Distribution patterns of selected PAHs in bulk peat and corresponding humic acids from a Swiss ombrotrophic bog profile

An ombrotrophic peat core was collected in 2005 from Etang de la Gruère, Jura Mountains, Switzerland. The concentrations of nine among the U.S. Environmental Protection Agency priority polycyclic aromatic hydrocarbons (PAHs) (i.e., acenaphthene, phenanthrene, fluorene, pyrene, fluoranthene, benzo[jbk]fluoranthene, benzo[a]pyrene, benzo[ghi]perylene, and indeno[1,2,3-cd]pyrene) were determined in both bulk peat and corresponding humic acids (HA) samples by gas chromatography equipped with a mass spectrometry detector (GC-MS). The maximum PAHs concentrations in peat (around 1,250 μg Σ PAHs kg^?1 dry matter) were found at 28–30 cm of depth, which correspond to ca. 1920–1930, when coal inputs to Switzerland reached their maximum level. Amongst the nine PAHs analyzed in the peat samples, pyrene (Pyr) was the predominant species, accounting for ca. 20–100% of the total PAHs throughout the profile. In the HA fraction, that represents 24.7% (average value) of the bulk peat, only phenanthrene (Phe), and sporadically Pyr and fluoranthene (Fth), were detected. In particular, HA showed Phe concentrations that were ten–150 times higher than corresponding bulk peat samples, thus suggesting its preservation against biodegradation due to the incorporation into HA molecules.     

Polynuclear Aromatic Hydrocarbons (PAHs) in fish from the Red Sea Coast of Yemen

A detailed analytical study using combined normal phase high pressure liquid chromatography (HPLC), gas chromatography (GC) and gas chromatography/mass spectrometry (GC/MS) of Polynuclear Aromatic Hydrocarbons (PAHs) in fish from the Red Sea was undertaken. This investigation involves a preliminary assessment of the sixteen parent compounds issued by the U.S. Environmental Protection Agency(EPA). The study revealed measurable levels of Σ PAHs (the sum of three to five or six ring parent compounds) (49.2 ng g⁻¹ dry weight) and total PAHs (all PAH detected) (422.1 ng g⁻¹ dry weight) in edible muscle of fishes collected from the Red Sea. These concentrations are within the range of values reported for other comparable regions of the world. Mean concentrations for individual parent PAH in fish muscles were; naphthalene 19.5, biphenyl 4.6, acenaphthylene 1.0, acenaphthene 1.2, fluorene 5.5, phenanthrene 14.0, anthracene 0.8, fluoranthene 1.5, pyrene 1.8, benz(a)anthracene 0.4, chrysene 1.9, benzo(b)fluoranthene 0.5, benzo(k)fluoranthene 0.5, benzo(e)pyrene 0.9, benzo(a)pyrene 0.5, perylene 0.2, and indeno(1,2,3-cd)pyrene 0.1 ng g⁻¹ dry weight respectively. The Red Sea fish extracts exhibit the low molecular weight aromatics as well as the discernible alkyl-substituted species of naphthalene, fluorene, phenanthrene and dibenzothiophene. Thus, it was suggested that the most probable source of PAHs is oil contamination originating from spillages and/or heavy ship traffic. It was concluded that the presence of PAHs in the fish muscles is not responsible for the reported fish kill phenomenon. However, the high concentrations of carcinogenic chrysene encountered in these fishes should be considered seriously as it is hazardous to human health. Based on fish consumption by Yemeni‘s population it was calculated that the daily intake of total carcinogens were 0.15 μg/person/day. This revised version was published online in August 2006 with corrections to the Cover Date.     

Seasonal Biotransformation of Naphthalene, Phenanthrene, and Benzo[a]pyrene in Surficial Estuarine Sediments

Transformation rates of naphthalene, phenanthrene, and benzo[a]pyrene in oxidized surficial sediments of a polluted urban estuary, Boston Harbor, Mass., were determined over a period of 15 months. Three sites characterized by muddy sediments were selected to represent a >300-fold range of ambient polycyclic aromatic hydrocarbon (PAH) concentration. Transformation rates were determined by a trace-level radiolabel PAH assay which accounted for PAH mineralization, the formation of polar metabolites, residue, and recovered parental PAHs in sediment slurries. Transformation rates of the model PAHs increased with increasing ambient PAH concentrations. However, turnover times for a given PAH were similar at all sites. The turnover times were as follows: naphthalene, 13.2 to 20.1 days; phenanthrene, 7.9 to 19.8 days, and benzo[a]pyrene, 53.7 to 82.3 days. At specific sites, rates were significantly affected by salinity, occasionally affected by temperature, but not affected by pH over the course of the study. Seasonal patterns of mineralization were observed for each of the PAHs at all sites. The timing of seasonal maxima of PAH mineralization varied from site to site. Seasonal potential heterotrophic activities as measured by acetate and glutamate mineralization rates did not always coincide with PAH mineralization maxima and minima, suggesting that the two processes are uncoupled in estuarine sediments.     

