Isolation of phenanthrene-degrading bacteria and characterization of phenanthrene metabolites

The discrepant metabolic pathways of PAHs by facultative anaerobic bacteria under aerobic and nitrate-reducing conditions

Studies regarding the facultative anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) were still in the initial stage. In this study, a facultative anaerobe which was identified as Bacillus Firmus and named as PheN7 was firstly isolated from the mixed petroleum-polluted soil samples using phenanthrene and nitrate as the solo carbon resource and electron acceptor under anaerobic condition. The degradation rates of PheN7 towards phenanthrene were detected as 33.17 μM/d, 13.81 μM/d and 7.11 μM/d at the initial phenanthrene concentration of 250.17 μM with oxygen, nitrate and sulfate as the electron acceptor, respectively. The metabolic pathways toward phenanthrene by PheN7 were deduced combining the metagenome analysis of PheN7 and intermediate metabolites of phenanthrene under aerobic and nitrate-reducing conditions. Dioxygenation and carboxylation were inferred as the initial activation reactions of phenanthrene degradation in these two pathways. This study highlighted the significance of facultative anaerobic bacteria in natural PAHs biodegradation, revealing the discrepant metabolic fates of PAHs by one solo bacteria under aerobic and anaerobic environments.

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.

Phenanthrene biodegradation in a fed-batch reactor treating a spent sediment washing solution: Techno-economic implications for the recovery of ethanol as extracting agent

The continuous dredging of sediments contaminated by polycyclic aromatic hydrocarbons such as phenanthrene (PHE) has required the employment of high-efficiency technologies, including sediment washing (SW). However, the large amount of generated spent SW effluents requires the development of effective, eco-friendly and cost-saving approaches, which can tackle the waste formation in favor of the recovery of chemicals. This study proposes the treatment of a spent SW solution containing ethanol (EtOH) as extracting agent, by testing different initial PHE concentrations (i.e. 20-140 mg L^-1) within six consecutive cycles in a fed-batch bioreactor under aerobic conditions. The biological process achieved a PHE removal of 63-91% after the enrichment of PHE-degrading bacteria and the proper supplementation of nutrients, and was mainly affected by the initial PHE concentration value and the excessive decrease of pH and dissolved oxygen. Achromobacter, Sphingobacterium and Dysgonomonas genera were mainly involved in PHE degradation, which followed a first-order kinetic model (R² = 0.652-0.928) with a degradation rate and half-life time of 0.127-1.177 d^-1 and 0.589-2.912 d, respectively. A techno-economic assessment revealed that a virtuous operation of SW, EtOH recovery and biodegradation of the SW solution can allow the recovery of up to 1.35 tons of EtOH per ton of remediated sediment and the decrease of the overall costs by 50%.

Biodegradation and metabolic pathway of phenanthrene by a newly isolated bacterium Gordonia sp. SCSIO19801

The bacterium Gordonia sp. SCSIO19801, which could effectively utilize phenanthrene as the sole carbon source, was isolated from the seawater of the South China Sea. Its biodegradation characteristics, whole genome sequence, and biodegradation pathway were investigated. The phenanthrene biodegradation process of Gordonia sp. SCSIO19801 was estimated to be a first-order kinetic model with a k value of 0.26/day. Based on the identification of metabolites, utilization of probable intermediates, and genomics analysis of related genes, the degradation of phenanthrene by Gordonia sp. SCSIO19801 was proposed to occur via the salicylate metabolic pathway. This is the first report of a phenanthrene degradation pathway in Gordonia species. In addition, the Gordonia sp. SCSIO19801 could use other aromatic compounds as the sole source of carbon and energy. These characteristics indicate that Gordonia sp. SCSIO19801 can be utilized for developing effective methods for the biodegradation of petroleum hydrocarbons in marine environments.

