5 ± 0.2. The wastewater was autoclaved for 20 min at 121 °C.

Bacillus subtilis X-12(A) was purchased from the China Center of Industrial Culture Collection (CICC) as CICC 21312. Candida bombicola C-15(B) was purchased from the American Type Culture Collection (ATCC) as ATCC 22214. Strains were maintained on LB medium or YPD medium at 4 °C. Pseudomonas aeruginosa A-21(C) was purchased from the CICC as CICC 10204. Arthrobacter sp .D-2 (D) was purchased from the CICC as CICC 10758.

LB medium: yeast extract, 5 g/L; peptone, 10 g/L; sodium chloride, 5 g/L; and agar 18 g/L.

YPD medium: yeast extract, 10 g/L; peptone, 20 g/L; glucose, 20 g/L; and agar 18 g/L.

Seed medium: yeast extract, 10 g/L; peptone, 20 g/L; and glucose, 20 g/L.

All media were autoclaved for 20 min at 121 °C.

Comparison of oil degradation rates between two strains and indigenous microorganisms

Two strains were actived in seed medium. The concentration of microbial cells was 1.5×10 8 CFU/mL. The oil contaminated soil was packed into 48 conical bottles (50 g each). The conical flasks were divided into three groups, with 16 flasks in each group. Then, 50 mL/kg of strain A and strain B suspension were added to two groups, and put in the incubator (28 °C). They were watered and ploughed every day to keep the water content around 20%. The remaining group (control group) did not receive strain suspension for investigating the effect of indigenous microorganisms. Samples were taken at intervals, and the oil degradation rate was calculatedby gravimetric method to checkthe mass fraction of oil in soil samples 14 .

Combinations of two strains were carried out. The mixed bacteria of different combinations were added into the oil-contaminated soil according to a certain amount of inoculation, and the total inoculation amount (50 mL/kg) of the mixed bacteria suspension in each group was equal. They were watered and ploughed every day to keep the water content around 20%. After 40 days in the incubator (28 °C), the mass fraction of oil in the soil samples was determined, and the oil degradation rate was calculated.

Three factors affecting the oil degradation rate (inoculation amount of mixed strains, the amount of wheat bran and the amount of swine wastewater) were selected. Box-Behnken design (BBD) was used to determine optimal concentrations of factors using Design-Expert software (Version 8.0.6, Stat-Ease, Inc, USA), and to understand the relationship among various factors. The three factors were studied at three levels (Table  1 ), and 17 sets of experiments were carried out (Table  2 ). All experiments were carried out in triplicate. The optimal values of factors were obtained by analysing 3D plots. The statistical analysis of the model was represented as an analysis of variance (ANOVA).

Analytical methods

The pH of soil samples was measured by potentiometric titration, and the volume ratio of water to soil was 2.5. The content of organic matter in soil samples was determined by potassium dichromate volumetric method. The total nitrogen content of the soil sample was determined by the semi-micro kjeldahl method. The content of total phosphorus in a soil sample was determined by the Mo-Sb antispetrophotography method 15 .

The total petroleum hydrocarbons (TPH) content in soil was determined by the gravimetric method 14 . The calculation formula for the oil degradation rate was as follows:

where ODR was the oil degradation rate (%), W 1 was the content of petroleum hydrocarbon in the soil before degradation, and W 2 was the content of petroleum hydrocarbon in the soil after degradation.

The amount of polycyclic aromatic hydrocarbon and alkane in soil were measured by the gravimetric method 14 .

Total nitrogen, total phosphorus, suspended solid, NH 3 -N, BOD 5 , and COD Cr in the swine wastewater were measured according to the procedure described in standard methods for the examination of water and wastewater 15 .

The activity of dehydrogenase was determined by using triphenyltetrazolium chloride as hydrogen acceptor, which was reduced to form red formazan. It was determined by colorimetry. The amount of formazan produced in 1 g of dry soil for 6 h was an active unit of dehydrogenase. The urease activity in the soil sample was determined by Nessler’s reagent colorimetry. The amount of NH 3 -N produced in 24 h in 1 g of dry soil was an activity unit of urease. Polyphenol oxidase activity in a soil sample was determined by pyrogallol colorimetry. The amount of gallic acid produced in 3 h in 1 g of dry soil was taken as an activity unit of polyphenol oxidase. Catalase activity in a soil sample was determined by Potassium Permanganate titration. The enzyme activity was expressed by the volume number of potassium permanganate consumed in 1 g dry soil in 1h 16 . The amount of microbial population in the soil was determined by colony forming unit 17 .

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Acknowledgements

This research was financially supported by State Key Laboratory of Microbial Technology (M2012-14), Shandong University.

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C.Z. and D.J.W. conceived of the study. C.Z. designed experiments, analyzed data, and performed experiments with assistance from H.X.R. C.Z. drafted the manuscript. All authors read and approved the final manuscript.

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Correspondence to Daoji Wu .

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Zhang, C., Wu, D. & Ren, H. Bioremediation of oil contaminated soil using agricultural wastes via microbial consortium. Sci Rep 10 , 9188 (2020). https://doi.org/10.1038/s41598-020-66169-5

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DOI : https://doi.org/10.1038/s41598-020-66169-5

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Bioremediation of Oil Spills: A Review of Challenges for Research Advancement

• Babajide Milton Macaulay University of Greenwich
• Deborah Rees University of Greenwich

As the demand for liquid petroleum increases, the need for reliable and efficient oil spill clean-up techniques is inevitable. Bioremediation is considered one of the most sustainable clean-up techniques but the potential has not been fully exploited in the field because it is too slow to meet the immediate demands of the environment. This study reviews the challenges to managing oil spills in terrestrial and marine environments to identify areas that require further research. Current challenges associated with bioremediation of spilled petroleum include resistance of asphalthenes to biodegradation; delay of heavy or high molar mass polycyclic aromatic hydrocarbon (PAH) biodegradation, eutrophication caused by biostimulation, unsustainability of bioaugmentation in the field, poor bioavailability of spilled petroleum, inefficiency of biodegradation in anoxic environments and failure of successful bioremediation laboratory studies in the field. Recommendations offered include encouraging asphalthene biodegradation by combining heat application (80°C), biosurfactant (thermophilic emulsifier) and bioaugmentation (using a consortium containing Bacillus lentus and Pleurotus tuberregium as members) but as a temporary measure, adopting the use of "booms and skimmers" and "organic sorbents" for water and land clean-up, respectively. Heavy PAHs may be rapidly degraded by applying nutrients (biostimulation) and biosurfactants to sites that are oleophilic microbe-rich. Oleophilic nutrients may be the most effective strategy to reduce eutrophication in marine environments whilst on land, slow-release nutrient application or organic-inorganic nutrient rotation may help prevent soil hardening and infertility. The use of encapsulating agents and genetically-engineered microbes (GEMs) may increase the efficiency of bioaugmentation in the field, but temporarily, indigenous oleophilic microbes may be employed in the field. Poor bioavailability of crude oil may be eliminated by the use of biosurfactants. In terrestrial anoxic sites, bioslurping-biosparging technology could be used whilst the marine anoxic site requires more research on how to transport nutrients and biosurfactants to oleophilic anaerobes residing in the ocean beds. The involvement of both governmental and non-governmental environmental institutions in sponsoring field studies in order to improve the reliability of bioremediation research. Further studies to test the practicability and cost of these recommendations in the field are needed.

