Microbial metabolism of polycyclic aromatic hydrocarbons

DNA adduct formation in Saccharomyces cerevisiae following exposure to environmental pollutants, as in vivo model for molecular toxicity studies

DNA adduction in the model yeast Saccharomyces cerevisiae was investigated after exposure to the fungicide penconazole and the reference genotoxic compound benzo(a)pyrene, for validating yeasts as a tool for molecular toxicity studies, particularly of environmental pollution. The effect of the toxicants on the yeast's growth kinetics was determined as an indicator of cytotoxicity. Fermentative cultures of S. cerevisiae were exposed to 2 ppm of Penconazole during different phases of growth; while 0.2 and 2 ppm of benzo(a)pyrene were applied to the culture medium before inoculation and on exponential cultures. Exponential respiratory cultures were also exposed to 0.2 ppm of B(a)P for comparison of both metabolisms. Penconazole induced DNA adducts formation in the exponential phase test; DNA adducts showed a peak of 54.93 adducts/109 nucleotides. Benzo(a)pyrene induced the formation of DNA adducts in all the tests carried out; the highest amount of 46.7 adducts/109 nucleotides was obtained in the fermentative cultures after the exponential phase exposure to 0.2 ppm; whereas in the respiratory cultures, 14.6 adducts/109 nucleotides were detected. No cytotoxicity was obtained in any experiment. Our study showed that yeast could be used to analyse DNA adducts as biomarkers of exposure to environmental toxicants.

The formation, reactivity, and fate of oxygen-containing organic compounds in petroleum-contaminated groundwaters: A state of the science review and future research directions

Hydrocarbon (HC) contamination in groundwater (GW) is a widespread environmental issue. Dissolved hydrocarbons in water are commonly utilized as an energy source by natural microbial communities, which can produce water soluble intermediate metabolite compounds, herein referred to as oxygen containing organic compounds (OCOCs), before achieving complete mineralization. This review aims to provide a comprehensive assessment of the literature focused on the state of the science for OCOCs detected and measured in GW samples collected from petroleum contaminated aquifers. In this review, we discuss and evaluate two hypotheses investigating OCOC formation, which are major points of contention in the freshwater oil spill community that need to be addressed. We reviewed over 150 articles compiling studies investigating OCOC formation and persistence to uncover knowledge gaps in the literature and studies that recommend quantitative and qualitative measurements of OCOCs in petroleum-contaminated aquifers. This review is essential because no consensus exists regarding specific compounds and related concerns. We highlight the knowledge gaps to progressing the discussion of hydrocarbon conversion products.

The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities

In microbial systems, a metabolic pathway can be either completed by one autonomous population or distributed among a consortium performing metabolic division of labor (MDOL). MDOL facilitates the system's function by reducing the metabolic burden; however, it may hinder the function by reducing the exchange efficiency of metabolic intermediates among individuals. As a result, the function of a community is influenced by the trade-offs between the metabolic specialization and versatility of individuals. To experimentally test this hypothesis, we deconstructed the naphthalene degradation pathway into four steps and introduced them individually or combinatorically into different strains with varying levels of metabolic specialization. Using these strains, we engineered 1,456 synthetic consortia and found that 74 consortia exhibited higher degradation function than both the autonomous population and rigorous MDOL consortium. Quantitative modeling provides general strategies for identifying the most effective MDOL configuration. Our study provides critical insights into the engineering of high-performance microbial systems.

DhDIT2 Encodes a Debaryomyces hansenii Cytochrome P450 Involved in Benzo(a)pyrene Degradation-A Proposal for Mycoremediation

Pollutants, such as polycyclic aromatic hydrocarbons (PAHs), e.g., benzo(a)pyrene (BaP), are common components of contaminating mixtures. Such compounds are ubiquitous, extremely toxic, and they pollute soils and aquatic niches. The need for new microorganism-based remediation strategies prompted researchers to identify the most suitable organisms to eliminate pollutants without interfering with the ecosystem. We analyzed the effect caused by BaP on the growth properties of Candida albicans, Debaryomyces hansenii, Rhodotorula mucilaginosa, and Saccharomyces cerevisiae. Their ability to metabolize BaP was also evaluated. The aim was to identify an optimal candidate to be used as the central component of a mycoremediation strategy. The results show that all four yeast species metabolized BaP by more than 70%, whereas their viability was not affected. The best results were observed for D. hansenii. When an incubation was performed in the presence of a cytochrome P450 (CYP) inhibitor, no BaP degradation was observed. Thus, the initial oxidation step is mediated by a CYP enzyme. Additionally, this study identified the D. hansenii DhDIT2 gene as essential to perform the initial degradation of BaP. Hence, we propose that D. hansenii and a S. cerevisiae expressing the DhDIT2 gene are suitable candidates to degrade BaP in contaminated environments.

A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils

The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.

Leaching of microplastic-associated additives in aquatic environments: A critical review

Microplastic pollution has attracted significant attention as an emerging global environmental problem. One of the most important issues with microplastics is the leaching of harmful additives. This review summarizes the recent advances in the understanding of the leaching phenomena in the context of the phase equilibrium between microplastics and water, and the release kinetics. Organic additives, which are widely used in plastic products, have been introduced because they have diverse physicochemical properties and mass fractions in plastics. Many theoretical and empirical models have been utilized in laboratory and field studies. However, the partition or distribution constant between microplastics and water (K_p) and the diffusivity of an additive in microplastics (D) are the two key properties explaining the leaching equilibrium and kinetics of hydrophobic organic additives. Because microplastics in aquatic environments undergo dynamic weathering, leaching of organic additives with high K_p and/or low D cannot be described by a leaching model that only considers microplastic and water phases with a fixed boundary. Surface modifications of microplastics as well as biofilms colonizing microplastic surfaces can alter the leaching equilibrium and kinetics and transform additives. Further studies on the release of hydrophobic organic additives and their transformation products under various conditions are required to extend our understanding of the environmental fate and transport of these additives in aquatic environments.

