Identification of metabolites from the degradation of fluoranthene by Mycobacterium sp. strain PYR-1

Determination of the metabolic pathways for degradation of naphthalene and pyrene in Amycolatopsis sp. Poz14

Polycyclic aromatic hydrocarbons (PAHs) constitute important soil contaminants derived from petroleum. Poz14 strain can degrade pyrene and naphthalene. Its genome presented 9333 genes, among them those required for PAHs degradation. By phylogenomic analysis, the strain might be assigned to Amycolatopsis nivea. The strain was grown in glucose, pyrene, and naphthalene to compare their proteomes; 180 proteins were detected in total, and 90 of them were exclusives for xenobiotic conditions. Functions enriched with the xenobiotics belonged to transcription, translation, modification of proteins and transport of inorganic ions. Enriched pathways were pentose phosphate, proteasome and RNA degradation; in contrast, in glucose were glycolysis/gluconeogenesis and glyoxylate cycle. Proteins proposed to participate in the upper PAHs degradation were multicomponent oxygenase complexes, Rieske oxygenases, and dioxygenases; in the lower pathways were ortho-cleavage of catechol, phenylacetate, phenylpropionate, benzoate, and anthranilate. The catechol dioxygenase activity was measured and found increased when the strain was grown in naphthalene. Amycolatopsis sp. Poz14 genome and proteome revealed the PAHs degradation pathways and functions helping to contend the effects of such process.

A review on the enzymes and metabolites identified by mass spectrometry from bacteria and microalgae involved in the degradation of high molecular weight PAHs

High molecular weight PAHs (HMW PAHs) are dangerous pollutants widely distributed in the environment. The use of microorganisms represents an important tool for HMW PAHs bioremediation, so, the understanding of their biochemical pathways facilitates the development of biodegradation strategies. For this reason, the potential role of species of microalgae, bacteria, and microalga-bacteria consortia in the degradation of HMW PAHs is discussed. The identification of their metabolites, mostly by GC-MS and LC-MS, allows a better approach to the enzymes involved in the key steps of the metabolic pathways of HMW PAHs biodegradation. So, this review intends to address the proteomic research on enzyme activities and their involvement in regulating essential biochemical functions that help bacteria and microalgae in the biodegradation processes of HMW PAHs. It is noteworthy that, given that to the best of our knowledge, this is the first review focused on the mass spectrometry identification of the HMW PAHs metabolites; whereby and due to the great concern of the presence of HMW PAHs in the environment, this material could help the urgency of developing new bioremediation methods. The elucidation of the metabolic pathways of persistent pollutant degrading microorganisms should lead to a better knowledge of the enzymes involved, which could contribute to a very ecological route to the control of environmental contamination in the future.

Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us?

Petroleum is the major energy matrix in the world whose refining generates chemical byproducts that may damage the environment. Among such waste, polycyclic aromatic hydrocarbons (PAH) are considered persistent pollutants. Sixteen of these are considered priority for remediation, and among them is benzo(a)pyrene. Amid remediation techniques, bioremediation stands out. The genus Burkholderia is amongst the microorganisms known for being capable of degrading persistent compounds; its strains are used as models to study such ability. High-throughput sequencing allows researchers to reach a wider knowledge about biodegradation by bacteria. Using transcripts and mRNA analysis, the genomic regions involved in this aptitude can be detected. To unravel these processes, we used the model B. vietnamiensis strain G4 in two experimental groups: one was exposed to benzo(a)pyrene and the other one (control) was not. Six transcriptomes were generated from each group aiming to compare gene expression and infer which genes are involved in degradation pathways. One hundred fifty-six genes were differentially expressed in the benzo(a)pyrene exposed group, from which 33% are involved in catalytic activity. Among these, the most significant genomic regions were phenylacetic acid degradation protein paaN, involved in the degradation of organic compounds to obtain energy; oxidoreductase FAD-binding subunit, related to the regulation of electrons within groups of dioxygenase enzymes with potential to cleave benzene rings; and dehydrogenase, described as accountable for phenol degradation. These data provide the basis for understanding the bioremediation of benzo(a)pyrene and the possible applications of this strain in polluted environments.

Preparation of dihydroxy polycyclic aromatic hydrocarbons and activities of two dioxygenases in the phenanthrene degradative pathway

Dihydroxy phenanthrene, fluoranthene, and pyrene derivatives are intermediates in the bacterial catabolism of the corresponding parent polycyclic aromatic hydrocarbon (PAH). Ring-opening of the dihydroxy species followed by a series of enzyme-catalyzed reactions generates metabolites that funnel into the Krebs Cycle with the eventual production of carbon dioxide and water. One complication in delineating these pathways and harnessing them for useful purposes is that the initial enzymatic processing produces multiple dihydroxy PAHs with multiple ring opening possibilities and products. As part of a systematic effort to address this issue, eight dihydroxy species were synthesized and characterized as the dimethoxy or diacetate derivatives. Several dihydroxy compounds were examined with two dioxygenases in the phenanthrene degradative pathway in Mycobacterium vanbaalenii PYR-1. One, 3,4-dihydroxyphenanthrene, was processed by PhdF with a k_cat/K_m of 6.0 × 10⁶ M^-1s^-1, a value that is consistent with the annotated function of PhdF in the pathway. PhdI processed 1-hydroxy-2-naphthoate with a k_cat/K_m of 3.1 × 10⁵ M^-1s^-1, which is also consistent with the proposed role in the pathway. The observations provide the first biochemical evidence for these two reactions in M. vanbaalenii PYR-1 and, to the best of our knowledge, the first biochemical evidence for the reaction of PhdF with 3,4-dihydroxyphenanthrene. Although PhdF is upregulated in the presence of pyrene, it did not process two dihydroxypyrenes. Methodology was developed for product analysis of the extradiol dioxygenases.

