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Degradation of benzo[ a ]pyrene by bacterial isolates from human skin
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are some of the most widespread xenobiotic pollutants, with the potentially carcinogenic high molecular weight representatives being of particular interest. However, while in eukaryotes the cytochrome P450-mediated activation of benzo[a]pyrene (B[a]P) has become a model for metabolism-mediated carcinogenesis, the oxidative degradation of B[a]P by microbes is less well studied. This should be reason for concern as the human organ most exposed to environmental PAHs is the skin, which at the same time is habitat to a most diverse population of microbial commensals. Yet, nothing is known about the skin's microbiome potential to metabolise B[a]P. This study now reports on the isolation of 21 B[a]P-degrading microbes from human skin, 10 of which were characterised further. All isolates were able to degrade B[a]P as sole source of carbon and energy and degradation was found to be complete in at least 4 isolates. Substrate metabolism involved two transcripts that encode a putative DszA/NtaA-like monooxygenase and a NifH-like reductase, respectively. Analysis of the 16S-rRNA genes showed that the B[a]P-degrading isolates comprise Gram(+) as well as Gram(-) skin commensals, with Micrococci being predominant. Moreover, microbial B[a]P degradation was detected on all volunteers probed, indicating it to be a universal feature of the skin's microbiome. This article is protected by copyright. All rights reserved.
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... These include PAHs and nitrosamines, which have received the most attention because they are pro-carcinogens. Given that studies have revealed the existence of environmental microorganisms that have the ability to metabolize PAHs (Ghosal et al., 2016;Habe & Omori, 2003;Hadibarata et al., 2017;Hennessee & Li, 2016;Hesham et al., 2009;Husain, 2008;MacGillivray & Shiaris, 1993;Mallick, Chakraborty & Dutta, 2011;Mbachu, Chukwura & Mbachu, 2016;Sowada et al., 2014;Sutherland, 1992) and that bacteria with similar qualities exist on human skin (Sowada et al., 2017;Sowada et al., 2014) we looked for evidence of PAH metabolizing microbes on the oral mucosa. We used the same method that is used to detect PAH metabolizing microbes from environmental sites such as petroleum waste sites. ...
... These include PAHs and nitrosamines, which have received the most attention because they are pro-carcinogens. Given that studies have revealed the existence of environmental microorganisms that have the ability to metabolize PAHs (Ghosal et al., 2016;Habe & Omori, 2003;Hadibarata et al., 2017;Hennessee & Li, 2016;Hesham et al., 2009;Husain, 2008;MacGillivray & Shiaris, 1993;Mallick, Chakraborty & Dutta, 2011;Mbachu, Chukwura & Mbachu, 2016;Sowada et al., 2014;Sutherland, 1992) and that bacteria with similar qualities exist on human skin (Sowada et al., 2017;Sowada et al., 2014) we looked for evidence of PAH metabolizing microbes on the oral mucosa. We used the same method that is used to detect PAH metabolizing microbes from environmental sites such as petroleum waste sites. ...
... We used the same method that is used to detect PAH metabolizing microbes from environmental sites such as petroleum waste sites. Oral samples were incubated long term with PAHs as the sole carbon source to select for PAH metabolizers (Hennessee & Li, 2016;Husain, 2008;Juhasz, Stanley & Britz, 2000;Sowada et al., 2014). ...
Certain soil microbes resist and metabolize polycyclic aromatic hydrocarbons (PAHs). The same is true for a subset of skin microbes. In the human mouth, oral microbes have the potential to oxidize tobacco PAHs, thereby increasing these chemicals’ ability to cause cancer of adjacent epithelium. We hypothesized that we could identify, in smokers, the oral mucosal microbes that can metabolize PAH. We isolated bacteria and fungi that survived long-term in minimal media with PAHs as the sole carbon source, under aerobic conditions, from the oral mucosa in 17 of 26 smokers and two of 14 nonsmokers. Of bacteria genera that survived harsh PAH exposure in vitro , most were found at trace levels, except for Staphylococcus , Actinomyces, and Kingella, which were more abundant. Two PAH-resistant strains of Candida albicans (C. albicans) were isolated from smokers. C. albicans was a prime candidate to contribute to carcinogenesis in tobacco users as it is found orally at high levels in tobacco users on the mucosa, and some Candida species can metabolize PAHs. However, when C. albicans isolates were tested for metabolism of two model PAH substrates, pyrene and phenanthrene, they were not capable, suggesting they cannot metabolize PAH under the conditions used. In conclusion, evidence for large scale microbial degradation of tobacco PAHs under aerobic conditions on the oral mucosa remains lacking, though nonabundant PAH metabolizers are certainly present.
... Specifically, cutaneous exposure to PAHs has been linked to changes in the physiological properties of the skin, potentially leading to pigmented spots [11] and cancer [19]. While specific members of the skin microbiome have been shown to metabolize PAHs [20,21], the roles of PAH exposure in shaping the skin microbiome warrant further investigation. In our previous study [22], we demonstrated a dose-response relationship between the levels of exposure to various PAHs and changes in the taxonomic compositions of skin microbiomes, as well as variations in the abundances of microbial functional genes crucial for host-microbe interactions, virulence, and host immune modulation. ...
... The bacterial taxa previously documented to have biodegradation capabilities (e.g., Archromobacter, Caulobacter, Paracoccus, Pseudomonas, Rhodococcus, and Sphingomonas) [23,24] were enriched in cutotype 2, and a positive correlation was detected between acenaphthene exposure level and the inferred growth rate of a species in Janibacter, a genus capable of using multiple PAH types as carbon sources [41]. These observations together with the documented PAH metabolic capabilities of common skin colonizers [20,21] suggest that PAHs are actively metabolized by the skin microbiome. The species with biodegradation abilities may have been originated from the environment [24,42] and managed to transiently colonize on skin due to the presence of PAHs. ...
... In contrast, cutotype 2 was associated with dry skin and hyperpigmentation in subjects aged under 45. Diverse species, including Paracoccus [46], Sphingomonas [23], and Pseudomonas [20], that can reportedly degrade PAHs were found in cutotype 2. In particular, members of Corynebacterium were the key taxa in cutotype 2. These taxa were positively correlated with benzoate degradation and KOs in the TCA cycle (i.e., K01607 and K00262 [gdhA]). Growth in the presence of aromatic compounds has been shown to upregulate enzymes in the TCA cycle of Corynebacterium glutamicum (e.g., a fivefold increase in GdhA that leads to L-glutamate production) [47], which we speculate is similar to that in the microbiome of skin exposed to PAHs. ...
