Polycyclic aromatic hydrocarbon biodegradation rates: a structure-based study

Modeling sorption and biodegradation of phenanthrene in mangrove sediment slurry

A mathematical model, combining both sorption and biodegradation process, was developed to predict the biodegradation of phenanthrene by Sphingomonas sp. in different sediment slurries. The model includes two sorption parameters, α (the partition coefficient) and 1/K (the diffusion resistance); a kinetic parameter k (the first order rate constant); and a sediment parameter, A(V) (the specific sediment surface area in unit volume of slurry). These parameters were evaluated and verified in three types of sediment slurry systems (namely sandy clay loam Ho Chung sediment with fastest degradation, sandy Kei Ling Ha sediment with medium degradation, and clay Mai Po sediment with slowest degradation) at different initial phenanthrene concentrations. High R(2) values, ranging from 0.935 to 0.969, were obtained. Based on this integrated sorption-biodegradation model, the phenanthrene biodegradation in any sediment slurry could be predicted as long as the parameters of the specific sediment surface area in unit volume of slurry, total organic carbon and clay content were measured.

Effect of surfactant and oil additions in the biodegradation of hexane and toluene vapours in batch tests

The biological treatment of gaseous emissions of hydrophobic volatile organic compounds (VOCs) results in low rates of elimination partially because of the low solubility of VOCs in water. Recently, the use of two-phase partition bioreactors (TPPBs) was proposed to increase the bioavailability and consequently the elimination capacities of this kind of VOC. In the present study, TPPBs operating in a batch feed mode were tested for biodegradation of hexane and toluene vapours with a microbial consortium. The results obtained were compared with single-phase systems (control experiments). The liquid phase used was silicone oil (organic phase) with the surfactant Pluronic F-68. Experiments were named F1 and F2 for one and two phases, respectively, and F(1S) and F(2S) when the surfactant was included. The maximum specific rates (S(rates)) of hydrocarbon consumption for hexane and toluene were 539 and 773 mg(hydrocarbon)/(g(protein) x h), respectively. For both substrates, the systems that showed the highest S(rates) of hydrocarbon consumption were F2 and F(2S). In experiment F(1S) the surfactant Pluronic F-68 increased the solubility of hydrocarbons in the liquid phase, but did not increase the S(rates). The maximum percentages of mineralization were 51% and 72% for hexane and toluene, respectively. The results showed that simultaneous addition of silicone oil and surfactant favours the mineralization, but not the rate ofbiodegradation, of toluene and hexane vapours.

Evolution of bacterial community during bioremediation of PAHs in a coal tar contaminated soil

The monitoring of a windrow treatment applied to soil contaminated by mostly 2-, 3- and 4-ring PAHs produced by coal tar distillation was performed by following the evolution of both PAH concentration and the bacterial community. Total and PAH-degrading bacterial community structures were followed by 16S rRNA PCR-DGGE in parallel with quantification by bacterial counts and 16 PAH measurements. Six months of biological treatment led to a strong decrease in 2-, 3- and 4-ring PAH concentrations (98, 97 and 82% respectively). This result was associated with the activity of bacterial PAH-degraders belonging mainly to the Gamma-proteobacteria, in particular, the Enterobacteria and Pseudomonas genera, which were detected over the course of the treatment. This group was considered to be a good bioindicator to determine the potential PAH biodegradation of contaminated soil. Conversely, other species, like the Beta-proteobacteria, were detected after 3months, when 2-, 3- and 4-ring PAHs were almost completely degraded. Thus, presence of the Beta-proteobacteria group could be considered a good candidate indicator to estimate the endpoint of biotreatment of this type of PAH-contaminated soil.

Evaluation of bioaugmentation with entrapped degrading cells as a soil remediation technology

Soil augmentation with microbial degraders immobilized on carriers is evaluated as a potential remediation technology using a mathematical model that includes degradation within spatially distributed carriers and diffusion or advection-dispersion as contaminant mass transfer mechanisms. The total volume of carriers is a critical parameter affecting biodegradation performance. In the absence of advection, 320 and 20 000 days are required to mineralize 90% of the herbicide linuron by Variovorax sp. SRS16 encapsulated in 2 mm beads with 5 and 20 mm spacings, respectively. Given that many pesticide degraders have low intrinsic degradation rates and that only limited carrier to soil volume ratios are practically feasible, bioaugmented soils are characterized by low effective degradation rates and can be considered fully mixed. A simple exponential model is then sufficient to predict biodegradation as verified by comparisons with published experimental data. By contrast, the full spatially distributed model is needed to adequately model the degradation of faster degrading contaminants such as naphthalene and benzene which can be mass-transfer limited. Dimensionless Damköhler numbers are proposed to determine whether the spatially distributed model is required. Results show that field scale applications of immobilized degraders will be limited by the amount of carriers required to reach acceptable degradation rates.

