Biodegradation of phenanthrene by biodemulsifier-producing strain Achromobacter sp. LH-1 and the study on its metabolisms and fermentation kinetics

Characteristics and functional bacteria of an efficient benzocaine-mineralizing bacterial consortium

The extensive use of pharmaceutical and personal care products (PPCPs) has led to widespread residual pollution, which increases the risk of the development of drug resistance in pathogenic microorganisms. Benzocaine is a PPCP that is widely used medical anesthesia and in sunscreen. Microorganisms are essential for the degradation of residual PPCPs. However, no studies have reported the microbial degradation of benzocaine. In this study, through continuous enrichment of the initial consortium HJ1, the highly efficient benzocaine-degrading consortium HJ7 was obtained, HJ7 exhibited a degradation rate that was 1.92 times greater than that of HJ1. Methyl 4-aminobenzoate and 4-aminobenzoic acid were identified as major intermediate products during benzocaine biodegradation by consortium HJ1 or HJ7. Methylobacillus (57.8 % ± 0.9 %) and Pseudomonas (22.1 % ± 0.7 %), which are thought to harbor essential species for benzocaine degradation, were significantly enriched in consortium HJ7. Two benzocaine-degrading strains, Pseudomonas sp. A8 and Microbacterium sp. A741, and one methyl 4-aminobenzoate-degrading strain, Achromobacter sp. A5, were isolated from consortium HJ7, and they synergistically mineralized benzocaine. These findings not only provide new insights into the biotransformation of benzocaine but also provide strain resources for the bioremediation of residual benzocaine in the environment.

Enhancing bacterial biodegradation of n-hexane by utilizing the adsorption capacity of non-degrading fungi

Biodegradation of hydrophobic volatile organic compounds (VOCs) such as n-hexane is limited by their poor accessibility. Constructing fungal-bacterial degradation alliances is an effective approach, but the role of those fungi without the capability to degrade VOCs may have been overlooked. In this study, a non-n-hexane-degrading fungus, Fusarium keratoplasticum FK, was utilized to enhance n-hexane degradation by the bacterium Mycobacterium neworleansense WCJ. It was shown that strain WCJ removed 64.84% of n-hexane (at a concentration of 648.20 mg L-1) over 3 d, and 84.04% after introducing strain FK. Microbial growth kinetic studies revealed that the growth of strain WCJ was also promoted. Through a stepwise adsorption-degradation experiment combined with qPCR technology, it was found that the strain WCJ could utilize the n-hexane pre-adsorbed by strain FK, with an increase in copy number from 108.2662 to 108.7731. Therefore, the non-degrading fungi can improved the accessibility of n-hexane by providing n-hexane adsorbed by the mycelium to the degrading bacteria. In addition, the adsorption tests and characterization of the fungal samples before and after Soxhlet extraction indicated that the adsorption of n-hexane on strain FK conformed to Lagergren's pseudo-second-order kinetics and Freundlich adsorption isotherms, and was correlated with the presence of lipids and nonpolar groups. This study emphasizes the potential role of non-degrading fungi in bioremediation and proposes a viable strategy to enhance the bacterial degradation of hydrophobic VOCs.

High phenanthrene degrading efficiency by different microbial compositions construction

Microbial remediation has become the most promising technical means for the remediation of polycyclic aromatic hydrocarbons (PAHs) non-point source contaminated soil due to its low cost of treatment, complete degradation of pollutants, and in-situ remediation. In this study, in order to demonstrate the phenanthrene degrading microbial diversity, phenanthrene was chosen as the representative of PAHs and strains capable of degrading phenanthrene were isolated and screened from the sedimentation sludge and the bottom sludge of oil tank trucks, and high throughput sequencing was used to check the dominant strains with a good degrading effect on phenanthrene. Results showed even more than 50% of phenanthrene was degraded in all samples, the composition of PAH-degrading bacteria was diverse, and different environments constructed different functional microbial groups, which resulted in the microbial adapting to the diversity of the environment. Finally, a series of bacterial species with phenanthrene-degrading functions such as Achromobacter, Pseudomonas, Pseudochelatococcus, Bosea was enriched after nine transferring process. Overall, our study offers value information for the enrichment of functional degrading microbes of phenanthrene or other pollutants that more concern should be paid in not only the degradation rate, but also the diversity variation of microbial community composition.

Isolation and characterization of a newly chrysene-degrading Achromobacter aegrifaciens

Polycyclic aromatic hydrocarbons (PAHs) are considered substances of potential human health hazards because of their resistance to biodegradation and carcinogenic index. Chrysene is a PAH with a high molecular weight (HMW) that poses challenges for its elimination from the environment. However, bacterial degradation is an effective, environmentally friendly, and cost-effective solution. In our study, we isolated a potential chrysene-degrading bacteria from crude oil-contaminated seawater (Bizerte, Tunisia). Based on 16SrRNA analysis, the isolate S5 was identified as Achromobacter aegrifaciens. Furthermore, the results revealed that A. aegrifaciens S5 produced a biofilm on polystyrene at 20 °C and 30 °C, as well as at the air-liquid (A-L) interface. Moreover, this isolate was able to swim and produce biosurfactants with an emulsification activity (E24%) over 53%. Chrysene biodegradation by isolate S5 was clearly assessed by an increase in the total viable count. Confirmation was obtained via gas chromatography-mass spectrometry (GC-MS) analyses. A. aegrifaciens S5 could use chrysene as its sole carbon and energy source, exhibiting an 86% degradation of chrysene on day 7. In addition, the bacterial counts reached their highest level, over 25 × 1020 CFU/mL, under the conditions of pH 7.0, a temperature of 30 °C, and a rotary speed of 120 rpm. Based on our findings, A. aegrifaciens S5 can be a potential candidate for bioremediation in HMW-PAH-contaminated environments.