Permanent URL: http://hdl.handle.net/2047/d20018675

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BIOREMEDIATION OF OIL SPILLS: A REVIEW OF CHALLENGES FOR RESEARCH ADVANCEMENT

2014, Annals of Environmental Science

As the demand for liquid petroleum increases, the need for reliable and efficient oil spill clean-up techniques is inevitable. Bioremediation is considered one of the most sustainable clean-up techniques but the potential has not been fully exploited in the field because it is too slow to meet the immediate demands of the environment. This study reviews the challenges to managing oil spills in terrestrial and marine environments to identify areas that require further research. Current challenges associated with bioremediation of spilled petroleum include resistance of asphalthenes to biodegradation; delay of heavy or high molar mass polycyclic aromatic hydrocarbon (PAH) biodegradation, eutrophication caused by biostimulation, unsustainability of bioaugmentation in the field, poor bioavailability of spilled petroleum, inefficiency of biodegradation in anoxic environments and failure of successful bioremediation laboratory studies in the field. Recommendations offered include encouraging asphalthene biodegradation by combining heat application (80°C), biosurfactant (thermophilic emulsifier) and bioagumentation (using a consortium containing Bacillus lentus and Pleurotus tuberregium as members) but as a temporary measure, adopting the use of ‘booms and skimmers’ and ‘organic sorbents’ for water and land clean-up, respectively. Heavy PAHs may be rapidly degraded by applying nutrients (biostimulation) and biosurfactants to sites that are oleophilic microbe-rich. Oleophilic nutrients may be the most effective strategy to reduce eutrophication in marine environments whilst on land, slow-release nutrient application or organic-inorganic nutrient rotation may help prevent soil hardening and infertility. The use of encapsulating agents and genetically-engineered microbes (GEMs) may increase the efficiency of bioaugmentation in the field, but temporarily, indigenous oleophilic microbes may be employed in the field. Poor bioavailability of crude oil may be eliminated by the use of biosurfactants. In terrestrial anoxic sites, bioslurping-biosparging technology could be used whilst the marine anoxic site requires more research on how to transport nutrients and biosurfactants to oleophilic anaerobes residing in the ocean beds. The involvement of both governmental and non-governmental environmental institutions in sponsoring field studies in order to improve the reliability of bioremediation research. Further studies to test the practicability and cost of these recommendations in the field are needed.

Related Papers

Babajide Macaulay

Petroleum-contamination of both terrestrial and marine environments have persisted as a result of the increasing demand on liquid petroleum globally which has led to the need to clean up spilled petroleum using eco-friendly methods. Of all the petroleum-cleaning techniques explored, the use of petroleum-degrading microbes has received most attention. The microbial remediation of spilled petroleum has been proved to be cost-effective, eco-friendly and sustainable. However, these microbes have been found to thrive under certain environmental/nutritional conditions which influence their behaviour towards spilled petroleum. This study aims to identify the factors responsible for the change in behaviour of oil-degrading microbes which might help facilitate better petroleum spill management. Some of these factors include: the physical nature of the spilled petroleum; chemical nature of the spilled petroleum; availability of nutrients; water temperature; concentration of oxygen; soil region/soil particle size; competition from other micro-organisms. Petroleum-degrading microbes were also found to degrade specific hydrocarbon components in liquid petroleum due to the specific metabolic pathway utilized by individual microbes. This makes the use of a microbial consortium a more aggressive option for the microbial degradation of spilled petroleum than the use of microbial isolates. However, more research on the factors influencing theabundance and productivity of oil-degrading anaerobes may need to be carried out. Also, how oil-degrading microbes can be aided to break down asphalthenes should be investigated.

Biodegradation

Carla C C R de Carvalho , M Manuela da Fonseca , Meenu Tyagi

Journal of Chemical Technology & Biotechnology

Maria Nikolopoulou , Nicolas Kalogerakis

Mohamed Hussein

Stimulation of indigenous degraders with suitable nutrient s can significantly enhance bioremediation rates of marine environments polluted with petroleum hydrocarbons. Biostimu lation is emerging as the best strategy for combating oil spills following first response actions. This mini review is focused on t he conditions under which biostimulation leads to increased effectiveness and strategies for successful biostimulation to fresh and chronically polluted sites are suggested.

Coastal and Deep Ocean Pollution

Lautaro Girones , Analía Serra

Remediation of marine systems, which could be polluted by both organic and inorganic contaminants, is a complex process. Traditional remediation strategies include chemical, physico-chemical and thermal techniques, which are still widely used. However, biological techniques have begun to be applied, as they are eco-friendly and low cost alternatives. Biological remediation includes bioremediation and phytoremediation, which are defined as the use of microorganisms and plants, respectively, to remediate polluted sites. This chapter first describes briefly the physico-chemical factors that can affect bioremediation and phytoremediation and, in the case of bioremediation, the microorganisms that could be involved. Then, the different bioremediation (bioaugmentation, biostimulation, bioventing, bioleaching, etc.) and phytoremediation (phytoextraction, phytostabiliazation, phytovolatilization, etc.) strategies are defined. Finally, emphasis is placed on the biological remediation of marine systems, both in seawater and in sediments. This part is divided into inorganic (namely metals) and organic (oil spills and persistent organic pollutants) pollutants, discussing the different bioremediation and phytoremediation strategies that are applied or could be applied in marine systems. Combinations of techniques and novel approaches including genetic engineering are also considered.

Microbial Action on Hydrocarbons

Milene Gomes

Petroleum pollution is an environmental issue often reported, including oil spills that occur accidentally worldwide. The release of large quantities of oil causes directly or indirectly huge environmental and economic impacts and may persist for decades. Bioremediation processes, such as biostimulation and bioaugmentation, among others, represent an eco-friendly and effective way to treat impacted areas based on the use of biological agents, associated or not to other compounds like biosurfactants in order to mineralize or complex organic and inorganic pollutant compounds. Therefore, this book chapter will review some topics related to bioremediation, including several in situ and ex situ techniques employed to treat polluted areas and the use of biosurfactants produced by several microorganisms. Moreover, oil spills and how they can affect marine and terrestrial environments are also mentioned, based on recent reports available in literature and according to organizations responsible for environmental impact monitoring. Hydrocarbonoclastic microorganisms have been described in both environments as well as the community dynamics of specific groups as a function of oil compounds input. In marine environments, a high abundance increase of a specific group called “obligate hydrocarbonoclastic bacteria (OHCB)” has been reported after an event involving petroleum contamination. Similar observation has been reported for mangroves, showing that oil or its derivatives allow the selection of microorganisms capable to degrade hydrocarbons. Petroleum contamination in cold environments, as Arctic and Antarctic regions, represents a huge challenge since management of contaminated sites and bioremediation effectiveness in these regions depend on several factors influencing oil degradation under cold conditions facing intrinsic limiting factors. In conclusion, bioremediation is not only a scientific concept described in literature but a concrete and applied efficient tool to treat polluted environments. The increasing number of bioremediation companies and patents also corroborates the tendency in search for new technologies and approaches focusing on sustainable management of polluted areas.

Jacob Alberto Valdivieso Ojeda

Andrea M. Garcia

Marine Pollution Bulletin

European Journal of Soil Biology

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Recent Strategies for Bioremediation of Emerging Pollutants: A Review for a Green and Sustainable Environment

1 Department of Microbiology, Punjab Agriculture University, Ludhiana 141001, India

Diksha Garg

Banjagere veerabhadrappa thirumalesh.

2 Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India

Minaxi Sharma

3 Laboratoire de Chimie Verte et Produits Biobasés, Département Agro Bioscience et Chimie, Haute Ecole Provinciale de Hainaut-Condorcet, 11 Rue de la Sucrerie, 7800 Ath, Belgium

Kandi Sridhar

4 UMR1253, Science et Technologie du Lait et de l’œuf, INRAE, L’Institut Agro Rennes-Angers, 65 Rue de Saint Brieuc, F-35042 Rennes, France

Baskaran Stephen Inbaraj

5 Department of Food Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan

Manikant Tripathi

6 Biotechnology Program, Dr. Rammanohar Lohia Avadh University, Ayodhya 224001, India

Associated Data

Data that support these findings available within the article.