Widespread Ability of Ligninolytic Fungi to Degrade Hazardous Organic Pollutants as the Basis for the Self-Purification Ability of Natural Ecosystems and for Mycoremediation Technologies

The ability of sixteen wood- and soil-inhabiting basidiomycete strains and four ascomycete strains to degrade the most hazardous, widespread, and persistent pollutants (polycyclic aromatic hydrocarbons, oxyethylated nonylphenol, alkylphenol, anthraquinone-type synthetic dyes, and oil) was found. The disappearance of the pollutants, their main metabolites, and some adaptive properties (activities of ligninolytic enzymes, the production of emulsifying compounds and exopolysaccharides) were evaluated. The toxicity of polycyclic aromatic hydrocarbons decreased during degradation. New data were obtained regarding (1) the dependence of the completeness of polycyclic aromatic hydrocarbon degradation on the composition of the ligninolytic enzyme complex; (2) the degradation of neonol AF9-12 by higher fungi (different accessibilities of the oxyethyl chain and the aromatic ring of the molecules to different fungal genera); and (3) the production of an emulsifying agent in response to the presence in the cultivation medium of hydrophobic pollutants as the common property of wood- and soil-inhabiting basidiomycetes and ascomycetes. Promise for use in mycoremediation was shown in the wood-inhabiting basidiomycetes Pleurotus ostreatus f. Florida, Schizophyllum commune, Trametes versicolor MUT 3403, and Trametes versicolor DSM11372; the litter-decomposing basidiomycete Stropharia rugosoannulata; and the ascomycete Cladosporium herbarum. These fungi degrade a wide range of pollutants without accumulation of toxic metabolites and produce ligninolytic enzymes and emulsifying compounds.

Biodiversity and biocatalyst activity of culturable hydrocarbonoclastic fungi isolated from Marac-Moruga mud volcano in South Trinidad

Mud volcanoes (MVs) are visible signs of oil and gas reserves present deep beneath land and sea. The Marac MV in Trinidad is the only MV associated with natural hydrocarbon seeps. Petrogenic polyaromatic hydrocarbons (PAHs) in its sediments must undergo biogeochemical cycles of detoxification as they can enter the water table and aquifers threatening ecosystems and biota. Recurrent hydrocarbon seep activity of MVs consolidates the growth of hydrocarbonoclastic fungal communities. Fungi possess advantageous metabolic and ecophysiological features for remediation but are underexplored compared to bacteria. Additionally, indigenous fungi are more efficient at PAH detoxification than commercial/foreign counterparts and remediation strategies remain site-specific. Few studies have focused on hydrocarbonoclastic fungal incidence and potential in MVs, an aspect that has not been explored in Trinidad. This study determined the unique biodiversity of culturable fungi from the Marac MV capable of metabolizing PAHs in vitro and investigated their extracellular peroxidase activity to utilize different substrates ergo their extracellular oxidoreductase activity (> 50% of the strains decolourized of methylene blue dye). Dothideomycetes and Eurotiomycetes (89% combined incidence) were predominantly isolated. ITS rDNA sequence cluster analysis confirmed strain identities. 18 indigenous hydrocarbonoclastic strains not previously reported in the literature and some of which were biosurfactant-producing, were identified. Intra-strain variability was apparent for PAH utilization, oil-tolerance and hydroxylase substrate specificity. Comparatively high levels of extracellular protein were detected for strains that demonstrated low substrate specificity. Halotolerant strains were also recovered which indicated marine-mixed substrata of the MV as a result of deep sea conduits. This work highlighted novel MV fungal strains as potential bioremediators and biocatalysts with a broad industrial applications.

Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation

Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.

Dioxin impacts on lipid metabolism of soil microbes: towards effective detection and bioassessment strategies

Dioxins are the most toxic known environmental pollutants and are mainly formed by human activities. Due to their structural stability, dioxins persist for extended periods and can be transported over long distances from their emission sources. Thus, dioxins can be accumulated to considerable levels in both human and animal food chains. Along with sediments, soils are considered the most important reservoirs of dioxins. Soil microorganisms are therefore highly exposed to dioxins, leading to a range of biological responses that can impact the diversity, genetics and functional of such microbial communities. Dioxins are very hydrophobic with a high affinity to lipidic macromolecules in exposed organisms, including microbes. This review summarizes the genetic, molecular and biochemical impacts of dioxins on the lipid metabolism of soil microbial communities and especially examines modifications in the composition and architecture of cell membranes. This will provide a useful scientific benchmark for future attempts at soil ecological risk assessment, as well as in identifying potential dioxin-specific-responsive lipid biomarkers. Finally, potential uses of lipid-sequestering microorganisms as a part of biotechnological approaches to the bio-management of environmental contamination with dioxins are discussed.

Network Analysis for Prioritizing Biodegradation Metabolites of Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are a diverse group of environmental contaminants released during the combustion of organic materials and the production and utilization of fossil fuels. Once released, PAHs deposit in soil and water bodies where they are subjected to environmental transport and transformations. As they degrade, intermediate transformation products may play an important role in their environmental impact. However, studying the effects of these degradation products has proven challenging because of the complexity, transience, and low concentration of many intermediates. Herein, a novel integration of a pathway prediction system and network theory was developed and applied to a set of four PAHs to demonstrate a possible solution to this challenge. Network analysis techniques were employed to refine the thousands of potential outputs and elucidate compounds of interest. Using these tools, we determined correlations between PAH degradation network data and intermediate metabolite structures, gaining information about the chemical characteristics of compounds based on their placement within the degradation network. Upon applying our developed filtering algorithm, we are able to predict up to 48% of the most common transformation products identified in a comprehensive empirical literature review. Additionally, our integrated approach uncovers potential metabolites which connect those found by past empirical studies but are currently undetected, thereby filling in the gaps of information in PAH degradation pathways.