A novel remediation strategy of mixed calcium peroxide and degrading bacteria for polycyclic aromatic hydrocarbon contaminated water

Polycyclic aromatic hydrocarbons (PAHs) are a class of toxic organic pollutants commonly detected in the aqueous phase. Traditional biodegradation is inefficient and advanced oxidation technologies are expensive. In the current study, a novel strategy was developed using calcium peroxide (CP) and PAH-degrading bacteria (PDB) to effectively augment PAH degradation by 28.62-59.22%. The PDB consisted of the genera Acinetobacter, Stenotrophomonas, and Comamonas. Applying the response surface model (RSM), the most appropriate parameters were identified, and the predictive degradation rates of phenanthrene (Phe), pyrene (Pyr), and ΣPAHs were 98%, 76%, and 84%, respectively. The constructed mixed system could reduce 90% of Phe and more than 60% of ΣPAHs and will perform better at pH 5-7 and lower salinity. Because PAHs tend to bind to dissolved organic matter (DOM) with larger molecular weights, humic acid (HA) had a larger negative effect on the PAH-degradation efficiency of the CP-PDB mixed system than fulvic acid (FA). The proposed PAH-degradation pathways in the mixed system were based on the detection of intermediates at different times. The investigation constructed and optimized a novel environmental PAH-degradation strategy. The synergistic application of PDB and oxidation was extended for organic contaminant degradation in aqueous environments.

Biodegradation of polystyrene nanoplastics by Achromobacter xylosoxidans M9 offers a mealworm gut-derived solution for plastic pollution

Nanoplastics pose significant environmental problems due to their high mobility and increased toxicity. These particles can cause infertility and inflammation in aquatic organisms, disrupt microbial signaling and act as pollutants carrier. Despite extensive studies on their harmful impact on living organisms, the microbial degradation of nanoplastics is still under research. This study investigated the degradation of nanoplastics by isolating bacteria from the gut microbiome of Tenebrio molitor larvae fed various plastic diets. Five bacterial strains capable of degrading polystyrene were identified, with Achromobacter xylosoxidans M9 showing significant nanoplastic degradation abilities. Within 6 days, this strain reduced nanoplastic particle size by 92.3%, as confirmed by SEM and TEM analyses, and altered the chemical composition of the nanoplastics, indicating a potential for enhanced bioremediation strategies. The strain also caused a 7% weight loss in polystyrene film over 30 days, demonstrating its efficiency in degrading nanoplastics faster than polystyrene film. These findings might enhance plastic bioremediation strategies.

Isolation of Diaphorobacter sp. LW2 capable of degrading Phenanthrene and its migration mediated by Pythium ultimum

Phenanthrene, one of the polycyclic aromatic hydrocarbons, is stubborn and persistent and exists widely in petroleum-contaminated soil. Filamentous fungi are good assistants to bacterial transport, by hyphae passing through soil pores and reaching further positions. An isolated bacterial strain, from the contaminated soil of the coking plant, was identified as Diaphorobacter and named LW2, which could use phenanthrene as the only carbon source and energy for its growth. LW2 could degrade phenanthrene in a wide range of pH, temperature and initial concentration. When pH was 6 and 10, the removal rate of phenanthrene was 38.59% and 76.44%, respectively, and the removal rate of phenanthrene was 68.25% at 15 ℃. And LW2 could degrade 86.64% phenanthrene when the initial concentration was 100 mg L-1. The detection of DI-N-octyl phthalate, phthalic acid and p-hydroxybenzoic acid revealed that the strain LW2 metabolised phenanthrene through the phthalic acid pathway. Meanwhile, swimming and swarming test results suggested that LW2 was motile. The auxiliary effect of Pythium ultimum on LW2 migration was assessed. In the presence of Pythium ultimum, LW2 could migrate within the range of centimters by its mycelium, which was also observed by fluorescence microscopy. Meanwhile, the degradation ability of LW2 after the migration was also explored. The results proved that the migration process had no significant effect on its degradation ability, and LW2 still showed good phenanthrene metabolism ability. This study provides more possibilities for the bioremediation of phenanthrene-contaminated soil by screening the degradation bacteria and testing the effect of fungi on its migration.

Accelerated deterioration corrosion of X70 steel by oxidation acid-producing process catalyzed by Acinetobacter soli in oil-water environment

Deterioration corrosion occurs between the external surface of oil pipelines and aerobic oil-degrading microorganisms in oil fields. Microorganisms with aerobic oil pollution remediation capabilities may catalyze more serious anaerobic microbial corrosion due to the carbon source supply. In this study, Acinetobacter soli strains were isolated from oil-contaminated environments, and their role in the deterioration corrosion behavior of X70 steel in an oil-water environment was investigated using the EDS multipoint scanning method. The presence of oil controls the deposition of carbon and phosphorus and diffusion of oxygen, leading to significant adhesion attraction and initial growth inhibition of biofilm on the metal surface. A. soli facilitates oxygen transfer and iron ion dissolution, thereby accelerating the pitting corrosion of X70 steel. This corrosion of the X70 steel, in turn, further accelerates the microbial degradation of oil, inhibiting the appearance of calcareous scale in the later stage of corrosion. The corrosion of X70 steel is influenced by microbial degradation, and the specific corrosion behaviors are related to the activity of A. soli in the petroleum environment. This study sheds light on the corrosion mechanisms of X70 steel by A. soli at different stages, providing insights into the interactions between microorganisms, oil pollution, and metal corrosion in oil fields.