Background
The effects of air pollutants, particularly polycyclic aromatic hydrocarbons (PAHs), on the skin microbiome remain poorly understood. Thus, to better understand the interplay between air pollutants, microbiomes, and skin conditions, we applied metagenomics and metabolomics to analyze the effects of PAHs in air pollution on the skin microbiomes of over 120 subjects residing in two cities in China with different levels of air pollution.
Results
The skin microbiomes differentiated into two cutotypes (termed 1 and 2) with distinct taxonomic, functional, resistome, and metabolite compositions as well as skin phenotypes that transcended geography and host factors. High PAH exposure was linked to dry skin and cutotype 2, which was enriched with species with potential biodegradation functions and had reduced correlation network structure integrity. The positive correlations identified between dominant taxa, key functional genes, and metabolites in the arginine biosynthesis pathway in cutotype 1 suggest that arginine from bacteria contributes to the synthesis of filaggrin-derived natural moisturizing factors (NMFs), which provide hydration for the skin, and could explain the normal skin phenotype observed. In contrast, no correlation with the arginine biosynthesis pathway was observed in cutotype 2, which indicates the limited hydration functions of NMFs and explains the observed dry skin phenotype. In addition to dryness, skin associated with cutotype 2 appeared prone to other adverse conditions such as inflammation.
Conclusions
This study revealed the roles of PAHs in driving skin microbiome differentiation into cutotypes that vary extensively in taxonomy and metabolic functions and may subsequently lead to variations in skin–microbe interactions that affect host skin health. An improved understanding of the roles of microbiomes on skin exposed to air pollutants can aid the development of strategies that harness microbes to prevent undesirable skin conditions.
... However, it is influenced by a variety of factors, including age (12,13), gender (14), and environmental variables such as climate (8), season (15), geography (16), hygiene practices (17), and urbanization (18,19). Among the environmental variables, air pollutants are an important factor that disturbs the skin microbiota (20)(21)(22)(23)(24). ...
... Several studies have assessed the effects of pollutants on the skin microbiota (20)(21)(22)(23)(24). Exposure to O 3 and NO 2 significantly reduced the viability of skin bacteria (20,22). ...
... Several studies have assessed the effects of pollutants on the skin microbiota (20)(21)(22)(23)(24). Exposure to O 3 and NO 2 significantly reduced the viability of skin bacteria (20,22). Different polycyclic aromatic hydrocarbons and related xenobiotic chemicals have been shown to be degraded by skin bacteria (23,24). Alterations in the composition and functional characteristics of the skin microbiota have been linked to chronic exposure levels of polycyclic aromatic hydrocarbon pollutants according to Leung et al. (21). ...
Haze pollution has been a public health issue. The skin microbiota, as a component of the first line of defense, is disturbed by environmental pollutants, which may have an impact on human health. A total of 74 skin samples from healthy students were collected during haze and nonhaze days in spring and winter. Significant differences of skin fungal community composition between haze and nonhaze days were observed in female and male samples in spring and male samples in winter based on unweighted UniFrac distance analysis. Phylogenetic diversity whole-tree indices and observed features were significantly increased during haze days in male samples in winter compared to nonhaze days, but no significant difference was observed in other groups. Dothideomycetes, Capnodiales, Mycosphaerellaceae, etc. were significantly enriched during nonhaze days, whereas Trichocomaceae, Talaromyces, and Pezizaceae were significantly enriched during haze days. Thus, five Talaromyces strains were isolated, and an in vitro culture experiment revealed that the growth of representative Talaromyces strains was increased at high concentrations of particulate matter, confirming the sequencing results. Furthermore, during haze days, the fungal community assembly was better fitted to a niche-based assembly model than during nonhaze days. Talaromyces enriched during haze days deviated from the neutral assembly process. Our findings provided a comprehensive characterization of the skin fungal community during haze and nonhaze days and elucidated novel insights into how haze exposure influences the skin fungal community. IMPORTANCE Skin fungi play an important role in human health. Particulate matter (PM), the main haze pollutant, has been a public environmental threat. However, few studies have assessed the effects of air pollutants on skin fungi. Here, haze exposure influenced the diversity and composition of the skin fungal community. In an in vitro experiment, a high concentration of PM promoted the growth of Talaromyces strains. The fungal community assembly is better fitted to a niche-based assembly model during haze days. We anticipate that this study may provide new insights on the role of haze exposure disturbing the skin fungal community. It lays the groundwork for further clarifying the association between the changes of the skin fungal community and adverse health outcomes. Our study is the first to report the changes in the skin fungal community during haze and nonhaze days, which expands the understanding of the relationship between haze and skin fungi.
... These include PAHs and nitrosamines, which have received the most attention because they are pro-carcinogens. Given that studies have revealed the existence of environmental microorganisms that have the ability to metabolize PAHs, 12-14, 15 ,16-22 and that bacteria with similar qualities exist on human skin 21,23 , we looked for evidence of the same in the oral cavity. We used the same method for selection of environmental microbes, obtained for example from petroleum waste sites, that have the ability to survive long term in minimal media with PAHs as the sole carbon Page 3/23 source 15,17,21,24 . ...
... Given that studies have revealed the existence of environmental microorganisms that have the ability to metabolize PAHs, 12-14, 15 ,16-22 and that bacteria with similar qualities exist on human skin 21,23 , we looked for evidence of the same in the oral cavity. We used the same method for selection of environmental microbes, obtained for example from petroleum waste sites, that have the ability to survive long term in minimal media with PAHs as the sole carbon Page 3/23 source 15,17,21,24 . In the current work, microorganisms were harvested from the oral mucosa surfaces and then exposed over weeks in vitro to a cocktail of PAHs with no other carbon source to determine if smokers preferentially harbored microbes tolerant of tobacco smoke PAHs. ...
... In this experiment the PAHs tested were phenanthrene and pyrene. These chemicals were chosen because they can be found at relatively high levels in the oral cavity in tobacco users 25,26 and they are readily digested by many environment microbes [13][14][15][16][17][18][19][20][21][22] . A soil-derived strain, Mycobacterium rutilum, capable of metabolizing pyrene or phenanthrene as sole carbon source was used as a positive control. ...