Identification of proteins induced by polycyclic aromatic hydrocarbon and proposal of the phenanthrene catabolic pathway in Amycolatopsis tucumanensis DSM 45259

In the present study the polycyclic aromatic hydrocarbon removal and metabolic adaptation of Amycolatopsis tucumanensis DSM 45259 were investigated. Analysis of one-dimensional gel electrophoresis of crude cell extracts revealed differential synthesis of proteins which were identified by MALDI-TOF. To elucidate the phenanthrene metabolic pathway in A. tucumanensis DSM45259, two-dimensional electrophoresis and detection of phenanthrene degradation intermediates by GS-MS were performed. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in the metabolism of aromatic compounds, oxidative stress response, energy production and protein synthesis. The obtained results allowed us to clarify the phenanthrene catabolic pathway, by confirming the roles of several proteins involved in the degradation process and comprehensive adaptation. This may clear the way for more efficient engineering of bacteria in the direction of more effective bioremediation applications.

Genome Sequence and Metabolic Analysis of a Fluoranthene-Degrading Strain Pseudomonas aeruginosa DN1

Pseudomonas aeruginosa DN1, isolated from petroleum-contaminated soil, showed excellent degradation ability toward diverse polycyclic aromatic hydrocarbons (PAHs). Many studies have been done to improve its degradation ability. However, the molecular mechanisms of PAHs degradation in DN1 strain are unclear. In this study, the whole genome of DN1 strain was sequenced and analyzed. Its genome contains 6,641,902 bp and encodes 6,684 putative open reading frames (ORFs), which has the largest genome in almost all the comparative Pseudomonas strains. Results of gene annotation showed that this strain harbored over 100 candidate genes involved in PAHs degradation, including those encoding 25 dioxygenases, four ring-hydroxylating dioxygenases, five ring-cleaving dioxygenases, and various catabolic enzymes, transcriptional regulators, and transporters in the degradation pathways. In addition, gene knockout experiments revealed that the disruption of some key PAHs degradation genes in DN1 strain, such as catA, pcaG, pcaH, and rhdA, did not completely inhibit fluoranthene degradation, even though their degradative rate reduced to some extent. Three intermediate metabolites, including 9-hydroxyfluorene, 1-acenaphthenone, and 1, 8-naphthalic anhydride, were identified as the dominating intermediates in presence of 50 μg/mL fluoranthene as the sole carbon source according to gas chromatography mass spectrometry analysis. Taken together, the genomic and metabolic analysis indicated that the fluoranthene degradation by DN1 strain was initiated by dioxygenation at the C-1, 2-, C-2, 3-, and C-7, 8- positions. These results provide new insights into the genomic plasticity and environmental adaptation of DN1 strain.

Structural Characterization of the Hydratase-Aldolases, NahE and PhdJ: Implications for the Specificity, Catalysis, and N-Acetylneuraminate Lyase Subgroup of the Aldolase Superfamily

NahE and PhdJ are bifunctional hydratase-aldolases in bacterial catabolic pathways for naphthalene and phenanthrene, respectively. Bacterial species with these pathways can use polycyclic aromatic hydrocarbons (PAHs) as sole sources of carbon and energy. Because of the harmful properties of PAHs and their widespread distribution and persistence in the environment, there is great interest in understanding these degradative pathways, including the mechanisms and specificities of the enzymes found in the pathways. This knowledge can be used to develop and optimize bioremediation techniques. Although hydratase-aldolases catalyze a major step in the PAH degradative pathways, their mechanisms are poorly understood. Sequence analysis identified NahE and PhdJ as members of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. Both have a conserved lysine and tyrosine (for Schiff base formation) as well as a GXXGE motif (to bind the pyruvoyl carboxylate group). Herein, we report the structures of NahE, PhdJ, and PhdJ covalently bound to substrate via a Schiff base. Structural analysis and dynamic light scattering experiments show that both enzymes are tetramers. A hydrophobic helix insert, present in the active sites of NahE and PhdJ, might differentiate them from other NAL subgroup members. The individual specificities of NahE and PhdJ are governed by Asn-281/Glu-285 and Ser-278/Asp-282, respectively. Finally, the PhdJ complex structure suggests a potential mechanism for hydration of substrate and subsequent retro-aldol fission. The combined findings fill a gap in our mechanistic understanding of these enzymes and their place in the NAL subgroup.

Comprehensive database of Manufactured Gas Plant tars. Part C. Heterocyclic and hydroxylated polycyclic aromatic hydrocarbons

RATIONALE

Coal tars are a mixture of organic and inorganic compounds that were by-products from the manufactured gas and coke making industries. The tar compositions varied depending on many factors such as the temperature of production and the type of retort used. For this reason a comprehensive database of the compounds found in different tar types is of value to understand both how their compositions differ and what potential chemical hazards are present. This study focuses on the heterocyclic and hydroxylated compounds present in a database produced from 16 different tars from five different production processes.

METHODS

Samples of coal tar were extracted using accelerated solvent extraction (ASE) and derivatized post-extraction using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS). The derivatized samples were analysed using two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GCxGC/TOFMS).

RESULTS

A total of 865 heterocyclic compounds and 359 hydroxylated polycyclic aromatic hydrocarbons (PAHs) were detected in 16 tar samples produced by five different processes. The contents of both heterocyclic and hydroxylated PAHs varied greatly with the production process used, with the heterocyclic compounds giving information about the feedstock used. Of the 359 hydroxylated PAHs detected the majority would not have been be detected without the use of derivatization.

CONCLUSIONS

Coal tars produced using different production processes and feedstocks yielded tars with significantly different heterocyclic and hydroxylated contents. The concentrations of the individual heterocyclic compounds varied greatly even within the different production processes and provided information about the feedstock used to produce the tars. The hydroxylated PAH content of the samples provided important analytical information that would otherwise not have been obtained without the use of derivatization and GCxGC/TOFMS.

Comprehensive composition of Creosote using comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC-TOFMS)

Creosote is a distillation product of coal tar and is widely used as wood preservative for railway sleepers, utility poles and for other applications. Creosote can have potentially negative effects on the environment and many of the components are toxic. This study presents the analysis of a Creosote sample from a former wood impregnation plant located in the UK. The sample was analysed using two dimensional gas chromatography time-of-flight mass spectrometry (GCxGC-TOFMS) and a database of compounds that could be detected was produced. The GCxGG-TOFMS was capable of detecting 1505 individual compounds, which is far more than previous estimates for the number of compounds present within Creosote. Post extraction derivatization using BTSFA with 1% TMCS was employed to increase the potential number of compounds detected with 255 derivatized compounds detected, 231 of which would not have been detected without prior derivatization. Selected derivatized compounds were quantified with limits of detection ranging from 0.6 mg/kg to 1.6 mg/kg from a concentrated dense non-aqueous phase liquid (DNAPL). This work presents the first published full analysis of a Creosote using GCxGC-TOFMS combined with derivatization.