Potential of Inactivated Bifidobacterium Strain in Attenuating Benzo(A)Pyrene Exposure-Induced Damage in Colon Epithelial Cells In Vitro

Long-term exposure to benzo(a)pyrene (BaP) poses a serious genotoxic threat to human beings. This in vitro study investigated the potential of inactivated Bifidobacterium animalis subsp. lactis BI-04 in alleviating the damage caused by BaP in colon epithelial cells. A concentration of BaP higher than 50 μM strongly inhibited the growth of colon epithelial cells. The colon epithelial cells were treated with 50 μM BaP in the presence or absence of inactivated strain BI-04 (~5 × 10⁸ CFU/mL). The BaP-induced apoptosis of the colon epithelial cells was retarded in the presence of B. lactis BI-04 through activation of the PI3K/ AKT signaling pathway, and p53 gene expression was decreased. The presence of the BI-04 strain reduced the intracellular oxidative stress and DNA damage incurred in the colon epithelial cells by BaP treatment due to the enhanced expression of antioxidant enzymes and metabolism-related enzymes (CYP1A1). The data from comet assay, qRT-PCR, and western blot analysis showed that the cytotoxic effects of BaP on colon epithelial cells were largely alleviated because the bifidobacterial strain could bind to this carcinogenic compound. The in vitro study highlights that the consumption of commercial probiotic strain BI-04 might be a promising strategy to mitigate BaP cytotoxicity.

Hydroxylated polycyclic aromatic hydrocarbons in surface soil in an emerging urban conurbation in South China

To investigate the effects of human activity on contaminants in regional soil, hydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) were measured in 187 surface soil samples of different land-use types collected from the Pearl River Delta (PRD), South China. The concentrations of Σ₉OH-PAH (sum of nine target analytes) ranged from 0.36 to 252ng/g (median: 5.98ng/g), with phenanthrene derivatives as the dominant components, accounting for ~70%. Among different land-use types, residency soil contained the highest levels of Σ₉OH-PAH (median: 11.3ng/g), followed by landfill soil (9.28ng/g), industry soil (7.51ng/g), agriculture soil (6.04ng/g), forestry soil (4.28ng/g) and drinking water source soil (4.20ng/g). A higher value was also observed in soil from the central PRD (6.94ng/g) than the surrounding areas (5.94ng/g), which indicated a significant impact of human activity on OH-PAH contamination in soil. Correlation and principal component analysis indicated that OH-PAHs in PRD soil are likely derived from the degradation of their parent PAHs in the atmosphere and/or soil and not directly from the same source as the parent PAHs. The ratios of OH-PAHs to their parent PAHs also varied among different land-use types, which may be partly attributed to the different populations of microorganisms in different soil types or the different chemical properties of PAHs and their metabolites.

Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

Pyrene degradation by marine-derived ascomycete: process optimization, toxicity, and metabolic analyses

Marine-derived fungi are relevant genetic resources for bioremediation of saline environments/processes. Among the five fungi recovered from marine sponges able to degrade pyrene (Py) and benzo[a]pyrene (BaP), Tolypocladium sp. strain CBMAI 1346 and Xylaria sp. CBMAI 1464 presented the best removal rates of Py and BaP, respectively. Since the decrease in BaP was related to mycelial adsorption, a combined strategy was applied for the investigation of Py degradation by the fungus Tolypocladium sp. CBMAI 1346. The selected fungus was able to degrade about 95% of Py after 7 days of incubation (optimized conditions), generating metabolites different from the ones found before optimization. Metabolites and transcriptomic data revealed that the degradation occurred mainly by the cytochrome P450 pathway. Putative monooxygenases and dioxygenases found in the transcriptome may play an important role. After 21 days of degradation, no toxicity was found in the optimized culture conditions. The findings from the present study highlight the potential of marine-derived fungi to degrade environmental pollutants and convey innovative information related to the metabolism of pyrene.

Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia

Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.

State of the art and future challenges for polycyclic aromatic hydrocarbons is sediments: sources, fate, bioavailability and remediation techniques

Polycyclic aromatic hydrocarbons (PAHs) are amongst the most abundant contaminants found in the aquatic environment. Due to their toxicity and carcinogenicity, their sources, fate, behaviour, and cleanup techniques have been widely investigated in the last several decades. When entering the sediment-water system, PAH fate is determined by particular PAH and sediment physico-chemical properties. Most of the PAHs will be associated with fine-grained, organic-rich, sediment material. This makes sediment an ultimate sink for these pollutants. This association results in sediment contamination, and in this manner, sediments represent a permanent source of water pollution from which benthic organisms may accumulate toxic compounds, predominantly in lipid-rich tissues. A tendency for biomagnification can result in critical body burdens in higher trophic species. In recent years, researchers have developed numerous methods for measuring bioavailable fractions (chemical methods, non-exhaustive extraction, and biomimetic methods), as valuable tools in a risk-based approach for remediation or management of contaminated sites. Contaminated sediments pose challenging cleanup and management problems, as conventional environmental dredging techniques are invasive, expensive, and sometimes ineffective or hard to apply to large and diverse sediment sites. Recent studies have shown that a combination of strategies including in situ approaches is likely to provide the most effective long-term solution for dealing with contaminated sediments. Such in situ approaches include, but are not limited to: bioaugmentation, biostimulation, phytoremediation, electrokinetic remediation, surfactant addition and application of different sorbent amendments (carbon-rich such as activated carbon and biochar) that can reduce exposure and limit the redistribution of contaminants in the environment.