Environmental pollution brought on by xenobiotics and other related recalcitrant compounds have recently been identified as a major risk to both human health and the natural environment. Due to their toxicity and non-biodegradability, a wide range of pollutants, such as heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals are present in the environment. Bioremediation is an effective cleaning technique for removing toxic waste from polluted environments that is gaining popularity. Various microorganisms, including aerobes and anaerobes, are used in bioremediation to treat contaminated sites. Microorganisms play a major role in bioremediation, given that it is a process in which hazardous wastes and pollutants are eliminated, degraded, detoxified, and immobilized. Pollutants are degraded and converted to less toxic forms, which is a primary goal of bioremediation. Ex situ or in situ bioremediation can be used, depending on a variety of factors, such as cost, pollutant types, and concentration. As a result, a suitable bioremediation method has been chosen. This review focuses on the most recent developments in bioremediation techniques, how microorganisms break down different pollutants, and what the future holds for bioremediation in order to reduce the amount of pollution in the world.

1. Introduction

Pollution of the environment, freshwater, and topsoil has evolved from global industrialization. Water quality has worsened as a result of human activity, such as due to mining and ultimate removal of toxic metal effluents from steel mills, battery companies, and electricity generation, posing major environmental concerns. Effluents like petroleum, polythenes, and trace metals harm the environment. Heavy metals are pollutants that exist in nature in the Earth’s crust and are difficult to decompose. They exist as ores in rocks and are recovered as minerals. High-level exposures can release heavy metals into the environment. Once in the environment, they remain toxic for much longer [ 1 ]. Many of these pollutants are mutagenic to both humans along with their surroundings. Absorbing heavy metals accumulates in the brain, liver, and kidney. Other effects on animals include cancer, nervous system damage, stunted growth, and even death [ 2 ]. Heavy metals in soils reduce food quality and quantity by inhibiting nutrient absorption, plant growth, and physiological metabolic processes. Metal-contaminated soils are being remedied using chemical, biological, and physical methods. However, physicochemical methods produce a lot of waste and pollution, so they are not valued [ 3 ]. Bioremediation is a cost-effective and practical solution for removing environmental contaminants [ 4 ]. Plant growth promotion, insect control, soil conservation, nutrient recycling, and pollutant reduction are all key functions of soil microorganisms [ 5 ]. Bioremediation has come a long way in terms of efficiency, cost, and social acceptability [ 6 ]. Bioremediation research has largely focused on bacterial processes, which have numerous applications. Archaea are known to play a role in bioremediation in many applications where bacteria are involved. Many hostile situations have degraded, requiring bioremediation. Microbes can also assist in the elimination of pollutants from hyperthermal, acidic, hypersaline, or basic industrial waste [ 7 , 8 ]. Recent research suggests that using more than one living organism will improve the efficiency and results, and allow for greater microbial diversity in bioremediation [ 8 , 9 ]. Many researchers employed bioremediation technology for the removal of organic and inorganic pollutants [ 10 , 11 , 12 ]. In a study, bioremediation technology was used for the treatment of various pollutants, including organophosphate pesticides such as chlorpyrifos, methyl parathion, and profenofos, by Aspergillus sydowii , and chloramphenicol by endophytic fungi, respectively [ 13 , 14 ]. In another study, Cymbella sp. has been shown to detoxify naproxen-polluted water with an efficiency of 97.1% [ 15 ].

A bioremediation approach requires the use of microbial enzymes to break down hydrocarbons into less harmful compounds. The widespread use of genetically-modified microorganisms that can also help to eliminate petroleum, naphthalene, toluene, benzene, and other xenobiotic chemicals is now being studied [ 16 ]. Several factors, such as temperature of the surrounding environment, aerobic or anaerobic conditions, and nutrient availability, all influence bioremediation for better outcomes. Emerging environmental pollutants, such as persistent organic compounds, heavy metals, toxins, and air pollutants that are of synthetic or natural origin, reach ecosystems mainly through anthropogenic activities and pose adverse threats to lifeforms like plants, animals, and humans [ 17 ]. One of the most economical and environmentally favorable biotechnological innovations is bioremediation. Waste management mainly relies on bioremediation. It can remove persistent organic pollutants, which are hard to breakdown and are thought to be heterologous biological substances. This review addresses the recent approaches and updated information of bioremediation strategies for eco-friendly detoxification and the effective degradation of various organic and inorganic contaminants to control environmental pollution.

2. Microorganisms Used in Bioremediation

Biological equilibrium is maintained in part by the contribution of microorganisms to nutritional chains. Bioremediation is the process of using bacteria, algae, fungi, and yeast to remove contaminated materials from the environment [ 18 ]. In the presence of hazardous compounds or any waste stream, microbes can grow at temperatures as low as −196 degrees Fahrenheit and as high as 1200 degrees Fahrenheit. The adaptability and biological systems of microbes make them an ideal choice for remediation [ 19 ]. Carbon is the most important nutrient for microorganisms. Microbes from a variety of environments were used to perform bioremediation. Achromobacter , Alcaligenes , Xanthobacter , Arthrobacter , Pseudomonas , Bacillus , Mycobacterium , Corynebacterium , Flavobacterium , Nitrosomonas , and other microorganisms [ 9 ] are examples of microbes.

2.1. Aerobic

Several microorganisms have the ability to bioremediate different types of environmental pollutants under aerobic conditions. Bacillus , Pseudomonas , Sphingomonas , Flavobacterium , Nocardia , Rhodococcus , and Mycobacterium are aerobic bacteria that can degrade a variety of complex organic compounds [ 20 ]. Pesticides, alkane hydrocarbons, and polyaromatic compounds have been shown to be degraded by these microbes. Several of these microorganisms make use of these contaminants as a source of carbon and energy [ 21 ]. In the aerobic bioremediation process, oxygen is the limiting factor for the growth of microorganisms.

2.2. Anaerobic

Amphibious bacteria that degrade and convert pollutants to fewer toxic forms are becoming increasingly popular for the bioremediation of polychlorinated biphenyls, chlorine compounds, and the chlorinated solvents, trichlorethylene and chloroform [ 22 ]. Several bacteria, such as Pseudomonas , Aeromonas, and sulfate-reducing bacteria, have been used in the bioremediation process under anaerobic conditions. Garg and Tripathi [ 23 ] reported microbial discoloration of azo dyes under different environmental situations. Azo dyes can decompose anaerobically through reduction reactions using electrons produced by the oxidation of the organic substrate(s). Due to such controlled dye decolorization events, microbe electrochemical properties would have a major impact on the effectiveness of color removal. Dyes were anaerobically decolored for industrial activities to progressively acquire such time-variant decolorized-metabolites (DMs). However, external augmentation of DMs gathered under certain conditions was carried out for improved research so that a precise system can be used [ 24 ].