Sensitivity of laccase activity to the fungicide tebuconazole in decomposing litter

The present study investigates the sensitivity of laccase activity to the fungicide tebuconazole (TBZ) in order to seek for new functional toxicity descriptors in aquatic microbial communities associated to decomposing litter. With this aim, we analyzed the sensitivity of laccase from the different microbial components (fungi and bacteria growing separately and in co-existence), as well as that of their corresponding enzyme fractions (cell bound and diffusible), forming microbial communities in Alnus glutinosa leaves. Results show that fungi are pivotal for laccase activity in leaves and that their activity is repressed when they co-exist with bacteria. The sensitivity of laccase activity to the TBZ was only detectable in leaves colonized by fungi separately (Alatospora acuminata populations), but absent in those colonized by bacteria separately and/or mixed fungi plus bacteria. Specifically, the increase of TBZ concentration enhances laccase activity in Alatospora acuminata populations but decreases ergosterol concentration as well as the amount of 18S RNA gene copies. This activity response suggests a detoxification mechanism employed by the fungus in order to reduce TBZ toxicity. Besides, enzyme fractioning showed that laccase activity in the cell bound fraction (76% of the total activity) was sensitive to the fungicide, but not that in the diffusible fraction (24% of total activity). Hence, TBZ would influence laccase activity in the presence of fungal cells but not in enzymes already synthesized in the extracellular space. The present study highlights the importance of the biological complexity level (i. e. population, community, ecosystem) when seeking for appropriate functional ecotoxicity descriptors in aquatic microbial communities.

Fluoranthene degradation and binding mechanism study based on the active-site structure of ring-hydroxylating dioxygenase in Microbacterium paraoxydans JPM1

In this study, a gram-positive fluoranthene-degrading bacterial strain was isolated from crude oil in Dagang Oilfield and identified as Microbacterium paraoxydans JPM1 by the analysis of 16S rDNA sequence. After 25 days of incubation, the strain JPM1 could degrade 91.78 % of the initial amount of fluoranthene. Moreover, four metabolites 9-fluorenone-1-carboxylic acid, 9-fluorenone, phthalic acid, and benzoic acid were detected in the culture solution. The gene sequence encoding the aromatic-ring-hydroxylating dioxygenase was amplified in the strain JPM1 by PCR. Based on the translated protein sequence, a homology modeling method was applied to build the crystal structure of dioxygenase. Subsequently, the interaction mechanism between fluoranthene and the active site of dioxygenase was simulated and analyzed by molecular docking. Consequently, a feasible degrading pathway of fluoranthene in the strain JPM1 was proposed based on the metabolites and the interaction analyses. Additionally, the thermodynamic analysis showed that the strain JPM1 had high tolerance for fluoranthene, and the influence of fluoranthene for the bacterial growth activity was negligible under 100 to 400 mg L^-1 concentrations. Taken together, this study indicates that the strain JPM1 has high potential for further study in bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sites.

Biodegradation of fluoranthene by a newly isolated strain of Bacillus stratosphericus from Mediterranean seawater of the Sfax fishing harbour, Tunisia

A physico-chemical characterization of seawater taken from the fishing harbour of Sfax, Tunisia, revealed a contamination by organic and inorganic micropollutants. An aerobic marine halotolerant Bacillus stratosphericus strain FLU5 was isolated after enrichment on fluoranthene, a persistent and toxic polycyclic aromatic hydrocarbon (PAH). GC-MS analyses showed that strain FLU5 was capable of degrading almost 45 % of fluoranthene (100 mg l(-1)), without yeast extract added, after 30 days of incubation at 30 g l(-1) NaCl and 37 °C. In addition, the isolate FLU5 showed a remarkable capacity to grow on a wide range of aliphatic, aromatic and complex hydrocarbons. This strain could also synthesize a biosurfactant which was capable of reducing the surface tension of the cell-free medium, during the growth on fluoranthene. The biodegradative abilities of PAHs are promising and can be used to perform the bioremediation strategies of seawaters and marine sediments contaminated by hydrocarbons.

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.

Bacteria induced degradation of fluoranthene in minimal salt medium mediated by catabolic enzymes in vitro condition

Fluoranthene is highly toxic and ubiquitous in the environment. A study on degradation of 200 ppm of fluoranthene in MSM by two bacterial strains Pseudomonas aeruginosa PSA5, Rhodococcus sp. NJ2 and their consortium revealed that fluoranthene was degraded 74% by Rhodococcus sp. NJ2, 61% by Pseudomonas sp. PSA5 and 97% by their consortium. Higher degradation in the consortium may be attributed to synergistic action between two bacteria. It was also observed that several degradative enzymes catechol 1,2 dioxygenase, catechol 2,3 dioxygenase, protocatechuate 2,3 dioxygenase, protocatechuate 3,4 dioxygenase, protocatechuate 4,5 dioxygenase, salicylate hydroxylase and 2-carboxybenzaldehyde dehydrogenase were differentially induced at different stages of fluoranthene degradation. Biodegradation kinetics indicated half life period of fluoranthene degradation. Besides, glycolipid, as a biosurfactant, was induced to facilitate the degradation process. Hence, both the bacteria may be used individually or in combination for effective decontamination of oil and sludge contaminated soil.