Certain soil microbes resist and metabolize polycyclic aromatic hydrocarbons (PAHs). The same is true for certain skin microbes. Oral microbes have the potential to oxidize tobacco PAHs to increase their ability to cause cancer. We hypothesized that oral microbes that resist high levels of PAH in smokers exist and can be identified based on their resistance to PAHs. We isolated bacteria and fungi that survived long term in minimal media with PAHs as the sole carbon source from the oral cavity in 11 of 14 smokers and only 1 of 6 nonsmokers. Of bacteria genera that included species that survived harsh PAH exposure in vitro , all were found at trace levels on the oral mucosa, except for Staphylococcus and Actinomyces . Two PAH-resistant strains of Candida albicans (C. albicans) were isolated from smokers. C. albicans is found orally at high levels in tobacco users and some Candida species can metabolize PAHs. The two C. albicans strains were tested for metabolism of two model PAH substrates, pyrene and phenanthrene. The result showed that the PAH-resistant C. albicans strains did not metabolize the two PAHs. In conclusion, evidence for large scale oral microbial metabolism of tobacco PAHs by common oral microbes remains lacking.
... Some of the bacterial genes for the respective underlying metabolic pathways were identified and shown to be detectable in situ on human skin, as were the associated bacteria. Concomitantly carbon-limited batch cultures showed the corresponding bacterial metabolism of B[a]P to result in the formation and excretion of highly cytotoxic and genotoxic metabolites (26,27). Similar observations have been reported for the intestinal microbiota, where commensals are known to directly metabolize xenobiotic substances, as well as impacting the host's capacity for xenobiotic metabolism by affecting phase I and phase II enzymes (28)(29)(30). ...
... The aim of the study was to investigate the effects of commensal skin colonization on B[a]P-metabolism in situ using a microbially competent 3D skin model (31). The model was colonized with two previously isolated skin commensals, namely, Micrococcus luteus 1B and Pseudomonas oleovorans 1C (26,27). While both organisms have been established using B[a]P as the sole source of carbon and energy, including the metabolites formed by M. luteus, the nature of the metabolites formed by P. oleovorans remained unknown (27). ...
... P. oleovorans B[a]P metabolites. The analytical examination of the respective culture supernatants confirmed this strain's ability to partially metabolize B[a]P (26). The dominant metabolites formed were B[a]P-1,6-dione, B[a]P-7,8-dione, B[a]P-7,10-dione, and 3-OH-B[a]P (Fig. S4A). ...
Polycyclic aromatic hydrocarbons (PAH) such as benzo[a]pyrene (B[a]P) are among the most abundant environmental pollutants, resulting in continuous exposure of human skin and its microbiota. However, effects of the latter on B[a]P toxicity, absorption, metabolism, and distribution in humans remain unclear. Here, we demonstrate that the skin microbiota does metabolize B[a]P on and in human skin in situ, using a recently developed commensal skin model. In this model, microbial metabolism leads to high concentrations of known microbial B[a]P metabolites on the surface as well as in the epider-mal layers. In contrast to what was observed for uncolonized skin, B[a]P and its metabo-lites were subject to altered rates of skin penetration and diffusion, resulting in up to 58% reduction of metabolites recovered from basal culture medium. The results indicate the reason for this altered behavior to be a microbially induced strengthening of the epider-mal barrier. Concomitantly, colonized models showed decreased formation and penetration of the ultimate carcinogen B[a]P-7,8-dihydrodiol-9,10-epoxide (BPDE), leading, in consequence , to fewer BPDE-DNA adducts being formed. Befittingly, transcript and expression levels of key proteins for repairing environmentally induced DNA damage such as xeroderma pigmentosum complementation group C (XPC) were also found to be reduced in the commensal models, as was expression of B[a]P-associated cytochrome P450-dependent monooxygenases (CYPs). The results show that the microbiome can have significant effects on the toxicology of external chemical impacts. The respective effects rely on a complex interplay between microbial and host metabolism and microbe-host interactions, all of which cannot be adequately assessed using single-system studies. IMPORTANCE Exposure to xenobiotics has repeatedly been associated with adverse health effects. While the majority of reported cases relate to direct substance effects, there is increasing evidence that microbiome-dependent metabolism of xenobiotic substances likewise has direct adverse effects on the host. This can be due to microbial bio-transformation of compounds, interaction between the microbiota and the host's en-dogenous detoxification enzymes, or altered xenobiotic bioavailability. However, there are hardly any studies addressing the complex interplay of such interactions in situ and less so in human test systems. Using a recently developed microbially competent three-dimensional (3D) skin model, we show here for the first time how commensal influence on skin physiology and gene transcription paradoxically modulates PAH toxicity.
... The azo dyes are regularly used in cosmetics, tattoo inks, and other products, and the reduction of these dyes due to their undesirable metabolism by the skin microbiome-harbored metabolic enzymes can produce carcinogenic aromatic amines, which poses significant health risks (Chung, 1983;Nakayama et al., 1983). Another example is the aerobic oxidative metabolism of an abundant environment pollutant BaP by monooxygenase enzymes from different bacterial species of skin microbiome (Sowada et al., 2014). The anaerobic metabolism of different skin secretion substances such as triglyceride lipids and secretory proteins by lipases and proteases has also been reported by experimental studies (Byrd et al., 2018). ...
... BaP is an abundant environmental pollutant found in almost all types of soot and smoke generated by the incomplete combustion of fossil fuel, coal, and other biomass including tobacco. The metabolism of this polycyclic aromatic hydrocarbon molecule by oxidation reaction through cytochrome P450 enzyme from human host and monooxygenases and dioxygenase enzymes from bacterial species of skin microbiome is known from experimental studies, and reference databases such as the University of Minnesota (Gelboin, 1980;Gibson et al., 1975;Jiang et al., 2007;Schwarz et al., 2001;Sowada et al., 2014). For this molecule, SkinBug correctly predicted its metabolism by skin microbiome as shown by an experimental study from Sowada et al., 2014, and predicted its oxidation by naphthalene 1,2-dioxygenase and monooxygenase enzymes from multiple species of Burkholderia, Polaromonas, Pseudomonas, and Ralstonia genera from the skin microbiome. ...
... The metabolism of this polycyclic aromatic hydrocarbon molecule by oxidation reaction through cytochrome P450 enzyme from human host and monooxygenases and dioxygenase enzymes from bacterial species of skin microbiome is known from experimental studies, and reference databases such as the University of Minnesota (Gelboin, 1980;Gibson et al., 1975;Jiang et al., 2007;Schwarz et al., 2001;Sowada et al., 2014). For this molecule, SkinBug correctly predicted its metabolism by skin microbiome as shown by an experimental study from Sowada et al., 2014, and predicted its oxidation by naphthalene 1,2-dioxygenase and monooxygenase enzymes from multiple species of Burkholderia, Polaromonas, Pseudomonas, and Ralstonia genera from the skin microbiome. This case study further supports the validity, accuracy, and utility of SkinBug tool. ...