3. Factors Affecting Microbial Bioremediation

Bioremediation is the process of using microorganisms such as bacteria, algae, fungi, and plants to break down, change, remove, immobilize, or detoxify various physical and chemical pollutants in the environment. Microorganisms’ enzymatic metabolic pathways speed up biochemical reactions that break down pollutants [ 25 , 26 ]. In order for microorganisms to combat pollutants, they must come into contact with compounds that provide them with the energy and nutrients they need to multiply. There are several factors such as physical, chemical, biological, soil-type, carbon and nitrogen source, type of microorganisms—i.e., single or consortium—and others that affect the process of bioremediation [ 27 ]. Microbial consortiums often have both multifunctionality and resistance because different species work together to use all substrates in the best way possible, thereby increasing the bioremediation efficiency compared to single microorganism [ 28 ]. In a study, carbon is one of the most important nutrients that help in situ bioremediation by increasing the metabolic activity of natural microbial communities and speeding up the bioremediation process to break down existing pollutants. Bioremediation may use organic carbon more than any other additive. In an anaerobic environment, many microorganisms can ferment organic carbon and make hydrogen gas [ 29 ]. In a study, bioremediation was found to be significantly affected by soil types, and the removal efficiency of pollutants varied in sandy soil and clay soil, respectively [ 30 ]. For bioremediation to be a success, it must be able to access existing microorganisms as well as the environment’s physicochemical characteristics ( Table 1 ). The microbial population responsible for degrading pollutants, the accessibility of contaminants, and the following factors are taken into consideration.

Critical factors for microbial bioremediation.

4. Principle of Bioremediation

When organic wastes are biologically degraded under controlled conditions, “bioremediation” is the term used to describe this process. Using bioremediation, harmful substances can be degraded or detoxified by providing the organisms with the nutrients and other chemicals they need to function optimally. Enzymes play a critical role in every stage of the metabolic process [ 24 , 43 ]. It is part of the family of oxidoreductases, lyases, transferases, and hydrolases. Non-specific and specific substrate affinities allow many enzymes to degrade a wide range of substrates. There must be enzymatic action on the pollutants in order for bioremediation to be successful. In order to speed up microbial growth and degradation, environmental parameters must often be manipulated during bioremediation [ 38 , 43 ]. This is because bioremediation only works when the environment is right for microbes to grow and move around.

Living organisms and fertilizers can aid in the process of bioremediation, which occurs naturally and is encouraged. Biodegradation is a key component of bioremediation technology. It’s the process of converting harmful organic pollutants like carbon dioxide and water into non-toxic or naturally-occurring inorganic compounds that are safe for use by humans, plants, animals, and aquatic life [ 44 ].

5. Types of Bioremediations

Bioremediation can be used in a plethora of ways, and some of the most commonly used methods are presented here ( Figure 1 ).

Diverse bioremediation techniques.

5.1. Biopile

In bioremediation, aeration and nutrient supplementation are used to enhance microbial metabolic activities in the piled-up polluted soil above ground. Aeration, nutrients, irrigation, leachate collection, and treatment bed systems are all included in this procedure. When it comes to ex situ biodegradation, this method is becoming increasingly popular because of its cost-effectiveness and useful features, such as pH and nutrient control. Using the biopile to clean up polluted cold environments and treat low-molecular-weight volatile pollutants is an option [ 15 , 45 ]. The biopile’s adaptability allows for a reduction in remediation time by increasing microbial activity and contaminant availability while also increasing biodegradation rate. When warm air is introduced into the biopile system to provide air and heat simultaneously, bioremediation is improved. The biopile’s remediation process has been helped by the addition of bulking agents like straw, sawdust, or wood chips. To replenish the air supply to polluted piled soil in biopiles, ex situ bioremediation techniques such as land farming, biosparging, and bioventing can be applied [ 46 ]. However, these techniques are expensive to implement and require a power supply at remote locations. Bioremediation may be slowed down by extreme air temperatures that dry soil and make it more likely to be vaporized than to be broken down by living organisms [ 47 ]. Bio-available organic carbon (BOC) plays an important role in bioremediation through the biopile method. Petroleum contaminated soil has been bioremediated using mesophillic conditions (30 °C–40 °C) and a low aeration rate for the removal of total petroleum hydrocarbon (TPH) using alpha , beta , and gamma proteobacteria [ 48 ]. Biopile systems have also been utilized for treating the diesel contaminated soil of the sub-Antarctic region. A total of 93% of the total petroleum hydrocarbon (TPH) was removed using the biopile system within one year [ 49 ].

5.2. Windrows

Windrows boosts bioremediation by enhancing the biodegradation processes of native and transitory hydrocarbon plastic found in the contaminated soils when spinning the heaped contaminated soils. The aeration, mineralization, and biotransformation of toxic soil can be performed through acclimation, biological treatment, and mineralization [ 50 ], can speed up bioremediation. The biopile approach can remove more hydrocarbons from soil than windrow treatment [ 15 , 51 ], which was more efficient in terms of hydrocarbon removal. The periodic rotation connected with windrow remediation is not a better selection approach for the bioremediation of soil affected by harmful volatile chemicals. Windrow treatment is a source of greenhouse gas (CH 4 ) due to the anaerobic system generated inside the heaped contaminated soil [ 52 ]. The windrow method of has been applied for the bioremediation of the Gurugram–Faridabad dumpsite in Bandhwari, India by forming terraces and windrows and utilizing bio-culture, and the results showed a decrease in the garbage [ 53 ].

5.3. Land Farming

Land farming is the most significant and simple bioremediation method because of its low operating costs and lack of specialized equipment [ 54 ]. Ex situ bioremediation is the most common method, but it can also occur with in situ bioremediation. The reason for this is the location of the treatment. It is common practice in land farming to remove and till polluted soils on a regular basis, and the location of treatment dictates the type of bioremediation. On-site treatment is classified as in situ , whereas ex situ bioremediation approaches are used for the treatment of the contaminated soil [ 55 ]. Extracted contaminated soils are usually placed on a permanent layer of substrate well above Earth’s surface to permit native microorganisms to aerobically degrade contaminants [ 56 ]. Land bioremediation of polluted soil using land farming bioremediation technology is a reasonably simple process that takes little capital, has little ecological footprint, and uses very little energy [ 57 ].

5.4. Bioreactor

Following a series of biological reactions, bioreactors transform raw materials into specific products. Bioremediation thrives in a bioreactor, which provides the ideal conditions for growth [ 58 ]. The remediation samples are placed in a bioreactor. There are a number of advantages to using a bioreactor to treat contaminated soil as opposed to ex situ bioremediation methods. An efficient bioremediation process based on bioreactors that can precisely regulate pH, agitation, temperature, aeration, substrate concentration, and inoculum concentration significantly reduce the time required for bioremediation [ 59 ]. Biological reactions can take place when the bioreactor can be controlled and manipulated. Given their adaptability, bioreactor designs are able to maximize microbial degradation while abiotic losses are kept to a minimum.

In Situ Bioremediation Techniques

These methods entail cleaning up polluted substances right where they were created. It does not necessitate any digging or disturbance of the surrounding soil. These techniques ought to be more cost-effective in comparison to the ex situ bioremediation techniques. Bioventing, phytoremediation, and biosparging are examples of in situ bioremediation techniques that can be improved, while intrinsic bioremediation and natural attenuation are examples of in situ bioremediation techniques that cannot be improved [ 60 ]. In situ bioremediation approaches have effectively treated chlorine, paints, toxic metals, and hydrocarbon-contaminated areas [ 61 ]. The practice of in situ bioremediation can be categorized into two distinct types: intrinsic and engineered.

• (a) Intrinsic in situ bioremediation:

Natural reduction is another term for in situ bioremediation. Intrinsic bioremediation utilizes polluted sites in a non-invasive manner (human intervention) [ 62 ]. The goal of this procedure is to stimulate an already existing microbial population. The biodegradation of polluting constituents, including those that are recalcitrant, is based on aerobic and anaerobic processes in microorganisms. It costs less because there isn’t a lot of force behind this technique [ 63 ]. Intrinsic in situ bioremediation can be performed using anaerobic reductive dechlorination, aerobic treatment, amendment delivery, biosparging, and bioslurping [ 64 ]. Using a stimulation–optimization approach that is powered by machine learning and particle swarm optimization (ELM–PSO) techniques, in situ bioremediation has been used as a method for the biological treatment of clogged groundwater [ 65 ]. This technique was implemented through the use of in situ bioremediation. This results in cheaper technology for the pumping system and requires less capital for the whole process. The concentration of contaminants was reduced from 40 ppm to 5 ppm (within permissible range) in 3 years using in situ bioremediation. In situ remediation has also been explored for the decontamination of Cr (VI) found in shallow unsaturated soil. Microorganisms possess the capability to survive under high concentrations of Cr (VI) in the soil and their sub-cellular machinery was utilized to interact with heavy metals. Microbial inoculants can be utilized for the in situ treatment of heavy metals [ 66 ]. Cr (VI) interacts with Fe (II) ions also through the redox reactions, and the release of iron in soluble forms promotes the reductive reactions [ 67 ].