The cytochrome P450BM-1 of Bacillus megaterium A14K is induced by 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin: Biophysical, molecular and biochemical determinants

The current study describes biological changes in Bacillus megaterium A14K cells growing in the presence of 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin (TCDD), the most potent congener of dioxins. The results indicate that the metabolizing of 2,3,7,8-TCDD by BmA14K was accompanied with a novel morphological and biophysical profile typified by the growth of single cells with high levels of biosurfactant production, surface hydrophobicity and cell membrane permeability. Moreover, the TCDD-grown bacteria exhibited a specific fatty acid profile characterized by low ratios of branched/straight chain fatty acids (BCFAs/SCFAs) and saturated/unsaturated fatty acids (SFAs/USFAs) with a specific "signature" due to the presence of branched chain unsaturated fatty acids (BCUFAs). This was synchronized with a significant induction of P450_BM-1, an unsaturated fatty acid-metabolizing enzyme in B. megaterium. Subsequently, the profile of oxygenated fatty acids in the TCDD-grown bacteria was typified by the presence of 5,6-epoxy derived from unsaturated C15, C16 and C17 fatty acids, that were absent in control bacteria. A net increase was also detected in both hydroxylated and epoxidized fatty acids, especially those derived from C15:0 and C16:1, respectively, suggesting a specific TCDD-induced "signature" of oxygenated fatty acids in BmA14K. Overall, this study sheds light on the use of B. megaterium A14K as a promising bioindicator/biodegrader of dioxins.

Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils

Soil pollution is an unavoidable evil; many crude-oil exploring communities have been identified to be the most ecologically impacted regions around the world due to hydrocarbon pollution and their concurrent health risks. Several clean-up technologies have been reported on the removal of hydrocarbons in polluted soils but most of them are either very expensive, require the integration of advanced mechanization and/or cannot be implemented in small scale. However, "Bioremediation" has been reported as an efficient, cost-effective and environment-friendly technology for clean-up of hydrocarbon"s contaminated soils. Here, we suggest the implementation of synergistic mechanism of bioremediation such as the use of rhizosphere mechanism which involves the actions of plant and microorganisms, which involves the exploitation of plant and microorganisms for effective and speedy remediation of hydrocarbon"s contaminated soils. In this mechanism, plant"s action is synergized with the soil microorganisms through the root rhizosphere to promote soil remediation. The microorganisms benefit from the root metabolites (exudates) and the plant in turn benefits from the microbial recycling/solubilizing of mineral nutrients. Harnessing the abilities of plants and microorganisms is a potential headway for cost-effective clean-up of hydrocarbon"s polluted sites; such technology could be very important in countries with great oil producing activities/records over many years but still developing.

Distributions and compositional patterns of polycyclic aromatic hydrocarbons (PAHs) and their derivatives in three edible fishes from Kharg coral Island, Persian Gulf, Iran

This is the first report on bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) and their derivatives (oxygen, nitrogen, sulfur, hydroxyl, carbonyl and methyl-containing PAHs) in three edible marine fishes, namely Lutjanus argentimaculatus, Lethrinus microdon and Scomberomorus guttatus, from Kharg Island, Persian Gulf, Iran. The concentrations (ng g^-1dw) of Σ39PAHs resulted significantly higher in fish liver than muscle, with the PAH composition pattern dominated by low molecular weight compounds (naphthalene, alkyl-naphthalenes and phenanthrene). The highest mean concentrations of ∑9 oxygenated and ∑15 hydroxylated PAHs (ng g^-1dw) were found ound in L. microdon and L. argentimaculatus, respectively, while the lowest values in S. guttatus. Additionally, the highest mean concentrations of Σ5 carbonylic PAHs (ng g^-1dw) were found in L. argentimaculatus, followed by L. microdon. The PAHs levels and distribution in fish liver and muscle were dependent on both the K_ow of PAHs congeners and fish lipid contents. Overall, the present findings provide important baseline data for further research on the ecotoxicity of PAHs in aquatic organisms, and consequent implications for human health.

Catechol 1,2-Dioxygenase is an Analogue of Homogentisate 1,2-Dioxygenase in Pseudomonas chlororaphis Strain UFB2

Catechol dioxygenases in microorganisms cleave catechol into cis-cis-muconic acid or 2-hydroxymuconic semialdehyde via the ortho- or meta-pathways, respectively. The aim of this study was to purify, characterize, and predict the template-based three-dimensional structure of catechol 1,2-dioxygenase (C12O) from indigenous Pseudomonas chlororaphis strain UFB2 (PcUFB2). Preliminary studies showed that PcUFB2 could degrade 40 ppm of 2,4-dichlorophenol (2,4-DCP). The crude cell extract showed 10.34 U/mL of C12O activity with a specific activity of 2.23 U/mg of protein. A 35 kDa protein was purified to 1.5-fold with total yield of 13.02% by applying anion exchange and gel filtration chromatography. The enzyme was optimally active at pH 7.5 and a temperature of 30 °C. The Lineweaver⁻Burk plot showed the v_max and K_m values of 16.67 µM/min and 35.76 µM, respectively. ES-MS spectra of tryptic digested SDS-PAGE band and bioinformatics studies revealed that C12O shared 81% homology with homogentisate 1,2-dioxygenase reported in other Pseudomonas chlororaphis strains. The characterization and optimization of C12O activity can assist in understanding the 2,4-DCP metabolic pathway in PcUFB2 and its possible application in bioremediation strategies.

Genome analysis and -omics approaches provide new insights into the biodegradation potential of Rhodococcus

The past few years observed a breakthrough of genome sequences of bacteria of Rhodococcus genus with significant biodegradation abilities. Invaluable knowledge from genome data and their functional analysis can be applied to develop and design strategies for attenuating damages caused by hydrocarbon contamination. With the advent of high-throughput -omic technologies, it is currently possible to utilize the functional properties of diverse catabolic genes, analyze an entire system at the level of molecule (DNA, RNA, protein, and metabolite), simultaneously predict and construct catabolic degradation pathways. In this review, the genes involved in the biodegradation of hydrocarbons and several emerging plasticizer compounds in Rhodococcus strains are described in detail (aliphatic, aromatics, PAH, phthalate, polyethylene, and polyisoprene). The metabolic biodegradation networks predicted from omics-derived data along with the catabolic enzymes exploited in diverse biotechnological and bioremediation applications are characterized.