Isolation and identification of a yeast strain capable of degrading four and five ring aromatic hydrocarbons

A yeast strain AEH was isolated from oil contaminated soil and identified by analysis of 18S and 26S ribosomal DNA sequences asPichia anomala. Strain AEH was capable of degrading naphthalene, phenanthrene and chrysene, singly, and benzo(a)pyrene in combination. The yeast degraded 5.36 mg naphthalene l^?1 within 2 days, and 5.04 mg phenanthrene l^?1 and 1.54 mg chrysene 1^?1 within 10 days. When a mixture of the four polycyclic aromatic hydrocarbons (PAHs) was treated at a concentration between 2.98 mg l^?1 and 6.89 mg l^?1, degradation rates were delayed for naphthalene and phenanthrene (3.79 mg l^?1 and, 4.20 mg l^?1 within 10 days, respectively), but enhanced for chrysene and benzo(a)pyrene (3.37 mg l^?1 and, 1.91 mg l^?1 within 10 days, respectively). In a binary system, all of the other 3 PAHs could be utilized as the carbon source for the cometabolic degradation of benzo(a)pyrene with naphthale ne as the best one.     

Ca2+ Promoted the Low Transformation Efficiency of Plasmid DNA Exposed to PAH Contaminants

The effects of interactions between genetic materials and polycyclic aromatic hydrocarbons (PAHs) on gene expression in the extracellular environment remain to be elucidated and little information is currently available on the effect of ionic strength on the transformation of plasmid DNA exposed to PAHs. Phenanthrene and pyrene were used as representative PAHs to evaluate the transformation of plasmid DNA after PAH exposure and to determine the role of Ca²⁺ during the transformation. Plasmid DNA exposed to the test PAHs demonstrated low transformation efficiency. In the absence of PAHs, the transformation efficiency was 4.7 log units; however, the efficiency decreased to 3.72–3.14 log units with phenanthrene/pyrene exposures of 50 µg·L^–1. The addition of Ca²⁺ enhanced the low transformation efficiency of DNA exposed to PAHs. Based on the co-sorption of Ca²⁺ and phenanthrene/pyrene by DNA, we employed Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and mass spectrometry (MS) to determine the mechanisms involved in PAH-induced DNA transformation. The observed low transformation efficiency of DNA exposed to either phenanthrene or pyrene can be attributed to a broken hydrogen bond in the double helix caused by planar PAHs. Added Ca²⁺ formed strong electrovalent bonds with “–POO^––” groups in the DNA, weakening the interaction between PAHs and DNA based on weak molecular forces. This decreased the damage of PAHs to hydrogen bonds in double-stranded DNA by isolating DNA molecules from PAHs and consequently enhanced the transformation efficiency of DNA exposed to PAH contaminants. The findings provide insight into the effects of anthropogenic trace PAHs on DNA transfer in natural environments.     

Microbial degradation of high and low molecular weight polyaromatic hydrocarbons in a two-phase partitioning bioreactor by two strains of Sphingomonas sp.

A mixture of six polyaromatic hydrocarbons (naphthalene, phenanthrene, fluoranthene, pyrene, chyrysene and benzo[a]pyrene), varying in size from 2 to 5 rings, was dissolved in dodecane, and used as the delivery phase of a partitioning bioreactor. Two species of Sphingomonas were then used individually, and as a consortium, to determine which of the PAHs were degraded. Only low molecular weight PAHs (naphthalene, phenanthrene and fluoranthene) were degraded by the individual strains, but the consortium degraded all substrates either to completion or near completion.     

Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil

Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p < 0.001) increases in the abundance of the GP PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial community in soil. The current study provides information on the response of soil bacterial, archaeal and fungal communities during the degradation of three priority pollutants and contributes to a knowledge base that can inform the development of effective bioremediation strategies for contaminated sites.     