Potential of some microbial isolates on diesel hydrocarbons removal, bio surfactant production and biofilm formation

Potential of Arthrobacter citreus B27Pet, Bacillus thuringiensis B48Pet and Candida catnulata to produce biosurfactant using four different carbon sources (naphthalene, hexadecane, diesel and petroleum crude oil) was investigated. Removal of petroleum crude oil from aqueous culture and degradation of diesel were also determined using single and mixed culture of strains. The biofilm existence in single and mixed culture of strains was considered using naphthalene, hexadecane and diesel in culture medium. Cell surface hydrophobicity of A. citreus was higher than other isolates which also showed maximum surface tension reduction and emulsification index. As a whole, remarkable biosurfactant production occurred using petroleum crude oil as a carbon source in medium. A. citreus was found to be more robust than other tested strains in removal efficiency of crude oil due to its biosurfactant production capability. Statistically significant positive correlation was observed between biofilm existence and surface tension using diesel and hexadecane as carbon source. Overall diesel biodegradation efficiency by the mix culture of three applied strains was about 75% within a short period of time (10 days) which was accompanied with high biofilm production.

Tributyltin degrading microbial enzymes: A promising remediation approach

Brazil is one of the countries most impacted along the entire coastline by the presence of tributyltin (TBT), a biocide used in antifouling paints. Despite being banned since 2008, its use is still registered in the country, and it is possible to find recent inputs of this substance in places under the influence of shipyards, marinas, and fishing ports. In this study, a bacterium isolated from TBT-contaminated sediment from Santos and São Vicente Estuarine System (SESS) in Brazil, identified as Achromobacter sp., proved to be resistant to this compound. Furthermore, its crude enzymatic extract presented the ability to reduce up to 25 % of the initial TBT concentration in the liquid phase in 1 h, demonstrating to be a simple, fast, effective procedure and a potential tool for the environmental attenuation of TBT.

Efficient elimination of nonylphenol and 4-tert-octylphenol by weak electrical stimulated anaerobic microbial processes

The investigation into the degradation of alkylphenol pollutants (APs) has become a hotspot due to their harmful effects on the environment and human health. In this study, microbial electrolysis cells (MECs) were used to degrade nonylphenol (NP) and 4-tert-octylphenol (4-tert-OP). The study found that the degradation rates of NP and 4-tert-OP for a 6-day period were 83.6% and 96.3%, respectively, which were 30.53% and 26.7% higher than those of the group without applied voltage. The double layer area in the degradation of 4-tert-OP was larger than that of NP, and the resistance exhibited by 4-tert-OP (87.47 Ω) in MEC was lower than that of NP (99.42 Ω). Meanwhile, NP had a greater effect on the bioenzyme activity than 4-tert-OP. GC-MS analysis showed that the degradation pathways of both pollutants mainly included oxidation and hydroxylation reactions. Furthermore, the microbial community analysis indicated that the main functional bacteria in NP degradation were Citrobacter, Desulfovibrio and Advenella, and those in 4-tert-OP degradation were Stenotrophomonas, Chryseobacterium, Dokdonella, and the key microbiomes underlying the cooperative relationship. The biotoxicity test indicated that the toxicity of residual substances was significantly reduced. Therefore, the MEC system is efficient and environmentally friendly and has broad application prospects in phenol refractory organics.

Metaproteomic and gene expression analysis of interspecies interactions in a PAH-degrading synthetic microbial consortium constructed with the key microbes of a natural consortium

Polycyclic Aromatic Hydrocarbons (PAHs) impose adverse effects on the environment and human life. The use of synthetic microbial consortia is promising in bioremediation of contaminated sites with these pollutants. However, the design of consortia taking advantage of natural interactions has been poorly explored. In this study, a dual synthetic bacterial consortium (DSC_AB) was constructed with two key members (Sphingobium sp. AM and Burkholderia sp. Bk), of a natural PAH degrading consortium. DSC_AB showed significantly enhanced degradation of PAHs and toxic intermediary metabolites relative to the axenic cultures, indicating the existence of synergistic relationships. Metaproteomic and gene-expression analyses were applied to obtain a view of bacterial performance during phenanthrene removal. Overexpression of the Bk genes, naph, biph, tol and sal and the AM gene, ahdB, in DSC_AB relative to axenic cultures, demonstrated that both strains are actively participating in degradation, which gave evidence of cross-feeding. Several proteins related to stress response were under-expressed in DSC_AB relative to axenic cultures, indicating that the division of labour reduces cellular stress, increasing the efficiency of degradation. This is the one of the first works revealing bacterial relationships during PAH removal in a synthetic consortium applying an omics approach. Our findings could be used to develop criteria for evaluating the potential effectiveness of synthetic bacterial consortia in bioremediation.

Evaluation of aerobic biodegradation of phenanthrene using Pseudomonas turukhanskensis: an optimized study

The ability of Pseudomonas turukhanskensis GEEL-01 to degrade the phenanthrene (PHE) was optimized by response surface methodology (RSM). Three factors as independent variables (including temperature, pH, and inoculum) were studied at 600 mg/L PHE where the highest growth of P. turukhanskensis GEEL-01 was observed. The optimum operating conditions were evaluated through the fit summary analysis, model summary statistics, fit statistics, ANOVA analysis, and model graphs. The degradation of PHE was monitored by high-performance liquid chromatography (HPLC) and the metabolites were identified by gas chromatography-mass spectrometry (GC-MS). The results showed that the correlation among independent variables with experimental and predicted responses was significant (p < 0.0001). The optimal temperature, pH, and inoculum were 30 ℃, 8, and 6 mL respectively. The HPLC peaks exhibited a reduction in PHE concentration from 600 mg/L to 4.97 mg/L with 99% degradation efficiency. The GC-MS peaks indicated that the major end products of PHE degradation were 1-Hydroxy-2-naphthoic acid, salicylic acid, phthalic acid, and catechol. This study demonstrated that the optimized parameters by RSM for P. turukhanskensis GEEL-01 could degrade PHE by phthalic and salicylic acid pathways.

