Biodegradation, bioaccessibility, and genotoxicity of diffuse polycyclic aromatic hydrocarbon (PAH) pollution at a motorway site

Bacterial communities of the Black Sea exhibit activity against persistent organic pollutants in the water column and sediments

The ability of bacteria to degrade organic pollutants influences their fate in the environment, impact on the other biota and accumulation in the food web. The aim of this study was to evaluate abundance and expression activity of the catabolic genes targeting widespread pollutants, such as polyaromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and hexachloro-cyclohexane (HCH) in the Black Sea water column and sediments. Concentrations of PAHs, PCBs and HCH were determined by gas chromatography (GC) coupled to mass spectrometry (MS) and electron capture (ECD) detectors. bphA1, PAH-RHDα, nahAc, linA and linB that encode biphenyl 2,3 dioxygenase, α-subunits of ring hydroxylating dioxygenases, naphthalene dioxygenase, dehydrochlorinase and halidohydrolase correspondently were quantified by quantitative PCR. More recalcitrant PAHs, PCBs and HCH tended to accumulate in the Black Sea environments. In water samples, 3- and 4-ringed PAHs outnumbered naphthalene, while PAHs with > 4 rings prevailed in the sediments. Congeners with 4-8 chlorines with ortho-position of the substituents were the most abundant among the PCBs. β-HCH was determined at highest concentration in water samples, and total amount of HCH exceeded its legacy Environmental Quality Standard value. bphA1, was the most numerous gene in water layers (105 copies/mL) and sediments (105 copies/mg), followed by linB and PAH-RHDα genes (103 copies/mL; 105 copies/mg). The least abundant genes were linA (103 copies/mL; 104 copies/mg) and nahAc (102 copies/mL; 104 copies/mg). The most widely distributed gene bphА1 was one of the least expressed (10-3-10-2 copies/mL; 10-1 copies/mg). The most actively expressed genes were linB (101-102 copies/mL; 103 copies/mg), PAH-RHDα (101 copies/mL; 102 copies/mg) and linA (10-1-100 copies/mL; 100 copies/mg). Interaction of bacteria with PAHs, PCBs and HCH is evidenced by high copy numbers of the catabolic genes that initiate their degradation. More persistent compounds, such as high-molecular weight PAHs or β-HCH are accumulating in the Black Sea water and sediments, albeit microbial activity is directed against them.

Roads with underlying tar asphalt - spreading, bioavailability and toxicity of their polycyclic aromatic hydrocarbons

Some of the older Swedish roads contain road tar underneath a surface layer of bituminous asphalt. This road tar, also known as tar asphalt, contains large amounts of polycyclic aromatic hydrocarbons (PAHs). There is concern about PAHs spreading from the bottom layers of these older roads to the surrounding environment, and that because of this spreading road tar asphalt should not be recycled but rather placed in landfills. However, a risk assessment of PAH spreading below roads has not yet been conducted. The first aim of this study was to assess this potential spreading of PAHs from underlying tar asphalt to the sand beneath, the soil next to the roads, as well as nearby groundwater. The second aim was to measure the bioavailability and estimate the toxicity of PAHs in all relevant media using polyoxymethylene (POM) passive samplers. Four road sections and nearby groundwater in northern Sweden were investigated, including a control road without tar asphalt. PAHs were detected in all analysed solid media at varying concentrations: in asphalt from 2.3 to 4800 mg kg^-1, in underlying sand from <1.5 to 460 mg kg^-1 and in slope soil from <1.5 to 36 mg kg^-1. However, the spread of PAHs from the asphalt to roadside soil and groundwater was very limited. Groundwater at most of the road sections contained very low or non-detectable levels of PAHs (<0.08-0.53 μg L^-1, excluding one site where fuel contamination is hypothesized). The PAHs generally showed low bioavailability. Only asphalt with PAH content >1200 mg kg^-1 exhibited bioavailable concentrations that exceeded threshold concentrations for serious risk. The most PAH contaminated sand and soil samples exhibited low toxicity when considering bioavailability, only in some cases exceeding chronic toxicity threshold concentrations. These results were compared with the Swedish EPA's guideline values for PAH in contaminated soil, which is shown to overpredict toxicity for these sites. Further research on the leaching and transportation processes of PAHs from subsurface tar asphalt is recommended for developing risk analysis approaches.