Biotransformation of the high-molecular weight polycyclic aromatic hydrocarbon (PAH) benzo[k]fluoranthene by Sphingobium sp. strain KK22 and identification of new products of non-alternant PAH biodegradation by liquid chromatography electrospray ionization tandem mass spectrometry

A pathway for the biotransformation of the environmental pollutant and high-molecular weight polycyclic aromatic hydrocarbon (PAH) benzo[k]fluoranthene by a soil bacterium was constructed through analyses of results from liquid chromatography negative electrospray ionization tandem mass spectrometry (LC/ESI(–)-MS/MS). Exposure of Sphingobium sp. strain KK22 to benzo[k]fluoranthene resulted in transformation to four-, three-and two-aromatic ring products. The structurally similar four-and three-ring non-alternant PAHs fluoranthene and acenaphthylene were also biotransformed by strain KK22, and LC/ESI(–)-MS/MS analyses of these products confirmed the lower biotransformation pathway proposed for benzo[k]fluoranthene. In all, seven products from benzo[k]fluoranthene and seven products from fluoranthene were revealed and included previously unreported products from both PAHs. Benzo[k]fluoranthene biotransformation proceeded through ortho-cleavage of 8,9-dihydroxy-benzo[k]fluoranthene to 8-carboxyfluoranthenyl-9-propenic acid and 9-hydroxy-fluoranthene-8-carboxylic acid, and was followed by meta-cleavage to produce 3-(2-formylacenaphthylen-1-yl)-2-hydroxy-prop-2-enoic acid. The fluoranthene pathway converged with the benzo[k]fluoranthene pathway through detection of the three-ring product, 2-formylacenaphthylene-1-carboxylic acid. Production of key downstream metabolites, 1,8-naphthalic anhydride and 1-naphthoic acid from benzo[k]fluoranthene, fluoranthene and acenaphthylene biotransformations provided evidence for a common pathway by strain KK22 for all three PAHs through acenaphthoquinone. Quantitative analysis of benzo[k]fluoranthene biotransformation by strain KK22 confirmed biodegradation. This is the first pathway proposed for the biotransformation of benzo[k]fluoranthene by a bacterium.

Comparative assessment of growth and biodegradation potential of soil isolate in the presence of pesticides

In Pakistan, to increase agricultural production, higher amounts of fertilizers and pesticides are being used. The residues of the applied pesticides stay in the environment and therefore causing contamination of air, water and land. Moreover, agricultural industries are also contributing relatively high quantities of toxic pesticides into the environment. Since most of them have no treatment facilities. These pesticides may be toxic, mutagenic or carcinogenic. They may be bioaccumulated or biomagnified by the biota. Therefore its removal from environmental systems needs special attention. In this study, bacterial isolate, Pseudomonas, designated as IES-Ps-1, was used to assess its potential for pesticide removal from industrial wastewater using the biosimulator (activated sludge process). During experimental studies conducted in the flask as well as in biosimulator, it was observed that IES-Ps-1 grows normally at low concentrations of added insecticides when compared with the control test (without pesticide). However, at high concentrations the microbial count decreased but no death occurred and the culture remained in lag phase. In many cases, the growth of organisms in the presence of the particular substrate serves as an indication about its metabolic potential. However, to confirm these results, chemical oxygen demand (COD) and HPLC analysis were performed. Under aerobic culture conditions using mechanical aerators in biosimulator, almost complete removal of Cypermethrin at 20 mg/L dose occurred during 48 h. The study findings indicate that IES-Ps-1 strain, can be used for the treatment of the pesticide contaminated environment. Such study may be valuable to scientist and engineers, who are trying to develop methods for the treatment of toxic organic waste using the biological treatment process.

Distribution and characterization of organochlorine pesticides and polycyclic aromatic hydrocarbons in surface sediment from Poyang Lake, China

The concentrations of organochlorine pesticides (OCPs) and 16 priority polycyclic aromatic hydrocarbons (PAHs) were investigated in the sediments from Poyang Lake, the largest freshwater lake in China. The results showed that the total concentrations of four hexachlorocyclohexane (HCH) isomers (α-HCH, β-HCH, γ-HCH, δ-HCH), three dichlorodiphenyltrichloroethane (DDT) homologs and their metabolites (p,p'-DDD, o,p'-DDD, p,p'-DDE, p,p'-DDT, o,p'-DDT, o,p'-DDE), sodium pentachlorophenate and PAHs varied from 0.536±0.330 to 6.937±2.655, 14.421±5.260 to 82.871±31.258, 15.346±6.935 to 48.254±16.836, and 33.0±11.5 to 369.1±138.5 μg/kg, respectively. The concentrations of HCH isomers followed the order: γ-HCH>β-HCH>δ-HCH>α-HCH. The most dominant γ-HCH ranged from 0.253±0.155 to 3.465±1.010 μg/kg, suggesting a recent input of lindane. p,p'-DDD was the most dominant pollutant of DDTs, with a mean concentration of 31.684±13.530 μg/kg. The ratios of (DDE+DDD)/DDT ranged from 75±24 to 360±115, indicating no recent input of DDTs. The PAHs were mainly originated from liquid fossil fuel combustion and leakage, except at Pojiang River estuary, where the pyrogenic source (coal, grass and wood combustion) was dominant. Several PAH metabolites were identified and the possible degradation pathways were proposed.

Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil

Soil microbial community response to phenanthrene was evaluated by metatranscriptomics. A marked increase in transcripts involved in aromatic compound metabolism, respiration and stress responses, and concurrent decreases in virulence, carbohydrate, DNA metabolism and phosphorus metabolism transcripts was revealed. Phenanthrene addition led to a 1.8-fold to 33-fold increase in the abundance of dioxygenase, stress response and detoxification transcripts, whereas those of general metabolism were little affected. Heavy metal P-type ATPases and thioredoxin transcripts were more abundant in the phenanthrene-amended soil, and this is the first time these proteins have been associated with polycyclic aromatic hydrocarbon (PAH) stress in microorganisms. Annotation with custom databases constructed with bacterial or fungal PAH metabolism protein sequences showed that increases in PAH-degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed widespread changes in the bacteria, archaea and fungi, and the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This is the first report of an experimental metatranscriptomic study detailing microbial community responses to a pollutant in soil, and offers information on novel in situ effects of PAHs on soil microbes that can be explored further.

Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1

This study investigated a metabolic network (MN) from Mycobacterium vanbaalenii PYR-1 for polycyclic aromatic hydrocarbons (PAHs) from the perspective of structure, behavior, and evolution, in which multilayer omics data are integrated. Initially, we utilized a high-throughput proteomic analysis to assess the protein expression response of M. vanbaalenii PYR-1 to seven different aromatic compounds. A total of 3,431 proteins (57.38% of the genome-predicted proteins) were identified, which included 160 proteins that seemed to be involved in the degradation of aromatic hydrocarbons. Based on the proteomic data and the previous metabolic, biochemical, physiological, and genomic information, we reconstructed an experiment-based system-level PAH-MN. The structure of PAH-MN, with 183 metabolic compounds and 224 chemical reactions, has a typical scale-free nature. The behavior and evolution of the PAH-MN reveals a hierarchical modularity with funnel effects in structure/function and intimate association with evolutionary modules of the functional modules, which are the ring cleavage process (RCP), side chain process (SCP), and central aromatic process (CAP). The 189 commonly upregulated proteins in all aromatic hydrocarbon treatments provide insights into the global adaptation to facilitate the PAH metabolism. Taken together, the findings of our study provide the hierarchical viewpoint from genes/proteins/metabolites to the network via functional modules of the PAH-MN equipped with the engineering-driven approaches of modularization and rationalization, which may expand our understanding of the metabolic potential of M. vanbaalenii PYR-1 for bioremediation applications.

In vitro degradation of fluoranthene by bacteria isolated from petroleum sludge

An investigation was carried out for in vitro degradation of fluoranthene by four bacterial strains (PSM6, PSM7, PSM10 and PSM11) isolated from the petroleum sludge. Although all the strains registered their growth in MSM with 100 ppm fluoranthene, PSM11 growth was better than other strains. Growth of bacterial strains invariably corresponded to their degradation potential of fluoranthene. After 168 h of incubation, 61% fluoranthene was degraded by PSM11, followed by PSM10 (48%) and PSM6 (42%) and the least was recorded in PSM7 (41%). Besides, 11% loss in fluoranthene was attributed to abiotic factors. Thirty-eight times more activity of catechol 2,3-dioxygenase than catechol 1,2-dioxygenase showed that it played a significant role in fluoranthene degradation. Molecular weight of catechol 2,3-dioxygenase isolated from PSM11 was determined as ∼ 136 kDa by size exclusion chromatography and 34 kDa on denaturing SDS-PAGE, indicating tetrameric nature of the enzyme.

Metabolism of Pyrene by the Basidiomycete Crinipellis stipitaria and Identification of Pyrenequinones and Their Hydroxylated Precursors in Strain JK375

The metabolism of pyrene, a polycyclic aromatic hydrocarbon, by submerged cultures of the basidiomycete Crinipellis stipitaria was studied. After incubation for 68 h at 25 degrees C in a 20-liter fermentor with complex medium and 20 mg of pyrene per liter, five metabolites were detected. The compounds were isolated by preparative high-performance liquid chromatography on RP18 and DIOL gels. By UV, infrared, and H nuclear magnetic resonance spectroscopy and mass spectrometry, 1-hydroxypyrene, 1,6-dihydroxypyrene, 1,8-dihydroxypyrene, 1,6-pyrenequinone, and 1,8-pyrenequinone were identified. 1,6- and 1,8-dihydroxypyrene were obtained from fungal cultures for the first time. The formation of these metabolites was confirmed by investigations with [4,5,9,10-C]pyrene.

Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria

Interest in understanding prokaryotic biotransformation of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) has continued to grow and the scientific literature shows that studies in this field are originating from research groups from many different locations throughout the world. In the last 10 years, research in regard to HMW PAH biodegradation by bacteria has been further advanced through the documentation of new isolates that represent diverse bacterial types that have been isolated from different environments and that possess different metabolic capabilities. This has occurred in addition to the continuation of in-depth comprehensive characterizations of previously isolated organisms, such as Mycobacterium vanbaalenii PYR-1. New metabolites derived from prokaryotic biodegradation of four- and five-ring PAHs have been characterized, our knowledge of the enzymes involved in these transformations has been advanced and HMW PAH biodegradation pathways have been further developed, expanded upon and refined. At the same time, investigation of prokaryotic consortia has furthered our understanding of the capabilities of microorganisms functioning as communities during HMW PAH biodegradation.

Bacterial degradation of aromatic compounds

Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.

Removal of PAHs from laboratory columns simulating the humus upper layer of vertical flow constructed wetlands

Removal of three polycyclic aromatic hydrocarbons or PAHs (fluoranthene, pyrene and benzo(k)fluoranthene) from two types of PAH-contaminated effluents was investigated using four laboratory columns filled with two different organic media: a green compost and a layer coming from the first stage of vertical flow constructed wetlands. Synthetic runoff polluted by polycyclic aromatic hydrocarbons were fed through the columns during a period of two months. After a period of hydrodynamic stabilisation, the results showed a great adsorption of PAHs (>95%) on the solid media due to their large adsorption capacities. Leaching of these compounds by water was monitored. The concentrations of PAHs in leaching samples indicated that PAHs were strongly adsorbed on organic substrates and that lixiviation was limited. Fluoranthene metabolites were also investigated. Accumulation of metabolites was transitory and located in the first few cm of the media, as was observed for PAH concentrations. A toxicity test of leachates based on the inhibition of the bioluminescence of luminescent bacteria Vibrio fischeri indicated a low inhibition which can be enhanced by metal traces.

Accumulation and biodegradation of phenanthrene and fluoranthene by the algae enriched from a mangrove aquatic ecosystem

This study focused on the accumulation and biodegradation of two typical polycyclic aromatic hydrocarbons (PAHs), phenanthrene (PHE) and fluoranthene (FLA), by the diatoms enriched from a mangrove aquatic ecosystem in the Jiulong River estuary, China. After separation, purification and culture, Skeletonema costatum (Greville) Cleve and Nitzschia sp. were exposed to different concentrations of PHE, FLA, and a mixture of the two. The results showed that the tolerance of S.costatum to PHE and FLA was greater than that of Nitzschia sp., and that the toxic effect of FLA on S. costatum and Nitzschia sp. was higher than that of PHE. The microalgal species S. costatum and Nitzschia sp. were capable of accumulating and degrading the two typical PAHs simultaneously. The accumulation and degradation abilities of Nitzschia sp. were higher than those of S. costatum. Degradation of FLA by the two algal species was slower, indicating that FLA was a more recalcitrant PAH compound. The microalgal species also showed comparable or higher efficiency in the removal of the PHE-FLA mixture than PHE or FLA singly, suggesting that the presence of one PAH stimulated the degradation of the other.