Mediational influence of spent mushroom compost on phytoremediation of black-oil hydrocarbon polluted soil and response of Megathyrsus maximus Jacq

Ability of a plant to develop different adaptive strategies can also determine its capability for effective soil remediation. In this study, influence of spent mushroom compost (SMC) was tested on the phytoremediation of black oil hydrocarbon polluted soil and the response of Megathyrsus maximus (guinea grass). Studies were carried out in microcosm conditions by mixing different concentration of SMC viz., 10, 20, 30 and 40% in a 5 kg of contaminated soil along with control. Seeds of M. maximus was sown in tray for two weeks and allowed to grow for height of 10 cm and transplanted in to the different experimental pots. Soil nutrient, heavy metal and PAH contents were analyzed before and after the experiment. Ecophysiological and anatomical responses due to the contaminants in the soil by M. Maximus were analyzed after 120 days. Phytomass efficiency, potential photosynthesis (Amax) and contents of chlorophylls (a and b) as well as the total chlorophyll along with anatomical evaluations were recorded. Plant alone (control) reduced the soil heavy metal and PAH contents but further improvements were observed in SMC treatments, similar results were also observed as regards to the plant's phytoremediation efficiency (PE), phytomass and potential photosynthetic rates (m mol O₂ M^-2S^-1). The plant's root and shoot anatomical responses were enhanced in treatments compared to control, study infers that the treatment enhances the biostimulation and development of adaptive characteristics for M. maximus survival in contaminated soils and promotes its co-degradation of hydrocarbon. SMC supports remediation and as well enhances the anatomical evaluations, we therefore recommend the use of SMC on response of Megathyrsus maximus Jacq for remediation of petrochemical based phytoremediation.

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by fungal enzymes: A review

Polycyclic aromatic hydrocarbons (PAHs) are a large group of chemicals. They represent an important concern due to their widespread distribution in the environment, their resistance to biodegradation, their potential to bioaccumulate and their harmful effects. Several pilot treatments have been implemented to prevent economic consequences and deterioration of soil and water quality. As a promising option, fungal enzymes are regarded as a powerful choice for degradation of PAHs. Phanerochaete chrysosporium, Pleurotus ostreatus and Bjerkandera adusta are most commonly used for the degradation of such compounds due to their production of ligninolytic enzymes such as lignin peroxidase, manganese peroxidase and laccase. The rate of biodegradation depends on many culture conditions, such as temperature, oxygen, accessibility of nutrients and agitated or shallow culture. Moreover, the addition of biosurfactants can strongly modify the enzyme activity. The removal of PAHs is dependent on the ionization potential. The study of the kinetics is not completely comprehended, and it becomes more challenging when fungi are applied for bioremediation. Degradation studies in soil are much more complicated than liquid cultures because of the heterogeneity of soil, thus, many factors should be considered when studying soil bioremediation, such as desorption and bioavailability of PAHs. Different degradation pathways can be suggested. The peroxidases are heme-containing enzymes having common catalytic cycles. One molecule of hydrogen peroxide oxidizes the resting enzyme withdrawing two electrons. Subsequently, the peroxidase is reduced back in two steps of one electron oxidation. Laccases are copper-containing oxidases. They reduce molecular oxygen to water and oxidize phenolic compounds.

Bioremediation of Polycyclic Aromatic Hydrocarbon (PAHs): A Perspective

Hydrocarbon pollution is a perennial problem not only in India but throughout the globe. A plethora of microorganisms have been reported to be efficient degraders of these recalcitrant pollutants. One of the major concerns of environmental problem is the presence of hydrocarbons due to the various anthropogenic activities. PAHs are ubiquitous in naturei.e.present in soil, water and air. Presence of PAHs in environment creates problem as their presence have deleterious effect on human and animals. They also have the ability to cause the tumors in human and animals. Some of the microorganisms are capable of transforming and degrading these PAHs and remove them from the environment. The present review describes about the sources, structure, fate and toxicity of PAHs as well as different bioremediation techniques involved in the removing of contaminants from the environment which are efficient and cost-effective. The conventional approaches used for removal of PAH are not only environment friendly but also are able to reduce the risk to human and ecosystem.

Emerging trends in photodegradation of petrochemical wastes: a review

Various human activities like mining and extraction of mineral oils have been used for the modernization of society and well-beings. However, the by-products such as petrochemical wastes generated from such industries are carcinogenic and toxic, which had increased environmental pollution and risks to human health several folds. Various methods such as physical, chemical and biological methods have been used to degrade these pollutants from wastewater. Advance oxidation processes (AOPs) are evolving techniques for efficient sequestration of chemically stable and less biodegradable organic pollutants. In the present review, photocatalytic degradation of petrochemical wastes containing monoaromatic and poly-aromatic hydrocarbons has been studied using various heterogeneous photocatalysts (such as TiO₂, ZnO and CdS. The present article seeks to offer a scientific and technical overview of the current trend in the use of the photocatalyst for remediation and degradation of petrochemical waste depending upon the recent advances in photodegradation of petrochemical research using bibliometric analysis. We further outlined the effect of various heterogeneous catalysts and their ecotoxicity, various degradation pathways of petrochemical wastes, the key regulatory parameters and the reactors used. A critical analysis of the available literature revealed that TiO₂ is widely reported in the degradation processes along with other semiconductors/nanomaterials in visible and UV light irradiation. Further, various degradation studies have been carried out at laboratory scale in the presence of UV light. However, further elaborative research is needed for successful application of the laboratory scale techniques to pilot-scale operation and to develop environmental friendly catalysts which support the sustainable treatment technology with the "zero concept" of industrial wastewater. Nevertheless, there is a need to develop more effective methods which consume less energy and are more efficient in pilot scale for the demineralization of pollutant.

Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review

Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.

A Critical Review about the Health Risk Assessment of PAHs and Their Metabolites in Foods

Polycyclic aromatic hydrocarbons (PAHs) are a family of toxicants that are ubiquitous in the environment. These contaminants generate considerable interest, because some of them are highly carcinogenic in laboratory animals and have been implicated in breast, lung, and colon cancers in humans. Dietary intake of PAHs constitutes a major source of exposure in humans. Factors affecting the accumulation of PAHs in the diet, their absorption following ingestion, and strategies to assess risk from exposure to these hydrocarbons following ingestion have received very little attention. This review, therefore, focuses on concentrations of PAHs in widely consumed dietary ingredients along with gastrointestinal absorption rates in humans. Metabolism and bioavailability of PAHs in animal models and the processes, which influence the disposition of these chemicals, are discussed. Finally, based on intake, disposition, and tumorigenesis data, the exposure risk to PAHs from diet is presented. This information is expected to provide a framework for refinements in risk assessment of PAHs.

Application of compost for effective bioremediation of organic contaminants and pollutants in soil

Soils contaminated with hazardous chemicals worldwide are awaiting remediation activities; bioremediation is often considered as a cost-effective remediation approach. Potential bioapproaches are biostimulation, e.g. by addition of nutrients, fertiliser and organic substrates, and bioaugmentation by addition of compound-degrading microbes or of organic amendments containing active microorganisms, e.g. activated sludge or compost. In most contaminated soils, the abundance of the intrinsic metabolic potential is too low to be improved by biostimulation alone, since the physical and chemical conditions in these soils are not conducive to biodegradation. In the last few decades, compost or farmyard manure addition as well as composting with various organic supplements have been found to be very efficient for soil bioremediation. In the present minireview, we provide an overview of the composting and compost addition approaches as 'stimulants' of natural attenuation. Laboratory degradation experiments are often biased either by not considering the abiotic factors or by focusing solely on the elimination of the chemicals without taking the biotic factors and processes into account. Therefore, we first systemise the concepts of composting and compost addition, then summarise the relevant physical, chemical and biotic factors and mechanisms for improved contaminant degradation triggered by compost addition. These factors and mechanisms are of particular interest, since they are more relevant and easier to determine than the composition of the degrading community, which is also addressed in this review. Due to the mostly empirical knowledge and the nonstandardised biowaste or compost materials, the field use of these approaches is highly challenging, but also promising. Based on the huge metabolic diversity of microorganisms developing during the composting processes, a highly complex metabolic diversity is established as a 'metabolic memory' within developing and mature compost materials. Compost addition can thus be considered as a 'super-bioaugmentation' with a complex natural mixture of degrading microorganisms, combined with a 'biostimulation' by nutrient containing readily to hardly degradable organic substrates. It also improves the abiotic soil conditions, thus enhancing microbial activity in general. Finally, this minireview also aims at guiding potential users towards full exploitation of the potentials of this approach.

Determination of oxygen, nitrogen, and sulfur-containing polycyclic aromatic hydrocarbons (PAHs) in urban stream sediments

Recent studies indicate that PAH transformation products such as ketone or quinone-substituted PAHs (OPAHs) are potent aryl hydrocarbon receptor (AhR) activators that elicit toxicological effects independent of those observed for PAHs. Here, we measured eight OPAHs, two sulfur-containing (SPAH), one oxygen-containing (DBF), and one nitrogen-containing (CARB) heterocyclic PAHs (i.e. ΣONS-PAHs = OPAH8 + SPAH + DBF + CARB) in 35 stream sediments collected from a small (∼1303 km(2)) urban watershed located in south-central Pennsylvania, USA. Combined ΣONS-PAH concentrations ranged from 59 to 1897 μg kg(-1) (mean = 568 μg kg(-1); median = 425 μg kg(-1)) and were 2.4 times higher in urban versus rural areas, suggesting that activities taking place on urban land serve as a source of ΣONS-PAHs to sediments. To evaluate urban land use metrics that might explain these data, Spearman rank correlation analyses was used to evaluate the degree of association between ΣONS-PAH concentrations and urban land-use/land-cover metrics along an urban-rural transect at two spatial scales (500-m and 1000-m upstream). Combined ΣONS-PAH concentrations showed highly significant (p < 0.0001) correlations with ΣPAH19, residential and commercial/industrial land use (RESCI), and combined state and local road miles (MILES), suggesting that ΣONS-PAHs originate from similar sources as PAHs. To evaluate OPAH sources, a subset of ΣONS-PAHs for which reference assemblages exist, an average OPAH fractional assemblage for urban sediments was derived using agglomerative hierarchal cluster (AHC) analysis, and compared to published OPAH source profiles. Urban sediments from the Condoguinet Creek (n = 21) showed highly significant correlations with urban particulate matter (X(2) = 0.05, r = 0.91, p = 0.0047), suggesting that urban particulate matter is an important OPAH source to sediments in this watershed. Results suggest the inclusion of ΣONS-PAH measurements adds value to traditional PAH analyses, and may help elucidate and refine pollutant source identification in urban watersheds.

