Biodegradation of 1-nitropyrene

Molecular Basis and Evolutionary Origin of 1-Nitronaphthalene Catabolism in Sphingobium sp. Strain JS3065

Nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) enter the environment from natural sources and anthropogenic activities. To date, microorganisms able to mineralize nitro-PAHs have not been reported. Here, Sphingobium sp. strain JS3065 was isolated by selective enrichment for its ability to grow on 1-nitronaphthalene as the sole carbon, nitrogen, and energy source. Analysis of the complete genome of strain JS3065 indicated that the gene cluster encoding 1-nitronaphthalene catabolism (nin) is located on a plasmid. Based on the genetic and biochemical evidence, the nin genes share an origin with the nag-like genes encoding naphthalene degradation in Ralstonia sp. strain U2. The initial step in degradation of 1-nitronaphthalene is catalyzed by a three-component dioxygenase, NinAaAbAcAd, resulting in formation of 1,2-dihydroxynaphthalene which is also an early intermediate in the naphthalene degradation pathway. Introduction of the ninAaAbAcAd genes into strain U2 enabled its growth on 1-nitronaphthalene. Phylogenic analysis of NinAc suggested that an ancestral 1-nitronaphthalene dioxygenase was an early step in the evolution of nitroarene dioxygenases. Based on bioinformatic analysis and enzyme assays, the subsequent assimilation of 1,2-dihydroxynaphthalene seems to follow the well-established pathway for naphthalene degradation by Ralstonia sp. strain U2. This is the first report of catabolic pathway for 1-nitronaphthalene and is another example of how expanding the substrate range of Rieske type dioxygenase enables bacteria to grow on recalcitrant nitroaromatic compounds. IMPORTANCE Nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) have been widely detected in the environment and they are more toxic than their corresponding parent PAHs. Although biodegradation of many PAHs has been extensively described at genetic and biochemical levels, little is known about the microbial degradation of nitro-PAHs. This work reports the isolation of a Sphingobium strain growing on 1-nitronaphthalene and the genetic basis for the catabolic pathway. The pathway evolved from an ancestral naphthalene catabolic pathway by a remarkably small modification in the specificity of the initial dioxygenase. Data presented here not only shed light on the biochemical processes involved in the microbial degradation of globally important nitrated polycyclic aromatic hydrocarbons, but also provide an evolutionary paradigm for how bacteria evolve a novel catabolic pathway with minimal alteration of preexisting pathways for natural organic compounds.

Biodegradation of anthracene and several PAHs by the marine-derived fungus Cladosporium sp. CBMAI 1237

The biodegradation of polycyclic aromatic hydrocarbons (PAHs) by marine-derived fungi was reported in this work. Marine-derived fungi (Trichoderma harzianum CBMAI 1677, Cladosporium sp. CBMAI 1237, Aspergillus sydowii CBMAI 935, Penicillium citrinum CBMAI 1186 and Mucor racemosus CBMAI 847) biodegraded anthracene (14days, 130rpm, 50mgmL^-1 initial concentration in malt 2% medium). Cladosporium sp. CBMAI 1237 was the most efficient strain and biodegraded more anthracene in the presence (42% biodegradation) than in the absence (26%) of artificial seawater, suggesting that the biodegradation of PAHs may be faster in seawater than in non-saline environment. After 21days, Cladosporium sp. CBMAI 1237 biodegraded anthracene (71% biodegradation), anthrone (100%), anthraquinone (32%), acenaphthene (78%), fluorene (70%), phenanthrene (47%), fluoranthene (52%), pyrene (62%) and nitropyrene (64%). Previous undocumented metabolites were identified and, anthraquinone was a common product of different PAHs biodegradation. The marine-derived fungus Cladosporium sp. CBMAI 1237 showed potential for bioremediation of PAHs.

Nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) in the environment - A review

Nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) are derivatives of PAHs with at least one nitro-functional group (-NO₂) on the aromatic ring. The toxic effects of several nitro-PAHs are more pronounced than those of PAHs. Some nitro-PAHs are classified as possible or probable human carcinogens by the International Agency for Research on Cancer. Nitro-PAHs are released into the environment from combustion of carbonaceous materials (e.g. fossil fuels, biomass, waste) and post-emission transformation of PAHs. Most studies on nitro-PAHs are about air (gas-phase and particulate matter), therefore less is known about the occurrence, concentrations, transport and fate of nitro-PAHs in soils, aquatic environment and biota. Studies on partition and exchange of nitro-PAHs between adjacent environmental compartments are also sparse. The concentrations of nitro-PAHs cannot easily be predicted from the intensity of anthropogenic activity or easily related to those of PAHs. This is because anthropogenic source strengths of nitro-PAHs are different from those of PAHs, and also nitro-PAHs have additional sources (formed by photochemical conversion of PAHs). The fate and transport of nitro-PAHs could be considerably different from their related PAHs because of their higher molecular weights and considerably different sorption mechanisms. Hence, specific knowledge on nitro-PAHs is required. Regulations on nitro-PAHs are also lacking. We present an extensive review of published literature on the sources, formation, physico-chemical properties, methods of determination, occurrence, concentration, transport, fate, (eco)toxicological and adverse health effects of nitro-PAHs. We also make suggestions and recommendations about data needs, and future research directions on nitro-PAHs. It is expected that this review will stimulate scientific discussion and provide the basis for further research and regulations on nitro-PAHs.

Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil

We investigated the response of the hydrocarbon-degrading Mycobacterium vanbaalenii PYR-1 to crude oil from the BP Deepwater Horizon (DWH) spill, using substrate depletion, genomic, and proteome analyses. M. vanbaalenii PYR-1 cultures were incubated with BP DWH crude oil, and proteomes and degradation of alkanes and polycyclic aromatic hydrocarbons (PAHs) were analyzed at four time points over 30 days. Gas chromatography-mass spectrometry (GC-MS) analysis showed a chain length-dependent pattern of alkane degradation, with C12 and C13 being degraded at the highest rate, although alkanes up to C28 were degraded. Whereas phenanthrene and pyrene were completely degraded, a significantly smaller amount of fluoranthene was degraded. Proteome analysis identified 3,948 proteins, with 876 and 1,859 proteins up- and downregulated, respectively. We observed dynamic changes in protein expression during BP crude oil incubation, including transcriptional factors and transporters potentially involved in adaptation to crude oil. The proteome also provided a molecular basis for the metabolism of the aliphatic and aromatic hydrocarbon components in the BP DWH crude oil, which included upregulation of AlkB alkane hydroxylase and an expression pattern of PAH-metabolizing enzymes different from those in previous proteome expression studies of strain PYR-1 incubated with pure or mixed PAHs, particularly the ring-hydroxylating oxygenase (RHO) responsible for the initial oxidation of aromatic hydrocarbons. Based on these results, a comprehensive cellular response of M. vanbaalenii PYR-1 to BP crude oil was proposed. This study increases our fundamental understanding of the impact of crude oil on the cellular response of bacteria and provides data needed for development of practical bioremediation applications.

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.

Organic pollution and genotoxicity of sediments of the Palun marshes (Berre lagoon, France)

The impact of industrial, rural, and urban activities on two runnels (B1, B2, and B3 from Beausset runnel and V1 and V2 from Vallat du Ceinturon runnel) located in the Palun marshes (Berre lagoon, France) was evaluated by analyzing 16 polycyclic aromatic hydrocarbons (PAHs), 1-nitropyrene (1-NP), 1-aminopyrene (1-AP), and six pesticides in sediment samples. The mutagenicity was assessed with the Salmonella mutagenicity test using tester strains TA98+S9 Mix and YG1041 +/- S9 Mix. The clastogenicity was evaluated with the micronucleus assay on Chinese Ovarian cells +/- S9 Mix. A gradient of PAHs concentrations was observed from B1 (3359 microg kg(-1) dry weight [dw]), close to industrial zones, to V2 (497 microg kg(-1) dw), away from the source of pollution. Similar gradient was noted for 1-AP (from B1: 11.8 microg kg(-1) dw to V2: 0.6 microg kg(-1) dw). However, this trend was not observed in 1-NP concentrations (concentrations ranged from 1.2 microg kg(-1) dw [V1] to 0.4 microg kg(-1) dw [B1]). Pesticides were detected in all samples. Diazinon and dieldrin were found in high concentrations in B1 extracts (74.5 and 39.9 microg.kg(-1) dw, respectively). All the sediments except V2 were mutagenic with strain TA98+S9 Mix. The mutagenicity was linked to the presence of PAHs (V1), nitroarenes (B1 and B3) and aromatic amines (B2). All sediments were clastogenic with and without S9 Mix except V1 extract, which was negative without S9 Mix. Overall, the two runnels in the Palun marshes were found to be polluted by many organic compounds that originate from direct human activities and pose a significant genotoxic risk.