Structure-based interpretation of biotransformation pathways of amide-containing compounds in sludge-seeded bioreactors

Partial microbial degradation of xenobiotic compounds in wastewater treatment plants (WWTPs) results in the formation of transformation products, which have been shown to be released and detectable in surface waters. Rule-based systems to predict the structures of microbial transformation products often fail to discriminate between alternate transformation pathways because structural influences on enzyme-catalyzed reactions in complex environmental systems are not well understood. The amide functional group is one such common substructure of xenobiotic compounds that may be transformed through alternate transformation pathways. The objective of this work was to generate a self-consistent set of biotransformation data for amide-containing compounds and to develop a metabolic logic that describes the preferred biotransformation pathways of these compounds as a function of structural and electronic descriptors. We generated transformation products of 30 amide-containing compounds in sludge-seeded bioreactors and identified them by means of HPLC-linear ion trap-orbitrap mass spectrometry. Observed biotransformation reactions included amide hydrolysis and N-dealkylation, hydroxylation, oxidation, ester hydrolysis, dehalogenation, nitro reduction, and glutathione conjugation. Structure-based interpretation of the results allowed for identification of preferences in biotransformation pathways of amides: primary amides hydrolyzed rapidly; secondary amides hydrolyzed at rates influenced by steric effects; tertiary amides were N-dealkylated unless specific structural moieties were present that supported other more readily enzyme-catalyzed reactions. The results allowed for the derivation of a metabolic logic that could be used to refine rule-based biotransformation pathway prediction systems to more specifically predict biotransformations of amide-containing compounds.

Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation.

Oxidation of PAHs in a simplified system using peroxy-acid and glass beads: Identification of oxidizing species

Polycyclic aromatic hydrocarbons (PAHs) are organic contaminants of concern due to their ubiquity, persistence in the natural environment and adverse health effects. Numerous studies have looked into the removal and treatment of these contaminants, with mixed results. High molecular weight PAHs have been particularly problematic due to their hydrophobicity and high affinity for organics, resulting in mass transfer limitations for even the fastest advanced oxidation processes (AOPs). The peroxy-acid process has been used to successfully treat PAH contaminated matrices. Experiments were conducted on benzo[a]pyrene contaminated glass beads in order to elucidate the reaction mechanisms responsible for the effectiveness of this process. For the first time peracetic acid (PAA) was identified as the important oxidant in this reaction. Different v/v/v ratios of hydrogen peroxide/acetic acid/DI water were studied which illustrated the importance of reaction ratio on oxidant concentration and rate of formation. Approximately 60% degradation of benzo[a]pyrene was achieved in 24 hours with 1.7% PAA. Observations of the reaction kinetics suggest that the slow desorption/dissolution of benzo[a]pyrene limits the efficiency of the peroxy-acid process. Modifications of the reaction setup supported this observation as treatment efficiencies increased with reactive surface area, and an increase in system agitation. These limitations were also overcome by increasing the concentration of PAA delivered to the contaminated matrix. Greater than 80% degradation of benzo[a]pyrene was achieved in 24 hours with approximately 9.2% PAA.

Bacterial communities from shoreline environments (costa da morte, northwestern Spain) affected by the prestige oil spill

The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution-affected areas with similar characteristics.