Genome-to-function characterization of novel fungal P450 monooxygenases oxidizing polycyclic aromatic hydrocarbons (PAHs)

Fungi, particularly the white rot basidiomycetes, have an extraordinary capability to degrade and/or mineralize (to CO₂) the recalcitrant fused-ring high molecular weight (?4 aromatic-rings) polycyclic aromatic hydrocarbons (HMW PAHs). Despite over 30 years of research demonstrating involvement of P450 monooxygenation reactions in fungal metabolism of HMW PAHs, specific P450 monooxygenases responsible for oxidation of these compounds are not yet known. Here we report the first comprehensive identification and functional characterization of P450 monooxygenases capable of oxidizing different ring-size PAHs in the model white rot fungus Phanerochaete chrysosporium using a successful genome-to-function strategy. In a genome-wide P450 microarray screen, we identified six PAH-responsive P450 genes (Pc-pah1-Pc-pah6) inducible by PAHs of varying ring size, namely naphthalene, phenanthrene, pyrene, and benzo(a)pyrene (BaP). Using a co-expression strategy, cDNAs of the six Pc-Pah P450s were cloned and expressed in Pichia pastoris in conjunction with the homologous P450 oxidoreductase (Pc-POR). Each of the six recombinant P450 monooxygenases showed PAH-oxidizing activity albeit with varying substrate specificity towards PAHs (3-5 rings). All six P450s oxidized pyrene (4-ring) into two monohydroxylated products. Pc-Pah1 and Pc-Pah3 oxidized BaP (5-ring) to 3-hydroxyBaP whereas Pc-Pah4 and Pc-Pah6 oxidized phenanthrene (3-ring) to 3-, 4-, and 9-phenanthrol. These PAH-oxidizing P450s (493-547 aa) are structurally diverse and novel considering their low overall homology (12-23%) to mammalian counterparts. To our knowledge, this is the first report on specific fungal P450 monooxygenases with catalytic activity toward environmentally persistent and highly toxic HMW PAHs.     

Effects of Crude Oil Exposure on Bioaccumulation of Polycyclic Aromatic Hydrocarbons and Survival of Adult and Larval Stages of Gelatinous Zooplankton

Gelatinous zooplankton play an important role in marine food webs both as major consumers of metazooplankton and as prey of apex predators (e.g., tuna, sunfish, sea turtles). However, little is known about the effects of crude oil spills on these important components of planktonic communities. We determined the effects of Louisiana light sweet crude oil exposure on survival and bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) in adult stages of the scyphozoans Pelagia noctiluca and Aurelia aurita and the ctenophore Mnemiopsis leidyi, and on survival of ephyra larvae of A. aurita and cydippid larvae of M. leidyi, in the laboratory. Adult P. noctiluca showed 100% mortality at oil concentration ≥20 µL L⁻¹ after 16 h. In contrast, low or non-lethal effects were observed on adult stages of A. aurita and M. leidyi exposed at oil concentration ≤25 µL L⁻¹ after 6 days. Survival of ephyra and cydippid larva decreased with increasing crude oil concentration and exposition time. The median lethal concentration (LC₅₀) for ephyra larvae ranged from 14.41 to 0.15 µL L⁻¹ after 1 and 3 days, respectively. LC₅₀ for cydippid larvae ranged from 14.52 to 8.94 µL L⁻¹ after 3 and 6 days, respectively. We observed selective bioaccumulation of chrysene, phenanthrene and pyrene in A. aurita and chrysene, pyrene, benzo[a]pyrene, benzo[b]fluoranthene, benzo[k]fluoranthene, and benzo[a]anthracene in M. leidyi. Overall, our results indicate that (1) A. aurita and M. leidyi adults had a high tolerance to crude oil exposure compared to other zooplankton, whereas P. noctiluca was highly sensitive to crude oil, (2) larval stages of gelatinous zooplankton were more sensitive to crude oil than adult stages, and (3) some of the most toxic PAHs of crude oil can be bioaccumulated in gelatinous zooplankton and potentially be transferred up the food web and contaminate apex predators.     

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.     