Analysis of interdomain taxonomic patterns in urban street mats

Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well-being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co-occurrences analysis confirmed contrasting non-random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.

Characterization of a Dibenzofuran-degrading strain of Pseudomonas aeruginosa, FA-HZ1

Dibenzofuran (DBF) derivatives have caused serious environmental problems, especially those produced by paper pulp bleaching and incineration processes. Prominent for its resilient mutagenicity and toxicity, DBF poses a major challenge to human health. In the present study, a new strain of Pseudomonas aeruginosa, FA-HZ1, with high DBF-degrading activity was isolated and identified. The determined optimum conditions for cell growth of strain FA-HZ1 were a temperature of 30 °C, pH 5.0, rotation rate of 200 rpm and 0.1 mM DBF as a carbon source. The biochemical and physiological features as well as usage of different carbon sources by FA-HZ1 were studied. The new strain was positive for arginine double hydrolase, gelatinase and citric acid, while it was negative for urease and lysine decarboxylase. It could utilize citric acid as its sole carbon source, but was negative for indole and H₂S production. Intermediates of DBF 1,2-dihydroxy-1,2-dihydrodibenzofuran, 1,2-dihydroxydibenzofuran, 2-hydroxy-4-(3'-oxo-3'H-benzofuran-2'-yliden)but-2-enoic acid, 2,3-dihydroxybenzofuran, 2-oxo-2-(2'-hydrophenyl)lactic acid, and 2-hydroxy-2-(2'-hydroxyphenyl)acetic acid were detected and identified through liquid chromatography-mass analyses. FA-HZ1 metabolizes DBF by both the angular and lateral dioxygenation pathways. The genomic study identified 158 genes that were involved in the catabolism of aromatic compounds. To identify the key genes responsible for DBF degradation, a proteomic study was performed. A total of 1459 proteins were identified in strain FA-HZ1, of which 100 were up-regulated and 104 were down-regulated. A novel enzyme "HZ6359 dioxygenase", was amplified and expressed in pET-28a in E. coli BL21(DE3). The recombinant plasmid was successfully constructed, and was used for further experiments to verify its function. In addition, the strain FA-HZ1 can also degrade halogenated analogues such as 2, 8-dibromo dibenzofuran and 4-(4-bromophenyl) dibenzofuran. Undoubtedly, the isolation and characterization of new strain and the designed pathways is significant, as it could lead to the development of cost-effective and alternative remediation strategies. The degradation pathway of DBF by P. aeruginosa FA-HZ1 is a promising tool of biotechnological and environmental significance.

Sedimentary organic biomarkers suggest detrimental effects of PAHs on estuarine microbial biomass during the 20th century in San Francisco Bay, CA, USA

Hydrocarbon contaminants are ubiquitous in urban aquatic ecosystems, and the ability of some microbial strains to degrade certain polycyclic aromatic hydrocarbons (PAHs) is well established. However, detrimental effects of petroleum hydrocarbon contamination on nondegrader microbial populations and photosynthetic organisms have not often been considered. In the current study, fatty acid methyl ester (FAME) biomarkers in the sediment record were used to assess historical impacts of petroleum contamination on microbial and/or algal biomass in South San Francisco Bay, CA, USA. Profiles of saturated, branched, and monounsaturated fatty acids had similar concentrations and patterns downcore. Total PAHs in a sediment core were on average greater than 20× higher above ∼200 cm than below, which corresponds roughly to the year 1900. Isomer ratios were consistent with a predominant petroleum combustion source for PAHs. Several individual PAHs exceeded sediment quality screening values. Negative correlations between petroleum contaminants and microbial and algal biomarkers - along with high trans/cis ratios of unsaturated FA, and principle component analysis of the PAH and fatty acid records - suggest a negative impacts of petroleum contamination, appearing early in the 20th century, on microbial and/or algal ecology at the site.