The influence of Sarcocornia fruticosa on retention of PAHs in salt marsh sediments (Sado estuary, Portugal)

Depth concentration profiles of PAHs, organic carbon and dissolved oxygen in non-colonised sediments and sediments colonised by Sarcocornia fruticosa from Mitrena salt marsh (Sado, Portugal) were determined in November 2004 and April 2005. Belowground biomass and PAH levels in below and aboveground material were also determined. In both periods, colonised sediments were oxygenated until 15-cm, rich in organic carbon (max 4.4%) and presented much higher PAH concentrations (max. 7.1 microg g(-1)) than non-colonised sediments (max. 0.55 microg g(-1)). Rooting sediments contained the highest PAH concentrations. The five- and six-ring compounds accounted to 50-75% of the total PAHs in colonised sediments, while only to 30% in non-colonised sediments. The elevated concentrations of PAHs in colonised sediments may be attributed to the transfer of dissolved PAH compounds towards the roots as plant uptake water and subsequent sequestration onto organically rich particles. A phase-partitioning mechanism probably explains the higher retention of the heavier PAHs. In addition oxygenated conditions of the rooting sediments favour the degradation of the lighter PAHs and explain the elevated proportion of the heavier compounds. Below and aboveground materials presented lower PAH concentrations (0.18-0.38 microg g(-1)) than colonised sediments. Only 3- and 4-PAHs were quantified in aboveground material, reflecting either preferential translocation of lighter compounds from roots or atmospheric deposition.

Multi-factors on biodegradation kinetics of polycyclic aromatic hydrocarbons (PAHs) by Sphingomonas sp. a bacterial strain isolated from mangrove sediment

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) in contaminated sediment is an attractive remediation technique and its success depends on biodegradation kinetics, and the optimal condition for the PAH-degrading isolates; however, information on this aspect is still scarce. The effects of multi-factors on biodegradation of phenanthrene, a 3-ring model PAH, in contaminated sediment slurry by Sphingomonas sp. a bacterial strain isolated from surface mangrove sediment, were investigated using the orthogonal experimental design (form L(16)(4(5))). The most significant factors were salinity and inoculum size, while the effects of phenanthrene concentrations, nutrient addition and temperatures were insignificant. The optimal biodegradation condition in contaminated mangrove sediment slurry was 30 degrees C, 15 ppt salinity, a carbon/nitrogen ratio of 100:1 (the background ratio in sediment) and an inoculum size of 10(6) most probable number g(-1) sediment. The phenanthrene biodegradation could be best described by the first order rate model, C=C(0)e(-kt), where k (the rate constant) is equaled to 0.1185, under the optimal condition. The kinetic model was verified and its validity in predicting biodegradation by Sphingomonas sp. at various phenanthrene concentrations was proved by experimental data.

Direct link between fluoranthene biodegradation and the mobility and sequestration of its residues during aging

The aim of this study was to assess the influence of the polycyclic aromatic hydrocarbons (PAH)-degrading activity in the fate of fluoranthene in soils. Three soil samples with different degrading activities (an industrial soil, the same industrial soil after biostimulation, and an agricultural soil) were spiked with 14C-fluoranthene and incubated for 6 mo with monitoring of biodegradation and mineralization. To follow the distribution of the 14C-fluoranthene residues (i.e., 14C-fluoranthene and its degradation products) among the soil compartments, we performed successively leaching, centrifugation (to collect intra-aggregate pore water), solvent extraction, and combustion of the soil columns. In the industrial soil, no mineralization of 14C-fluoranthene was observed, and only 3% of the initial 14C-activity was non-extractable (with acetone:dichloromethane) after 165 d of incubation. The biostimulation (addition of unlabeled polycyclic aromatic hydrocarbons) increased the degrading activity in this soil (59% of 14C-fluoranthene was mineralized) and increased the residues sequestration (13% of 14C-activity was non-extractable). The microflora of the agricultural soil mineralized 14C-fluoranthene more slowly and to a lesser extent (25%) than the biostimulated soil, but a higher amount of 14C-activity was sequestered (41%). Thus, the rate and extent of 14C-fluoranthene mineralization seemed to be related to the 14C-activity sequestration by controlling the accumulation of degradation products in the soil. 14C-Fluoranthene biodegradation enhanced the concentration of 14C-polar compounds in the intra-aggregate pore water. Our results point out the close link between fluoranthene biodegradation and two key aging processes, diffusion and sequestration, in soils. Biodegradation controls the mobility and sequestration of residues by transforming fluoranthene into more polar molecules that can diffuse into the intra-aggregate pore water and then might become bound to the matrix or entrapped in the microporosity.