Simultaneous Biodegradation of Polyaromatic Hydrocarbons by a <Emphasis Type="Italic">Stenotrophomonas</Emphasis> sp: Characterization of <Emphasis Type="Italic">nid</Emphasis> Genes and Effect of Surfactants on Degradation

A polyaromatic hydrocarbon degrading bacterium was isolated from a petroleum contaminated site and designated as Stenotrophomonas sp. strain IITR87. It was found to utilize pyrene, phenanthrene and benzo(a)pyrene as sole carbon source, but not anthracene, chrysene and fluoranthene. Gas chromatography and mass spectroscopy analysis resulted in identification of pyrene metabolites namely monohydroxypyrene, 4-oxa-pyrene-5-one, dimethoxypyrene and monohydroxyphenanthrene. Southern hybridization using naphthalene dioxygenase gene (nidA) as probe against the DNA of strain IITR87 revealed the presence of nidA gene. PCR analysis suggests dispersed occurrence of nid genes in the genome instead of a cluster as reported in a PAH-degrading Mycobacterium vanbaalenii PYR-1. The nid genes in strain IITR87, dioxygenase large subunit (nidA), naphthalene dioxygenase small subunit (nidB) and aldehyde dehydrogenase gene (nidD) showed more than 97 % identity to the reported nid genes from Mycobacterium vanbaalenii PYR-1. Most significantly, the biodegradation of PAHs was enhanced 25–60 % in the presence of surfactants rhamnolipid and Triton X-100 due to increased solubilization and bioavailability. These results could be useful for the improved biodegradation of high-molecular-weight PAHs in contaminated habitats.     

Aryl hydrocarbon receptor-mediated activity of mutagenic polycyclic aromatic hydrocarbons determined using in vitro reporter gene assay

Activation of aryl hydrocarbon receptor (AhR) by 30 polycyclic aromatic hydrocarbons (PAHs) was determined in the chemical-activated luciferase expression (CALUX) assay, using two exposure times (6 and 24h), in order to reflect the metabolization of PAHs. AhR-inducing potencies of PAHs were expressed as induction equivalency factors (IEFs) relative to benzo[a]pyrene and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). In 24h exposure assay, the highest IEFs were found for benzo[k]fluoranthene, dibenzo[a,h]anthracene and dibenzo[a,k]fluoranthene (approximately three orders of magnitude lower than TCDD) followed by dibenzo[a,j]anthracene, benzo[j]fluoranthene, indeno[1,2,3-cd]pyrene, and naphtho[2,3-a]pyrene. The 6h exposure to PAHs led to a significantly higher AhR-mediated activity than the 24h exposure (generally by two orders of magnitude), probably due to the high rate of PAH metabolism. The strongest AhR inducers showed IEFs approaching that of TCDD. Several PAHs, including some strong mutagens, such as dibenzo[a,l]pyrene, cyclopenta[cd]pyrene, and benzo[a]perylene, elicited only partial agonist activity. Calculation of IEFs based on EC25 values and/or 6h exposure data is suggested as an alternative approach to estimation of toxic potencies of PAHs with high metabolic rates and/or the weak AhR agonists. The IEFs, together with the recently reported relative mutagenic potencies of PAHs [Mutat. Res. 371 (1996) 123; Mutat. Res. 446 (1999) 1] were combined with data on concentrations of PAHs in extracts of model environmental samples (river sediments) to calculate AhR-mediated induction equivalents and mutagenic equivalents. The highest AhR-mediated induction equivalents were found for benzo[k]fluoranthene and benzo[j]fluoranthene, followed by indeno[1,2,3-cd]pyrene, dibenzo[a,h]anthracene, benzo[a]pyrene, dibenzo[a,j]anthracene, chrysene, and benzo[b]fluoranthene. High mutagenic equivalents in the river sediments were found for benzo[a]pyrene, dibenzo[a,e]pyrene, and naphtho[2,3-a]pyrene and to a lesser extent also for benzo[a]anthracene, benzo[b]fluoranthene, indeno[1,2,3-cd]pyrene, benzo[j]fluoranthene, dibenzo[a,e]fluoranthene and dibenzo[a,i]pyrene. These data illustrate that AhR-mediated activity of PAHs, including the highly mutagenic compounds, occurring in the environment but not routinely monitored, could significantly contribute to their adverse effects.     

Isolation and Characterization of a Mycobacterium Species Capable of Degrading Three- and Four-Ring Aromatic and Aliphatic Hydrocarbons

Mycobacterium sp. strain CH1 was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated freshwater sediments and identified by analysis of 16S rDNA sequences. Strain CH1 was capable of mineralizing three- and four-ring PAHs including phenanthrene, pyrene, and fluoranthene. In addition, strain CH1 could utilize phenanthrene or pyrene as a sole carbon and energy source. A lag phase of at least 3 days was observed during pyrene mineralization. This lag phase decreased to less than 1 day when strain CH1 was grown in the presence of phenanthrene or fluoranthene. Strain CH1 also was capable of using a wide range of alkanes as sole carbon and energy sources. No DNA hybridization was detected with the nahAc gene probe, indicating that enzymes involved in PAH metabolism are not related to the well-characterized naphthalene dioxygenase gene. DNA hybridization was not detected when the alkB gene from Pseudomonas oleovorans was used under high-stringency conditions. However, there was slight but detectable hybridization under low-stringency conditions. This suggests a distant relationship between genes involved in alkane oxidation.     