Isomer-specific biodegradation of methylphenanthrenes by soil bacteria

It is assumed that bacteria generally degrade 2-methylphenanthrene (2MPhe) in preference to 1-methylphenanthrene (1MPhe), and that environmental biodegradation of methylated PAHs therefore can be described qualitatively by changes in relative concentrations of these isomers. Our objective was to investigate whether microbial phenanthrene degraders (Sphingomonas and Mycobacterium) show such isomer-specific PAH degradation. Eleven out of twenty-nine phenanthrene degraders could grow on methylphenanthrene. The mycobacteria grew only on 2MPhe, the sphingomonads grew mostly on 1MPhe, and one sphingomonad could utilize both substrates. Seven strains were tested in a two-phase system where 1MPhe and 2MPhe were supplied in heptamethylnonane. For these strains, a consistent description of biodegradation based on the 2MPhe/1MPhe diagnostic ratio would not be possible because three Mycobacterium and one Sphingomonas degraded 2MPhe faster than 1MPhe, another Sphingomonas degraded 1MPhe and 2MPhe at almost equal rates, and two Sphingomonas degraded 1MPhe faster than 2MPhe. Thus, environmental biodegradation of phenanthrenes may theoretically proceed with only minor changes in 2MPhe/1MPhe ratios if individual members of the degrader community have different isomer preferences. However, two soil microcosms polluted with bunker oil confirmed the general decline in 2MPhe/1MPhe ratio during oil biodegradation.

Bacterial degradation of phthalate isomers and their esters

Phthalate isomers and their esters are used heavily in various industries. Excess use and leaching from the product pose them as major pollutants. These chemicals are toxic, teratogenic, mutagenic and carcinogenic in nature. Various aspects like toxicity, diversity in the aerobic bacterial degradation, enzymes and genetic organization of the metabolic pathways from various bacterial strains are reviewed here. Degradation of these esters proceeds by the action of esterases to form phthalate isomers, which are converted to dihydroxylated intermediates by specific and inducible phthalate isomer dioxygenases. Metabolic pathways of phthalate isomers converge at 3,4-dihydroxybenzoic acid, which undergoes either ortho- or meta- ring cleavage and subsequently metabolized to the central carbon pathway intermediates. The genes involved in the degradation are arranged in operons present either on plasmid or chromosome or both, and induced by specific phthalate isomer. Understanding metabolic pathways, diversity and their genetic regulation may help in constructing bacterial strains through genetic engineering approach for effective bioremediation and environmental clean up.

Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1

Mycobacterium vanbaalenii PYR-1 is well known for its ability to degrade a wide range of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs). The genome of this bacterium has recently been sequenced, allowing us to gain insights into the molecular basis for the degradation of PAHs. The 6.5 Mb genome of PYR-1 contains 194 chromosomally encoded genes likely associated with degradation of aromatic compounds. The most distinctive feature of the genome is the presence of a 150 kb major catabolic region at positions 494 approximately 643 kb (region A), with an additional 31 kb region at positions 4,711 approximately 4,741 kb (region B), which is predicted to encode most enzymes for the degradation of PAHs. Region A has an atypical mosaic structure made of several gene clusters in which the genes for PAH degradation are complexly arranged and scattered around the clusters. Significant differences in the gene structure and organization as compared to other well-known aromatic hydrocarbon degraders including Pseudomonas and Burkholderia were revealed. Many identified genes were enriched with multiple paralogs showing a remarkable range of diversity, which could contribute to the wide variety of PAHs degraded by M. vanbaalenii PYR-1. The PYR-1 genome also revealed the presence of 28 genes involved in the TCA cycle. Based on the results, we proposed a pathway in which HMW PAHs are degraded into the beta-ketoadipate pathway through protocatechuate and then mineralized to CO2 via TCA cycle. We also identified 67 and 23 genes involved in PAH degradation and TCA cycle pathways, respectively, to be expressed as proteins.

Involvement of Tetrahymena pyriformis and selected fungi in the elimination of anthracene, and toxicity assessment of the biotransformation products

Anthracene (AC) is a non-mutagenic and non-carcinogenic, low-molecular-weight polycyclic aromatic hydrocarbon present in the environment. Its toxicity can be dramatically increased after solar-light exposure. Biotransformation capacities of AC by Tetrahymena pyriformis and a selection of eight micromycetes were studied, and the ability of these microorganisms to detoxify the polluted ecosystems was assessed. We showed that T. pyriformis was able to accumulate high amounts of AC without any transformation. In contrast, the fungi Cunninghamella elegans, Absidia fusca, Absidia cylindrospora, Rhodotorula glutinis, and Aspergillus terreus were able to transform AC with a high efficiency. Cytotoxicity assays conducted on HeLa cells and T. pyriformis showed that crude extract from A. fusca culture medium obtained after AC biotransformation was not toxic. For A. fusca and A. cylindrospora, 1-4 dihydroxyanthraquinone was shown to be the major product during the biotransformation process. This compound seemed to be a dead-end metabolite at least for the Absidia strains. The cytotoxicity of 1-4 dihydroxyanthraquinone was higher than that of AC to T. pyriformis but lower to HeLa cells. On the whole our results showed that the microorganisms studied were all able to decontaminate an AC-polluted ecosystem, either by accumulating or transforming the compound. A possible detoxification process resulting from AC biotransformation can be considered only using the human cell model.