In addition to being pivotal for the host health, the skin microbiome possesses a large reservoir of metabolic enzymes, which can metabolise molecules (cosmetics, medicines, pollutants, etc.) that form a major part of the skin exposome. Therefore, to predict the complete metabolism of any molecule by skin microbiome, a curated database of metabolic enzymes (1,094,153), reactions, and substrates from ∼900 bacterial species from 19 different skin sites were used to develop “SkinBug”. It integrates machine learning, neural networks, and chemoinformatics methods, and displayed a multiclass multilabel accuracy of up to 82.4% and binary accuracy of up to 90.0%. SkinBug predicts all possible metabolic reactions and associated enzymes, reaction centers, skin microbiome species harbouring the enzyme, and the respective skin sites. Thus, SkinBug will be an indispensable tool to predict xenobiotic/biotic metabolism by skin microbiome, and will find applications in exposome and microbiome studies, dermatology, and skin cancer research.
... Beyond extensively characterised immunomodulation dysbiosis of the skin's microbiome has been associated with conditions such as atopic dermatitis or allergies and recent work highlighted the potential of skin commensals to form highly carcinogenic by-products from benzo[a]pyrene and other polycyclic aromatic hydrocarbons (Platzek et al. 1999;Sowada et al. 2014;Stingley et al. 2010). Yet, for many of the observed microbial dysbalances it still remains unclear if they are cause or rather consequence of the respective condition (Tralau et al. 2015). ...
... Yet, for many of the observed microbial dysbalances it still remains unclear if they are cause or rather consequence of the respective condition (Tralau et al. 2015). Even the presumably more straightforward hazard of carcinogenic metabolites remains challenging to assess, not the least due to the aforementioned lack of suitable model systems (Sowada et al. 2014(Sowada et al. , 2017. We now report on the development of a test system designed to study skin-microbe interactions in situ. ...
... Moreover, the model was previously pre-validated for metabolically competent toxicity testing in vitro (Brinkmann et al. 2013;Hu et al. 2010) and genotoxicity testing using micronucleus and COMET assays (Pfuhler et al. 2014). In a proof-of-concept, this model has now been colonised using two previously isolated skin isolates, namely Micrococcus luteus 1B and Pseudomonas oleovorans 1C (Sowada et al. 2014). The selection of these organisms followed practical considerations and with the intended later application of studying potential microbiome-mediated substance toxification in mind. ...
The skin`s microbiome is predominantly commensalic, harbouring a metabolic potential far exceeding that of its host. While there is clear evidence that bacteria-dependent metabolism of pollutants modulates the toxicity for the host there is still a lack of models for investigating causality of microbiome-associated pathophysiology or toxicity. We now report on a biologically characterised microbial–skin tissue co-culture that allows studying microbe–host interactions for extended periods of time in situ. The system is based on a commercially available 3D skin model. In a proof-of-concept, this model was colonised with single and mixed cultures of two selected skin commensals. Two different methods were used to quantify the bacteria on the surface of the skin models. While Micrococcus luteus established a stable microbial–skin tissue co-culture, Pseudomonas oleovorans maintained slow continuous growth over the 8-day cultivation period. A detailed skin transcriptome analysis showed bacterial colonisation leading to up to 3318 significant changes. Additionally, FACS, ELISA and Western blot analyses were carried out to analyse secretion of cytokines and growth factors. Changes found in colonised skin varied depending on the bacterial species used and comprised immunomodulatory functions, such as secretion of IL-1α/β, Il-6, antimicrobial peptides and increased gene transcription of IL-10 and TLR2. The colonisation also influenced the secretion of growth factors such as VFGFA and FGF2. Notably, many of these changes have already previously been associated with the presence of skin commensals. Concomitantly, the model gained first insights on the microbiome’s influence on skin xenobiotic metabolism (i.e., CYP1A1, CYP1B1 and CYP2D6) and olfactory receptor expression. The system provides urgently needed experimental access for assessing the toxicological impact of microbiome-associated xenobiotic metabolism in situ.
... Cutaneous exposure to PAHs has been linked to changes in the physiological properties of the skin 17 , potentially leading to pigmented spots 18 , wrinkle formation 18 , premature skin aging 18 , and cancer 19 . While speci c members of the skin microbiome have been shown to metabolize PAHs 20,21 , the roles of PAH exposure in shaping the skin microbiome warrant further investigation. In our previous study 22 , we demonstrated a dose-response relationship between the levels of exposure to various PAHs and changes in the taxonomic compositions of skin microbiomes, as well as variations in the abundances of microbial functional genes crucial for host-microbe interactions, virulence, and host immune modulation. ...
... The bacterial taxa previously documented to have biodegradation capabilities were enriched in cutotype 2, and a positive correlation was detected between acenaphthene exposure level and the inferred growth rate of a species in Janibacter, a genus capable of using multiple PAH types as carbon sources 37 . These observations together with the documented PAH metabolic capabilities of common skin colonizers 20,21 suggest that PAHs are actively metabolized by the skin microbiome. However, PAHs do not appear to greatly in uence fungal community composition. ...
Background
The effects of air pollutants, particularly polycyclic aromatic hydrocarbons (PAHs), on the skin microbiome remain poorly understood. Thus, to better understand the interplay between air pollutants, microbiomes, and skin conditions, we applied metagenomics and metabolomics to analyze the effects of PAHs in air pollution on the skin microbiomes of over 120 subjects residing in two cities in China with different levels of air pollution.
Results
The skin microbiomes differentiated into two cutotypes (termed 1 and 2) with distinct taxonomic, functional, resistome, and metabolite compositions as well as skin phenotypes that transcended geography and host factors. High PAH exposure was linked to dry skin and cutotype 2, which was enriched with species with potential biodegradation functions and had reduced correlation network structure integrity. The positive correlations identified between dominant taxa, key functional genes, and metabolites in the arginine biosynthesis pathway in cutotype 1 suggest that arginine from bacteria contributes to the synthesis of filaggrin-derived natural moisturizing factors (NMFs), which provide hydration for the skin, and could explain the normal skin phenotype observed. In contrast, no correlation with the arginine biosynthesis pathway was observed in cutotype 2, which indicates the limited hydration functions of NMFs and explains the observed dry skin phenotype. In addition to dryness, skin associated with cutotype 2 appeared prone to other adverse conditions such as inflammation.
Conclusions
This study revealed the roles of PAHs in driving skin microbiome differentiation into cutotypes that vary extensively in taxonomy and metabolic functions and may subsequently lead to variations in skin–microbe interactions that affect host skin health. An improved understanding of the roles of microbiomes on skin exposed to air pollutants can aid the development of strategies that harness microbes to prevent undesirable skin conditions.