• (b) Engineered in-situ bioremediation

In the second method, a specific microorganism is brought into the area of contamination to clean it up. In situ bioremediation is a technique that employs microorganisms that have undergone genetic engineering in order to hasten the decomposition process. This is accomplished by enhancing the physicochemical conditions that foster the growth of microorganisms [ 68 ].

5.5. Bioventing

Bioventing is a technique that uses controlled airflow to increase the activity of indigenous microbes for bioremediation by delivering oxygen to the unsaturated zone. The bioremediation process is aided by the addition of nutrients and moisture during the bioventing process. This will lead to the microbial transformation of pollutants into harmless substances. Other in situ bioremediation methods have flocked to this one in recent years [ 69 ]. Bioventing is a technique that helps in stimulating the indigenous microflora through ample amounts of aeration to enhance the biodegradation ability of the various microbes and promote decontamination of the heavy metal pollutants by precipitation [ 70 ].

5.6. Bioslurping

A direct oxygen supply and stimulation of contaminant biodegradation are used in conjunction with vacuum-assisted pumping, bioventing, and soil vapour extraction (SVE) in order to reach soil and groundwater levels for restoration [ 71 ]. This approach can be used to recover unsaturated and saturated zones as well as light non-aqueous phase liquids (LNAPLs). This technology can be used to remediate soils contaminated with flammable and moderately-flammable organic substances. Liquid is drawn from the free product layer by means of a “slurp” that spreads into the layer. LNAPLs are lifted to the surface by the pumping machine, where they are separated from the surrounding air and water [ 72 ]. To reduce microbial activity, soil moisture is used in this technique to reduce air permeability and oxygen transfer rate. Given that it uses less groundwater, this method saves money on storage, disposal, and treatment, even though it’s not ideal for remediation in low-permeable soils. Bioslurping requires 25 feet of digging below the ground surface and then the contaminants floating on the water can be removed. It combines both the approaches of bioventing, which utilize aerobic bioremediation of contaminated soil in situ. Free product is recovered by a vacuum-enhanced system that utilizes LNAPLs from the capillary fringe [ 73 ]. Free product is “slurped” up the bioslurping tube into a trap or oil–water separator for further treatment after the bioslurping tube is vacuumed. When the LNAPL is removed, the height of the LNAPL drops, which encourages the flow of LNAPL from distant locations into the bioslurping well. The bioslurping tube starts to remove vapours from the unsaturated zone when the fluid level in the bioslurping well decreases as a result of the vacuum extraction of LNAPL. This vapour extraction encourages soil gas movement, which in turn boosts aerobic biodegradation and aeration [ 74 ].

5.7. Biosparging

Air is introduced into the soil’s core, just like bioventing, to encourage microbiological activity, which in turn removes pollutants from polluted sites. As an alternative to conventional biodegradation methods, bioventing involves injecting air into a saturated zone in order to encourage the movement of flammable organic chemicals upward to an unsaturated zone nearby [ 75 ]. The success of biosparging is dependent on soil porosity and contaminant biodegradability. When it comes to bioventing and soil vapour extraction (SVE), in situ air sparging (IAS) uses high air-flow rates to volatilize contaminants, while biosparging encourages microbial degradation [ 76 ]. It is common practice to use biosparging to remove diesel and kerosene from water supplies. In order to hasten the biodegradation processes, oxygen is supplied into microorganisms during enhanced bioremediation [ 77 ]. The removal of organic pollutants (BTEX) can be accomplished using a variety of technologies, including adsorption, microbial degradation, biosparging, PRBs, and the use of modified or synthesized zeolites. However, there aren’t many investigations on readily available, inexpensive materials like natural zeolite for BTEX adsorption [ 78 ].

5.8. Phytoremediation

Contaminated soils can be cleaned up using phytoremediation. In contaminated areas, this method uses plant interactions at the physical, biological, chemical, biochemical, and microbiological levels to reduce pollutant toxicity. Depending on the quantity and form of the pollutant, phytoremediation employs a variety of processes [ 79 ]. Extraction, sequestration, and transformation are common methods for removing pollutants like heavy metals. When using plants like willow or alfalfa, the decay, immobilization, rhizoremediation, and evaporation of organic contaminants such as oils and chloro-compounds is feasible [ 80 ]. Tap root system or fibrous root system, penetration, toxicity levels, adaptability to the harsh environmental conditions of the contaminants, plant annual growth, supervision, and, notably, the time needed to reach standard of cleanliness are all important factors in plants that serve as phytoremediators. The plant must also be disease and insect resistant [ 81 ]. An important part of phytoremediation is removing pollutants from the roots and shoots. The movement of water and nutrients is also dependent on transpiration and partitioning [ 82 ]. When it comes to contaminants and plant nature, it is possible to alter this process. Phytoremediation can be accomplished with the help of the majority of the plants present at a polluted site. In polluted environments, native plants can be bioaugmented by natural or anthropogenic plants, or a combination of both. Phytomining, the process of extracting precious metals from polluted sites with plants, is one of them [ 83 ].

Numerous plants (over 300) are better candidates for phytoremediation because they ideally absorb Cu, Zn, and Ni. Phytostabilization, sometimes referred to as in situ inactivation or immobilisation of heavy metals, reduces their bioavailability and prevents their off-site transfer. At the plant roots, it absorbs metals and restores them. Several species, notably Acanthus ilicifolius and Virola surinamensis , are capable of Cd photostability. Cinnamomum camphora , Osmanthus fragrans , Euonymus japonicus , Ligustrum vicaryi , and Loropetalum chinense are five decorative plants chosen for their capacity to phytostabilize Cd [ 84 ]. Water from various places that has been contaminated with metal can be successfully treated using bacterially-aided phytoremediation. The phytoremediation method of metal reduction in wastewater utilising plants can be used by coalitions of growth-promoting rhizobacteria, degrading bacteria, as well as endophytic bacteria [ 85 ]. There are a few limitations to bioremediation techniques, as presented in Table 2 .

Limitations of various bioremediation techniques.

6. Bioremediation of Various Pollutants

6.1. bioremediation for organic pollutants.

Organic compounds (OCs) such as biocides and flame retardants have been widely used and are now considered a threat to nearly all forms of life on the planet because of the widespread and massive use of these chemicals in the environment. Most OCs, such as polychlorinated biphenyls (PCBs), polybrominated biphenyl ethers (PBEs), and polycyclic aromatic hydrocarbons (PAHs), can be degraded in the environment by microbes. Biodegradation is the process by which microbes break down organic compounds into less toxic or entirely non-toxic residues [ 91 ]. In order to obtain organic carbons and energy, the microbes consume the organic substrate. Isolated from other microbes, an individual microbial species usually does not degrade any organic substrate [ 92 ] and does well in a community. As a result of community microbe interactions, resistance, chemical-degrading ability, and tolerance are all conferred by the exchange of genetic information among microbial species. Many OC-degrading microorganisms are misidentified due to a lack of internationally agreed-upon methods and protocols for microbial identification [ 93 ]. This underlines the significance of studies into microbial consortiums using metagenomics tools and conventional genetic engineering protocols. Bacteria and other microorganisms have the ability to degrade a wide range of organic compounds, depending on the chromosomal genes, as well as the extracellular enzymatic activity (in the case of bacteria) (fungal degradation process). The varying environmental conditions that affect the microbe growth pattern further complicate these processes [ 94 ].