Conversion of polycyclic aromatic hydrocarbons by <Emphasis Type="Italic">Sphingomonas</Emphasis> sp. VKM B-2434

A versatile bacterial strain able to convert polycyclic aromatic hydrocarbons (PAHs) was isolated, and a conversion by the isolate of both individual substances and PAH mixtures was investigated. The strain belonged to the Sphingomonas genus as determined on the basis of 16S rRNA analysis and was designated as VKM B-2434. The strain used naphthalene, acenaphthene, phenanthrene, anthracene and fluoranthene as a sole source of carbon and energy, and cometabolically oxidized fluorene, pyrene, benz[a]anthracene, chrysene and benzo[a]pyrene. Acenaphthene and fluoranthene were degraded by the strain via naphthalene-1,8-dicarboxylic acid and 3-hydroxyphthalic acid. Conversion of most other PAHs was confined to the cleavage of only one aromatic ring. The major oxidation products of naphthalene, phenanthrene, anthracene, chrysene, and benzo[a]pyrene were identified as salicylic acid, 1-hydroxy-2-naphthoic acid, 3-hydroxy-2-naphthoic acid, o-hydroxyphenanthroic acid and o-hydroxypyrenoic acid, respectively. Fluorene and pyrene were oxidized mainly to hydroxyfluorenone and dihydroxydihydropyrene, respectively. Oxidation of phenanthrene and anthracene to the corresponding hydroxynaphthoic acids occurred quantitatively. The strain converted phenanthrene, anthracene, fluoranthene and carbazole of coal-tar-pitch extract.     

Succession of Phenotypic, Genotypic, and Metabolic Community Characteristics during In Vitro Bioslurry Treatment of Polycyclic Aromatic Hydrocarbon-Contaminated Sediments

Dredged harbor sediment contaminated with polycyclic aromatic hydrocarbons (PAHs) was removed from the Milwaukee Confined Disposal Facility and examined for in situ biodegradative capacity. Molecular techniques were used to determine the successional characteristics of the indigenous microbiota during a 4-month bioslurry evaluation. Ester-linked phospholipid fatty acids (PLFA), multiplex PCR of targeted genes, and radiorespirometry techniques were used to define in situ microbial phenotypic, genotypic, and metabolic responses, respectively. Soxhlet extractions revealed a loss in total PAH concentrations of 52%. Individual PAHs showed reductions as great as 75% (i.e., acenapthene and fluorene). Rates of ¹⁴C-PAH mineralization (percent/day) were greatest for phenanthrene, followed by pyrene and then chrysene. There was no mineralization capacity for benzo[a]pyrene. Ester-linked phospholipid fatty acid analysis revealed a threefold increase in total microbial biomass and a dynamic microbial community composition that showed a strong correlation with observed changes in the PAH chemistry (canonical r² of 0.999). Nucleic acid analyses showed copies of genes encoding PAH-degrading enzymes (extradiol dioxygenases, hydroxylases, and meta-cleavage enzymes) to increase by as much as 4 orders of magnitude. Shifts in gene copy numbers showed strong correlations with shifts in specific subsets of the extant microbial community. Specifically, declines in the concentrations of three-ring PAH moieties (i.e., phenanthrene) correlated with PLFA indicative of certain gram-negative bacteria (i.e., Rhodococcus spp. and/or actinomycetes) and genes encoding for naphthalene-, biphenyl-, and catechol-2,3-dioxygenase degradative enzymes. The results of this study suggest that the intrinsic biodegradative potential of an environmental site can be derived from the polyphasic characterization of the in situ microbial community.     