Biosurfactant Production from the Biodegradation of n-Paraffins, Isoprenoids and Aromatic Hydrocarbons from Crude Petroleum by Yarrowia lipolytica IMUFRJ 50682

Yarrowia lipolytica is a unique, strictly aerobic yeast with the ability to degrade efficiently hydrophobic substrates. In the present work, we evaluated the degrading potential of Yarrowia lipolytica IMUFRJ 50682, isolated from tropical estuarine water in Rio de Janeiro (Brazil), and the possible biomolecules produced during this process. To investigate which crude oil compounds are degraded by Y. lipolytica IMUFRJ 50682, this microorganism was grown in a medium containing Marlim petroleum (19 °API, American Petroleum Institute gravity) at 28 °C and 160 rpm for 5 days. The residual petroleum was submitted to gas chromatograph-mass spectrometric analysis (GC-MS). The chromatographic fingerprints of the residual petroleum were compared with the abiotic control test incubated in the same conditions. Y. lipolytica assimilates high molecular weight hydrocarbons, such as n-alkanes (C11-C19), isoprenoids (pristane and phytane), aromatics with two or three aromatics rings (naphthalene, methylnaphthalenes, dimethylnaphthalenes, trimethylnaphthalenes, phenanthrene, methylphenanthrenes, dimethylphenanthrenes, anthracene). This strain was also capable of consuming more complex hydrocarbons, such as tricyclic terpanes. During this biodegradation, the emulsification index of the culture medium increased significantly, showing that biosurfactant molecules can be produced from this process. Therefore, Y. lipolytica IMUFRJ 50682 showed to be a potential crude oil degrading yeast, which can be used for bioremediation processes and simultaneously produce bioproducts of commercial interest.

A novel Diaphorobacter sp. strain isolated from saponification wastewater shows highly efficient phenanthrene degradation

Polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene, are a type of organic pollutants that exist widely in the environment. Of the currently known degradation methods, bioremediation is a desirable and feasible option. A novel Diaphorobacter sp. Strain MNS-0 was isolated from saponification wastewater and showed the ability to degrade phenanthrene, fluorene, acenaphthene, anthracene, benzo[a]anthracene, or chrysene using phenanthrene as the sole carbon source. Gas chromatography mass spectroscopy analysis of catabolic intermediates indicates that phenanthrene degradation occurs through the phthalic acid pathway in strain MNS-0. Genome sequencing shows that strain MNS-0 has two plasmids and one chromosome containing a presumptive phenanthrene degradation gene cluster. Strain MNS-0 was able to completely degrade 100 mg/L phenanthrene within 40 h and tolerate up to 10 g/L NaCl at pH 9.0, while maintaining phenanthrene degradation activity. We thus propose that strain MNS-0 is an effective degrader for bioremediation of PAHs pollution, even in relatively harsh alkali environments such as saponification wastewater.

Indigenous oil-degrading bacteria more efficient in soil bioremediation than microbial consortium and active even in super oil-saturated soils

A microbial consortium of the hydrocarbonoclastic bacterial species, comprising Actinotalea ferrariae, Arthrobacter ginsengisoli, Dietzia cinnamea, Dietzia papillomatosis, and Pseudomonas songnenensis, isolated from oil-saturated desert soil did not consume more oil in batch cultures than the individual species with the maximum oil consumption. In oil-polluted desert soil microcosms, the rate of oil removal in the soil samples bioaugmented with the microbial consortium was similar to the rate of oil removal in the unbioaugmented ones through a 6-month bioremediation experiment. Although the composition of hydrocarbonoclastic bacterial communities in the unbioaugmented and bioaugmented soil samples was different, the predominant bacterial species during most of the months were the same. Toward the end of the bioremediation experiment, Ar. ginsengisoli prevailed in both soil samples, suggesting its important role in oil removal. Self-cleaning proceeded in desert soil samples artificially polluted with 1, 10, 20, and 30% of crude oil and incubated at 30 °C for 6 months. Oil was removed effectively at rates reaching 73.6 and 69.3% in the soils polluted with 1 and 10% oil concentrations, respectively, and reached 50% in desert soils polluted with 20 and 30% oil concentrations. The bacterial numbers increased in all soil samples from hundreds of thousands per gram of soil samples at time zero to millions and tens of millions per gram of soil samples after 6 months. It was concluded that bioaugmenting oil-polluted soil samples with microbial consortium of hydrocarbonoclastic bacterial species with high oil removal potential did not drastically enhance oil bioremediation and that even in super oil-saturated soils, indigenous oil-degrading bacteria will prevail and effectively contribute to oil removal from the surrounding environment.

Advances in Biochar and PGPR engineering system for hydrocarbon degradation: A promising strategy for environmental remediation

In soil, polycyclic aromatic hydrocarbons (PAHs) have resulted in severe environmental deterioration, compromised soil characteristics, and negatively affect all life forms, including humans. Developing appropriate and effective clean-up technology is crucial in solving the contamination issues. The traditional methods to treat PHAs contaminated soil are less effective and not ecofriendly. Bioremediation, based on bioaugmentation and biostimulation approaches, is a promising strategy for remediating contaminated soil. The use of plant growth-promoting rhizobacteria (PGPR) as a bioaugmentation tool is an effective technique for treating hydrocarbon contaminated soil. Plant growth-promoting rhizobacteria (PGPR) are group of rhizospheric bacteria that colonize the roots of plants. Biochar is a carbon-rich residue, which acts as a source of nutrients, and is also a bio-stimulating candidate to enhance the activities of oil-degrading bacteria. The application of biochar as a nutrient source to bioremediate oil-contaminated soil is a promising approach for reducing PHA contamination. Biochar induces polyaromatic hydrocarbons (PAHs) immobilization and removes the contaminants by various methods such as ion exchange electrostatic attractions and volatilization. In comparison, PGPR produce multiple types of biosurfactants to enhance the adsorption of hydrocarbons and mineralize the hydrocarbons with the conversion to less toxic substances. During the last few decades, the use of PGPR and biochar in the bioremediation of hydrocarbons-contaminated soil has gained greater importance. Therefore, developing and applying a PGPR-biochar-based remediating system can help manage hazardous PAH contaminated soil. The goal of this review paper is to (i) provide an overview of the PGPR mechanism for degradation of hydrocarbons and (ii) discuss the contaminants absorbent by biochar and its characteristics (iii) critically discuss the combined effect of PGPR and biochar for degradation of hydrocarbons by decreasing their mobility and bioavailability. The present review focuses on techniques of bioaugmentation and biostimulation based on use of PGPR and biochar in remediating the oil-contaminated soil.