Traceability of polychlorinated dibenzo-dioxins/furans pollutants in soil and their ecotoxicological effects on genetics, functions and composition of bacterial community

Dioxins (PCDD/Fs) are persistent organic pollutants. Their accumulation in soil is a crucial step in their transmission through the ecosystem. Traceability of dioxin in soil was evaluated in four sites A, B, C and D considered as potential industrial PCDD/Fs sources in Syria. Our results showed that the highest pollution with dioxin (⩾50 ppt) was found in site C (vicinity of Homs refinery). In parallel, analysis of physicochemical proprieties and bacterial density of soil samples were carried out. Bacterial density differed significantly among samples between 68×10(4) and 64×10(6) CFU g(-1)DW. Analysis of 16S rRNA encoding sequences showed that the genus Bacillus was the most abundant (74.7%) in all samples, followed by the genera Arthrobacter and Klebsiella with 5.2% and 4.7%, respectively. The genera Microbacterium, Pantoea, Pseudomonas, Enterobacter and Exiguobacterium formed between 2.1% and 2.6%. Cellulomonas, Kocuria, Lysinibacillus, Staphylococcus and Streptomyces were in a minority (0.5-1%). The bacterial richness and biodiversity, estimated by DMg and H' index, were highest in the heavily polluted site. Molecular screening for angular dioxygenase (AD α-subunit) and the cytochrome P450 (CYPBM3) genes, led to identification of 41 strains as AD-positive and 31 strains as CYPBM3-positive. RT-real-time PCR analysis showed a significant abundance of AD α-subunit transcript in the heavily dioxin-polluted soils, while the expression of CYPBM3 was highest in the moderately polluted soils. Our results illustrate the microbial diversity and functionality in soil exposed to dioxin pollution. Identification of dioxin-degrading bacteria from polluted sites should allow bioremediation to be carried out.

The prediction of PAHs bioavailability in soils using chemical methods: state of the art and future challenges

The evaluation of the available fraction of hydrophobic organic contaminants (HOCs) is extremely important for assessing their risk to the environment and human health. This available fraction, which can be solubilized and/or easily extracted, is believed to be the most accessible for bioaccumulation, biosorption and/or transformation by organisms. Based on this, two main types of chemical methods have been developed, closely related to the concepts of bioaccessibility and freely available concentrations: non-exhaustive extractions and biomimetic methods. Since bioavailability is species and compound specific, this work focused only in one of the most widespread group of HOCs in soils: polycyclic aromatic hydrocarbons (PAHs). This study aims at producing a state of the art knowledge base on bioavailability and chemical availability of PAHs in soils, clarifying which chemical methods can provide a better prediction of an organism exposure, and which are the most promising ones. Therefore, a review of the processes involved on PAHs availability to microorganisms, earthworms and plants was performed and the outputs given by the different chemical methods were evaluated. The suitability of chemical methods to predict bioavailability of the 16 US EPA PAHs in dissimilar naturally contaminated soils was not yet demonstrated, being especially difficult for high molecular weight compounds. Even though the potential to predict microbial mineralization using non-exhaustive extractions is promising, it will be very difficult to achieve for earthworms and plants, due to the complexity of accumulation mechanisms which are not taken into account by chemical methods. Yet, the existing models could be improved by determining compound, species and site specific parameters. Moreover, chemical availability can be very useful to understand the bioavailability processes and the behavior of PAHs in soils. The inclusion of chemical methods on risk assessment has been suggested and it is promising, despite some methods overpredict risks.

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.

Monitoring of soil and groundwater contamination following a pipeline explosion and petroleum product spillage in Ijegun, Lagos Nigeria