Application of resazurin for estimating abundance of contaminant-degrading micro-organisms

AIMS

The aim of the current study was to test whether resazurin changed colour when incubated with a range of organic chemicals used as growth substrates in bioremediation studies and to determine whether resazurin was more effective in estimating microbial growth than turbidity alone (i.e. no resazurin) or use of the dye, methylene blue.

METHODS AND RESULTS

Resazurin was incubated with a range of organic chemicals that were used as substrates in an MPN assay. Only 1,2-dichlorobenzene, 2,4-D, glycol sulphite and sulphinol reacted to generate false positives. Resazurin was also used to estimate micro-organisms in a series of bioremediation studies.

CONCLUSION

The results showed that resazurin was more sensitive than methylene blue or turbidity alone as an indicator of microbial growth.

SIGNIFICANCE AND IMPACT OF THE STUDY

The significance of the current study is that resazurin should be used in MPN assays for estimating contaminant-degrading micro-organisms instead of turbidity alone or other dyes such as methylene blue.

Degradation of phenanthrene and anthracene by cell suspensions of Mycobacterium sp. strain PYR-1

Cultures of Mycobacterium sp. strain PYR-1 were dosed with anthracene or phenanthrene and after 14 days of incubation had degraded 92 and 90% of the added anthracene and phenanthrene, respectively. The metabolites were extracted and identified by UV-visible light absorption, high-pressure liquid chromatography retention times, mass spectrometry, (1)H and (13)C nuclear magnetic resonance spectrometry, and comparison to authentic compounds and literature data. Neutral-pH ethyl acetate extracts from anthracene-incubated cells showed four metabolites, identified as cis-1,2-dihydroxy-1,2-dihydroanthracene, 6,7-benzocoumarin, 1-methoxy-2-hydroxyanthracene, and 9,10-anthraquinone. A novel anthracene ring fission product was isolated from acidified culture media and was identified as 3-(2-carboxyvinyl)naphthalene-2-carboxylic acid. 6,7-Benzocoumarin was also found in that extract. When Mycobacterium sp. strain PYR-1 was grown in the presence of phenanthrene, three neutral metabolites were identified as cis- and trans-9,10-dihydroxy-9,10-dihydrophenanthrene and cis-3,4-dihydroxy-3,4-dihydrophenanthrene. Phenanthrene ring fission products, isolated from acid extracts, were identified as 2,2'-diphenic acid, 1-hydroxynaphthoic acid, and phthalic acid. The data point to the existence, next to already known routes for both gram-negative and gram-positive bacteria, of alternative pathways that might be due to the presence of different dioxygenases or to a relaxed specificity of the same dioxygenase for initial attack on polycyclic aromatic hydrocarbons.

Reduction and mutagenic activation of nitroaromatic compounds by a Mycobacterium sp

Mycobacterium sp. strain Pyr-1 cells, which were grown to the stationary phase in media with and without pyrene, were centrifuged and resuspended in a medium containing 1-nitropyrene. Cells that had been grown with pyrene oxidized up to 20% of the added 1-nitropyrene to 1-nitropyrene-cis-9,10- and 4,5-dihydrodiols. However, cells that had been grown without pyrene reduced up to 70% of the 1-nitropyrene to 1-aminopyrene but did not produce dihydrodiols. The nitroreductase activity was oxygen insensitive, intracellular, and inducible by nitro compounds. Nitroreductase activity was inhibited by p-chlorobenzoic acid, o-iodosobenzoic acid, menadione, dicumarol, and antimycin A. Extracts from cells that had been grown without pyrene activated 1-nitropyrene, 1-amino-7-nitrofluorene, 2,7-dinitro-9-fluorenone, 1,3-dinitropyrene, 1,6-dinitropyrene, and 6-nitrochrysene to DNA-damaging products, as shown in Salmonella typhimurium tester strains by the reversion assay and by induction of the umuC gene. Activation of nitro compounds, as shown by the umu test, was enhanced by NADPH. This study shows that Mycobacterium sp. strain Pyr-1 metabolizes nitroaromatic compounds by both oxidative and reductive pathways. During reduction, it generates products that are mutagenic.