Partially oxidized polycyclic aromatic hydrocarbons show an increased bioavailability and biodegradability

Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source

In this study, we conducted an extensive investigation of the biodegradation capabilities and stress response of the newly isolated strain Pseudomonas veronii SM-20 in order, to assess its potential for bioremediation of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Initially, phenotype microarray technology demonstrated the strain's proficiency in utilizing various carbon sources and its resistance to certain stressors. Genomic analysis has identified numerous genes involved in aromatic hydrocarbon metabolism. Biodegradation assay analyzed the depletion of phenanthrene (PHE) when it was added as a sole carbon and energy source. We found that P. veronii strain SM-20 degraded approximately 25% of PHE over a 30-day period, starting with an initial concentration of 600 µg/mL, while being utilized for growth. The degradation process involved PHE oxidation to an unstable arene oxide and 9,10-phenanthrenequinone, followed by ring-cleavage. Comparative proteomics provided a comprehensive understanding of how the entire proteome responded to PHE exposure, revealing the strain's adaptation in terms of aromatic metabolism, surface properties, and defense mechanism. In conclusion, our findings shed light on the promising attributes of P. veronii SM-20 and offer valuable insights for the use of P. veronii species in environmental restoration efforts targeting PAH-impacted sites.

Structural, metabolic, and functional characteristics of soil microbial communities in response to benzo[a]pyrene stress

Understanding the characteristics of soil microbes responding to benzo[a]pyrene (BaP) helps to deepen the knowledge of the risks of BaP to soil ecosystem. In this study, the structural, metabolic, and functional responses of soil microbial communities to BaP (8.11 mg kg^-1) were investigated. Analysis of microbial community structure based on 16 S rRNA and ITS gene sequencing indicated that BaP addition enriched microbes associated with aromatic compound degradation (Sphingomonas, Bacilli, Fusarium) and oligotrophs (Blastocatellaceae, Rokubacteriales), but inhibited Cyanobacteria involved in nitrogen-fixing process. Network analysis showed that the bacterial community enhanced intraspecific cooperation, while fungal community mainly altered the keystone taxa under BaP stress. Biolog EcoPlate assay demonstrated that microbial metabolism of carbon sources, especially nitrogen-containing sources, was stimulated by BaP addition. Functional analysis based on enzyme activity tests, functional gene quantification, and function annotation showed that nitrogen-cycling processes, especially nitrogen fixation, were significantly inhibited. These results suggest that BaP-tolerant microbes may establish cooperative relationships and compete for resources and ecological niches with sensitive microbes, especially those associated with nitrogen cycling, ultimately leading to enhanced carbon source utilization and restricted nitrogen cycling. This study clearly elucidates the adaptation strategies and functional shifts of soil microbial communities to BaP contamination.

Mineralization of pyrene (polycyclic aromatic hydrocarbon) in clay soil supplemented with animal organic carbon source

Biostimulation of polycyclic aromatic hydrocarbons (PAHs) is a major concern in the environment due to their toxic nature and ubiquitous occurrence. The study aimed to determine the best animal supplement of organic carbon source (cow dung, goat dung, pig dung and poultry (fowl droppings) and indigenous microbes capable of mineralizing pyrene in clay soil. Clay soil sample was collected from the top surface soil (0 - 15 cm) in Ikpoba River and upper Lawani river bank, both in Benin City with the aid of stainless steel trowel and gloved hands and stored in a polyethylene bag. The isolation and identification process were evaluated by staining method, microscopic examination and biochemical tests. The degradation experiment was conducted in bioreactors and supplemented cow dung, pig dung, goat dung and fowl droppings were added in varying amounts of 25 g/l, 50 g/l, 75 g/l and 100 g/l. The potential effects of animal organic carbon as nutrient supplements to enhance mineralization of pyrene were investigated. The rates of mineralization of pyrene were studied for a remediation period of 35 days at room temperature of about 25 °C. Results obtained from microbial isolation showed that B. substilis and A. niger were the most populated in the soil and were therefore selected. The degradation experiment showed that mixed culture of B. substilis and A. niger using 50 g/l supplement with the dungs and droppings gave the highest percentage degradation with fowl droppings 98.3%, pig dung 98.1%, goat dung 97.8%, and cow dung 97.7%. The least degradation was observed in supplement with 100 g/l in a single culture of A. niger with fowl droppings yielded 64.5% degradation, pig dung 63.8%, goat dung 63.7% and cow dung 62.7%. The overall results of the study showed that 50 g/l of animal wastes supplement in the ratio of 1:4 with pyrene contaminated soils are most effective in degradation processes. Also the mixed culture of bacteria and fungi enhanced pyrene mineralization and degradation more than single culture.

Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives

Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.

Synergy between fungi and bacteria promotes polycyclic aromatic hydrocarbon cometabolism in lignin-amended soil

Lignin enhanced biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but collaboration among soil microorganisms during this process remains poorly understood. Here we explored the relations between microbial communities and PAH transformation in soil microcosms amended with lignin. Mineralization of the four-ring benzo(a)anthracene (BaA), which was selected as a model, was determined by using an isotope-labeled tracer. The eukaryotic inhibitor cycloheximide and redox mediator ABTS were used to validate the fungal role, while microbial communities were monitored by amplicon sequencing. The results demonstrated that lignin significantly promoted BaA mineralization to CO₂, which was inhibited and enhanced by cycloheximide and ABTS, respectively. Together with the increased abundance of Basidiomycota, these observations suggested an essential contribution of fungi to BaA biodegradation, which possibly through a ligninolytic enzyme-mediated pathway. The enrichment of Methylophilaceae and Sphingomonadaceae supported bacterial utilization of methyl and aryl groups derived from lignin, implicating cometabolic BaA degradation. Co-occurrence network analysis revealed increased interactions between fungi and bacteria, suggesting they played synergistic roles in the transformation of lignin and BaA. Collectively, these findings demonstrate the importance of synergy between fungi and bacteria in PAH transformation, and further suggest that the modulation of microbial interplay may ameliorate soil bioremediation with natural materials such as lignin.