In May 2008, an accidental damage of a Nigerian National Petroleum Corporation (NNPC) pipeline occurred in Ijegun area of Lagos, Nigeria, resulting in oil spillage and consequent contamination of the environment. The residual concentration of the total hydrocarbon (THC) and benzene, toluene, ethylbenzene, and xylene (BTEX) in the groundwater and soil was therefore investigated between March 2009 and July 2010. Results showed elevated THC mean levels in groundwater which were above the World Health Organization maximum admissible value of 0.1 mg/l. THC values as high as 757.97 mg/l in groundwater and 402.52 mg/l in soil were observed in March 2009. Pronounced seasonal variation in the concentration of THC in groundwater and soil samples show that there was significant (P < 0.05) difference in the measured concentration of THC between each season (dry and wet), with the highest being in the dry season and between the years 2009 and 2010. Significant hydrocarbon contamination, 500 m beyond the explosion site and 25 months after the incident, was observed revealing the extent of the spillage of petroleum products. The highest concentrations of 16.65 μg/l (benzene), 2.08 μg/l (toluene), and 4864.79 μg/l (xylene) were found in stations within the 100 m buffer zone. Most of the samples of groundwater taken were above the target value of 0.2 μg/l set for BTEX compounds by the Environmental Guidelines and Standards for Petroleum Industry in Nigeria. The level of hydrocarbon in the impacted area calls for concern and remediation of the area is urgently needed to reduce further negative impact on the ecosystem.

Impact of different land uses on polycyclic aromatic hydrocarbon contamination in coastal stream sediments

PAHs are ubiquitous environmental pollutants that can cause adverse health and ecological effects. In the present study, we examined the impact of land use on the concentration and composition of PAHs in 28 coastal stream sediments on the Island of Oahu, Hawaii. In densely populated urban areas, the concentration range of total PAHs in the stream sediments affected by mixed residential and industrial activities (RI) are 0.40-9.05 ppm, which is significantly higher than the 0.36-4.21 ppm detected in the stream sediments affected predominantly by urban residential land uses (UR). The stream sediments affected by agricultural activities (AG) reported a concentration range of 0.09-2.14 ppm, which is lower than those of the RI and UR stream sediments. The molecular weight of PAH is a factor, as only high molecular weight (HMW) PAHs were significantly affected by land uses (ANOVA P=0.009). Correlation analysis showed that only in the UR stream sediments were significant correlations observed between PAH concentration and two anthropogenic indicators: population density (r=0.57, P=0.027) and vehicle density (r=0.55, P=0.034). The fractional concentrations of PAHs were analyzed by using PCA analysis, which led to the separate clustering of the RI and AG stream sediments and suggest distinct PAH sources between the two land uses. Two PAH source indicators, including Ant/(Ant+Phe) and Fl/(Fl+Py), indicates that PAHs sources in the RI stream sediments are most likely of petroleum origin, while PAHs in the UR and AG stream sediments most likely came from combustion activities. In addition, the concentration and relative potency of carcinogenic PAHs in the coastal stream sediments exhibited similar patterns as the total PAH concentration with respect to land uses.

Impact of black carbon originated from fly ash and soot on the toxicity of pentachlorophenol in sediment

The widely existing fly ash and soot produced during the process of combustion, which are often known as waste but also an important source of black carbon (BC) in the environment, were treated by HCl and HF solution for this study, and recorded as FC and SC, respectively. A series of experiments were carried out to investigate the toxicity of pentachlorophenol (PCP) in sediment, influence of various BCs in sediment with different contents (0%, 0.5%, 1%, 2%, 5% and 10%) on the extractability and toxicity of PCP (50mg/kg), and toxicity of various BC in sediment. The results demonstrated that the PCP exposure to wheat seed exhibited a dose-dependent behavior, and the extractability and toxicity of PCP decreased with the increasing content of BC in sediment. The PCP extractable rate was significantly (P<0.01) influenced by the higher content of BCs. Noticeably, each BC had no toxic but stimulative effect on root elongation and early seedling growth. Furthermore, it was found that the inhibitive effect on the extractability and toxicity of PCP and the stimulative effect on root elongation and early seedling growth caused by SC were more evident than FC.

Quantification of centimeter-scale spatial variation in PAH, glucose and benzoic acid mineralization and soil organic matter in road-side soil

The aim of the study was to determine centimeter-scale spatial variation in mineralization potential in diffusely polluted soil. To this end we employed a 96-well microplate method to measure the mineralization of 14C-labeled organic compounds in deep-well microplates and thereby compile mineralization curves for 348 soil samples of 0.2-cm3. Centimeter-scale spatial variation in organic matter and the mineralization of glucose, benzoic acid, and PAHs (phenanthrene and pyrene) was determined for urban road-side soil sampled as arrays (7×11cm) of 96 subsamples. The spatial variation in mineralization was visualized by means of 2-D contour maps and quantified by means of semivariograms. The geostatistical analysis showed that the easily degradable compounds (glucose and benzoic acid) exhibited little spatial variation in mineralization potential, whereas the mineralization was highly heterogeneous for the PAH compounds that require specialized degraders. The spatial heterogeneity should be taken into account when estimating natural attenuation rates.