A successfully bioengineered microbe requires the identification of the relevant species and strains for each substrate. A viable alternative to the recombinant degradation of resistant organic compounds is biodegradation by microbes using readily-available organic carbon and energy sources in the surrounding environment. Microbes use the fluctuation in chemical gradients in their environment to determine the most favourable conditions for growth. This allows them to thrive in an optimal environment [ 95 ]. Microbial consortia and microbial fuel cells (MFCs and bioreactors) are two new developments in microbiological bioremediation that are being used to degrade recalcitrant organic compounds. Toxic organics can be remedied more effectively using fungi rather than bacteria because the latter cannot grow at high concentrations of toxic organics [ 96 ]. For example, the enzymes, laccase (LAC), lignin peroxidase (Lip), and manganese decarboxylase (MDA), are active in the metabolism of lignocellulosic compounds by the white rot fungus Phanerochaete chrysosporium [ 97 ].

6.2. Bioremediation for Inorganic Pollutants

Toxic heavy metals and their compounds resulting from mining, power plants, metallurgy, and chemical manufacturing processes are among the most common inorganic contaminants [ 98 ]. One of the main concerns of environmentalists is toxic elemental pollution because the disposal of toxic metals to soils and waters on or below the surface causes unacceptable health risks [ 99 ]. Microbes cannot degrade metal ions; it is essential to know that they are only capable of changing the oxidation states of the metals to stabilize them [ 100 ]. They can metabolize and detoxify metals like any other nutrient in the cells. Several microorganisms have been reported for the bioremediation of organic and inorganic pollutants ( Table 3 ). Microbes that release chelating agents and acids, as well as those that alter physicochemical properties such as redox potential in their environment can cause significant changes in the environment by increasing the bioavailability of metal ions [ 101 ]. Physical adsorption, biosorption, and ion complexation are the first steps in the interaction between metals and microbial cells [ 102 ]. Enzymes for oxidation, methylation, reduction, precipitation, and dealkylation are involved in the biochemical transformation of metal ions by microorganisms. The adaptability of microbes to heavy metals, such as iron, zinc, chrome, magnesium, mercury, and barium in textile waste, was demonstrated in the multidrug-resistant Pseudomonas aeruginosa T-3 isolate from tannery effluent [ 67 , 83 ]. This shows that microbes can adapt to changing environmental conditions. A plasmid-encoded copper and cadmium metal resistance gene in the bacteria, Pseudomonas putida PhCN, has also been discovered [ 103 ]. Plasmid-encoded biochemical information and genetic engineering techniques were used to create recombinant Escherichia coli that expresses the metallothionein gene ( Neurospora crasa ) for Cd uptake, resulting in significantly faster Cd uptake than the donor microbe [ 104 ]. A poly-histidyl peptide was introduced into Staphylococcus xylosus and Staphylococcus carnosus that encoded genes that allowed these microbes to bind nickel [ 105 ].

Potentially hazardous organic and inorganic pollutants and their degrading microbes (bacteria, fungi, and algae).

7. Recent Advancement and Challenges in Bioremediation

7.1. bioinformatics approaches in bioremediation.

When it comes to waste management, bioremediation is a useful technique that can be used to remove waste from contaminated areas and sites. It is particularly concerned with the utilization of organisms to consume or neutralize pollutants [ 20 ]. Using data from various biological databases, such as databases of chemical structure and composition, RNA/protein expression, organic compounds, catalytic enzymes, microbial degradation pathways, and comparative genomics to interpret the underlying degradation mechanism carried out by a particular organism for a specific pollutant is the goal of bioremediation [ 133 ]. A variety of bioinformatics tools are used to interpret all of these sources in order to study bioremediation in order to develop more effective environmental cleaning technology. There has been a scarcity of data on the factors that control the growth and metabolism of microbes with bioremediation potential, which has resulted in a limited number of bioremediation applications [ 134 ]. These microorganisms with bioremediation capabilities have been profiled and their mineralization pathways and mechanisms have been mapped out using bioinformatics [ 135 ]. The use of proteomic approaches such as two-dimensional polyacrylamide gel electrophoresis, microarrays, and mass spectrometry is also critical in the investigation of bioremediation methods and technologies. It significantly improves the structural characterization of microbial proteins that have contaminant-degradable properties, according to the researchers [ 135 ]. The structural characterization of microbial proteins capable of degrading contaminants has greatly improved. Research in this field crosses the boundaries between computer science and biology. For example, computers are used to store, manipulate, and retrieve information linked to the DNA, RNA, and proteins of the genome [ 133 , 135 ].

7.1.1. Bioremediation Tools Based on Omics

Bioremediation studies can benefit from the use of genomics, transcriptomics, metabolomics, and proteomics. Given its ability to correlate DNA sequences with the abundance of metabolites, proteins, and mRNA, this technology aids in the in situ bioremediation process’s evaluation [ 136 , 137 ].

7.1.2. Genomics

There is a new field in genomics for the study of bioremediation microbes. This strategy is based on microbes’ ability to fully analyze their genetic information within the cell. Bioremediation uses a wide variety of microorganisms [ 138 ]. To better understand the biodegradation process, genomic tools such as PCR, analysis of isotope distribution, DNA hybridization, molecular connectivity, metabolic footprinting, and metabolic engineering are used. For genotypic fingerprinting, a variety of PCR-based techniques are available, including amplified fragment length polymorphisms (AFLP), amplified ribosomal DNA restriction analysis (ARDRA), automated ribosomal intergenic spacer analysis (ARISA), terminal-restriction fragment length polymorphism (T-RFLP), randomly amplified polymorphic DNA analysis (RAPD), single strand conformation polymorphism (SSCP), and length heterogeneity [ 139 ]. When it comes to studying soil microbial communities, RAPD can be utilized for assessing inherently related bacterial species, constructing functional structural models, and generating genetic fingerprints [ 140 ]. In microbial communities, LH-PCR may be used to detect natural length variations of various SSU rRNA genes. Multiple taxonomic groups of microbes can be profiled simultaneously using T-RFLP [ 141 ]. Research into how soil microbes interact with natural factors can also make use of a combination of molecular tools, such as genetic fingerprinting, microradiography, FISH, stable isotope probing, and quantitative PCR. A PCR-based quantitative analysis of soil microbial communities can be used to determine the abundance and appearance of taxonomic and operational gene markers in the soil. Techniques for analysing a person’s DNA use amplified PCR products as a starting point for the direct analysis of specific molecular biomarker genes [ 142 ]. In order to better understand the relationship between diverse microbial communities, cluster-assisted analysis, which compares fingerprints from different samples, could be used.

7.1.3. Transcriptomics and Metatranscriptomics

The transcriptome is a crucial link between cellular phenotype, interactome, genome, and proteome because it represents the set of genes that are being transcribed at a specific time and condition. The ability to control gene expression is critical to adapting to changes in the environment and thus ensuring survival. Transcriptomics provides a comprehensive view of this process across the entire human genome. In transcriptomics, DNA microarray analysis is a powerful tool for determining mRNA expression levels [ 143 ]. To perform a transcriptomic analysis, one must first isolate and enrich the total mRNA, then synthesize cDNA, and then sequence the cDNA transcriptome. Using a DNA microarray as a transcriptomics tool, almost every gene in an organism’s mRNA expression can be examined and studied [ 144 ]. The study of transcriptional mRNA profiles, also known as transcriptomics or metatranscriptomics, is critical for gaining functional insights into the activities of environmental microbial communities [ 145 ]. Syntrophism between microbes and complementary metabolic pathways can be discovered using metagenomics and genome binning as well as metatranscriptomics during the entire biodegradation process [ 146 ]. Metatranscriptomics is a way to look at gene expression that can be used by researchers [ 147 ].