Differential regulation of phenanthrene biodegradation process by kaolinite and quartz and the underlying mechanism

Natural and cost-effective materials such as minerals can serve as supportive matrices to enhance biodegradation of polycyclic aromatic hydrocarbons (PAHs). In this study we evaluated and compared the regulatory role of two common soil minerals, i.e. kaolinite and quartz in phenanthrene (a model PAH) degradation by a PAH degrader Sphingomonas sp. GY2B and investigated the underlying mechanism. Overall kaolinite was more effective than quartz in promoting phenanthrene degradation and bacterial growth. And it was revealed that a more intimate association was established between GY2B and kaolinite. Si and O atoms on mineral surface were demonstrated to be involved in GY2B-mineral interaction. There was an higher polysaccharide/lipid content in the EPS (extracellular polymeric substances) secreted by GY2B on kaolinite than on quartz. Altogether, these results showed that differential bacterial growth, enzymatic activity, EPS composition as well as the interface interaction may explain the effects minerals have on PAH biodegradation. It was implicated that different interface interaction between different minerals and bacteria can affect microbial behavior, which ultimately results in different biodegradation efficiency.

In situ long-term modeling of phenanthrene dynamics in an aged contaminated soil using the VSOIL platform

Management and remediation actions of polycyclic aromatic hydrocarbons (PAH) contaminated sites require an accurate knowledge of the dynamics of these chemicals in situ under real conditions. Here we developed, under the Virtual Soil Platform, a global model for PAH that describes the principal physical and biological processes controlling the dynamics of PAH in soil under real climatic conditions. The model was applied first to simulate the observed dynamics of phenanthrene in situ field experimental plots of industrial contaminated soil. In a second step, different long-term scenarios of climate change or bioavailability increase were applied. Our results show that the model can adequately predict the fate of phenanthrene and can contribute to clarify some of unexplored aspects regarding the behavior of phenanthrene in soil like its degradation mechanism and stabilization. Tested prospective scenarios showed that bioavailability increase (through the addition of solvent or surfactants) resulted in significant increase in substrate transfer rate, hence reducing remediation time. Regarding climate change effect, the model indicated that phenanthrene concentration decreased by 54% during 40years with a natural attenuation and both scenarios chosen for climatic boundaries provided very similar results.

Using a Bayesian approach to improve and calibrate a dynamic model of polycyclic aromatic hydrocarbons degradation in an industrial contaminated soil

A novel kinetics model that describes the dynamics of polycyclic aromatic hydrocarbons (PAHs) in contaminated soils is presented. The model includes two typical biodegradation pathways: the co-metabolic pathway using pseudo first order kinetics and the specific biodegradation pathway modeled using Monod kinetics. The sorption of PAHs to the solid soil occurs through bi-phasic fist order kinetics, and two types of non-extractible bounded residues are considered: the biogenic and the physically sequestrated into soil matrix. The PAH model was developed in Matlab, parameterized and tested successfully on batch experimental data using a Bayesian approach (DREAM). Preliminary results led to significant model simplifications. They also highlighted that the specific biodegradation pathway was the most efficient at explaining experimental data, as would be expected for an old industrial contaminated soil. Global analysis of sensitivity showed that the amount of PAHs ultimately degraded was mostly governed by physicochemical interactions rather than by biological activity.

Enhanced degradation of phenol by Sphingomonas sp. GY2B with resistance towards suboptimal environment through adsorption on kaolinite

The effects of clay minerals on microbial degradation of phenol under unfavorable environmental conditions were investigated. Degradation of phenol by Sphingomonas sp. GY2B adsorbed on kaolinite, montmorillonite, and vermiculite were evaluated in comparison with free bacteria under optimal conditions. Kaolinite was found to be the most effective in accelerating degradation rate (reducing the degradation time) as well as improving degradation efficiency (increasing the percentage of phenol degraded), with GY2B/kaolinite complex achieving a degradation efficiency of 96% within 6 h. GY2B adsorbed on kaolinite was more competent than free GY2B in degradation under conditions with high phenol concentrations and at alkaline pH. Kaolinite reduced the time required for degradation by 8-12 h and improved the degradation efficiency by as much as 82% at high phenol concentrations. Meanwhile, the GY2B/kaolinite complex reduced the degradation time by 24 h and improved the degradation efficiency by 46% at pH 12. The improvement was partially due to the buffering effects of kaolinite. It was also shown that Cr(VI) and kaolinite synergistically enhanced the degradation by GY2B, with Cr(VI) and kaolinite both increasing the degradation rate and kaolinite being primarily responsible for enhanced degradation efficiency. These results showed one of the common clay minerals, kaolinite, is able to significantly improve the microbial degradation performance, and protect microorganisms against unfavorable environment. Kaolinite can collaborate with Cr(VI) to further improve the microbial degradation performance. It is implied that clay minerals have great potential to be applied in enhancing the biodegradation of phenol.