Fluoranthene metabolism and associated proteins in Mycobacterium sp. JS14

Fluoranthene is a polycyclic aromatic hydrocarbon (PAH) commonly present in PAH-contaminated soils. We studied fluoranthene catabolism and associated proteins in Mycobacterium sp. JS14, a bacterium isolated from a PAH-contaminated soil in Hilo (HI, USA). Fluoranthene degrades in at least three separated pathways via 1-indanone, 2',3'-dihydroxybiphenyl-2,3,-dicarboxylic acid, and naphthalene-1,8-dicarboxylic acid. Part of the diverse catabolism is converged into phthalate catabolism. An increased expression of 25 proteins related to fluoranthene catabolism is found with 1-D PAGE or 2-DE and nano-LC-MS/MS. Detection of fluoranthene catabolism associated proteins coincides well with its multiple degradation pathways that are mapped via metabolites identified. Among the up-regulated proteins, PAH ring-hydroxylating dioxygenase alpha-subunit and beta-subunit and 2,3-dihydroxybiphenyl 1,2-dioxygenase are notably induced. The up-regulation of trans-2-carboxybenzalpyruvate hydratase suggests that some of fluoranthene metabolites may be further degraded through aromatic dicarboxylic acid pathways. Catalase and superoxide dismutase were up-regulated to control unexpected oxidative stress during the fluoranthene catabolism. The up-regulation of chorismate synthase and nicotine-nucleotide phosphorylase may be necessary for sustaining shikimate pathway and pyrimidine biosynthesis, respectively. A fluoranthene degradation pathway for Mycobacterium sp. JS14 was proposed and confirmed by proteomic study by identifying almost all the enzymes required during the initial steps of fluoranthene degradation.

Isolation and characterization of bacteria capable of degrading polycyclic aromatic hydrocarbons (PAHs) and organophosphorus pesticides from PAH-contaminated soil in Hilo, Hawaii

Nineteen bacterial strains were isolated from petroleum-contaminated soil in Hilo, HI, and characterized by two different spray-plated methods, turbidity test in liquid medium, and 16S rRNA gene sequence analysis. Analysis of the soil showed 13 polycyclic aromatic hydrocarbons (PAHs) in a range from 0.6 to 30 mg/kg of dry weight each and 12 PAH metabolites. Five distinct bacterial strains (C3, C4, P1-1, JS14, and JS19b1) selected from preliminary plating and turbidity tests were further tested for PAH degradation through single PAH degradation assay. Strains C3, C4, and P1-1 degraded phenanthrene (40 mg/L) completely during 7 days of incubation. Strain JS14 degraded fluoranthene (40 mg/L) completely during 10 days of incubation. Strain JS19b1 degraded 100% of phenanthrene (40 mg/L) in 7 days, 77% of fluorene (40 mg/L) in 14 days, 97% of fluoranthene (40 mg/L) in 10 days, and 100% of pyrene (40 mg/L) in 14 days. Turbidity tests showed that strains P1-1, JS14, and JS19b1 utilized several organophosphorus pesticides as growth substrate. P1-1 can degrade carbofenothion, chlorfenvinphos, diazinon, fonofos, and pirimiphos-methyl. JS14 can transform chlorfenvinphos and diazinon. JS19b1 can break down diazinon, pirimiphos-methyl, and temephos.

Influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons by Sphingomonas sp. strain PheB4

The influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated when Sphingomonas sp. strain PheB4 isolated from surface mangrove sediments was grown in either phenanthrene-containing mineral salts medium (PMSM) or nutrient broth (NB). The NB-grown culture exhibited a more rapid cometabolic degradation of single and mixed non-growth substrate PAHs compared to the PMSM-grown culture. The concentrations of PAH metabolites were also lower in NB-grown culture than in PMSM-grown culture, suggesting that NB-grown culture removed metabolites at a faster rate, particularly, for metabolites produced from cometabolic degradation of a binary mixture of PAHs. Cometabolic pathways of single PAH (anthracene, fluorene, or fluoranthene) in NB-grown culture showed similarity to that in PMSM-grown culture. However, cometabolic pathways of mixed PAHs were more diverse in NB-grown culture than that in PMSM-grown culture. These results indicated that nutrient rich medium was effective in enhancing cometabolic degradation of mixed PAHs concomitant with a rapid removal of metabolites, which could be useful for the bioremediation of mixed PAHs contaminated sites using Sphingomonas sp. strain PheB4.

A polyomic approach to elucidate the fluoranthene-degradative pathway in Mycobacterium vanbaalenii PYR-1

Mycobacterium vanbaalenii PYR-1 is capable of degrading a wide range of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs), including fluoranthene. We used a combination of metabolomic, genomic, and proteomic technologies to investigate fluoranthene degradation in this strain. Thirty-seven fluoranthene metabolites including potential isomers were isolated from the culture medium and analyzed by high-performance liquid chromatography, gas chromatography-mass spectrometry, and UV-visible absorption. Total proteins were separated by one-dimensional gel and analyzed by liquid chromatography-tandem mass spectrometry in conjunction with the M. vanbaalenii PYR-1 genome sequence (http://jgi.doe.gov), which resulted in the identification of 1,122 proteins. Among them, 53 enzymes were determined to be likely involved in fluoranthene degradation. We integrated the metabolic information with the genomic and proteomic results and proposed pathways for the degradation of fluoranthene. According to our hypothesis, the oxidation of fluoranthene is initiated by dioxygenation at the C-1,2, C-2,3, and C-7,8 positions. The C-1,2 and C-2,3 dioxygenation routes degrade fluoranthene via fluorene-type metabolites, whereas the C-7,8 routes oxidize fluoranthene via acenaphthylene-type metabolites. The major site of dioxygenation is the C-2,3 dioxygenation route, which consists of 18 enzymatic steps via 9-fluorenone-1-carboxylic acid and phthalate with the initial ring-hydroxylating oxygenase, NidA3B3, oxidizing fluoranthene to fluoranthene cis-2,3-dihydrodiol. Nonspecific monooxygenation of fluoranthene with subsequent O methylation of dihydroxyfluoranthene also occurs as a detoxification reaction.

Requirement of duplicated operons for maximal metabolism of phthalate by Rhodococcus sp. strain DK17

The operons encoding the transformation of phthalate to protocatechuate are duplicated and present on two different megaplasmids [pDK2 (330 kb) and pDK3 (750 kb)] in Rhodococcus sp. strain DK17. RT-PCR experiments using gene-specific primers showed that both the pDK2- and the pDK3-encoded dihydroxyphthalate decarboxylase genes are simultaneously expressed during growth on phthalate. The doubling time of the pDK2-cured mutant strain DK176 in minimal liquid medium with 5mM phthalate is 52.5% of that of the wild-type strain DK17. The data indicate that both copies of the phthalate operon are equally functional in DK17, and gene dosage is the main reason for slower growth of DK176 on phthalate.