Pyrene biodegradation in an industrial soil exposed to simulated rhizodeposition: how does it affect functional microbial abundance?

Rhizodeposition is an important biogeochemical process for the phytoremediation of contaminated substrates. This study investigated the effects of various rhizodeposition components from celery (Apium graveolens) on pyrene biodegradation and microbial abundance in a long-term contaminated soil. Batch microcosms simulating in situ contaminated soil were amended with lipophilic extract, water-soluble extract, or debris from celery root to mimic plant rhizodeposition within 70 days. Soil was intermittently analyzed for pyrene concentration and target gene abundance estimated by real-time PCR. Lipophilic extract was the major simulated rhizodeposit enhancing pyrene biodegradation, while water-soluble extract stimulated microbial growth most efficiently. The relative abundance of total polycyclic aromatic hydrocarbon (PAH) degraders was enhanced by lipophilic extract but inhibited by the other two rhizodeposits, indicating that these components exerted different selective pressures on PAH degrader community. Moreover, PAH catabolic pathway may involve in the pollutant detoxification and fatty acid metabolism by microorganisms, which were also affected by rhizodeposition. These results provide insights into plant-microbe interactions responsible for PAH biodegradation and offer opportunities to facilitate PAH phytoremediation in industrial sites.

New metabolites in dibenzofuran cometabolic degradation by a biphenyl-cultivated Pseudomonas putida strain B6-2

A biphenyl (BP)-utilizing bacterium, designated B6-2, was isolated from soil and identified as Pseudomonas putida. BP-grown B6-2 cells were capable of transforming dibenzofuran (DBF) via a lateral dioxygenation and meta-cleavage pathway. The ring cleavage product 2-hydroxy-4-(3'-oxo-3'H-benzofuran-2'-yliden)but-2-enoic acid (HOBB) was detected as a major metabolite. B6-2 growing cells could also cometabolically degrade DBF using BP as a primary substrate. A recombinant Escherichia coli strain DH10B (pUC118bphABC) expressing BP dioxygenase, BP-dihydrodiol dehydrogenase, and dihydroxybiphenyl dioxygenase was shown to be capable of transforming DBF to HOBB. Using purified HOBB that was produced by the recombinant as the substrate for B6-2, we newly identified a series of benzofuran derivatives as metabolites. The structures of these metabolites indicate that an unreported HOBB degradation pathway is employed by strain B6-2. In this pathway, HOBB is proposed to be transformed to 2-oxo-4-(3'-oxobenzofuran-2'-yl)butanoic acid and 2-hydroxy-4-(3'-oxobenzofuran-2'-yl)butanoic acid (D4) through two sequential double-bond hydrogenation steps. D4 is suggested to undergo reactions including decarboxylation and oxidation to produce 3-(3'-oxobenzofuran-2'-yl)propanoic acid (D6). 3-Hydroxy-3-(3'-oxobenzofuran-2'-yl)propanoic acid (D7) and 2-(3'-oxobenzofuran-2'-yl)acetic acid (D8) would represent metabolites involved in the processes of beta- and alpha-oxidation of D6, respectively. D7 and D8 are suggested to be transformed to their respective products 3-hydroxy-2,3-dihydrobenzofuran-2-carboxylic acid (D10) and 2-(3'-hydroxy-2',3'-dihydrobenzofuran-2'-yl)acetic acid. D10 is proposed to be transformed to salicylic acid (D14) via 2,3-dihydro-2,3-dihydroxybenzofuran, 2-oxo-2-(2'-hydroxyphenyl)acetic acid and 2-hydroxy-2-(2'-hydroxyphenyl)acetic acid. Further experimental results revealed that B6-2 was capable of growing with D14 as the sole carbon source. Because benzofuran derivatives may have biological, pharmacological, and toxic properties, the elucidation of this new pathway should be significant from both biotechnological and environmental views.