Differential repair of polycyclic aromatic hydrocarbon DNA adducts from an actively transcribed gene

Polycyclic aromatic hydrocarbons (PAHs) are carcinogens with varying potencies. These compounds are metabolized to diol epoxides that react to form DNA adducts. Nucleotide excision repair is a critical cellular defense against these bulky DNA adducts which, if not repaired, can lead to mutations and the initiation of cancer. The structural features of the PAH-adducts play a role in differential repair of these adducts by the global genomic repair subpathway of nucleotide excision repair. DNA adducts derived from the PAHs containing bay-regions are repaired more rapidly than adducts derived from PAHs containing fjord-regions. We have employed the host cell reactivation assay to examine the rate of repair of these adducts in an actively transcribing gene. The pGL3 plasmid containing a luciferase gene was damaged with diol epoxides of benzo[a]pyrene (B[a]P-DE), dibenzo[a,l]pyrene (DB[a,l]P-DE), benzo[g]chrysene (B[g]Ch-DE), and benzo[c]phenanthrene (B[c]Ph-DE). The plasmids were transfected into B-lymphocytes with normal repair capacity as well as lymphocytes derived from patients with the XP-A, XP-C and CS-B syndromes. We found that XPA cells were able to transcribe slowly past B[g]Ch-adducts but not the other PAHs. Using the amount of luciferase produced as a measure of DNA repair, we found that the relative rates of repair in the actively transcribing luciferase gene was B[a]P-DE > DB[a,l]P-DE, B[g]Ch-DE, >B[c]Ph-DE in repair proficient and XP-C cells. These results indicate that the abilities to transcribe past and to repair the PAH adducts are dependent on different structural features of the DNA adducts.     

Colonization on Root Surface by a Phenanthrene-Degrading Endophytic Bacterium and Its Application for Reducing Plant Phenanthrene Contamination

A phenanthrene-degrading endophytic bacterium, Pn2, was isolated from Alopecurus aequalis Sobol grown in soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Based on morphology, physiological characteristics and the 16S rRNA gene sequence, it was identified as Massilia sp. Strain Pn2 could degrade more than 95% of the phenanthrene (150 mg·L⁻¹) in a minimal salts medium (MSM) within 48 hours at an initial pH of 7.0 and a temperature of 30°C. Pn2 could grow well on the MSM plates with a series of other PAHs, including naphthalene, acenaphthene, anthracene and pyrene, and degrade them to different degrees. Pn2 could also colonize the root surface of ryegrass (Lolium multiflorum Lam), invade its internal root tissues and translocate into the plant shoot. When treated with the endophyte Pn2 under hydroponic growth conditions with 2 mg·L⁻¹ of phenanthrene in the Hoagland solution, the phenanthrene concentrations in ryegrass roots and shoots were reduced by 54% and 57%, respectively, compared with the endophyte-free treatment. Strain Pn2 could be a novel and useful bacterial resource for eliminating plant PAH contamination in polluted environments by degrading the PAHs inside plants. Furthermore, we provide new perspectives on the control of the plant uptake of PAHs via endophytic bacteria.     

Pleiotropic and Epistatic Behavior of a Ring-Hydroxylating Oxygenase System in the Polycyclic Aromatic Hydrocarbon Metabolic Network from Mycobacterium vanbaalenii PYR-1

Despite the considerable knowledge of bacterial high-molecular-weight (HMW) polycyclic aromatic hydrocarbon (PAH) metabolism, the key enzyme(s) and its pleiotropic and epistatic behavior(s) responsible for low-molecular-weight (LMW) PAHs in HMW PAH-metabolic networks remain poorly understood. In this study, a phenotype-based strategy, coupled with a spray plate method, selected a Mycobacterium vanbaalenii PYR-1 mutant (6G11) that degrades HMW PAHs but not LMW PAHs. Sequence analysis determined that the mutant was defective in pdoA2, encoding an aromatic ring-hydroxylating oxygenase (RHO). A series of metabolic comparisons using high-performance liquid chromatography (HPLC) analysis revealed that the mutant had a lower rate of degradation of fluorene, anthracene, and pyrene. Unlike the wild type, the mutant did not produce a color change in culture media containing fluorene, phenanthrene, and fluoranthene. An Escherichia coli expression experiment confirmed the ability of the Pdo system to oxidize biphenyl, the LMW PAHs naphthalene, phenanthrene, anthracene, and fluorene, and the HMW PAHs pyrene, fluoranthene, and benzo[a]pyrene, with the highest enzymatic activity directed toward three-ring PAHs. Structure analysis and PAH substrate docking simulations of the Pdo substrate-binding pocket rationalized the experimentally observed metabolic versatility on a molecular scale. Using information obtained in this study and from previous work, we constructed an RHO-centric functional map, allowing pleiotropic and epistatic enzymatic explanation of PAH metabolism. Taking the findings together, the Pdo system is an RHO system with the pleiotropic responsibility of LMW PAH-centric hydroxylation, and its epistatic functional contribution is also crucial for the metabolic quality and quantity of the PAH-MN.