Isolation and characterization of a gene cluster involved in PAH degradation in Mycobacterium sp. strain SNP11: Expression in Mycobacterium smegmatis mc2155

Mycobacterium sp. strain SNP11 is able to grow with pyrene, fluoranthene, phenanthrene and fluorene the sole carbon and energy sources. A probe based on the previously described gene pdoA2, which encodes the alpha subunit of a PAH ring-hydroxylating dioxygenase in Mycobacterium sp. strain 6PY1 [S. Krivobok et al., Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases, J. Bacteriol. 185(13) (2003) 3828-3841], was used to isolate a 14kb DNA fragment from strain SNP11. Twelve putative open reading frames (ORFs), divided into two groups by a promoter intergenic region, were detected in this DNA sequence. The first gene cluster, located upstream of the promoter region, showed low but significant deduced amino acid sequence homologies with enzymes involved in aromatic degradation. The second gene cluster, under control of the promoter, contained pdoA2 (designated phdA in this study) and several other ORFs with deduced amino acid sequences closely related to enzymes involved in the phenanthrene-degrading pathway of Nocardioides sp. strain KP7. Gene expression analysis in Mycobacterium smegmatis mc(2)155 revealed broad substrate specificity of the ring-hydroxylating dioxygenase, since transformant cells containing phdAB strongly oxidized fluoranthene, phenanthrene, anthracene, fluorine and dibenzofuran. Laser desorption/ionization time-of-flight mass spectrometry (LDI-ToF MS) analyses of culture media after PAH degradation by M. smegmatis transformants also revealed that the second gene cluster, located downstream of the promoter, takes an active share in initial phenanthrene and anthracene degradation by allowing transformation of these two PAHs in aromatic ring-cleaved metabolites.

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.

Ecotoxicological assessment of PAHs and their dead-end metabolites after degradation by Mycobacterium sp. strain SNP11

Mycobacterium sp. SNP11 has a high PAH biodegradation potential. In this paper, the toxicity of pyrene, fluoranthene, phenanthrene, and their dead-end metabolites, accumulated in the media after biodegradation by Mycobacterium sp. SNP11, were evaluated by a screening battery of acute, chronic, and genotoxic tests. According to the bioassays, performed on bacteria (Vibrio fischeri, Salmonella typhimurium strains TA1535/pSK1002, TA97a, TA98, TA100), algae (Pseudokirchneriella subcapitata), and crustaceans (Daphnia magna, Ceriodaphnia dubia), total disappearance or a very significant reduction of the (geno)toxic potential was observed after PAH degradation by Mycobacterium sp. SNP11.

Molecular cloning and expression of genes encoding a novel dioxygenase involved in low- and high-molecular-weight polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1

Mycobacterium vanbaalenii PYR-1 is able to metabolize a wide range of low- and high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs). A 20-kDa protein was upregulated in PAH-metabolizing M. vanbaalenii PYR-1 cells compared to control cultures. The differentially expressed protein was identified as a beta subunit of the terminal dioxygenase using mass spectrometry. PCR with degenerate primers designed based on de novo sequenced peptides and a series of plaque hybridizations were done to screen the M. vanbaalenii PYR-1 genomic library. The genes, designated nidA3B3, encoding the alpha and beta subunits of terminal dioxygenase, were subsequently cloned and sequenced. The deduced enzyme revealed close similarities to the corresponding PAH ring-hydroxylating dioxygenases from Mycobacterium and Rhodococcus spp. but had the highest similarity, 61.9%, to the alpha subunit from Nocardioides sp. strain KP7. The alpha subunit also showed 52% sequence homology with the previously reported NidA from M. vanbaalenii PYR-1. The genes nidA3B3 were subcloned into the expression vector pET-17b, and the enzyme activity in Escherichia coli cells was reconstituted through coexpression with the ferredoxin (PhdC) and ferredoxin reductase (PhdD) genes of the phenanthrene dioxygenase from Nocardioides sp. strain KP7. The recombinant PAH dioxygenase appeared to favor the HMW PAH substrates fluoranthene, pyrene, and phenanthrene. Several other PAHs, including naphthalene, anthracene, and benz[a]anthracene, were also converted to their corresponding cis-dihydrodiols. The recombinant E. coli, however, did not show any dioxygenation activity for phthalate and biphenyl. The upregulation of nidA3B3 in M. vanbaalenii PYR-1 induced by PAHs was confirmed by reverse transcription-PCR analysis.

Limited microbial degradation of pyrene metabolites from the estuarine polychaete Nereis diversicolor

We compared microbial mineralization of [4,5,9,10-14C]pyrene and its eukaryotic [4,5,9,10-14C]pyrene metabolites in estuarine sediments. Metabolites were obtained by exposing the estuarine deposit-feeding polychaete Nereis diversicolor to sediment-associated 14C-pyrene, followed by homogenization of the worms and extraction of the pyrene-metabolites. In sediment from a pristine Danish Fjord only 2.6% of the added metabolite-label and 1.7% of the pyrene-label were mineralized to 14CO2 during 175 days incubation. Pre-exposure of the pristine sediment to unlabelled pyrene for 60 days increased the mineralization potential for 14C-pyrene substantially, as 81.2% was mineralized to 14CO2 during 95 days incubation, whereas 14C-pyrene metabolite label was unaffected by pre-exposure to pyrene. In comparison, naturally aged bunker-oil contaminated sediment did not show elevated potentials for mineralization of neither 14C-pyrene nor 14C-metabolites. Six bacterial strains of known pyrene degraders were tested for growth on crystalline 1-hydroxypyrene. 1-Hydroxypyrene is the only intermediate eucaryotic metabolite of pyrene. The results indicate that 1-hydroxypyrene was not utilized as a sole source of carbon and energy by any of them. In addition, respiration was depressed in all six strains when exposed to crystalline 1-Hydroxypyrene, demonstrating an acute toxic effect of 1-hydroxypyrene. The results presented here suggest that microbial degradation of pyrene is not enhanced by release of aqueous and polar metabolites by marine invertebrates.