Oil Absorbent Polypropylene Particles Stimulate Biodegradation of Crude Oil by Microbial Consortia

Oil absorbent particles made from surface-modified polypropylene can be used to facilitate the removal of oil from the environment. In this study, we investigated to what extent absorbed oil was biodegraded and how this compared to the biodegradation of oil in water. To do so, we incubated two bacterial communities originating from the Niger Delta, an area subject to frequent oil spills, in the presence and absence of polypropylene particles. One community evolved from untreated soil whereas the second evolved from soil pre-exposed to oil. We observed that the polypropylene particles stimulated the growth of biofilms and enriched species from genera Mycobacterium, Sphingomonas and Parvibaculum. Cultures with polypropylene particles degraded more crude oil than those where the oil was present in suspension regardless of whether they were pre-exposed or not. Moreover, the community pre-exposed to crude oil had a different community structure and degraded more oil than the one from untreated soil. We conclude that the biodegradation rate of crude oil was enhanced by the pre-exposure of the bacterial communities to crude oil and by the use of oil-absorbing polypropylene materials. The data show that bacterial communities in the biofilms growing on the particles have an enhanced degradation capacity for oil.

Efficient biodegradation of phenanthrene using Pseudomonas stutzeri LSH-PAH1 with the addition of sophorolipids: Alleviation of biotoxicity and cometabolism studies

Phenanthrene (PHE) is widely distributed, and it can cause genotoxicity in humans by interacting with enzymes in the body. A current challenge for PHE bioremediation is the inhibitory effect of biotoxic intermediates on bacterial growth. Notably, the aerobic biotransformation processes for PHE in the presence of sophorolipids have been poorly studied. Here, a PHE-degrading strain was isolated from sediments and identified as Pseudomonas stutzeri and named LSH-PAH1. It was observed that 1-naphthol (a biotoxic substance that can inhibit strain growth) was produced during the PHE metabolism process of LSH-PAH1. The biodegradation ratio increased from 21.4% to 91.7% within 48 h after the addition of sophorolipids. Unexpectedly, this addition accelerated the metabolic process for 1-naphthol rather than causing its accumulation. The cometabolism of 1-naphthol and sophorolipids alleviated the biotoxic effects for the strain, which was verified by gene expression analysis. We identified a new PHE-degrading strain and provided a mechanism for PHE biodegradation using LSH-PAH1 with the addition of sophorolipids, which provides a reference for practical applications of the bioremediation of PHE and study of the cometabolism of biotoxic intermediates.

Bioremediation perspectives and progress in petroleum pollution in the marine environment: a review

The marine environment is often affected by petroleum hydrocarbon pollution due to industrial activities and petroleum accidents. This pollution has recalcitrant and persistent compounds that pose a high risk to the ecological system and human health. For this reason, the world claims to seek to clean up these pollutants. Bioremediation is an attractive approach for removing petroleum pollution. It is considered a low-cost and highly effective approach with fewer side effects compared to chemical and physical techniques. This depends on the metabolic capability of microorganisms involved in the degradation of hydrocarbons through enzymatic reactions. Bioremediation activities mostly depend on environmental conditions such as temperature, pH, salinity, pressure, and nutrition availability. Understanding the effects of environmental conditions on microbial hydrocarbon degraders and microbial interactions with hydrocarbon compounds could be assessed for the successful degradation of petroleum pollution. The current review provides a critical view of petroleum pollution in seawater, the bioavailability of petroleum compounds, the contribution of microorganisms in petroleum degradation, and the mechanisms of degradation under aerobic and anaerobic conditions. We consider different biodegradation approaches such as biostimulation, bioaugmentation, and phytoremediation.

Construction of biotreatment platforms for aromatic hydrocarbons and their future perspectives

Aromatic hydrocarbons (AHCs) are one of the major environmental pollutants introduced from both natural and anthropogenic sources. Many AHCs are well known for their toxic, carcinogenic, and mutagenic impact on human health and ecological systems. Biodegradation is an eco-friendly and cost-effective option as microorganisms (e.g., bacteria, fungi, and algae) can efficiently breakdown or transform such pollutants into less harmful and simple metabolites (e.g., carbon dioxide (aerobic), methane (anaerobic), water, and inorganic salts). This paper is organized to offer a state-of-the-art review on the biodegradation of AHCs (monocyclic aromatic hydrocarbons (MAHs) and polycyclic aromatic hydrocarbons (PAHs)) and associated mechanisms. The recent progress in biological treatment using suspended and attached growth bioreactors for the biodegradation of AHCs is also discussed. In addition, various substrate growth and inhibition models are introduced along with the key factors governing their biodegradation kinetics. The growth and inhibition models have helped gain a better understanding of substrate inhibition in biodegradation. Techno-economic analysis (TEA) and life cycle assessment (LCA) aspects are also described to assess the technical, economical, and environmental impacts of the biological treatment system.