7.1.4. Proteomics and Metabolomics

In contrast to metabolomics, which focuses on the total metabolites produced by an organism in a given period of time or environment, proteomics focuses on the total proteins expressed in a cell at a given location and time [ 148 ]. The analysis of protein abundance and changes in composition, as well as the identification of key microbe-related proteins, has been accomplished using proteomics [ 149 ]. In comparison to genomics, the functional analysis of microbial communities is more useful and holds more promise. There are two primary ways in which metabolomics studies can be used to analyze biological systems. It is not necessary to have any prior knowledge of the metabolic pathways of the biological system in order to conduct the first type of study. By employing this strategy, there are numerous metabolites in the sample that can be identified and recovered, which generates enormous amounts of data that can be used to establish the interconnectedness of various samples in metabolic pathways. Another option is to conduct a targeted study to identify specific metabolic pathways or metabolites based on prior research [ 150 ]. Metabolite profiling, foot printing, and target analysis are just some of the many tools in the toolbox of microbial metabolomics that can be used to identify and quantify the myriad of cellular byproducts present in living organisms [ 151 ]. Data from both the proteome and metabolome will be useful for cell-free bioremediation.

7.2. Bioremediation Using Nanotechnological Methods

A nanometer is the smallest unit of measurement used in nanotechnology. Many toxic substances can be removed with their help because of their unique abilities against various recalcitrant contaminants. Technology such as water treatment has been given a new perspective by nanotechnology. Techniques that are good for the environment can now be categorized as nanofiltration [ 151 ].

7.2.1. Microbe and Nanotechnology

When using effective microbes (EM) technology, wastewater can be treated with effective microbes, and the water can then be used for irrigation [ 152 ]. For water purification, nanotechnology and EM technology can be helpful. Innumerable and all-pervasive environmental issues arise from the presence of recalcitrant organic pollutants like polycyclic aromatic hydrocarbons (PAHs) with multiple benzene rings. Polycyclic aromatic hydrocarbons (PAHs) are mutagenic and non-biodegradable [ 153 ]. In a study, Ramos et al. [ 154 ] synthesized silver nanoparticles using whole cells of the fungi Trichoderma spp. for its application.

7.2.2. Engineered Polymeric Nanoparticles for Hydrophobic Contaminant Bioremediation

Soil sorption of organic pollutants, such as petroleum hydrocarbons and PAHs, reduces their solubility and mobility, which in turn reduces their environmental impact. The phenanthrene solubility and phenanthrene release from contaminated aquifer material are both improved by polymeric nano-network particles [ 155 ]. Precursor chains of poly-(ethylene) glycol-modified urethane acrylate (PMUA) are used to create polymeric nanoparticles. PMUA nanoparticles are designed to maintain their properties in the presence of a diverse range of bacterial populations [ 156 ].

7.3. Genetic and Metabolic Engineering

“Gene editing” refers to scientific technical developments that enable rational genetically-created fragments at genome level to provide exact addition, deletion, or substitution of pieces of DNA molecules. Transcription activators are utilized in a variety of gene editing methods, including TALENs, ZFNs, and CRISPRs, which are widely used in research. CRISPR-Cas has been dubbed the most efficient and straightforward gene editing tool [ 157 ]. A DNA-binding element in TALEN is complementary to the sequence of the host DNA. When TALEN attaches to DNA and exposes sticky ends for stabilization, it creates double-stranded breaks (DSBs). ZFNs also have a DNA-binding domain made up of 30 amino acids. At the target location of the host DNA, the Fok1 cleavage domain causes DSBs. A novel perspective on composite endonuclease comprising TALENs and ZFN nucleases was required to solve molecular problems [ 158 , 159 ]. Two of the CRISPR-Cas system’s unique properties are sequence similarity complementarity and simultaneous gene editing [ 160 , 161 ]. The bacteria, Streptococcus pyogenes, provides this unique ability as a sort of virus resistance. In the CRISPR-Cas system, guide RNA connects crisper-derived RNA (crRNA) and trans-acting antisense RNA (trcRNA). The Cas9 enzyme is able to carry out the requisite DSB when gRNA recognizes the target DNA sequence. These gene editing tools’ knock-in and knock-out effects are being analyzed for usage in bioremediation investigations [ 161 ]. In model organisms like Pseudomonas and Escherichia coli , the CRISPR-Cas system has been widely accepted by researchers [ 138 ]. In non-model species (such as Rhodococcus ruber TH, Achromobacter sp. HZ01, and Comamonas testosteroni ), the area of bioremediation is also exploring new insights into CRISPR toolkits and the synthesis of gRNA for the production of remediation-specific genes [ 162 ].

Pollutant-tolerant bacteria are the greatest choices for genetic manipulation and biochemical pathways since they are accustomed to tolerating and storing a variety of toxic, refractory, and non-degradable xenobiotic compounds under harsh circumstances. Furthermore, recognizing biochemical functions is critical for analyzing microbiological bioremediation, such as the bioremediation of harmful pollutants through the production of haloalkane dehalogenases and the disposal of pyrethrins from land through the anaerobic decomposition pathway of fenpropathrin studied in Bacillus sp. DG-02 [ 163 ]. The bioremediation process can be improved by metabolic engineering, which alters the existing pathway. The likelihood of obtaining recombinant enzymes increases significantly when using a genetic approach. Some extracellular enzymes have been found to play a role in enzymatic bioremediation, according to some studies. PAHs are degraded by LiPs ((lignin peroxidase) from P. chrysosporium that encode hemoproteins [ 164 ]. Even though contaminants can be consumed by microbes as substrates or intermediates in biological pathways, incomplete or partial degradation leads to simpler, non-toxic degradable compounds [ 136 ]. For example, LiP can degrade benzopyrene into three quinine compounds, namely 1,6-quinol, 3,6-quinine, and 6,12-quinine [ 165 ]. MnP (Mn (II) peroxidase) can also oxidise organic compounds in the presence of MnP (Manganese peroxidase) [ 166 ]. As well, laccase, glutathione S transferase, and cytochrome P 450 are involved in the biodegradation of recalcitrant compounds [ 167 ]. It has been shown that the immobilization of enzymes significantly increases enzyme stability, activity, and stability. Enzymatic bioremediation is a simple, environmentally-friendly, and fast method for removing and degrading persistent xenobiotic compounds by microorganisms [ 134 , 145 ]. Enzyme-producing microorganisms have been isolated and characterized with the limitation of low productivity. Insecticides’ main ingredients, organophosphates (OP) and organochlorines (OC), are found in agricultural soil and run-off into waterways.

Genetically-engineered microorganisms have demonstrated successful bioremediation of hexachlorocyclohexane and methyl parathion [ 135 , 146 ]. Genetically-modified P. putida KT2440 was used in organophosphate and pyrethroid bioremediation experiments [ 168 ]. The degradation and catabolism of a variety of persistent compounds has been documented since the advent of metabolic engineering. Sphingobium japonicum and Pseudomonas sp. WBC-3 showed bioremediation of methyl parathion and -hexachlorocyclohexane degradation pathways [ 169 ]. When three enzymes from two different microorganisms are combined in E. coli , a persistent fumigant called 1-, 2-, 3-trichloropropane is released into the environment via heterologous catabolism [ 137 , 148 ]. To do this, microbes can be used to turn persistent compounds into minerals [ 49 ].