Enhanced bioremediation of sediment contaminated with polycyclic aromatic hydrocarbons by combined stimulation with sodium acetate/phthalic acid

In this study, four groups of laboratory scale experiments were performed by adding sodium acetate (SA), phthalic acid (PA), and SA-PA to river sediment to observe the microbial response and biodegradation efficiency of polycyclic aromatic hydrocarbons (PAHs). The results showed that the amount of total organic carbon consumed and the amount of sulfate reduction were both positively correlated (p < 0.01) with the biodegradation efficiency of the sum (∑) PAHs (∼40.5%). The lower the number of rings, the more PAHs were biodegraded, with an efficiency of 63.0% for ∑ (2 + 3) ring PAHs. Based on high-throughput sequencing and molecular ecological network analysis, it was found that the combined stimulation of SA and PA not only increased the relative abundance of PAHs-degrading bacterial (eg., Proteobacteria, Desulfobacterota, Campilobacterota and Firmicutes), but also had a strengthening effect on microbes in sediments. The altered microbial structure caused a variation in metabolic functions, which increased the amino acid metabolism to 12.2%, thus increasing the positive correlations among genera and improving the connectivity of the microbial network (p < 0.01). These changes may be responsible for the enhanced biodegradation of PAHs under SA-PA dosing in comparison to SA or PA dosing alone. This study revealed that the microbial community was stimulated by the combined addition of SA and PA, and indicated its role in enhancing biodegradation of PAHs in contaminated river sediments.

Extra-Heavy Crude Oil Degradation by Alternaria sp. Isolated from Deep-Sea Sediments of the Gulf of Mexico

The Gulf of Mexico (GoM) is an important source of oil for the United States and Mexico. There has been growing interest, particularly after the Deepwater Horizon oil spill, in characterizing the fungal diversity of the GoM and identifying isolates for use in the bioremediation of petroleum in the event of another spill. Most studies have focused on light crude oil bioremediation processes, while heavy crude oil (HCO) and extra-heavy crude oil (EHCO) have been largely ignored. In this work, we evaluated the ability of fungal isolates obtained from deep-sea sediments of the Mexican economic exclusive zone (EEZ) of the GoM to degrade HCO (16–20° API) and EHCO (7–10° API). Alternaria sp., Penicillium spp., and Stemphylium sp. grew with HCO as the sole carbon source. Remarkably, Alternaria sp. was the only isolate able to grow with EHCO as the sole carbon source, degrading up to 25.6% of the total EHCO and 91.3% of the aromatic fraction, as demonstrated by gas chromatography analysis of the saturate, aromatic, and polar fractions. These findings proved to be significant, identifying Alternaria sp. as one of the few fungi reported so far capable of degrading untreated EHCO and as a suitable candidate for bioremediation of EHCO in future studies.

Bioaugmentation of Native Fungi, an Efficient Strategy for the Bioremediation of an Aged Industrially Polluted Soil With Heavy Hydrocarbons

The concurrence of structurally complex petroleum-associated contaminants at relatively high concentrations, with diverse climatic conditions and textural soil characteristics, hinders conventional bioremediation processes. Recalcitrant compounds such as high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) and heavy alkanes commonly remain after standard soil bioremediation at concentrations above regulatory limits. The present study assessed the potential of native fungal bioaugmentation as a strategy to promote the bioremediation of an aged industrially polluted soil enriched with heavy hydrocarbon fractions. Microcosms assays were performed by means of biostimulation and bioaugmentation, by inoculating a defined consortium of six potentially hydrocarbonoclastic fungi belonging to the genera Penicillium, Ulocladium, Aspergillus, and Fusarium, which were isolated previously from the polluted soil. The biodegradation performance of fungal bioaugmentation was compared with soil biostimulation (water and nutrient addition) and with untreated soil as a control. Fungal bioaugmentation resulted in a higher biodegradation of total petroleum hydrocarbons (TPH) and of HMW-PAHs than with biostimulation. TPH (C14-C35) decreased by a 39.90 ± 1.99% in bioaugmented microcosms vs. a 24.17 ± 1.31% in biostimulated microcosms. As for the effect of fungal bioaugmentation on HMW-PAHs, the 5-ringed benzo(a)fluoranthene and benzo(a)pyrene were reduced by a 36% and 46%, respectively, while the 6-ringed benzoperylene decreased by a 28%, after 120 days of treatment. Biostimulated microcosm exhibited a significantly lower reduction of 5- and 6-ringed PAHs (8% and 5% respectively). Higher TPH and HMW-PAHs biodegradation levels in bioaugmented microcosms were also associated to a significant decrease in acute ecotoxicity (EC50) by Vibrio fischeri bioluminiscence inhibition assays. Molecular profiling and counting of viable hydrocarbon-degrading bacteria from soil microcosms revealed that fungal bioaugmentation promoted the growth of autochthonous active hydrocarbon-degrading bacteria. The implementation of such an approach to enhance hydrocarbon biodegradation should be considered as a novel bioremediation strategy for the treatment of the most recalcitrant and highly genotoxic hydrocarbons in aged industrially polluted soils.