Enhanced biodegradation of hydrocarbons by Pseudomonas aeruginosa-encapsulated alginate/gellan gum microbeads

Pseudomonas aeruginosa-encapsulated alginate/gellan gum microbeads (PAGMs) were prepared at the condition of 10 g/L alginate, 1 g/L gellan gum, and 2.57 mM calcium ions, and investigated for the biodegradation of a diesel-contaminated groundwater. The degradation of diesel with PAGMs reached 71.2% after 10days in the aerobic condition, while that of suspended bacteria was only 32.0% even after 30days. The kinetic analysis showed that PAGMs had more than two-order higher second-order kinetic constant than that of the suspended bacteria. Interestingly, the degradation of diesel was ceased due to the depletion of the dissolved oxygen after 10 day in the PAGM reactor, but the microbial degradation activity was immediately restored after the addition of oxygen to 10.5 mg/L. The change in ATP concentration and the viability of bacteria showed that the microbial activity in PAGMs were maintained (66.4%, and 84.3%, respectively) even after 30days of experiment with PAGMs due to the protective barrier of the microbeads, whereas those of suspended bacteria showed significant decrease to 6.2% and 14.4% of initial value, respectively, due to the direct contact to toxic hydrocarbons. The results suggested that encapsulation of bacterial cells could be used for the enhanced biodegradation of diesel hydrocarbons in aqueous systems.

Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation

Freshwater lake ecosystem is a reservior of valuable microbial diversity. It needs to be explored for addressing key environmental issues like petroleum-hydrocarbon contamination. In this work, the microbial communities (pre and post enriched with petroleum-hydrocarbons) from different layers of freshwater lake, i.e. surface water, sediments and deepwater, were explored through metagenomic and culture-dependent approaches. A total of 41 bacterial phyla were retrieved from pre-enriched samples, which were significantly reduced in enriched samples where Proteobacteria were dominant (87% to 100%) followed by Bacteroidetes (7.37%) and Verrucomicrobia (3.06%). The most dominant hydrocarbon-degrading genera were extensively verified as Pseudomonas (48.65%), Acinetobacter (45.38%), Stenotrophomonas (3.16%) and Brevundimonas (2.07%) in surface water (S1WCC); Acinetobacter (62.46%), Aeromonas (10.7%), Sphingobacterium (5.20%) and Pseudomonas (4.23%) in sediment (S2MCC); and Acinetobacter (46.57%), Pseudomonas (13.10%), Comamonas (12.93%), Flavobacterium (12.18%) and Enterobacter (9.62%) in deep water (S4WCC). Additionally, the maximum biodegradation of petroleum-hydrocarbons (i.e. used engine oil or UEO) was achieved by microbiome of S2MCC (67.60 ± 0.08%) followed by S4WCC (59.70 ± 0.12%), whereas only 36.80 ± 0.10% degradation was achieved by S1WCC microbiome. On the other hand, UEO degradation by cultivable biosurfactant-producing single cultures such as Pseudomonas sp. S2WE, Pseudomonas sp. S2WG, Pseudomonas sp. S2MS, Ochrobactrum sp. S1MM and Bacillus nealsonii S2MT showed 31.10 ± 0.08% to 40.50 ± 0.11% biodegradation. Comparatively, the biodegradation efficiency was found higher (i.e. 42.20 ± 0.12% to 56.10 ± 0.12%) in each consortia comprising of two, three, four, and five bacterial cultures. Conclusively, the isolated culturable biosurfactants-producing bacterial consortium of freshwater lake demonstrated >80% contribution in the total petroleum-hydrocarbons degradation by the natural microbiome of the ecosystem.

Production, functional stability, and effect of rhamnolipid biosurfactant from Klebsiella sp. on phenanthrene degradation in various medium systems

The present study investigated the stability and efficacy of a biosurfactant produced by Klebsiella sp. KOD36 under extreme conditions and its potential for enhancing the solubilization and degradation of phenanthrene in various environmental matrices. Klebsiella sp. KOD36 produced a mono-rhamnolipids biosurfactant with a low critical micelle concentration (CMC) value. The biosurfactant was stable under extreme conditions (60 °C, pH 10 and 10% salinity) and could lower surface tension by 30% and maintained an emulsification index of > 40%. The emulsion index was also higher (17-43%) in the presence of petroleum hydrocarbons compared to synthetic surfactant Triton X-100. Investigation on phenanthrene degradation in three different environmental matrices (aqueous, soil-slurry and soil) confirmed that the biosurfactant enhanced the solubilization and biodegradation of phenanthrene in all matrices. The high functional stability and performance of the biosurfactant under extreme conditions on phenanthrene degradation show the great potential of the biosurfactant for remediation applications under harsh environmental conditions.

A high-efficiency phenanthrene-degrading Diaphorobacter sp. isolated from PAH-contaminated river sediment

Polycyclic aromatic hydrocarbons (PAHs) are typical persistent organic pollutants that accumulate in the environment, mainly from anthropogenic activities. Microbial degradation is the main pathway of PAHs degradation in the natural environment. Therefore, the widen of the available bank of microbial resources and exploration of the molecular degradation mechanisms of PAHs are crucial to the proper management of PAHs-polluted sites. In this work, a bacterial strain, YM-6, which has a high ability to utilize phenanthrene (PHE) as its sole source of carbon and energy, was isolated from sediment contaminated with PAHs. The strain YM-6 was found to degrade 96.3% of 100 mg/L of PHE in liquid cultures within 52 h. The strain was identified as Diaphorobacter sp. by 16S rDNA sequencing. The optimum growth conditions of the YM-6 strain were studied, and the results indicated that the optimum growth temperature of the strain was 30 °C, and the optimum growth pH was 7. The stain is well-suited for high-temperature stress (40 °C), and it could withstand 400 mg/L of PHE. The strain's PHE metabolism was assayed using GC-MS analyses. The results revealed that the YM-6 strain metabolized PHE via the phthalic acid pathway because the intermediates, such as phthalic acid, diethyl ester and phthalaldehydic acid, methyl ester, were detected. The use of this strain may be an attractive alternative for the bioremediation of polycyclic aromatic hydrocarbons in an aquatic environment.