... Some species of the genus Bacillus are well known to degrade hydrocarbons, pyrene, and other PAH (Sowada et al. 2014). B. thuringiensis strain was able to degrade anthracene (Tarafdar et al. 2017), whereas B. thuringiensis B3, and B. cereus B6, were able to live and metabolize crude oil-contaminated sites in Ecuador, metabolizing PAHs from diesel. ...
... The alternative metabolism to degrade benzo [a] pyrene was previously proved by Sowada et al. (2014), who isolated B. licheniformis from human skin, and showed their metabolic capabilities, degrading BaP under mesophilic conditions. Another work supporting this metabolic diversity was that of Bahuguna et al. (2012), which analyzed growth kinetics of B. licheniformis BMIT5ii MTCC 9446 able to grow on naphthalene (0.5 mg/mL). ...
Petroleum derivates used in energy production are gravely pollutants for the ecosystem, especially for aquatic environments and human health. This study aimed to isolate hydrocarbons-degrading bacteria from hot springs. Three strains of hydrocarbondegrading bacteria strains, belonging to the Bacillus and one of the genus Lysinibacillus were isolated. These strains tolerate temperatures from 65 to 100 ºC and were able to degrade and grow on BH medium supplemented with gasoline and diesel. Strain M2-7 shared 100 % 16S rRNA identity with Bacillus licheniformis and was the only able to degrade pyrene and benzopyrene among these isolated strains. The results indicate that B. licheniformis M2-7 could degrade a wider range of hydrocarbons and some recalcitrant hydrocarbon components, which could be particularly helpful for the treatment and bioremediation of hydrocarbon-polluted systems.
... Cette liaison induit le recrutement de la machinerie transcriptionnelle et la transcription des gènes XRE impliqués dans la modulation de la prolifération cellulaire, l'inflammation et la mélanogenèse cutanée(Mancebo and Wang, 2015;Koohgoli et al., 2017).• Altération du microbiote cutanéUn nombre grandissant d'études souligne indépendamment l'impact délétère des polluants atmosphériques sur des bactéries isolées et sur la peau directement, peu d'études traitent de l'impact de la pollution sur le microbiote cutané(Sowada et al., 2014;Araviiskaia et al., 2019).Une nouvelle approche consiste à considérer l'altération du microbiote cutané par les polluants comme une action indirecte de ces polluants sur la peau. Une première étude par méthodes culturales de He et al. a permis de démontrer que l'O3 avait un effet bactéricide et entrainait une réduction de 50% de la densité du microbiote bactérien cutané résident(He et al., 2006). ...
... métabolisme des glucides, lipides et acides aminés) ainsi qu'une augmentation du potentiel pathogène. Ces études ont également démontré que certaines bactéries de la peau peuvent métaboliser les HAP en produits bénins ou produire des métabolites intermédiaires à toxicité accrue exacerbant l'impact sur le peau(Sowada et al., 2014(Sowada et al., , 2017Leung et al., 2020). De manière plus générale, l'urbanisation est reconnue comme étant un facteur majeur d'altération du microbiote cutané ( §II.4.b).b. ...
Le dioxyde d’azote (NO2), en tant que second polluant atmosphérique le plus meurtrier en Europe est un des plus préoccupants pour la santé humaine selon l’Agence Européenne de l’Environnement. Il est notamment connu pour être responsable de maladies cardiovasculaires, respiratoires ainsi que pour contribuer au vieillissement cutané et au développement de la dermatite atopique. Des facteurs endogènes à l’hôte tels que le microbiote cutané interviennent également dans cette pathologie. En effet, de nombreuses pathologies cutanées sont corrélées à un déséquilibre (dysbiose) du microbiote bactérien, un acteur essentiel du maintien de l’homéostasie de la peau. Or, il est fortement soupçonné que l’effet des polluants sur la peau implique des mécanismes d’action directe mais également un mécanisme d’action indirecte lié à l’altération du microbiote cutané par le polluant. En conséquence, il est pertinent d’aborder l’effet du NO2 gazeux (gNO2) sur le microbiote cutané bactérien. Cette thèse a donc pour objectif d’évaluer l’impact physiologique, morphologique et moléculaire du NO2 sur des souches bactériennes commensales d’espèces représentatives du microbiote cutané (Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus capitis, Pseudomonas fluorescens, Corynebacterium tuberculostearicum). Selon l’espèce, des réponses différentes au stress nitrosant généré par le gNO2 ont ainsi été mises en évidence ainsi qu’une tolérance plus importante au gNO2 pour certaines d’entre elles. Ces travaux suggèrent par conséquent que le NO2 pourrait contribuer à la formation d’un état dysbiotique du microbiote cutané et participer à l’action indirect du polluant sur la peau.
... The bacterial isolates include (1 Figure S1 shows the phylogenetic trees of the identified bacteria based on their 16S rRNA gene sequences. Four bacterial species were identified, i.e., Paracoccus yeei, Pseudomonas geniculate, Microbacterium laevaniformans, and Pseudomonas stutzeri which are known to be widely distributed in PBDE/ECs-contaminated soil (Chou et al. 2013;Sowada et al. 2014;Wu et al. 2018). ...
... Microbacterium sp. have been shown to biodegrade BDE-47 as sole carbon source under aerobic condition (Zhang et al. 2013a). A Stenotrophomonas strain isolated from soils at a PBDEs-contaminated e-waste recycling site was able to effectively degrade BDE-209 (55.15% of 65 μg l -1 ) under aerobic conditions during a 30-day incubation (Wu et al. 2018), and Paracoccus yeei has been shown to utilize benzo[a]pyrene as a sole carbon and energy source (Sowada et al. 2014). UVA irradiation can adversely affect microbial activity and hence inhibit biochemical reactions in the NBB. Figure 3 shows that the number of bacteria present during the coupled UV photolysis-biodegradation process is less than for biodegradation alone. ...
The commercial flame retardant is an emerging contaminant (EC) commonly found in soils and sediments. A coupled UV-photolysis-biodegradation process was used to decompose decabromodiphenyl ether (BDE-209) in clay slurries. A novel bioslurry bioreactor (NBB) was employed in which BDE-209 degradation was maximized by the simultaneous application of LED UVA irradiation and biodegradation by a mixed bacterial culture. The rate of BDE-209 degradation decreased in the order: coupled UV photolysis-biodegradation (1.31 × 10-2 day-1) > UV photolysis alone (1.10 × 10-2 day-1) > biodegradation alone (1.00 × 10-2 day-1). Degradation intermediates detected included hydroxylated polybrominated diphenylethers, partially debrominated PBDE congeners and polybrominated dibenzofuran. The UV-resistant bacterial strains isolated that could utilize BDE-209 as a sole carbon source included Stenotrophomonas sp., Pseudomonas sp., and Microbacterium sp. These strains encoded important functional genes such as dioxygenase and reductive dehalogenases. Continuous UV irradiation during the NBB process affected various biochemical oxidative reactions during PBDEs biodegradation. Simultaneous photolysis and biodegradation in the NBB system described reduces operational time, energy, expense, and maintenance-demands required for the remediation of BDE-209 when compared to sequential UV-biodegradation process or to biodegradation alone.