Biogenic fenton-like reaction involvement in aerobic degradation of C60 by Labrys sp. WJW

Buckminster fullerene (C₆₀), the most representative type among fullerenes, has attracted widely attentions because of its many potential applications. The increasing application of fullerene and limited knowledge of its environmental fate are required concerns. Herein, the biotransformation of C₆₀ by Labrys sp. WJW was investigated. Cell numbers reached 25.76 ± 1.85 folds within 8 days using 100 mg/L C₆₀ as sole carbon source. The biotransformation of C₆₀ by Labrys sp. WJW was analyzed by various characterization methods. Raman spectra indicated that strain WJW broke the soccer ball like structure of C₆₀. After 12 days, over 60% of C₆₀ was degraded evidenced by UV-vis spectrophotometry and liquid chromatography-mass spectrometry. The underlying biotransformation mechanism of C₆₀ through an extracellular Fenton-like reaction was illustrated. In this reaction, the ^•OH production was mediated by reduction of H₂O₂ involving a continuous cycle of Fe(II)/Fe(III). Bacterial transformation of C₆₀ will provide new insights into the understanding of C₆₀ bioremediation process.

Bacteria mediated Fenton-like reaction drives the biotransformation of carbon nanomaterials

Carbon nanomaterials (CNs), which gain heightened attention as novel materials, are increasingly incorporated into daily products and thus are released into the environment. Limited research on CNs environmental fates lags their industry growth, only few bacteria have been confirmed to biotransform CNs and the mechanism behind has not been revealed yet. In this study, four types of commercial CNs, i.e. graphene oxide (GO), reduced graphene oxide (RGO), single walled carbon nanotubes (SWCNTs), and oxidized (carboxylated) SWCNTs, were selected for investigation. The biotransformation of CNs by Labrys sp. WJW, which could grow with these CNs as the sole carbon source, was investigated. The bacterial transformation was proved by qPCR, transmission electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, liquid chromatography/time-of-flight/mass spectrometry, and gas chromatograph-mass spectrometry analyses. The biotransformation resulted in morphology change, defect increase and functional group change of these CNs. Furthermore, the underlying mechanism of CNs biodegradation mediated by extracellular Fenton-like reaction was demonstrated. In this reaction, the OH production was mediated by reduction of H₂O₂ involved a continuous cycle of Fe(II)/Fe(III). These findings reveal a novel degradation mechanism of microorganism towards high molecular weight substrate, which will provide a new insight into the environmental fate of CNs and the guidance for their safer use.

Growth management of white-rot fungus Phlebia brevispora improved degradation of high-molecular-weight polycyclic aromatic hydrocarbons

The effect of co-culturing white-rot fungus Phlebia brevispora with growth-promoting bacterial strains Enterobacter sp. TN3W-14 and Pseudomonas sp. TN3W-8 on the degradation of polycyclic aromatic hydrocarbons (PAHs) was evaluated in liquid culture. In axenic cultures, P. brevispora strains TN3F and TMIC33929 showed high degradation of phenanthrene (> 98%) within 15 days, and degraded 65% and 63% of pyrene, and 12% and 8% of benzo(a)pyrene, respectively. This low level of degradation ability toward benzo(a)pyrene was improved significantly by co-culturing the fungi with a mixture of bacterial strains TN3W-8 and TN3W-14 (mixed bacterial co-culture; MBC). Within 15 days, P. brevispora TN3F with MBC achieved about 86% pyrene and 53% benzo(a)pyrene degradation; P. brevispora TMIC33929 with MBC showed 92% pyrene and 72% benzo(a)pyrene degradation. The MBC alone degraded little PAH, as its growth was inhibited by PAH; however, its co-culture with P. brevispora improved mycelial growth of the fungus, which led to improved degradation of the PAHs. A possible dihydrodiol metabolite of pyrene from fungal cultures suggests that hydroxylation was the first step in the degradation of pyrene by P. brevispora.

Environmentally Persistent Free Radical (EPFR) Formation by Visible-Light Illumination of the Organic Matter in Atmospheric Particles

A secondary process may be an important source of environmentally persistent free radicals (EPFRs) in atmospheric particulates; yet, this process remains to be elucidated. This study demonstrated that secondary EPFRs could be generated by visible-light illumination of atmospheric particulate matter (PM), and their lifetimes were only 30 min to 1 day, which were much shorter than the lifetimes of the original EPFRs in PM. The yields of secondary EPFRs produced by PM could reach 15-60% of those of the original EPFRs. The extractable organic matter contributed to the formation of secondary EPFRs (∼55%), and a humic-like substance was the main precursor of the secondary EPFRs and was also the most productive precursor compared to the other aerosol components. The results of simulation experiments showed that the secondary EPFRs generated by the extractable and nonextractable PM components were similar to those produced by phenolic compounds and polycyclic aromatic hydrocarbons, respectively. We have found that oxygen molecules play an important role in the photochemical generation and decay of EPFRs. The reactive oxygen capture experiments showed that the original EPFRs may contribute to singlet oxygen generation, while the secondary EPFRs generated by photoexcitation may not produce singlet oxygen or hydroxyl radicals.

Simultaneous determination of dissolved phenanthrene and its metabolites by derivative synchronous fluorescence spectrometry with double scans method in aqueous solution

A simple and sensitive derivative synchronous fluorescence spectrometry with double scans (DS-DSFS) method was developed for simultaneous determination of dissolved Phenanthrene (Phe) and its metabolites 1-hydroxy-2-naphthoic acid (1H2NA) and salicylic acid (SA) in aqueous solution. The value of 69 nm was selected as the optimal Δλ conditions for Phe and 1H2NA, and the Δλ value of 55 nm was selected for SA. The overlapping fluorescence emission spectra of Phe, 1H2NA and SA were resolved by DS-DSFS. The signals detected at wavelength of 296 nm for Phe, 352 nm for 1H2NA and 307 nm for SA vary linearly when the concentrations in the range of 4.0-1.0 × 10³ μg L^-1, 4.0-1.2 × 10³ μg L^-1 and 4.0-8.0 × 10² μg L^-1, respectively. The detection limits were 0.08, 0.07 and 0.88 μg L^-1 for Phe, 1H2NA and SA, with the relatively standard deviations less than 5.0%. The established method was successfully applied in the determination of Phe and the metabolites during the biodegradation of dissolved Phe in the lab. It was evidenced that the method has potential for the in situ investigation of PAH biodegradation.