Streptomyces sp. S501, a Marine Petroleum-Degrading Actinobacterium Isolated from Sediment of Yalujiang Estuary, Northern China, and Its Genome Annotation

Streptomyces sp. S501, which was isolated from the sediment of Yalujiang Estuary in China, was the first marine Streptomyces species discovered to act as an excellent petroleum degrader. We analyzed the effect of pH, temperature, and concentration of NH₄NO₃ on the petroleum degradation of strain S501, and the optimum biodegradation rate reached 63.02% under the condition of 2 g/L NH₄NO₃ addition at 30 °C and pH 8. The complete genome sequence of Streptomyces sp. S501 was determined by using the PacBio RSII platform, which contains a linear chromosome with 7,173,651 bp and a linear plasmid with 288,181 bp, with GC contents of 71.19% and 67.57%, respectively. The genome sequence suggests that Streptomyces sp. S501 has the ability to degrade several hazardous pollutants, as well as the ability to biosynthesize diverse secondary metabolites and enzymes. There are fifty annotated genes involved in oil component degradation, and there are three genes without known annotation information in Streptomyces sp. S501, which have high homology with genes encoding P450 family enzymes and should be novel genes involved in alkane degradation. This study provides useful genetic information for investigating the molecular mechanisms of marine Streptomyces, with biodegradation and application potential.

Characterization and genome functional analysis of an efficient nitrile-degrading bacterium, Rhodococcus rhodochrous BX2, to lay the foundation for potential bioaugmentation for remediation of nitrile-contaminated environments

Nitriles are a class of extremely toxic chemicals with extensive applications, and these compounds pose potential risks to humans and ecosystems. The activated sludge isolate Rhodococcus rhodochrous BX2 efficiently metabolizes aliphatic nitriles. However, the molecular underpinnings of the degradation mechanism of aliphatic nitriles by BX2 remain unknown, and the metabolic fate of aliphatic nitriles also has not been elucidated. Here, strain BX2 was capable of completely mineralizing three aliphatic nitriles. Bioinformatic analysis yielded a deeper insight into the genetic basis of BX2 for efficient degradation of aliphatic nitriles and adaptation to harsh environments. Transcriptional, enzyme activity and metabolite analyses confirmed that the intracellular inducible nitrile hydratase/amidase pathway is the preferred metabolic pathway. Our findings provide an in-depth understanding of the environmental fate of aliphatic nitriles and, most importantly, offer a new perspective on the potential applications of the genus Rhodococcus in bioremediation and the development of degradation enzyme resources.

Bioaugmentation Treatment of a PAH-Polluted Soil in a Slurry Bioreactor

A bioslurry reactor was designed and used to treat loamy clay soil polluted with polycyclic aromatic hydrocarbons (PAHs). To this end, biostimulation alone, or combined with bioaugmentation with two bacterial strains (Rhodocccus erythropolis and Pseudomonas stuzeri) previously isolated from the polluted site, was applied. The PAH concentrations decreased notably after 15 days in all of the treatments. The concentrations of the two- and three-ring compounds fell by >80%, and, remarkably, the four- to six-ring PAHs also showed a marked decrease (>70%). These results thus indicate the capacity of bioslurry treatments to improve, notably, the degradation yields obtained in a previous real-scale remediation carried out using biopiles. In this sense, the remarkable results for recalcitrant PAHs can be attributed to the increase pollutants’ bioavailability achieves in the slurry bioreactors. Regarding bioaugmentation, although treatment with R. erythropolis led to a somewhat greater reduction of lighter PAHs at 15 days, the most time-effective treatment was achieved using P. stutzeri, which led to an 84% depletion of total PAHs in only three days. The effects of microbial degradation of other organic compounds were also monitored by means of combined qualitative and quantitative gas chromatography mass spectrometry (GC–MS) tools, as was the evolution of microbial populations, which was analyzed by culture and molecular fingerprinting experiments. On the basis of our findings, bioslurry technology emerges as a rapid and operative option for the remediation of polluted sites, especially for fine soil fractions with a high load of recalcitrant pollutants.

Hydroponic approach to assess rhizodegradation by sudangrass (Sorghum x drummondii) reveals pH- and plant age-dependent variability in bacterial degradation of polycyclic aromatic hydrocarbons (PAHs)

Rhizodegradation of polycyclic aromatic hydrocarbons (PAHs) is a product of complex interactions between plant and bacteria. In this study, hydroponic culture of sudangrass was established in order to investigate the effects of the plant on PAHs degradation and vice versa through changes in rhizosphere bacterial community. Results showed a plant-induced variability in PAHs degradation dependent on a characteristic shift in bacterial community, with pH and plant age as driving factors. Moreover, bacterial communities with high diversity seemed to abate the phytotoxic effects of PAHs degradation as observed in the plant's gross health. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing revealed that regardless of plant age and culture conditions, the increase or decrease of Sphingobium sp. could dictate the PAHs degradation potential of the bacterial consortium. Overall, this study utilized hydroponic culture of sudangrass to show that plant even of same species can suppress, support, or enhance PAHs degradation of bacteria depending on specific factors.