Cyclodextrin enhanced biodegradation of polycyclic aromatic hydrocarbons and phenols in contaminated soil slurries

This work aimed to evaluate the relative contribution of soil catabolic activity, contaminant bioaccessibility, and nutrient levels on the biodegradation of field-aged polycyclic aromatic hydrocarbons and phenolic compounds in three municipal gas plant site soils. Extents of biodegradation achieved, in 6 week-long soil slurry assays, under the following conditions were compared: (i) with inoculation of catabolically active PAH and phenol-degrading microorganisms, (ii) with and without hydroxypropyl-beta-cyclodextrin supplementation (HPCD; 100 g L(-1)), and finally (iii) with the provision of additional inorganic nutrients in combination with HPCD. Results indicated no significant (p < 0.05) differences between biodegradation endpoints attained in treatments inoculated with catabolically active microorganisms as compared with the uninoculated control. Amendments with HPCD significantly (p < 0.05) lowered biodegradation endpoints for most PAHs and phenolic compounds. Only in one soil did the combination of HPCD and nutrients consistently achieve better bioremediation endpoints with respect to the HPCD-only treatments. Thus, for most compounds, biodegradation was not limited by the catabolic activity of the indigenous microorganisms but rather by processes resulting in limited availability of contaminants to degraders. It is therefore suggested that the bioremediation of PAH and phenol impacted soils could be enhanced through HPCD amendments. In addition, the biodegradability of in situ and spiked (deuterated analogues) PAHs following 120 days aging of the soils suggested that this contact time was not sufficient to obtain similar partitions to that observed for field-aged contaminants; with the spiked compounds being significantly (p < 0.05) more available for biodegradation.

Measurement of biodegradability parameters for single unsubstituted and methylated polycyclic aromatic hydrocarbons in liquid bacterial suspensions

Substrate depletion experiments were conducted to characterize aerobic biodegradation of 20 single polycyclic aromatic hydrocarbons (PAHs) by induced Sphingomonas paucimobilis strain EPA505 in liquid suspensions. PAHs consisted of low molecular weight, unsubstituted, and methyl-substituted homologs. A material balance equation containing the Andrews kinetic model, an extension of the Monod model accounting for substrate inhibition, was numerically fitted to batch depletion data to estimate extant kinetic parameters including the maximal specific uptake rates, q(max), the affinity coefficients, K(S), and the substrate inhibition coefficients, K(I). Strain EPA505 degraded all PAHs tested. Applied kinetic models adequately simulated experimental data. A cell proliferation assay involving reduction of the tetrazolium dye WST-1 was used to evaluate the ability of strain EPA505 to utilize individual PAHs as sole energy and carbon sources. Of the 22 PAHs tested, 9 supported bacterial growth. Evaluation of the biokinetic data showed that q(max) correlated highly with transmembrane flux as theoretically estimated by a diffusion model, pointing to transmembrane transport as a potential rate-determining process. The biodegradability data generated in this study is essential for the development of quantitative structure-activity relationships (QSARs) for biodegradability and for modeling biodegradation of simple PAH mixtures.

Electronic polarizability as a predictor of biodegradation rates of dimethylnaphthalenes. an ab initio and density functional theory study

Geometries, relative stabilities, electronic excited states, atomic charges, and electronic dipole polarizabilities of dimethylnaphthalene (DMN) isomers have been calculated in gas and aqueous phases by ab initio and DFT methods. At the highest levels of calculation, alpha,alpha-DMN (2,6-DMN, 2,7-DMN, and 2,3-DMN) are the lowest energy isomers, while 1,8-DMN is the less stable by 7-8 kcal mol(-1). The averaged electronic polarizability, <alpha>, is dependent on the position of the methyl substituents, increasing in the order alpha, alpha-DMN < (a, beta-DMN < beta, beta-DMN, with the largest values being obtained for 2,6-DMN and 2,7-DMN, while the lowest value is calculated for 1,8-DMN isomer. Polarizability differences among the isomers have been related to their spectroscopic properties. The computed <a> value of DMN isomers, with the notable exception of 2,7-DMN, is in excellent linear relationship with the observed first-order biomass-normalized rate coefficient, a parameter related to the rate of biodegradation of polycyclic aromatic hydrocarbons (PAHs). This result suggests that electronic polarizability may be a useful tool for prediction of biodegradation trends of series of compounds, and inductive and dispersive interactions play a fundamental role in the biodegradation process of DMNs. The present approach is potentially suitable for applications on PAHs with higher molecular weight.