A novel environmental fate of graphene oxide: Biodegradation by a bacterium Labrys sp. WJW to support growth

Graphene oxide (GO) is a new type of nanomaterial with unique physicochemical properties and diverse applications, whereas it poses potential risk to human and environment. By screening from natural soil exposed to GO in the laboratory, we successfully obtained a novel bacterium, Labrys sp. WJW, which was able to use GO as the sole carbon source for growth. Within 8 days, cell numbers increased 16.76 ± 3.21 folds using 100 mg/L GO as the carbon source by qPCR analysis. The bacterial biodegradation which resulted in formation of holes and functional group changes of GO was proved by Raman spectroscopy, atomic force microscopy, transmission electron microscopy and X-ray photoelectron spectroscopy analyses. Aromatic intermediates with structures of benzoic acid and phenol were identified using gas chromatograph-mass spectrometry and liquid chromatography/time-of-flight/mass spectrometry. Combination of genomic and proteomic analyses were performed to explore the proteins associated with GO degradation. A total of 644 proteins were significantly shifted. Bioinformatics analysis indicated that part of the up-regulated proteins were related to oxidation, ring cleavage and intermediates transmembrane processes, and GO was supposed to be degraded to benzoate and further degraded for downstream processes. This study enriches our understanding and provides new insights into the environmental fate of GO.

Occurrence, impact variables and potential risk of PPCPs and pesticides in a drinking water reservoir and related drinking water treatment plants in the Yangtze Estuary

PPCPs and pesticides have been documented throughout the world over the years, yet relatively little is known about the factors affecting their spatial distribution and temporal change in order to know their potential risk to the ecosystem or human health in the future. In our study, 5 PPCPs and 9 pesticides were selected to study their occurrence, impact variables and potential risk in a drinking water reservoir in Yangtze Estuary and related drinking water treatment plants (DWTPs) in China. The detection results showed the presence of PPCPs and pesticides reflected in a large part of croplands and urban and built-up land in the adjacent basin. The discrepancy of concentration among the different PPCPs and pesticides was mainly decided by their application amount or daily usage. Then, the major factors regulating the occurrence of these contaminants in the surface water were found as the living expenditure attributed to food and medicine based on a correlation analysis. Also, the PPCPs were found to negatively correlate to the effectiveness of sewage management. The detection of the PPCPs and pesticides in DWTPs indicated that, except for atrazine and simazine, the removal percentages were increased significantly in advanced DWTPs. Moreover, risk assessment estimated by a Risk Quotient and Hazard Quotient showed that while caffeine, bisphenol A, estrone and simazine were at a high-risk level in the reservoir water, all of the contaminants detected posed no risk to human health through drinking water. It's possible that atrazine could pose a high risk to the ecosystem while simazine could pose a risk to human health in the future considering the increasing expenditure attributed to food.

Natural Porphyrins Accelerating the Phototransformation of Benzo[a]pyrene in Water

Phototransformation is one of the most important transformation pathways of organic contaminants in the water environment. However, how active compounds enable and accelerate the phototransformation of organic pollutants remains to be elucidated. In this study, the phototransformation of benzo[a]pyrene (BaP, the first class "human carcinogens") by various natural porphyrins under solar irradiation was investigated, including chlorophyll a, sodium copper chlorophyllin, hematin, cobalamin, and pheophorbide a. Transformation efficiency of BaP varied considerably with chemical stabilities of the porphyrins. Porphyrins with a lower stability displayed higher BaP transformation efficiencies. BaP transformation had a significant positive correlation with the production of singlet oxygen. Identical phototransformation products of BaP were observed for all investigated porphyrins, and the main products were identified as BaP-quinones, including BaP-1,6-dione, BaP-3,6-dione, and BaP-6,12-dione. The mechanism of natural porphyrins accelerating the BaP phototransformation in water was proposed to proceed via the photocatalytic generation of singlet oxygen resulting in the transformation of BaP to quinones.

Exploring the potential of fungi isolated from PAH-polluted soil as a source of xenobiotics-degrading fungi

The aim of this study was to find polycyclic aromatic hydrocarbon (PAH)-degrading fungi adapted to polluted environments for further application in bioremediation processes. In this study, a total of 23 fungal species were isolated from a historically pyrogenic PAH-polluted soil in Spain and taxonomically identified. The dominant groups in these samples were the ones associated with fungi belonging to the Ascomycota phylum and two isolates belonging to the Mucoromycotina subphylum and Basiodiomycota phylum. We tested their ability to convert the three-ring PAH anthracene in a 42-day time course and analysed their ability to secrete extracellular oxidoreductase enzymes. Among the 23 fungal species screened, 12 were able to oxidize anthracene, leading to the formation of 9,10-anthraquinone as the main metabolite, a less toxic one than the parent compound. The complete removal of anthracene was achieved by three fungal species. In the case of Scopulariopsis brevicaulis, extracellular enzyme independent degradation of the initial 100 μM anthracene occurred, whilst in the case of the ligninolytic fungus Fomes (Basidiomycota), the same result was obtained with extracellular enzyme-dependent transformation. The yield of accumulated 9,10-anthraquinone was 80 and 91 %, respectively, and Fomes sp. could slowly deplete it from the growth medium when offered alone. These results are indicative for the effectiveness of these fungi for pollutant removal. Graphical abstract ᅟ.

Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review

Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.

Chlorophyll catalyse the photo-transformation of carcinogenic benzo[a]pyrene in water

Algal blooms cause great damage to water quality and aquaculture. However, this study showed that dead algal cells and chlorophyll could accelerate the photo-transformation of benzo[a]pyrene (BaP), a ubiquitous and persistent pollutant with potently mutagenic and carcinogenic toxicities, under visible light irradiation. Chlorophyll was found to be the major active substance in dead algal cells, and generated a high level of singlet oxygen to catalyse the photo-transformation of BaP. According to various BaP metabolites formed, the degradation mechanism was proposed as that chlorophyll in dead algal cells photo-oxidized BaP to quinones via photocatalytic generation of singlet oxygen. The results provided a good insight into the role of chlorophyll in the photo-transformation of organic contaminants and could be a possible remediation strategy of organic pollutants in natural environment.

Changes in the abundance of sugars and sugar-like compounds in tall fescue (Festuca arundinacea) due to growth in naphthalene-treated sand

The hydrophilic metabolome of tall fescue (Festuca arundinacea) adapted to grow in naphthalene-treated sand (0.8 g kg(-1) sand dw) was analysed using gas chromatography-mass spectrometry, and peaks corresponding to the more abundant compounds were tentatively identified from analysis of their mass spectral features and reference to the NIST Mass Spectral Database. Particular attention was paid to sugars as they are known to play important roles as stress regulators in plants. The results showed that the abundance of sugars was greater in the roots but lesser in the shoots of treated plants when compared to their control counterparts. The results for indole acetic acid (IAA) were notable: IAA was prominently less in the treated roots compared to shoots, and in treated shoots, IAA was particularly subdued compared to untreated shoots consistent with IAA degradation in treated plant tissues. The differences in the molecular phenotype between control and treated plants were expressed in root structural differences. The treated roots were modified to have greater suberisation, enhanced thickening in the endodermis and distortions in the cortical zone as demonstrated through scanning electron and epi-fluorescence microscopy.

Chemical measures of bioavailability/bioaccessibility of PAHs in soil: fundamentals to application

Risk assessment and remediation of contaminated land is inherently dependent on the contaminants present and their availability for interaction with soil biota. An ever-growing body of evidence suggests that current regulatory procedures over-estimate the 'true' fraction available to biota. Thus, a procedure that predicts the 'bioavailable fraction' would be useful for predicting 'actual' exposure limits and provide a more relevant basis for risk assessment. The aim of this paper is to address several important questions: "How should bioavailability be defined?" "What factors affect bioavailability measurement?" "To what extent have existing protocols measured bioavailability?" "What is actually measured by chemical techniques purported to determine bioavailability?" We offer two definitions (namely 'bioavailability' and 'bioaccessibility') and review commonly employed chemical extraction techniques to measure putative bioavailability. Relative advantages and disadvantages of the techniques are highlighted to elucidate underlying factors for the wide range of conclusions observed in the literature. Although the concept of bioavailability is implicit to contaminated land risk assessment and remediation, explicit reference to and use of adjustment factors is rare amongst regulatory bodies and remediators. Use of chemical determinants for bioavailability, applicable within current legislation and due consideration to inherent variability, are proposed and barriers to their implementation discussed.

Removal of polycyclic aromatic hydrocarbons from organic solvents by ashes wastes

Polycyclic aromatic hydrocarbons (PAHs) can be formed during the refinery processes of crude petroleum. Their removal is of great importance. The same happens with other organic solvents used for the extraction of PAHs (hexane, acetonitrile...), which can be polluted with PAHs. Kinetic and equilibrium batch sorption tests were used to investigate the effect of wood ashes wastes as compared to activated carbon on the sorption of three representative PAHs from n-hexane and acetonitrile. Mussel shell ashes were discarded for batch sorption experiments because they were the only ashes containing PAHs. The equilibrium time was reached at 16 h. Physical sorption caused by the aromatic nature of the compounds was the main mechanism that governed the PAHs removal process. Our investigation revealed that wood ashes obtained at lower temperature (300 degrees C) did not show any PAHs sorption, while ashes obtained at higher temperature (>500 degrees C) have adsorbent sites readily available for the PAH molecules. An increase in the molecular weight of PAHs has a strong effect on sorption wood ashes wastes. As low the wood ashes particle size as high the sorption of PAHs, as a result of differences in adsorbent sites. The performance of wood ash wastes vs. activated carbon to remove 10 PAHs from organic solvents is competitive in price, and a good way for waste disposal.

Inoculum carrier and contaminant bioavailability affect fungal degradation performances of PAH-contaminated solid matrices from a wood preservation plant

The objective of the study was to investigate the impact of chopped wheat straw (CWS), ground corn cobs (GCC) and commercial pellets (CP), as inoculum carriers, on both growth and polycyclic aromatic hydrocarbons (PAH) degradation performances of Dichomitus squalens, Pleurotus ostreatus and Coprinus comatus. A historically-contaminated soil (HCS) and creosote-treated shavings (CTS) from the Sobeslav wood preservation plant, characterized by different relative abundances of the PAH bioavailable fractions, were used to assess the contaminated matrix effect and its interaction with both carrier and fungal strain. In HCS, best results were obtained with CP-immobilized P. ostreatus, which was able to deplete benzo[a]anthracene, chrysene, benzo[b]fluoranthene (BbF), benzo[k]fluoranthene (BkF) and benzo[a]pyrene (BaP) by 69.1%, 29.7%, 39.7%, 32.8% and 85.2%, respectively. Only few high-molecular mass PAHs such as BbF, BkF and BaP were degraded beyond their respective bioavailable fractions and this effect was confined to a limited number of inoculants. In CTS, only phenanthrene degradation exceeded its respective bioavailability from 1.42 to 1.86-fold. Regardless of both inoculum carrier and fungal species, degradation was positively and significantly (P<0.001) correlated with bioavailability in fungal microcosms on HCS and CTS and such correlation was very similar in the two matrices (R(adj)(2) equal to 0.60 and 0.59, respectively). The ability of white-rot fungi to degrade certain PAHs beyond their bioavailability was experimentally proven by this study. Although CTS and HCS considerably differed in their physico-chemical properties, PAH contents and contaminant aging, the relationship between degradation and bioavailability was not significantly affected by the type of matrix.