... PAH exposure can also alter the diversity, taxonomic composition, and metabolic profiles of skin microbiome [14,15], consequently affecting skin phenotype [15]. For example, high levels of PAH exposure have been linked to skin dryness and hyperpigmentation [15] and to a skin microbiome enriched in bacterial species capable of degrading xenobiotics [16]. Recent studies on skin metagenomes have revealed the composition and potential functions of the skin microbiome [2,8,15,17] and the microbial taxonomy, functionality, and antimicrobial resistance profiles of skin-identified microbial sub-community clusters, denoted "cutotypes." ...
Exposure to polycyclic aromatic hydrocarbons (PAHs) in polluted air influences the composition of the skin microbiome, which in turn is associated with altered skin phenotypes. However, the interactions between PAH exposure and viromes are unclear. This study aims to elucidate how PAH exposure affects the composition and function of skin viruses, their role in shaping the metabolism of bacterial hosts, and the subsequent effects on skin phenotype. We analyzed metagenomes from cheek skin swabs collected from 124 Chinese women in our previous study and found that the viruses associated with the two microbiome cutotypes had distinct diversities, compositions, functions, and lifestyles following PAH exposure. Moreover, exposure to high concentrations of PAHs substantially increased interactions between viruses and certain biodegrading bacteria. Under high-PAH exposure, the viruses were enriched in xenobiotic degradation functions, and there was evidence suggesting that the insertion of bacteriophage-encoded auxiliary metabolic genes into hosts aids biodegradation. Under low-PAH exposure conditions, the interactions followed the “Piggyback-the-Winner” model, with Cutibacterium acnes being “winners,” whereas under high-PAH exposure, they followed the “Piggyback-the-Persistent” model, with biodegradation bacteria being “persistent.” These findings highlight the impact of air pollutants on skin bacteria and viruses, their interactions, and their modulation of skin health. Understanding these intricate relationships could provide insights for developing targeted strategies to maintain skin health in polluted environments, emphasizing the importance of mitigating pollutant exposure and harnessing the potential of viruses to help counteract the adverse effects.
... BaP is a highly recalcitrant PAH with a high molecular weight that is incorporated into the particles present in water, air, and soil (Fanali et al. 2018;Qin et al. 2018;Guevara-Luna et al. 2018). To date, few studies have addressed the genes and regulators involved in the degradation of BaP, as well as the enzymatic and physiological responses that cause changes in the metabolic pathways that are crucial for using BaP as the sole source of carbon and energy (Sowada et al. 2014;Eskandari et al. 2017). It has been reported that the enzymatic activity of catechol 2,3-dioxygenase, a product of the catE gene, is related to the catabolism of hydrocarbons in B. subtilis and is essential in the growth and viability of this bacterium in the presence of catechol (Tam et al. 2006). ...
Benzopyrene is a high-molecular-weight polycyclic aromatic hydrocarbon that is highly recalcitrant and induces carcinogenic effects. CsrA is a conserved regulatory protein that controls the translation and stability of its target transcripts, having negative or positive effects depending on the target mRNAs. It is known that Bacillus licheniformis M2-7 has the ability to grow and survive in certain concentrations of hydrocarbons such as benzopyrene, prompted in part by CsrA, as is present in gasoline. However, there are a few studies that reveal the genes involved in that process. To identify the genes involved in the Bacillus licheniformis M2-7 degradation pathway, the plasmid pCAT-sp containing a mutation in the catE gene was constructed and used to transform B. licheniformis M2-7 and generate a CAT1 strain. We determined the capacity of the mutant B. licheniformis (CAT1) to grow in the presence of glucose or benzopyrene as a carbon source. We observed that the CAT1 strain presented increased growth in the presence of glucose but a statistically considerable decrease in the presence of benzopyrene compared with the wild-type parental strain. Additionally, we demonstrated that the Csr system positively regulates its expression since it was observed that the expression of the gene in the mutant strain LYA12 (M2-7 csrA:: Sp, SpR) was considerably lower than that in the wild-type strain. We were thus able to propose a putative regulation model for catE gene in B. licheniformis M2-7 strain by CsrA regulator in the presence of benzopyrene.
... A study on polyaromatic hydrocarbons such naphthalene, phenanthrene, pyrene, and benzo(a) pyrene, revealed that colon bacteria produced estrogenic metabolites from such chemicals (Van De Wiele et al., 2005). Other groups characterized bacteria from skin that completely degraded benzo(a)pyrene (Sowada et al., 2014), but certain intermediate metabolites might have more toxicity impacts (Tralau et al., 2015). ...
... Furthermore, it has been found that M. luteus was as equally effective in removing PAHs in vitro when compared to various microbial consortia. M. luteus is an effective PAHs degrader that can utilize pyrene and benzo [a]pyrene as a sole carbon [36]. ...
Petroleum hydrocarbon contamination is a serious concern across the globe. Here, the capability of native bacterial consortium enriched from sediment samples of Map Ta Phut Industrial Estate (MTPIE), Rayong, Thailand was described. The distribution of PAHs was assessed from the sediment samples collected from MTPIE by GC-FID and the toxic unit (TU) was calculated to assess the potential ecological risk to the surrounding biota. This study investigated the degradation potential and determined the PAH-degrading bacterial cultures by enriching collected sediments in PAHs mixtures (naphthalene, phenanthrene, and pyrene). The TPH degradation capacity of each bacterial consortium was validated in a soil microcosm using aged crude oil-contaminated soil. The MTPIE sediments were highly contaminated with PAHs (843.99-3904.39 ng g-1) and posed extremely high ecological risks to benthic biota (TU > 1). The consortium S5-P most significantly removed naphthalene (90.03%) and phenanthrene (88.14%) while the highest removal of pyrene was achieved by the S3-P consortium. Other consortia only partially degraded the PAHs. The dominant microbes in the consortia were determined using PCR-DGGE, it was found that the PAH degrading consortia were known PAH degraders such as Annwoodia, Bacillus, Brevibacillus, Lysinibacillus, Paracoccus, Rhodococcus, Sphingopyxis, Sulfurovum, and Sulfurimonas species and unknown PAH degraders such as Lithuaxuella species. The consortium S5-P showed the highest degradation capacity, removing 74.99% of TPHs in the soil microcosm. Furthermore, the inoculation of PAH-biodegrading bacterial consortia significantly promoted the catechol-2,3-dioxygenase (C23O) and dehydrogenase (DHA) activities which directly correlated with the degradation efficiency of petroleum hydrocarbons (p < 0.05).