Effects of nano bamboo charcoal on PAHs-degrading strain Sphingomonas sp. GY2B

Nano bamboo charcoal (NBC) has been commonly used in the production of textiles, plastics, paint, etc. However, little is known regarding their effects towards the microorganisms. The effects of NBC on phenanthrene degrading strain Sphingomonas sp. GY2B were investigated in the present study. Results showed that the addition of NBC could improve the phenanthrene removal by Sphingomonas sp. GY2B, with removal efficiencies increased by 10.29-18.56% in comparison to the control at 24h, and phenanthrene was almost completely removed at 48h. With the presence of low dose of NBC (20 and 50mgL(-1)), strain GY2B displayed a better growth at 6h, suggesting that NBC was beneficial to the growth of GY2B and thus resulting in the quick removal of phenanthrene from water. However, the growth of strain GY2B in high dose of NBC (200mgL(-1)) was inhibited at 6h, and the inhibition could be attenuated and eliminated after 12h. NBC-effected phenanthrene solubility experiment suggested that NBC makes a negligible contribution to the solubilization of phenanthrene in water. Results of electronic microscopy analysis (SEM and TEM) indicated NBC may interact with the cell membrane, causing the enhanced membrane permeability and then NBC adsorbed on the membrane would enter into the cells. The findings of this work would provide important information for the future usage and long-term environmental risk assessment of NBC.

Effect of surfactants on PAH biodegradation by a bacterial consortium and on the dynamics of the bacterial community during the process

The aim of this work was to evaluate the effect of a non-biodegradable (Tergitol NP-10) and a biodegradable (Tween-80) surfactant on growth, degradation rate and microbial dynamics of a polycyclic aromatic hydrocarbon (PAHs) degrading consortium (C2PL05) from a petroleum polluted soil, applying cultivable and non cultivable techniques. Growth and degradation rate were significantly lower with Tergitol NP-10 than that with Tween-80. Toxicity did not show any significant reduction with Tergitol NP-10 whereas with Tween-80 toxicity was almost depleted (30%) after 40 days. Regarding to the cultured bacteria, Pseudomonas and Stenotrophomonas groups were dominant during PAH degradation with Tergitol NP-10, whereas Enterobacter and Stenotrophomonas were dominant with Tween-80. DGGE analyses (PRIMER and MDS) showed that bacteria composition was more similar between treatments when PAHs were consumed than when PAHs concentration was still high. Community changes between treatments were a consequence of Pseudomonas sp., Sphingomonas sp., Sphingobium sp. and Agromonas sp.

Biodegradation of phenanthrene using adapted microbial consortium isolated from petrochemical contaminated environment

In developing countries like India, there are many industrial areas discharging effluent containing large amount of polyaromatic hydrocarbon (PAH) which causes hazardous effect on the soil-water environment. The objective of this study was to isolate and characterize high-efficiency PAH-degrading microbial consortium from 3 decade old petrochemical refinery field located in Nagpur, Maharashtra with history of PAH disposal. Based on biochemical tests and 16S rDNA gene sequence analysis the consortium was identified as Sphingobacterium sp., Bacillus cereus and a novel bacterium Achromobacter insolitus MHF ENV IV with effective phenanthrene-degrading ability. The biodegradation data of phenanthrene indicates about 100%, 56.9% and 25.8% degradation at the concentration of 100mg/l, 250 mg/l and 500 mg/l respectively within 14 days. The consortium and its monoculture isolates also utilized variety of other hydrocarbons for growth. To best of our knowledge this is the first time that Achromobacter insolitus has been reported to mineralize phenanthrene effectively. GC-MS analysis of phenanthrene degradation confirmed biodegradation by detection of intermediates like salicylaldehyde, salicylic acid and catechol. All the results indicated that the microbial consortium have a promising application in bioremediation of petrochemical contaminated environments and could be potentially useful for the study of PAH degradation and for bioremediation purposes.