Fungal PAH-metabolites resist mineralization by soil microorganisms

This study investigated the mineralization of water-soluble polycyclic aromatic hydrocarbon (PAH) metabolites produced by the soil fungus Cunninghamella elegans. Eleven soil fungi were screened for their ability to metabolize (14)C-phenanthrene, (14)C-fluoranthene, and (14)C-pyrene into water-soluble compounds. Eight fungi produced water-soluble metabolites from all or some of the PAHs. The composition of the water-soluble PAH-metabolites from the most effective solubilizer C. elegans was analyzed by an ultraperformance liquid chromatograph interfaced to a quadrupole time-of-flight mass spectrometer. Thirty-eight metabolites were detected. All of 34 identified metabolites were sulfate-conjugated. The mineralization of (14)C-metabolites, produced by C. elegans, was compared to mineralization of the parent (14)C-PAHs in soil slurries. It was hypothesized that the increased bioavailability and metabolic activation of the metabolites would increase mineralization in soil slurries compared to mineralization of the parent PAHs. Unexpectedly, the mineralization of the (14)C-metabolites was in all cases extremely slow compared to the mineralization of the parent (14)C-PAHs. Slow (14)C-metabolite mineralization was not caused by metabolite toxicity, neither was cometabolic mineralization of (14)C-metabolites stimulated by the presence of active PAH-degraders. High water solubility, low lipophilicity, and extremely slow mineralization of the metabolites indicate a potential problem of leaching of fungal PAH-metabolites to the groundwater.

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.

Enzymatic degradation of low soluble compounds in monophasic water: solvent reactors. Kinetics and modeling of anthracene degradation by MnP

Polycyclic aromatic hydrocarbons (PAHs) are toxic compounds presenting low water solubility and high hydrophobicity, which greatly hampers their natural biodegradation. The enzymatic degradation of a model compound, anthracene, was evaluated in presence of a miscible solvent for an increased solubility. Manganese peroxidase, a ligninolytic enzyme from white-rot fungi, was used as biocatalyst in a medium containing acetone. The kinetic parameters of the enzymatic degradation of anthracene, obtained from fed-batch experiments, were applied to model the operation of a continuous reactor. Kinetics comprised a Michaelis-Menten equation, modified with an autocatalytic term, assumed to the effect of quinones acting as electron carriers, and a logistic function related to enzyme activity. The continuous reactor has been operated for 108 h, attaining a 90% of anthracene degradation, which demonstrated the feasibility of the system for its application in the removal of poorly soluble compounds. The model of this reactor permitted to predict accurately anthracene degradation in different conditions, such as external addition of anthraquinone and different enzymatic activities.

Microbial biodegradation of polyaromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are widespread in various ecosystems and are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Because of their hydrophobic nature, most PAHs bind to particulates in soil and sediments, rendering them less available for biological uptake. Microbial degradation represents the major mechanism responsible for the ecological recovery of PAH-contaminated sites. The goal of this review is to provide an outline of the current knowledge of microbial PAH catabolism. In the past decade, the genetic regulation of the pathway involved in naphthalene degradation by different gram-negative and gram-positive bacteria was studied in great detail. Based on both genomic and proteomic data, a deeper understanding of some high-molecular-weight PAH degradation pathways in bacteria was provided. The ability of nonligninolytic and ligninolytic fungi to transform or metabolize PAH pollutants has received considerable attention, and the biochemical principles underlying the degradation of PAHs were examined. In addition, this review summarizes the information known about the biochemical processes that determine the fate of the individual components of PAH mixtures in polluted ecosystems. A deeper understanding of the microorganism-mediated mechanisms of catalysis of PAHs will facilitate the development of new methods to enhance the bioremediation of PAH-contaminated sites.

Addition of allochthonous fungi to a historically contaminated soil affects both remediation efficiency and bacterial diversity

Botryosphaeria rhodina DABAC P82 and Pleurotus pulmonarius CBS 664.97 were tested for their ability to grow and to degrade aromatic hydrocarbons in an aged contaminated soil. To evaluate the impact of indigenous microflora on the overall process, incubations were performed on both fumigated and nonfumigated soils. Fungal colonization by B. rhodina was unexpectedly lower in the fumigated than in the nonfumigated soil while the growth of P. pulmonarius showed an opposite response. Degradation performances and detoxification by both fungi in the nonfumigated soil were markedly higher than those observed in the fumigated one. Heterotrophic bacterial counts in nonfumigated soil augmented with either B. rhodina or P. pulmonarius were significantly higher than those of the corresponding incubation control (6.7 +/- 0.3 x 10(8) and 8.35 +/- 0.6 x 10(8), respectively, vs 9.2 +/- 0.3 x 10(7)). Bacterial communities of both incubation controls and fungal-augmented soil were compared by numerical analysis of denaturing gradient gel electrophoresis profiles of polymerase chain reaction (PCR)-amplified 16S ribosomal RNA (rRNA) genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Besides increasing overall diversity, fungal augmentation led to considerable qualitative differences with respect to the pristine soil.