Determining the identity and roles of oil-metabolizing marine bacteria from the Thames estuary, UK

Crude oil is a complex mixture of different hydrocarbons. While diverse bacterial communities can degrade oil, the specific roles of individual members within such communities remain unclear. To identify the key bacterial taxa involved in aerobic degradation of specific hydrocarbons, microcosm experiments were established using seawater from Stanford le Hope, Thames estuary, UK, adjacent to a major oil refinery. In all microcosms, hydrocarbon degradation was significant within 10 weeks, ranging from > 99% of low-molecular-weight alkanes (C(10)-C(18)), 41-84% of high-molecular-weight alkanes (C(20)-C(32)) and pristane, and 32-88% of polycyclic aromatic hydrocarbons (PAHs). Analysis of 16S rRNA sequences from clone libraries and denaturing gradient gel electrophoresis (DGGE) indicated that, except when incubated with fluorene, PAH-degrading communities were dominated by Cycloclasticus. Moreover, PAH-degrading communities were distinct from those in microcosms containing alkanes. Degradation of the branched alkane, pristane, was carried out almost exclusively by Alcanivorax. Bacteria related to Thalassolituus oleivorans (99-100% identity) were the dominant known alkane degraders in n-alkane (C(12)-C(32)) microcosms, while Roseobacter-related bacteria were also consistently found in these microcosms. However, in contrast to previous studies, Thalassolituus, rather than Alcanivorax, was dominant in crude oil-enriched microcosms. The communities in n-decane microcosms differed from those in microcosms supplemented with less volatile alkanes, with a phylogenetically distinct species of Thalassolituus out-competing T. oleivorans. These data suggest that the diversity and importance of the genus Thalassolituus is greater than previously established. Overall, these experiments demonstrate how degradation of different petroleum hydrocarbons is partitioned between different bacterial taxa, which together as a community can remediate petroleum hydrocarbon-impacted estuarine environments.

Degradation of carbazole and its derivatives by a Pseudomonas sp

Carbazole, carbazoles with monomethyl or dimethyls substituted on different positions (C(1)-carbazoles or C(2)-carbazoles), and benzocarbazoles, as toxic and mutagenic components of petroleum and creosote contamination, were biodegradable by an isolated bacterial strain Pseudomonas sp. XLDN4-9. C(1)-carbazoles were degraded in preference to carbazole and C(2)-carbazoles. The biodegradation of C(1)-carbazoles or C(2)-carbazoles was influenced by the positions of methyl substitutions. Among C(1)-carbazole isomers, 1-methyl carbazole was the most susceptible. C(2)-carbazole isomers with substitutions on the same benzo-nucleus were more susceptible at a concentration of less than 3.4 microg g(-1) petroleum, especially when harboring one substitution on position 1. In particular, 1,5-dimethyl carbazole was the most recalcitrant dimethyl isomer.

Comparative assessment of coal tars obtained from 10 former manufactured gas plant sites in the eastern United States

A comparative analysis was performed on eleven coal tars obtained from former manufactured gas plant sites in the eastern United States. Bulk properties analyzed included percent ash, Karl Fisher water content, viscosity and average molecular weight. Chemical properties included monocyclic- and polycyclic-aromatic hydrocarbon (PAH) concentrations, alkylated aromatic concentrations, and concentrations of aliphatic and aromatic fractions. It was found that there was at least an order-of-magnitude variation in all properties measured between the eleven coal tars. Additionally, two coal tars obtained from the same manufactured gas plant site had very different properties, highlighting that there can be wide variations in coal tar properties from different samples obtained from the same site. Similarities were also observed between the coal tars. The relative chemical distributions were similar for all coal tars, and the coal tars predominantly consisted of PAHs, with naphthalene being the single-most prevalent compound. The C(9-22) aromatic fraction, an indicator of all PAHs up to a molecular weight of approximately 276 gmole(-1), showed a strong power-law relationship with the coal tar average molecular weight (MW (ct)). And the concentrations of individual PAHs decreased linearly as MW (ct) increased up to ca. 1000 gmole(-1), above which they remained low and variable. Implications of these properties and their variation with MW (ct) on groundwater quality are discussed. Ultimately, while these similarities do allow generalities to be made about coal tars, the wide range of coal tar bulk and chemical properties reported here highlights the complex nature of coal tars.