Disturbance in testosterone production in leydig cells by polycyclic aromatic hydevrepocarbons

Polycyclic aromatic hydevrepocarbons (PAHs), which are ubiquitous in the air, are present as volatile and particulate pollutants that result from incomplete combustion. Most PAHs have toxic, mutagenic, and/or carcinogenic properties. Among PAHs, benzo[a]pyrene (B[a]P) and dimethylbenz[a]anthracene (DMBA) are suspected endocrine disruptors. The testis is an important target for PAHs, yet effects on steroidogenesis in Leydig cells are yet to be ascertained. Particularly, disruption of testosterone production by these chemicals can result in serious defects in male reproduction. Exposure to B[a]P reduced serum and intratesticular fluid testosterone levels in rats. Of note, the testosterone level reductions were accompanied by decreased steroidogenic acute regulatory protein (StAR) and 3β-hydevrepoxysteroid dehydevrepogenase isomerase (3β-HSD) expression in Leydig cells. B[a]P exposure can decrease epididymal sperm quality, possibly by disturbing the testosterone level. StAR may be a key steroidogenic protein that is targeted by B[a]P or other PAHs.

Disturbance in testosterone production in leydig cells by polycyclic aromatic hydevrepocarbons

Polycyclic aromatic hydrocarbons (PAHs), which are ubiquitous in the air, are present as volatile and particulate pollutants that result from incomplete combustion. Most PAHs have toxic, mutagenic, and/or carcinogenic properties. Among PAHs, benzo[a]pyrene (B[a]P) and dimethylbenz[a]anthracene (DMBA) are suspected endocrine disruptors. The testis is an important target for PAHs, yet effects on steroidogenesis in Leydig cells are yet to be ascertained. Particularly, disruption of testosterone production by these chemicals can result in serious defects in male reproduction. Exposure to B[a]P reduced serum and intratesticular fluid testosterone levels in rats. Of note, the testosterone level reductions were accompanied by decreased steroidogenic acute regulatory protein (StAR) and 3β-hydroxysteroid dehydrogenase isomerase (3β-HSD) expression in Leydig cells. B[a]P exposure can decrease epididymal sperm quality, possibly by disturbing the testosterone level. StAR may be a key steroidogenic protein that is targeted by B[a]P or other PAHs.

Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology

The remediation of polluted sites has become a priority for society because of increase in quality of life standards and the awareness of environmental issues. Over the past few decades there has been avid interest in developing in situ strategies for remediation of environmental contaminants, because of the high economic cost of physicochemical strategies, the biological tools for remediation of these persistent pollutants is the better option. Major foci have been considered on persistent organic chemicals i.e. polyaromatic hydrocarbons (PAHs) due to their ubiquitous occurrence, recalcitrance, bioaccumulation potential and carcinogenic activity. Rhizoremediation, a specific type of phytoremediation that involves both plants and their associated rhizospheric microbes is the creative biotechnological approach that has been explored in this review. Moreover, in this review we showed the significance of rhizoremediation of PAHs from other bioremediation strategies i.e. natural attenuation, bioaugmentation and phytoremediation and also analyze certain environmental factor that may influence the rhizoremediation technique. Numerous bacterial species were reported to degrade variety of PAHs and most of them are isolated from contaminated soil, however few reports are available from non contaminated soil. Pseudomonas aeruginosa , Pseudomons fluoresens , Mycobacterium spp., Haemophilus spp., Rhodococcus spp., Paenibacillus spp. are some of the commonly studied PAH-degrading bacteria. Finally, exploring the molecular communication between plants and microbes, and exploiting this communication to achieve better results in the elimination of contaminants, is a fascinating area of research for future perspective.

A combined chemical and biological approach to transforming and mineralizing PAHs in runoff water

The water quality of lakes, rivers and streams associated with metropolitan areas is declining from increased inputs of urban runoff that contain polycyclic aromatic hydrocarbons (PAHs). Our objective was to transform and mineralize PAHs in runoff using a combined chemical and biological approach. Using (14)C-labeled phenanthrene, (14)C-benzo(a)pyrene and a mixture of 16 PAHs, we found that ozone transformed all PAHs in a H2O matrix within minutes but complete mineralization to CO2 took several weeks. When urban runoff water (7.6 mg CL(-1)) replaced H2O as the background matrix, some delays in degradation rates were observed but transforming a mixture of PAHs was still complete within 10 min. Comparing the biodegradability of the ozonated products to the parent structures in unsaturated soil microcosms showed that the 3-ring phenanthrene was more biodegradable (as evidence by (14)CO2 released) than its ozonated products but for the 5-ring benzo(a)pyrene, the products produced by ozone were much more biodegradable (22% vs. 3% mineralized). For phenanthrene, we identified diphenaldehyde as the initial degradation product produced from ozonation. By continuing to pump the ozonated products ((14)C-labeled diphenaldehyde or ozone-treated benzo(a)pyrene) onto glass beads coated with microorganisms, we verified that biological mineralization could be achieved in a flow-through system and mineralization rates improved with acclimation of the microbial population (i.e., time and exposure to the substrate). These results support a combined ozone and biological approach to treating PAHs in urban runoff water.

Biodegradation of Benzo[a]Pyrene through the use of algae

In this work for disposal of the biologically hard decomposed pollutant Benzo[a]Pyrene (BaP) photooxidation Chlorella kessleri was used. The simulation model system under the different experimental conditions (varying biomass and light intensity) was evaluated. For quantitative analysis of the decrease in BaP, GC/MS technique was used. The highest degradation efficiency was achieved in the case of biomass from the culture of live algae (29%) and light intensity at level of 13.5 W m−2. When the dry biomass was used, degradation under the same conditions was lower because of lack of enzymatic activity in the system.

Changes in the concentration and relative abundance of alkanes and PAHs from the Deepwater Horizon oiling of coastal marshes

We determined changes of 28 alkanes and 43 different PAHs in 418 wetland soil samples collected on ten sampling trips to three Louisiana estuaries before and after they were oiled from the 2010 Deepwater Horizon disaster. There was a significant decline in 22 of the 28 alkane analytes (0.42% day(-1)), no change in 6, over 2.5 years. The concentration of five aromatic petroleum hydrocarbons (PAHs) increased (range 0.25-0.70% day(-1)), whereas the total PAH pool did not change. Of these five, naphthalene and C-1-naphthalenes are suggested to be of higher toxicity than the other three because of their relatively higher volatility or solubility. The relative proportions of alkane analytes, but not PAHs, does not yet resemble that in the pre-oiled marshes after 3 years, The trajectories of nine indicators for degradation/weathering were either inconclusive or misleading (alkanes) or confirmed the relatively meager degradation of PAHs.