Enhanced degradation of benzo[a]pyrene by Mycobacterium sp. in conjunction with green alga

Previous work in this laboratory has confirmed that the bacteria Mycobacterium sp. strain RJGII.135 and Sphingomonas yanoikuyae strain B1 and the green alga Selanastrum capricornutum strain UTEX 1648 degrade benzo[a]pyrene (BaP) to various BaP intermediates. S. capricornutum was first grown with BaP for 4 days. The organic extract of this media was then introduced into separate cultures of strain RJGII.135 and strain B1; separate cultures were grown with BaP for comparison. Cultures grown with BaP and those grown with the algal/BaP extract showed similar mineralization patterns. The quantity of total metabolites formed was greater in bacterial cultures grown with the algal/BaP extract than those grown with BaP alone. For strain RJGII.135, only 27% of the original BaP remained in cultures grown with the algal/BaP extract; 59% remained in cultures grown with BaP. For strain B1, only 6% of the original BaP remained in cultures grown with the algal/BaP extract; 38% remained in cultures grown with BaP. These results indicate that strategies utilizing organisms together may be necessary in being able to degrade large, recalcitrant polycyclic aromatic hydrocarbons (PAHs) such as BaP.

Evaluation of cytochrome P450BSβ reactivity against polycyclic aromatic hydrocarbons and drugs

The oxidation of 10 polycyclic aromatic hydrocarbons (PAH) by cytochrome P450(BSbeta) using three different electron acceptors is reported. Three PAH were found to be substrates for the oxidation by P450(BSbeta), namely anthracene, 9-methyl-anthracene and azulene. The respective oxidation products were identified by reversed-phase high-performance liquid chromatography coupled to electrospray ionization-mass spectrometry. In addition, 10 drug-like compounds were investigated for their effects on the catalytic activity of P450(BSbeta) by carrying out inhibition studies. The stability of P450(BSbeta) against hydrogen peroxide, cumene, and ter-butyl hydroperoxide was determined. Overall, the results of this study suggested that the P450(BSbeta) enzyme represents a powerful catalyst in terms of the catalytic activity and operational stability.

Operation of a two-phase partitioning bioreactor for the oxidation of anthracene by the enzyme manganese peroxidase

A study was conducted to determine the potential of a two-phase partitioning bioreactor (TPPB) for the treatment of a poorly soluble compound, anthracene, by the enzyme manganese peroxidase (MnP) from the fungus Bjerkandera sp. BOS55. Silicone oil was used as the immiscible solvent, which contained anthracene at high concentrations. The optimization of the oxidation process was conducted taking into account the factors which may directly affect the MnP catalytic cycle (the concentration of H(2)O(2) and malonic acid) and those that affect the mass transfer of anthracene between the organic and the aqueous phase (solvent and agitation speed). The main objective was carried out in terms of improved efficiency, i.e., maximizing the anthracene oxidized per unit of enzyme used. The TPPB reached nearly complete oxidation of anthracene at a conversion rate of 1.8mgl(-1)h(-1) in 56h, which suggests the application of enzymatic TPPBs for the removal of poorly soluble compounds.

Enzymatic degradation of anthracene, dibenzothiophene and pyrene by manganese peroxidase in media containing acetone

The high hydrophobicity of polycyclic aromatic hydrocarbons (PAHs) greatly hamper their degradation in liquid media. The use of an organic solvent can assist the degradative action of ligninolytic enzymes from white rot fungi. The enzymatic action of the enzyme manganese peroxidase (MnP) in media containing a miscible organic solvent, acetone (36% v/v), was evaluated as a feasible system for the in vitro degradation of three PAHs: anthracene, dibenzothiophene and pyrene. These compounds were degraded to a large extent after a short period of time (7, 24 and 24h, respectively), at conditions maximizing the MnP-oxidative system. The initial amount of enzyme present in the reaction medium was determinant for the kinetics of the process. The order of degradability, in terms of degradation rates was as follows: anthracene>dibenzothiophene>pyrene. The intermediate compounds were determined using gas chromatography-mass spectrometry and the degradation mechanisms were proposed. Anthracene was degraded to phthalic acid. A ring cleavage product of the oxidation of dibenzothiophene, 4-methoxybenzoic acid, was also observed.

Effect of Modified Fenton’s Reaction on Microbial Activity and Removal of PAHs in Creosote Oil Contaminated Soil

This study describes the removal of polycyclic aromatic hydrocarbons (PAHs) from creosote oil contaminated soil by modified Fenton's reaction in laboratory-scale column experiments and subsequent aerobic biodegradation of PAHs by indigenous bacteria during incubation of the soil. The effect of hydrogen peroxide addition for 4 and 10 days and saturation of soil with H(2)O(2) on was studied. In both experiments the H(2)O(2) dosage was 0.4 g H(2)O(2)/g soil. In completely H(2)O(2)-saturated soil the removal of PAHs (44% within 4 days) by modified Fenton reaction was uniform over the entire soil column. In non-uniformly saturated soil, PAH removal was higher in completely saturated soil (52% in 10 days) compared to partially saturated soil, with only 25% in 10 days. The effect of the modified Fenton's reaction on the microbial activity in the soil was assessed based on toxicity tests towards Vibrio fischeri, enumeration of viable and dead cells, microbial extracellular enzyme activity, and oxygen consumption and carbon dioxide production during soil incubation. During the laboratory-scale column experiments, the toxicity of column leachate towards Vibrio fischeri increased as a result of the modified Fenton's reaction. The activities of the microbial extracellular enzymes acetate- and acidic phosphomono-esterase were lower in the incubated modified Fenton's treated soil compared to extracellular enzyme activities in untreated soil. Abundance of viable cells was lower in incubated modified Fenton treated soil than in untreated soil. Incubation of soil in serum bottles at 20 degrees C resulted in consumption of oxygen and formation of carbon dioxide, indicating aerobic biodegradation of organic compounds. In untreated soil 20-30% of the PAHs were biodegraded during 2 months of incubation. Incubation of chemically treated soil slightly increased PAH-removal compared to PAH-removal in untreated soil.