... Furthermore, it has been found that M. luteus was as equally effective in removing PAHs in vitro when compared to various microbial consortia. M. luteus is an effective PAHs degrader that can utilize pyrene and benzo [a]pyrene as a sole carbon [36]. ...
Petroleum hydrocarbon contamination is a serious concern across the globe. Here, the capability of native bacterial consortium enriched from sediment samples of Map Ta Phut Industrial Estate (MTPIE), Rayong, Thailand was described. The distribution of PAHs was assessed from the sediment samples collected from MTPIE by GC-FID and the toxic unit (TU) was calculated to assess the potential ecological risk to the surrounding biota. This study investigated the degradation potential and determined the PAH-degrading bacterial cultures by enriching collected sediments in PAHs mixtures (naphthalene, phenanthrene, and pyrene). The TPH degradation capacity of each bacterial consortium was validated in a soil microcosm using aged crude oil-contaminated soil. The MTPIE sediments were highly contaminated with PAHs (843.99-3904.39 ng g-1) and posed extremely high ecological risks to benthic biota (TU > 1). The consortium S5-P most significantly removed naphthalene (90.03%) and phenanthrene (88.14%) while the highest removal of pyrene was achieved by the S3-P consortium. Other consortia only partially degraded the PAHs. The dominant microbes in the consortia were determined using PCR-DGGE, it was found that the PAH degrading consortia were known PAH degraders such as Annwoodia, Bacillus, Brevibacillus, Lysinibacillus, Paracoccus, Rhodococcus, Sphingopyxis, Sulfurovum, and Sulfurimonas species and unknown PAH degraders such as Lithuaxuella species. The consortium S5-P showed the highest degradation capacity, removing 74.99% of TPHs in the soil microcosm. Furthermore, the inoculation of PAH-biodegrading bacterial consortia significantly promoted the catechol-2,3-dioxygenase (C23O) and dehydrogenase (DHA) activities which directly correlated with the degradation efficiency of petroleum hydrocarbons (p < 0.05).
... ATCC 17483, Pseudomonas putida PpG7, Pseudomonas putida, Pseudomonas aeruginosa, Pelomonas saccharophila (classified as Pseudomonas saccharophila before year 2005), Pseudomonas fluorescens, Pseudomonas sp., MTCC 2445, and Pseudomonas sp. JP1 (Aitken et al. 1998;Barnsley 1975;Guntupalli et al. 2016;Liang et al. 2014;Luo et al. 2009;Mishra and Singh 2014;Sowada et al. 2014;Trzesicka-Mlynarz and Ward 1995). Among them, one facultative anaerobe Pseudomonas sp. ...
Purpose
Polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons are common contaminants in soils. In PBDEs, decabromodiphenyl ether (BDE-209) is the most persistent, while benzo(a)pyrene (BaP) is an identified human carcinogen. This study is aimed to solve the contamination of BDE-209 and BaP in soils by adjusting environmental variables and amendments of microorganisms or nutrients.
Methods
A batch test and a sandbox test were performed. In the batch test on an artificial soil, the Taguchi method was applied to define optimum environmental factors. The sandbox test was conducted to verify if addition of soybean soil nanoemulsion (SONE) or acclimated microorganisms can assist the bioremediation of BDE-209 and BaP in rice-paddy soil under optimum volumetric water content (θW). Next-generation sequencing (NGS) was performed to observe the microbial profile, correlation, and interaction.
Results
The batch test revealed that the θW is the predominant factor for both contaminants. In the sandbox test, bioaugmentation with SONE-amended group achieved 55% and 74% removals in 70 days for fresh BDE-209 and BaP, respectively. Yet for weathered BDE-209, natural attenuation group was the best with about 75% removal in 70 days. NGS data showed that a few dominant genera formed a strong alliance against a large group of others.
Conclusions
The results suggest that the θW is the key parameter and proper amendment of soil organic matter, and SONE can enhance the bioremediation. The results implied that natural attenuation with water flooding could be effective for the soils historically contaminated by BDE-209.
... Cigarette smoke is another source of pollution stressors known to affect skin health (24). Certain bacteria of skin origin were reported to display a metabolic capacity to break down organic pollutants, like benzo(a)pyrene, that exist in both cigarette smoke and automobile exhaust fumes (25), suggesting a potential combinatorial effect of regional air pollution and a smoking lifestyle on the skin microbiome. Indeed, our MNI results indicated that Shanghai smokers (SS) had the least robust microbiome network compared with Chongming nonsmokers (CN). ...
Urban living has been reported to cause various skin disorders. As an integral part of the skin barrier, the skin microbiome is among the key factors associated with urbanization-related skin alterations. The role of skin microbiome in mediating the effect of urban stressors (e.g., air pollutants) on skin physiology is not well understood. We generated 16S sequencing data and constructed a microbiome network of individual (MNI) to analyze the effect of pollution stressors on the microbiome network and its downstream mediation effect on skin physiology in a personalized manner. In particular, we found that the connectivity and fragility of MNIs significantly mediated the adverse effects of air pollution on skin health, and a smoking lifestyle deepened the negative effects of pollution stress on facial skin microbiota. This is the first study that describes the mediation effect of the microbiome network on the skin’s physiological response toward environmental factors as revealed by our newly developed MNI approach and conditional process analysis.
IMPORTANCE The association between the skin microbiome and skin health has been widely reported. However, the role of the skin microbiome in mediating skin physiology remains a challenging and yet priority subject in the field. Through developing a novel MNI method followed by mediation analysis, we characterized the network signature of the skin microbiome at an individual level and revealed the role of the skin microbiome in mediating the skin’s responses toward environmental stressors. Our findings may shed new light on microbiome functions in skin health and lay the foundation for the design of a microbiome-based intervention strategy in the future.
... Increases in abundances of bacteria in the family Moraxellaceae, which contains several opportunistic pathogens (Austin and Austin, 2016), is associated with increased stress in fish (Boutin et al., 2013). Furthermore, these same taxa are capable of degrading BaP when isolated from human skin (Sowada et al., 2014). Although the taxa were not the same, a similar phenomenon of enrichment of taxa associated with hydrocarbon degradation was seen in (DeBofsky et al, (2020a)). ...