Microbial communities to mitigate contamination of PAHs in soil--possibilities and challenges: a review

BACKGROUND, AIM, AND SCOPE

Although highly diverse and specialized prokaryotic and eukaryotic microbial communities in soil degrade polycyclic aromatic hydrocarbons (PAHs), most of these are removed slowly. This review will discuss the biotechnological possibilities to increase the microbial dissipation of PAHs from soil as well as the main biological and biotechnological challenges.

DISCUSSION AND CONCLUSIONS

Microorganism provides effective and economically feasible solutions for soil cleanup and restoration. However, when the PAHs contamination is greater than the microbial ability to dissipate them, then applying genetically modified microorganisms might help to remove the contaminant. Nevertheless, it is necessary to have a more holistic review of the different individual reactions that are simultaneously taking place in a microbial cell and of the interactions microorganism-microorganism, microorganism-plant, microorganism-soil, and microorganisms-PAHs.

PERSPECTIVES

Elucidating the function of genes from the PAHs-polluted soil and the study in pure cultures of isolated PAHs-degrading organisms as well as the generation of microorganisms in the laboratory that will accelerate the dissipation of PAHs and their safe application in situ have not been studied extensively. There is a latent environmental risk when genetically engineered microorganisms are used to remedy PAHs-contaminated soil.

Role of oxygenases in guiding diverse metabolic pathways in the bacterial degradation of low-molecular-weight polycyclic aromatic hydrocarbons: a review

Widespread environmental pollution by polycyclic aromatic hydrocarbons (PAHs) poses an immense risk to the environment. Bacteria-mediated attenuation has a great potential for the restoration of PAH-contaminated environment in an ecologically accepted manner. Bacterial degradation of PAHs has been extensively studied and mining of biodiversity is ever expanding the biodegradative potentials with intelligent manipulation of catabolic genes and adaptive evolution to generate multiple catabolic pathways. The present review of bacterial degradation of low-molecular-weight (LMW) PAHs describes the current knowledge about the diverse metabolic pathways depicting novel metabolites, enzyme-substrate/metabolite relationships, the role of oxygenases and their distribution in phylogenetically diverse bacterial species.

Construction of an artificial microalgal-bacterial consortium that efficiently degrades crude oil

Four oil component-degrading bacteria and one oil-tolerant microalgae, Scenedesmus obliquus GH2, were used to construct an artificial microalgal-bacterial consortium for crude-oil degradation. The bacterial strains included Sphingomonas GY2B and Burkholderia cepacia GS3C, along with a mixed culture, named GP3, containing Pseudomonas GP3A and Pandoraea pnomenusa GP3B. GY2B could only degrade polycyclic aromatic hydrocarbons, GS3C was able to degrade aliphatic chain hydrocarbons, and GP3 could utilize both saturated and aromatic hydrocarbons. In combination with unialgal or axenic algae, the bacteria showed different effects on oil degradation. Unialgal GH2 was not suitable for the consortium construction, as it could not cooperate well with GS3C and GP3. The axenic GH2 exhibited no oil-degrading ability; however, it significantly promoted the degradation ability of the oil component-degrading bacteria, especially for degrading biorefractory polycyclic aromatic hydrocarbons. Axenic S. obliquus GH2, combined with the four bacteria mentioned above, formed an optimal algal-bacterial consortium. The artificial consortium demonstrated an elevated efficiency in degrading both aliphatic and aromatic hydrocarbons of crude oil.