Mechanistic investigations in ultrasound-assisted biodegradation of phenanthrene

This study has addressed the biodegradation of polycyclic aromatic hydrocarbon, phenanthrene using Candida tropicalis. Optimization using central composite statistical design yielded optimum experimental parameters as: pH = 6.2, temperature = 33.4 °C, mechanical shaking = 190 rpm and % inoculum = 9.26% v/v. Sonication of biodegradation mixture at 33 kHz and 10% duty cycle in log phase (12 h per day for 4 days) resulted in a 25% enhancement in phenanthrene removal. Profiles of specific growth rate (µ) and specific degradation rate (q) versus initial substrate concentration were fitted to Haldane substrate inhibition model. Both µ and q showed maxima for initial concentration of 100 mg L^-1. Kinetic analysis of degradation profiles showed higher biomass yield coefficient and smaller decay coefficient in presence of sonication. Expression of total intracellular proteins in control and test experiments were analyzed using SDS-PAGE. This analysis revealed overexpression of enzyme catechol 2,3-dioxygenase (in meta route metabolism) during sonication which is involved in ring cleavage of phenanthrene. Evaluation of cell viability after sonication by flow cytometry analysis revealed > 80% live cells. These effects are attributed to enhanced cellular transport induced by intense microturbulence generated by sonication.

One Biosurfactant-Producing Bacteria Achromobacter sp. A-8 and Its Potential Use in Microbial Enhanced Oil Recovery and Bioremediation

Biosurfactant plays an important role in bioremediation of crude oil contamination and microbial enhanced oil recovery (MEOR). In the present study, a salt-tolerant, biosurfactant-producing bacterium, designated A-8, was isolated from wastewater contaminated with petroleum collected from the Changqing reservoir in China. A phylogenetic analysis based on the 16S rRNA sequence suggests that strain A-8 belongs to the genus Achromobacter. The optimal growth conditions for strain A-8 in mineral salt (MS) medium were 30°C, pH 7, and 10 g/L NaCl, while the optimal conditions for biosurfactant production in a fermentation medium were 40-45°C, pH 7, and more than 70 g/L NaCl. Better biosurfactant production was obtained from strain A-8 when edible oil and liquid paraffin were used as carbon sources and when (NH4)2SO4 was used as an inorganic nitrogen source compared with other tested carbon and nitrogen sources. The biodegradation of petroleum in MS medium in different optimized conditions reached 56.23-73.87% for 20 days. The biodegradation of petroleum, together with the production of organic acid and biosurfactant, decreased the viscosity of petroleum by about 45%. The decrease in petroleum viscosity and the biodegradation of petroleum suggest the potential use of strain A-8 for MEOR and bioremediation of petroleum-contaminated environments.

Bacteria involved in biodegradation of creosote PAH - A case study of long-term contaminated industrial area

Polycyclic aromatic hydrocarbons (PAH) contained in creosote oil are particularly difficult to remove from the soil environment. Their hydrophobic character and low bioavailability to soil microorganisms affects their rate of biodegradation. This study was performed on samples of soil that were (for over forty years) subjected to contamination with creosote oil, and their metagenome and physicochemical properties were characterized. Moreover, the study was undertaken to evaluate the biodegradation of PAHs by autochthonous consortia as well as by selected bacteria strains isolated from long-term contaminated industrial soil. From among the isolated microorganisms, the most effective in biodegrading the contaminants were the strains Pseudomonas mendocina and Brevundimonas olei. They were able to degrade more than 60% of the total content of PAHs during a 28-day test. The biodegradation of these compounds using AT7 dispersant was enhanced only by Serratia marcescens strain. Moreover, the addition of AT7 improved the effectiveness of fluorene and acenaphthene biodegradation by Serratia marcescens 6-fold. Our results indicated that long-term contact with aromatic compounds induced the bacterial strains to use the PAHs as a source of carbon and energy. We observed that supplementation with surfactants does not increase the efficiency of hydrocarbon biodegradation.

Enhancement of atrazine biodegradation by marine isolate Bacillus velezensis MHNK1 in presence of surfactin lipopeptide

Atrazine is one of the widely used toxic herbicide and considered as serious environmental contaminant worldwide due to its long term use in crop production. In this study, the effect of surfactin lipopeptide produced by Bacillus velezensis MHNK1 on atrazine biodegradation was investigated. B. velezensis MHNK1 produced 0.83 ± 0.07 g/L of anionic biosurfactant that reduced surface tension from 72.12 ± 0.02 to 33.2 ± 0.61 mN/m and CMC was 40 mg/L with 85.21 ± 1.60% emulsification index. Further, biosurfactant was characterized as surfactin by TLC, HPLC, FTIR, ¹H and ¹³C NMR and LCMS-ESI. B. velezensis MHNK1 showed 87.10 ± 3.10% atrazine biodegradation within 5 days which was revealed by HPLC and MS analysis. Atrazine biodegradation using a combination of B. velezensis MHNK1 (2%) and surfactin (2 CMC) resulted in 100 ± 1.20% degradation within 4 days. Presence of atrazine degrading genes in B. velezensis MHNK1 was also confirmed by PCR. To the best of our knowledge, there are no previous reports available on atrazine degradation using B. velezensis strain and also in combination with surfactin. The results of this study reveal that strain B. velezensis MHNK1 and surfactin can be potential source of ecofriendly application for removal of atrazine from contaminated sites.

Petroleum Hydrocarbon-Degrading Bacteria for the Remediation of Oil Pollution Under Aerobic Conditions: A Perspective Analysis

With the sharp increase in population and modernization of society, environmental pollution resulting from petroleum hydrocarbons has increased, resulting in an urgent need for remediation. Petroleum hydrocarbon-degrading bacteria are ubiquitous in nature and can utilize these compounds as sources of carbon and energy. Bacteria displaying such capabilities are often exploited for the bioremediation of petroleum oil-contaminated environments. Recently, microbial remediation technology has developed rapidly and achieved major gains. However, this technology is not omnipotent. It is affected by many environmental factors that hinder its practical application, limiting the large-scale application of the technology. This paper provides an overview of the recent literature referring to the usage of bacteria as biodegraders, discusses barriers regarding the implementation of this microbial technology, and provides suggestions for further developments.