Novel alkane hydroxylase gene (alkB) diversity in sediments associated with hydrocarbon seeps in the Timor Sea, Australia

Hydrocarbon seeps provide inputs of petroleum hydrocarbons to widespread areas of the Timor Sea. Alkanes constitute the largest proportion of chemical components found in crude oils, and therefore genes involved in the biodegradation of these compounds may act as bioindicators for this ecosystem's response to seepage. To assess alkane biodegradation potential, the diversity and distribution of alkane hydroxylase (alkB) genes in sediments of the Timor Sea were studied. Deduced AlkB protein sequences derived from clone libraries identified sequences only distantly related to previously identified AlkB sequences, suggesting that the Timor Sea maybe a rich reservoir for novel alkane hydroxylase enzymes. Most sequences clustered with AlkB sequences previously identified from marine Gammaproteobacteria though protein sequence identities averaged only 73% (with a range of 60% to 94% sequence identities). AlkB sequence diversity was lower in deep water (>400 m) samples off the continental slope than in shallow water (<100 m) samples on the continental shelf but not significantly different in response to levels of alkanes. Real-time PCR assays targeting Timor Sea alkB genes were designed and used to quantify alkB gene targets. No correlation was found between gene copy numbers and levels of hydrocarbons measured in sediments using sensitive gas chromatography-mass spectrometry techniques, probably due to the very low levels of hydrocarbons found in most sediment samples. Interestingly, however, copy numbers of alkB genes increased substantially in sediments exposed directly to active seepage even though only low or undetectable concentrations of hydrocarbons were measured in these sediments in complementary geochemical analyses due to efficient biodegradation.

Influence of vegetation on the in situ bacterial community and polycyclic aromatic hydrocarbon (PAH) degraders in aged PAH-contaminated or thermal-desorption-treated soil

The polycyclic aromatic hydrocarbon (PAH) contamination, bacterial community, and PAH-degrading bacteria were monitored in aged PAH-contaminated soil (Neuves-Maisons [NM] soil; with a mean of 1,915 mg of 16 PAHs.kg(-1) of soil dry weight) and in the same soil previously treated by thermal desorption (TD soil; with a mean of 106 mg of 16 PAHs.kg(-1) of soil dry weight). This study was conducted in situ for 2 years using experimental plots of the two soils. NM soil was colonized by spontaneous vegetation (NM-SV), planted with Medicago sativa (NM-Ms), or left as bare soil (NM-BS), and the TD soil was planted with Medicago sativa (TD-Ms). The bacterial community density, structure, and diversity were estimated by real-time PCR quantification of the 16S rRNA gene copy number, temporal thermal gradient gel electrophoresis fingerprinting, and band sequencing, respectively. The density of the bacterial community increased the first year during stabilization of the system and stayed constant in the NM soil, while it continued to increase in the TD soil during the second year. The bacterial community structure diverged among all the plot types after 2 years on site. In the NM-BS plots, the bacterial community was represented mainly by Betaproteobacteria and Gammaproteobacteria. The presence of vegetation (NM-SV and NM-Ms) in the NM soil favored the development of a wider range of bacterial phyla (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi) that, for the most part, were not closely related to known bacterial representatives. Moreover, under the influence of the same plant, the bacterial community that developed in the TD-Ms was represented by different bacterial species (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Actinobacteria) than that in the NM-Ms. During the 2 years of monitoring, the PAH concentration did not evolve significantly. The abundance of gram-negative (GN) and gram-positive (GP) PAH-degrading bacteria was estimated by real-time PCR quantification of specific functional genes encoding the alpha subunit of PAH-ring hydroxylating dioxygenase (PAH-RHD(alpha)). The percentage of the PAH-RHD(alpha) GN bacterial genes relative to 16S rRNA gene density decreased with time in all the plots. The GP PAH-RHD(alpha) bacterial gene proportion decreased in the NM-BS plots but stayed constant or increased under vegetation influence (NM-SV, NM-Ms, and TD-Ms).