Biodegradation of 2-naphthol and its metabolites by coupling Aspergillus niger with Bacillus subtilis

To explore biodegradation of 2-naphthol and its metabolites accumulated in wastewater treatment, a series of bio-degradation experiments were conducted. Two main metabolites of 2-naphthol, 1,2-naphthalene-diol and 1,2-naphthoquinone, were identified by high-performance liquid chromatography with standards. Combining fungus Aspergillus niger with bacterium Bacillus subtilis in the treatment enhanced 2-naphthol degradation efficiency, lowered the accumulation of the two toxic metabolites. There were two main phases during the degradation process by the kinetic analysis: 2-naphthol was first partly degraded by the fungus, producing labile and easily accumulated metabolites, and then the metabolites were mainly degraded by the bacterium, attested by the degradation processes of 1,2-naphthalene-diol and 1,2-naphthoquinone as sole source of carbon and energy. Sodium succinate, as a co-metabolic substrate, was the most suitable compound for the continuous degradation. The optimum concentration of 2-naphthol was 50 mg/L. The overall 2-naphthol degradation rate was 92%, and the CODcr removal rate was 80% on day 10. These results indicated that high degradation rate of 2-naphthol should not be considered as the sole desirable criterion for the bioremediation of 2-naphthol-contaminated soils/wastewater.

Rapid degradation of phenanthrene by using Sphingomonas sp. GY2B immobilized in calcium alginate gel beads

The strain Sphingomonas sp. GY2B is a high efficient phenanthrene-degrading strain isolated from crude oil contaminated soils that displays a broad-spectrum degradation ability towards PAHs and related aromatic compounds. This paper reports embedding immobilization of strain GY2B in calcium alginate gel beads and the rapid degradation of phenanthrene by the embedded strains. Results showed that embedded immobilized strains had high degradation percentages both in mineral salts medium (MSM) and 80% artificial seawater (AS) media, and had higher phenanthrene degradation efficiency than the free strains. More than 90% phenanthrene (100 mg·L⁻¹) was degraded within 36 h, and the phenanthrene degradation percentages were >99.8% after 72 h for immobilized strains. 80% AS had significant negative effect on the phenanthrene degradation rate (PDR) of strain GY2B during the linear-decreasing stage of incubation and preadsorption of cells onto rice straw could improve the PDR of embedded strain GY2B. The immobilization of strain GY2B possesses a good potential for application in the treatment of industrial wastewater containing phenanthrene and other related aromatic compounds.

Flocculant in wastewater affects dynamics of inorganic N and accelerates removal of phenanthrene and anthracene in soil

Recycling of municipal wastewater requires treatment with flocculants, such as polyacrylamide. It is unknown how polyacrylamide in sludge affects removal of polycyclic aromatic hydrocarbons (PAH) from soil. An alkaline-saline soil and an agricultural soil were contaminated with phenanthrene and anthracene. Sludge with or without polyacrylamide was added while emission of CO(2) and concentrations of NH(4)(+), NO(3)(-), NO(2)(-), phenanthrene and anthracene were monitored in an aerobic incubation experiment. Polyacrylamide in the sludge had no effect on the production of CO(2), but it reduced the concentration of NH(4)(+), increased the concentration of NO(3)(-) in the Acolman soil and NO(2)(-) in the Texcoco soil, and increased N mineralization compared to the soil amended with sludge without polyacrylamide. After 112d, polyacrylamide accelerated the removal of anthracene from both soils and that of phenanthrene in the Acolman soil. It was found that polyacrylamide accelerated removal of phenanthrene and anthracene from soil.

Oxidoreductase activity of Sorghum root exudates in a phenanthrene-contaminated environment

The effect of the polycyclic aromatic hydrocarbon (PAH) phenanthrene on the enzymatic activity of root exudates of the phytoremediating plant Sorghum bicolor (L.) Moench was studied. Analysis of sorghum root exudates allowed us to reveal the activities of oxidase, peroxidase, and tyrosinase. The activities of these enzymes were progressive as the soil phenanthrene concentration increased. Using lyophilized samples, we found that as a result of the enzymatic activity of the root exudates, some of the PAHs and products of PAH degradation were oxidized in the reaction mixture supplemented with the mediating agents (ABTS or DL-DOPA) but that no oxidation was observed in the reaction mixtures without the mediators. The revealed enzymatic activity of the sorghum root exudates may indicate the involvement of the root-released oxidoreductases in rhizospheric degradation of PAHs and/or their derivatives. In addition, from the data obtained, the coupling of plant and microbial metabolisms of PAHs in the rhizosphere may be surmised.