Biodegradation of benzo[a]pyrene in soil by Mucor sp. SF06 and Bacillus sp. SB02 co-immobilized on vermiculite

Two indigenous microorganisms, Bacillus sp. SB02 and Mucor sp. SF06, capable of degrading polycyclic aromatic hydrocarbons (PAHs) were co-immobilized on vermiculite by physical adsorption and used to degrade benzo[a] pyrene (BaP). The characteristics of BaP degradation by both free and co-immobilized microorganism were then investigated and compared. The removal rate using the immobilized bacterial-fungal mixed consortium was higher than that of the freely mobile mixed consortium. 95.3% of BaP was degraded using the co-immobilized system within 42 d, which was remarkably higher than the removal rate of that by the free strains. The optimal amount of inoculated co-immobilized system for BaP degradation was 2%. The immobilized bacterial-fungal mixed consortium also showed better water stability than the free strains. Kinetics of BaP biodegradation by co-immobilized SF06 and SB02 were also studied. The results demonstrated that BaP degradation could be well described by a zero-order reaction rate equation when the initial BaP concentration was in the range of 10-200 mg/kg. The scanning electronic microscope (SEM) analysis showed that the co-immobilized microstructure was suitable for the growth of SF06 and SB02. The mass transmission process of co-immobilized system in soil is discussed. The results demonstrate the potential for employing the bacterial-fungal mixed consortium, co-immobilized on vermiculite, for in situ bioremediation of BaP.

Impact of microbial activity on copper, lead and nickel mobilization during the bioremediation of soil PAHs

A fungal bioremediation method using P. frequentans removed up to 75% of phenanthrene with the addition of water and nutrients over a period of 30 d. During the bioremediation process, changes in metal behavior were monitored by an in situ technique (diffusive gradients in thin-films, DGT) and by soil solution chemistry. DGT provided absolute data on fluxes from the solid phase to the DGT device and relative trends of concentrations of the most labile metal species. DGT response indicated that bioremediation increases metal mobilization from the solid phase. Filtration provided data on the concentrations of solution phase (<0.45 microm) metal. In all case, metal fluxes and concentrations significantly increased after the bioremediation process began. Fluxes increased from <0.1 pg cm(-2)s(-1) before bioremediation to between 0.2 and 0.5 pg cm(-2)s(-1) after bioremediation. Metal concentrations in the soils solution (filtration at 0.45 microm) increased from 2 to 10 microg l(-1) (Cu), 1-4 microgl(-1) (Pb) and from 40 to 140 microg l(-1) (Ni) after bioremediation. Although over a short time period, these data strongly indicated that there was remobilization of metal from solid to solution (and thus to the DGT device) directly due to the bioremediation process. Although the mechanism was not unambiguously identified, it was shown not to be related to small changes in bulk pH over time and was attributed to the microbial action on the surface of the soil solid phase, releasing metal into solution. Additionally, differences in metal concentration and flux were observed in sterilized and non-sterilized soils and in the absence or presence of phenanthrene. The results indicated that the bioremediation of soil by P. frequentans increased the flux, lability and mobility of trace metal species and therefore the likely metal bioavailability to plants.

Isolation and characterization of a white rot fungus Bjerkandera sp. strain capable of oxidizing phenanthrene

Strain BOL13 was selected from 18 fungal strains isolated from an oil-spill contaminated site in Oruro, Bolivia. It was identified as a basidiomycete with high homology to Bjerkandera. The fungus degraded 100 mg phenanthrene l(-1) at 0.17 mg l(-1) d(-1) at 30 degrees C at pH 7. During phenanthrene degradation, a maximum manganese peroxidase activity of 100-120 U l(-1) was measured after 10 days of incubation. The ability of Bjerkandera sp. to produce lignin-modifying enzymes and to oxidize phenanthrene under various pH and temperature conditions was confirmed.

Polycyclic aromatic hydrocarbon biodegradation in extracellular fluids and static batch cultures of selected sub-tropical white rot fungi

Four sub-tropical white rot fungi, Trametes versicolor, Trametes pocas, Trametes cingulata and isolate DSPM95 were studied alongside the well studied white rot fungus, Phanerochaete chrysosporium, for their ability to remove polycyclic aromatic hydrocarbons (PAHs) from culture media. Both static shallow cultures and extracellular fluids were studied using media contaminated with a defined mixture of the PAHs; fluorene, phenanthrene, anthracene, pyrene and benzo(a)anthracene. With all isolates, the total loss of the parent compound in 31 days was high for fluorene, at +60%, phenanthrene at +40% and anthracene at +42%. Biotransformation of pyrene and benzo(a)anthracene by all the isolates was low, with the highest reduction of pyrene of 15.2% and benzo(a)anthracene of 15.8% being achieved with P. chrysosporium. Disappearance of the more condensed PAHs, pyrene and benzo(a)anthracene, increased in shallow static cultures with the addition of glucose and glucose oxidase as a source of additional H2O2. The addition of Mn2+ and ABTS (2,2-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid)) to culture supernatants was associated with higher levels of biotransformation. Comparison of the isolates T. versicolor, T. pocas, T. cingulata and isolate DSPM95 with P. chrysosporium showed that these strains were competitive in the reduction of the PAHs, reducing the PAHs by more or less the same magnitude. Also these sub-tropical isolates did not accumulate a lot of HPLC detectable metabolites as much as P. chrysosporium.