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.

Experimental results and integrated modeling of bacterial growth on an insoluble hydrophobic substrate (phenanthrene)

Metabolism of a low-solubility substrate is limited by dissolution and availability and can hardly be determined. We developed a numerical model for simultaneously calculating dissolution kinetics of such substrates and their metabolism and microbial growth (Monod kinetics with decay) and tested it with three aerobic phenanthrene (PHE) degraders: Novosphingobium pentaromativorans US6-1, Sphingomonas sp. EPA505, and Sphingobium yanoikuyae B1. PHE was present as microcrystals, providing non-limiting conditions for growth. Total PHE and protein concentration were tracked over 6-12 days. The model was fitted to the test results for the rates of dissolution, metabolism, and growth. The strains showed similar efficiency, with vmax values of 12-18 g dw g(-1) d(-1), yields of 0.21 g g(-1), maximum growth rates of 2.5-3.8 d(-1), and decay rates of 0.04-0.05 d(-1). Sensitivity analysis with the model shows that (i) retention in crystals or NAPLs or by sequestration competes with biodegradation, (ii) bacterial growth conditions (dissolution flux and resulting chemical activity of substrate) are more relevant for the final state of the system than the initial biomass, and (iii) the desorption flux regulates the turnover in the presence of solid-state, sequestered (aged), or NAPL substrate sources.

A study of the phototoxic effect of Benzo[a] Pyrene on bacteria

Although Benzo[a]Pyrene (BaP) released to soils tends to bind very strongly to soil particles, however, small amounts have been shown to leach into groundwaters. This polycyclic aromatic hydrocarbon is stable and can stay (and travel) in the environment for an extended period of time. Release of BaP into the environment therefore causes concern at a global environmental level. In this paper we evaluated the effect of BaP on the cell growth of Escherichia coli and Enterococcus faecalis in aerobic conditions. Irradiation of BaP increased its antibacterial activity which suggests that this process produced a singlet oxygen. This way would be able to speed up the processes of photochemical degradation of BaP.

Comparative Bioremediation of Oil Contaminated Soil by Natural Attenuation, Biostimulation and Bioaugmentation

In most field studies, enhancing biodegradation of petroleum hydrocarbons depends on the specific microbial population present. It is a dispute whether inoculation microbial consortium improved the degradation of petroleum because indigenous microorganism can easily adapt to surroundings and contend for inoculation microbial consortium. Therefore, all of three technologies (natural attenuation, biostimulation and bioaugmentation) were evaluated. After 8 weeks of bioremediation, it was observed that bioaugmentation most effectively removed 53% of oil under inoculation condition. Poor oil removal of below 4% was observed under natural attenuation without inoculation. In addition, it was found that the degradation of oil in oil-polluted soil followed second-order model and acquired the dynamics equations. The half-life of natural attenuation, biostimulation and bioaugmentation was 833 days, 75days, 25days, respectively. The results indicated bioaugmentation could improve efficiently the degradation of TPH and shorten the bioremediation period.

Endophytic Burkholderia fungorum DBT1 can improve phytoremediation efficiency of polycyclic aromatic hydrocarbons

Burkholderia fungorum DBT1 is a bacterial strain isolated from an oil refinery discharge and capable of transforming dibenzothiophene, phenanthrene, naphthalene, and fluorene. In order to evaluate the influence of a policyclic aromatic hydrocarbon (PAH)-transforming bacterial strain on the phytoremediation of organic contaminants, B. fungorum DBT1 was inoculated into hybrid poplar (Populus deltoides×Populus nigra). The poplar plants were grown for 18-wk with or without naphthalene, phenanthrene, fluorene and dibenzothiophene (488mgkg(-1) soil each) in non-sterile sand-peat substrate. Evidences were gained that B. fungorum DBT1 was present in high concentration in poplar root tissues (2.9-9.5×10(3)CFUg(-1)), while the strain was not detected in stem, leaves and rhizosphere. When poplar was planted in uncontaminated substrate, the infection caused negative effects on biomass index, leaves and stem dry weight, without showing however any disease symptoms. On the other hand, plants inoculated with the strain DBT1 resulted in better tolerance against the toxic effects of PAHs, in terms of root dry weight. Although the presence of plants acted as the main effective treatment for PAH dissipation (82-87%), the inoculum with DBT1 strain lead to the highest PAH abatement (up to 99%). In the present study, an environmental isolate with proper metabolic features was demonstrated to be possibly suitable as a poplar endophyte for improving microbe-assisted phytoremediation in PAH contaminated matrices.

Biodegradability of Corexit 9500 and dispersed South Louisiana crude oil at 5 and 25 °C

The reported persistence of the dioctyl sodium sulfosuccinate (DOSS) surfactant in Corexit 9500 in the oil plumes formed during the Deepwater Horizon oil spill has contributed to concerns regarding the biodegradability and bioavailability of dispersed oil and dispersants used as an oil spill countermeasure in the Gulf of Mexico. We studied the biodegradation of DOSS and dispersed South Louisiana crude oil (SLC) in laboratory microcosms. Two oil-degrading cultures from the Gulf of Mexico were isolated, one from the surface (meso) and one from close to the area of the Macondo well (cryo). Each was enriched on SLC, the former at 25 °C, the latter at 5 °C. Results indicated that the meso culture rapidly and completely degraded DOSS, alkanes, and aromatics. The cryo culture metabolized the same compounds but with a lag of 28 d and a remaining residual of iso-alkanes, n-C(30-35), and the 4-ring PAHs.