Effects of native organic material and water on sorption properties of reference diesel soot

Soot has been considered as a potentially important sorbent for organic contaminants in soils, sediments, and aerosols. This paper demonstrates that native (authigenic) extractable organic material (EOM) and surface-covering water on soot may have a substantial influence on sorption properties of the soot. Sorption isotherms were determined for apolar and weakly polar sorbates (n-octane, cyclooctane, n-propylbenzene, naphthalene) from an aqueous solution to a standard reference material of diesel soot (SRM 2975) in the original state and after extraction with methanol. For all sorbates tested, removal of EOM from soot by methanol caused the sorption isotherms to be more nonlinear (decrease of Freundlich exponents by 0.19-0.25) compared to the untreated soot. The changes in the isotherms depend on both sorbate structure and sorbate concentration and can be accounted for by two opposing roles that EOM could have on the sorption properties of soot (i) enhancing the overall sorption by absorbing the sorbate into the EOM phase, and (ii) attenuating the sorbate adsorption to the soot carbon surface through sorption competition or site blockage. The n-alkane-to-cycloalkane sorption coefficient ratios (Kn/Kc) indicated that the removal of EOM altered the sorption mode for alkanes from absorption to adsorption. A comparison of the sorption isotherms measured in aqueous suspensions with the soot-air sorption coefficients reported for SRM 2975 in the literature showed that sorption to "soot in water" is significantly weaker than sorption to "soot in air", indicating that complete surface coverage with water suppresses the sorption by soot.

Human Health Risk Assessment Approach for Urban Park Development

A Human Health Risk Assessment (HHRA) was undertaken for a proposed park development "River Landing", to be constructed along the north bank of the South Saskatchewan River in the City of Saskatoon, Saskatchewan, Canada. The purpose of the HHRA was to determine whether chemical constituents identified at the site, including polycyclic aromatic hydrocarbons (PAHs), petroleum hydrocarbons (PHCs), and toxic and heavy metals, would adversely affect the health of construction workers and potential park users. Although more traditional remediation options were considered, the risk assessment approach was chosen since it represented the best available technology. The HHRA was undertaken using protocols and methodologies proposed and readily accepted by the Canadian Council of Ministers of the Environment (CCME), Health Canada, and the United States Environmental Protection Agency (US EPA). Results of the risk assessment revealed that the magnitude and distribution of the chemicals at the site were such that extensive remediation was not required, and that the site could be developed without any significant restrictions on the proposed use. The assessment revealed that potential exposure to soil constituents would not result in adverse health risk to construction workers involved in park development or future park users.

Impact of bioavailability restrictions on microbially induced stable isotope fractionation. 2. Experimental evidence

Stable isotope fractionation analysis (SIFA) of contaminants is an emerging technique to characterize in situ microbial activity. The kinetic isotope effect in microbial degradation reactions, or enzyme catalysis, is caused by the preferential cleavage of bonds containing light rather than heavy isotopes. This leads to a relative enrichment of the heavier isotopes in the residual substrate pool. However, a number of nonisotopically sensitive steps preceding the isotopically sensitive bond cleavage may affect the reaction kinetics of a degradation process, thus reducing the observed (i.e., the macroscopically detectable) isotope fractionation. Low bioavailability of contaminants poses kinetic limitations on the biodegradation process and can significantly reduce the observed kinetic isotope fractionation. Here we present experimental evidence for the influence of bioavailability-limited pollutant biodegradation on observed stable isotope fractionation. Batch laboratory experiments were performed to quantify the toluene hydrogen isotope fractionation of Pseudomonas putida mt-2 (pWWO) subjected to different small concentrations of toluene with and without deuterium label, which corresponded to realistic environmental mass transfer scenarios. Detected isotope fractionations depended significantly on the toluene concentration, hence confirming the influence of substrate mass transfer limitation on observed isotope fractionation, hypothesized by Thullner et al. (Environ. Sci. Technol. 2008, 42,6544-6551). Our results indicate that the bioavailability of a substrate should be considered during quantitative analysis of microbial degradation based on SIFA.

Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDalpha) genes from Gram positive and Gram negative bacteria in soil and sediment samples

Real-Time PCR based assays were developed to quantify Gram positive (GP) and Gram negative (GN) bacterial populations that are capable of degrading the polycyclic aromatic hydrocarbons (PAH) in soil and sediment samples with contrasting contamination levels. These specific and sensitive Real-Time PCR assays were based on the quantification of the copy number of the gene that encodes the alpha subunit of the PAH-ring hydroxylating dioxygenases (PAH-RHDalpha), involved in the initial step of the aerobic metabolism of PAH. The PAH-RHDalpha-GP primer set was designed against the different allele types present in the data base (narAa, phdA/pdoA2, nidA/pdoA1, nidA3/fadA1) common to the Gram positive PAH degraders such as Rhodococcus, Mycobacterium, Nocardioides and Terrabacter strains. The PAH-RHDalpha-GN primer set was designed against the genes (nahAc, nahA3, nagAc, ndoB, ndoC2, pahAc, pahA3, phnAc, phnA1, bphAc, bphA1, dntAc and arhA1) common to the Gram negative PAH degraders such as Pseudomonas, Ralstonia, Commamonas, Burkholderia, Sphingomonas, Alcaligenes, Polaromonas strains. The PCR clones for DNA extracted from soil and sediment samples using the designed primers showed 100% relatedness to the PAH-RHDalpha genes targeted. Deduced from highly sensitive Real-Time PCR quantification, the ratio of PAH-RHDalpha gene relative to the 16S rRNA gene copy number showed that the PAH-bacterial degraders could represent up to 1% of the total bacterial community in the PAH-contaminated sites. This ratio highlighted a positive correlation between the PAH-bacterial biodegradation potential and the PAH-contamination level in the environmental samples studied.

Diffuse PAH contamination of surface soils: environmental occurrence, bioavailability, and microbial degradation

The purpose of this review is to recognize the scientific and environmental importance of diffuse pollution with polycyclic aromatic hydrocarbons (PAHs). Diffuse PAH pollution of surface soil is characterized by large area extents, low PAH concentrations, and the lack of point sources. Urban and pristine topsoils receive a continuous input of pyrogenic PAHs, which induces a microbial potential for PAH degradation. The significance of this potential in relation to black carbon particles, PAH bioaccessibility, microbial PAH degradation, and the fate of diffuse PAHs in soil is discussed. Finally, the state-of-the-art methods for future investigations of the microbial degradation of diffuse PAH pollution are reviewed.

Strong impact on the polycyclic aromatic hydrocarbon (PAH)-degrading community of a PAH-polluted soil but marginal effect on PAH degradation when priming with bioremediated soil dominated by mycobacteria

Bioaugmentation of soil polluted with polycyclic aromatic hydrocarbons (PAHs) is often disappointing because of the low survival rate and low activity of the introduced degrader bacteria. We therefore investigated the possibility of priming PAH degradation in soil by adding 2% of bioremediated soil with a high capacity for PAH degradation. The culturable PAH-degrading community of the bioremediated primer soil was dominated by Mycobacterium spp. A microcosm containing pristine soil artificially polluted with PAHs and primed with bioremediated soil showed a fast, 100- to 1,000-fold increase in numbers of culturable phenanthrene-, pyrene-, and fluoranthene degraders and a 160-fold increase in copy numbers of the mycobacterial PAH dioxygenase gene pdo1. A nonpolluted microcosm primed with bioremediated soil showed a high rate of survival of the introduced degrader community during the 112 days of incubation. A nonprimed control microcosm containing pristine soil artificially polluted with PAHs showed only small increases in the numbers of culturable PAH degraders and no pdo1 genes. Initial PAH degradation rates were highest in the primed microcosm, but later, the degradation rates were comparable in primed and nonprimed soil. Thus, the proliferation and persistence of the introduced, soil-adapted degraders had only a marginal effect on PAH degradation. Given the small effect of priming with bioremediated soil and the likely presence of PAH degraders in almost all PAH-contaminated soils, it seems questionable to prime PAH-contaminated soil with bioremediated soil as a means of large-scale soil bioremediation.