7.4. Designing the Synthetic Microbial Communities

Synthetic biology advancements have had a significant impact on environmental issues in recent years. Toxic compounds, pesticides, and xenobiotics can be removed from the environment by using genetically-modified organisms (GMOs). Natural microbial communities must be understood in order to create a synthetic one [ 170 ]. Identifying which species are participating in bioremediation is difficult in a natural community. Through the use of a synthetic microbial community, the development of an artificial microbiome with functionally specific species is possible. Model systems for studying functional and structural characteristics can be found in these communities. Synthetic communities were formed by the co-culturing of two distinct microorganisms under precisely defined conditions, which were based on their interactions and functions [ 171 ]. The community’s dynamics and structure are determined by these variables; it is based on the discovery of bacterial processes and behaviors. Metabolism drives these patterns of microbial interaction, which in turn facilitates communication within communities [ 172 ]. Interactions between two microbial populations are social in nature (such as mutualism, competition, and cooperation). Cooperation is said to be a key factor in community structure and operation. Cooperation in community dynamics is influenced by the creation of synthetic communities [ 173 ] and it was found that modifying environmental conditions, such as deleting genes, could be used to engineer cooperation between two microbial strains. In addition to this, the synthetic community’s engineered microbial species have been examined for other patterns of interaction. Bioremediation strategies frequently make use of this type of engineered interaction [ 174 ]. It is possible to sustain the existence of microorganisms in a large population by using synthetic biology.

8. Advantages and Disadvantages

Due to the harm that pollutants exert on both humans and other living things, environmental pollution is a serious public health problem. The complete elimination of contaminants via chemical and physical methods of remediation is costly [ 175 ]. Additionally, both approaches may result in increased pollution and site disruption, which could have a detrimental effect on nearby humans and other biota. As a result, remediation techniques using chemicals and physical means are not regarded as eco-sustainable. Contrary to these techniques, bioremediation is the suggested solution to remove various persistent contaminants by relying on biological processes (mediated by various types of living organisms). However, all bioremediation techniques have their own advantages and disadvantages ( Figure 2 ) because they have their own specific applications [ 176 , 177 ].

Advantages and disadvantages of bioremediation.

9. Future Perspectives and Conclusions

Omics has gained prominence in the field of microbial remediation of the pulp and paper industry, textile industry, food industry, dairy industry, wood industry, fisheries, water and soil treatment industry, solid waste remediation, heavy metal pollution remediation, and hydrocarbon remediation. In order to better understand degradative pathways, bioremediation data must be mined, and new algorithms can be used to fit these data into simulation and numerical modeling with ease along with data assemblage, repositioning, exploration, and transmission, which necessitate standard protocols. Bioremediation processes may be better understood if new biomarkers are studied. Combining all the omics data with genetically-engineered tools could provide a comprehensive picture of the microbial remediation process. The role of phytoremediation in reducing environmental pollution can also be studied. The phytoremediation process has a number of advantages over other remediation strategies, including lower costs, greater public acceptance, and increased pollution degradation capacity [ 178 ]. Groundwater and air pollution, along with toxic waste generation as a by-product of semiconductor manufacturing, are problems for the environment; some examples include glycol ethers, hydrochloric acid (HCl), xylene, hydrogen fluoride (HF), and methanol [ 179 ]. In the case of pharmaceuticals that are designed to be long-lasting or even non-degradable, they pose a unique threat to the environment. The pharmaceutical pollutants are environmentally persistent substances. Trace amounts of pharmaceutical ingredients, such as birth control pills, anti-epileptics, pain relievers, and antidepressant medications, are found in many urban and rural sources of groundwater [ 180 ]. While operating, solar power generation facilities produce less greenhouse gas emissions, including air pollutants such as carbon monoxide, volatile organic compounds, nitrogen oxides, and carbon dioxide, than conventional fossil fuel-based power generation facilities [ 181 ]. Genetically-engineered plants can be able to bioremediate specific pollutants through discovered metabolic processes, enzymes, genes, or operons [ 182 ]. Although genomics, metabolomics, and proteomics in bioremediation aid in the exploration of possible solutions to specific pollutants, identifying and comparing gene and protein sequences that are effective at removing contaminants is the next step in bioremediation research. GMOs can clean up a wide range of waste effluents and polluted land [ 183 ]. When used in conjunction with other physical and chemical methods, bioremediation can provide a comprehensive approach toward removing pollution from the environment. Since it appears to be a long-term solution, there is a need for additional research in this area.

Acknowledgments

The author M.T. grateful to the Biotechnology Program, Department of Biochemistry, Dr. Rammanohar Lohia Avadh University, Ayodhya, India, for providing us with the research environment.

Funding Statement

This research received no external funding.

Author Contributions

Conceptualization, M.T., M.S., K.S. and B.S.I.; Writing—original draft preparation, S.B., D.G. and B.V.T.; Writing—review and editing, M.S., M.T., K.S. and B.V.T.; visualization, S.B. and D.G.; supervision, M.T., M.S., K.S. and B.S.I. All authors have read and agreed to the published version of the manuscript.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Data availability statement, conflicts of interest.

The authors declare no conflict of interest.

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Microbial remediation of oil-contaminated shorelines: a review

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• Xiaoli Dai   ORCID: orcid.org/0000-0002-7109-7511 1 ,
• Jing Lv 2 ,
• Pengcheng Fu 3 &
• Shaohui Guo 2  

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Frequent marine oil spills have led to increasingly serious oil pollution along shorelines. Microbial remediation has become a research hotspot of intertidal oil pollution remediation because of its high efficiency, low cost, environmental friendliness, and simple operation. Many microorganisms are able to convert oil pollutants into non-toxic substances through their growth and metabolism. Microorganisms use enzymes’ catalytic activities to degrade oil pollutants. However, microbial remediation efficiency is affected by the properties of the oil pollutants, microbial community, and environmental conditions. Feasible field microbial remediation technologies for oil spill pollution in the shorelines mainly include the addition of high-efficiency oil degrading bacteria (immobilized bacteria), nutrients, biosurfactants, and enzymes. Limitations to the field application of microbial remediation technology mainly include slow start-up, rapid failure, long remediation time, and uncontrolled environmental impact. Improving the environmental adaptability of microbial remediation technology and developing sustainable microbial remediation technology will be the focus of future research. The feasibility of microbial remediation techniques should also be evaluated comprehensively.

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The work is financially supported by the National Key Research and Development Program of China (No. 2022YFC3203001) and the Sprout Project of Beijing Academy of Science and Technology (No. 2022A-0006).

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Xiaoli Dai, Jing Lv, and Pengcheng Fu contributed equally to this work.

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Beijing Key Laboratory of Remediation of Industrial Pollution Sites, Institute of Resources and Environment, Beijing Academy of Science and Technology, Beijing, 10089, China

China University of Petroleum-Beijing, Beijing, 102249, China

Jing Lv & Shaohui Guo

State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Hainan, 570228, China

Pengcheng Fu

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XLD: writing—original draft, conceptualization, and resources; JL: writing—review and editing and resources; SHG: writing—review and editing; PCF: writing—review and editing, conceptualization, methodology, and supervision.

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Dai, ., Lv, J., Fu, P. et al. Microbial remediation of oil-contaminated shorelines: a review. Environ Sci Pollut Res 30 , 93491–93518 (2023). https://doi.org/10.1007/s11356-023-29151-y

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Received : 27 March 2023

Accepted : 31 July 2023

Published : 12 August 2023

Issue Date : September 2023

DOI : https://doi.org/10.1007/s11356-023-29151-y

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