The microbiome has been described as an additional host “organ” with well-established beneficial roles. However, the effects of exposures to chemicals on both structure and function of the gut microbiome of fishes are understudied. To determine effects of benzo[a]pyrene (BaP), a model persistent organic pollutant, on structural shifts of gut microbiome in juvenile fathead minnows (Pimephales promelas), fish were exposed ad libitum in the diet to concentrations of 1, 10, 100, or 1,000 μg BaP g⁻¹ food, in addition to a vehicle control, for two weeks. To determine the link between exposure to BaP and changes in the microbial community, concentrations of metabolites of BaP were measured in fish bile and 16S rRNA amplicon sequencing was used to evaluate the microbiome. Exposure to BaP only reduced alpha-diversity at the greatest exposure concentrations. However, it did alter community composition assessed as differential abundance of taxa and reduced network complexity of the microbial community in all exposure groups. Results presented here illustrate that environmentally-relevant concentrations of BaP can alter the diversity of the gut microbiome and community network connectivity.
... This enrichment was carried out in microplates in 200 µL, unlike the aforementioned studies, which were generally carried out in bigger volumes, equal or more than 50 mL. Twenty one species of BaP degrading bacteria were identified, and these belong to various genera, including Micrococcus, Bacillus, Pseudomonas and Staphylococcus, [48] (ST27). However, in this study, the BaP was dissolved in dimethyl sulfoxide (DMSO) during the enrichment procedures. ...
Benzo[a]pyrene (BaP) is one the main pollutants belonging to the high-molecular-weight PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important strategy for its removal from the environment. Extensive studies have been carried out on the isolation and characterisation of microorganisms that can actively degrade low-molecular-weight PAHs (LMW-PAHs), and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high chemical stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of “omics” approaches.
... This enrichment was carried out in microplates in 200 µL, unlike the aforementioned studies, which were generally carried out in bigger volumes, equal or more than 50 mL. Twenty one species of BaP degrading bacteria were identified, and these belong to various genera, including Micrococcus, Bacillus, Pseudomonas and Staphylococcus, [48] (ST27). However, in this study, the BaP was dissolved in dimethyl sulfoxide (DMSO) during the enrichment procedures. ...
Polycyclic aromatic hydrocarbons (PAHs), which consist of low-molecular-weight PAHs (LMW-PAHs) and high-molecular-weight PAHs (HMW-PAHs), form an important class of pollutants. Pyrene and benzo[a]pyrene (BaP) are the main pollutants belonging to HMW-PAHs, and their degradation by microorganisms remains an important strategy for their removal from the environments. Extensive studies have been carried out on the isolation and characterisation of microorganisms that actively degrade LMW-PAHs, and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of “omics” approaches
... Some of these species were investigated for the presence of catabolic genes/enzymes such as dehydrogenase, monooxygenase, catechol dioxygense, and aromatic-ring-hydroxylating dioxygenase in different studies. 12,14,29,30 Phylogenetic tree for analysis of evolutionary relationship of K. flava DTU-1Y with these identified 18 different bacterial species was constructed 13 NM, not mentioned; seq., sequence. ( Figure 1). ...
Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants, ubiquitously present and are hazardous to all forms of life due to their toxic, carcinogenic, and mutagenic nature. With enhanced understanding of adverse effects of PAHs on living organisms, reclamation of PAH-contaminated sites has become a global concern. In order to devise efficient bioremediation strategies for PAH-degradation, the identification and study of metabolic potential of microbial species is essential. The goal of this study is to isolate PAH-degrading bacterial strains from petroleum contaminated soil that can utilize PAHs as their sole carbon source and investigate their growth on medium containing PAHs as only carbon source. For the first time, the evolutionary relationship of isolated bacterial strains with known PAH-degrading bacterial strains having PAH-catabolic genes/enzymes involved in PAH-bioremediation was examined. Two strains isolated from contaminated soil, that is, Kocuria flava DTU-1Y and Rhodococcus pyridinivorans DTU-7P may have the ability to utilize PAHs as sole carbon source for their growth. Phylogenetic analysis for evolutionary relationship revealed that these strains are related to different known PAH-degrading bacterial strains which have catabolic genes/enzymes involved in degradation pathway. The bacterial strains reported in this study may also possess the genes responsible for PAH-degradation and can prove useful in devising sustainable bioremediation approach.
... This has been recently reviewed by Ostrem Loss and Yu (Ostrem Loss and Yu 2018). Research regarding benzo[a]pyrene metabolism by the human gut microbiota is lacking, with one report on bacterial isolates from the human skin microbiota found to degrade benzo[a]pyrene (Sowada et al. 2014). Unfortunately, these metabolites were found cytotoxic and genotoxic; therefore, it is critical to consider this metabolic pathway harbored by the human microbiota that could complicate how we perceive benzo[a]pyrene's toxicity (Sowada et al. 2017). ...
Food contaminants represent food constituents that are accidentally introduced during food preparation cycle. In addition to their direct toxic effects on human health at different levels, they influence both gut microbiota composition and function. This often leads to metabolic disorders linked to many aspects of the human body. Foods are poisoned with physical, chemical, or biological factors either in agriculture or during processing steps. These include naturally occurring compounds such as mycotoxins, agricultural chemicals such as pesticides and antibiotics, persistent organic pollutants, thermal process contaminants (e.g., furans, aromatic compounds, and nitrosamines), or heavy metals. These xenobiotics cause a wide range of toxicities. They also disturb gut homeostasis by inducing intestinal damage and inflammation and gut microbiota dysbio-sis. We present herein the first comprehensive review of how food contaminants can specifically influence gut microbiota and intestinal homeostasis, and likewise via gut microbiota-mediated contaminants metabolism. The first part summarizes the different classes of food contaminants and their impact on gut microbiota and its homeostasis, while, the second part discusses the promising role of the gut microbiota in the biodegradation of these xenobiotics and the possible unfortunate exaggerated toxicities in some cases. Finally, we summarize the novel strategies to minimize toxic effects of food contaminants and future directions needed to explore the interactions between food contaminants and the gut microbiota.
... Micrococcus is one of the most common PAH-degrading bacterial isolates (Nwachukwu et al. 2001). An analysis of 16S rRNA genes from human skin also showed that the B[a]P-degrading isolates comprise Gram(+) as well as Gram(−) skin commensals, with Micrococcus being predominant (Sowada et al. 2014). In addition, Bacillus-like genera (Firmicutes) in the atmosphere were correlated with 3-4 ring PAHs, including Ant, Fla, Flu, and Phe. ...
The purpose of this study was to investigate the association among polycyclic aromatic hydrocarbons (PAHs) exposure and air pollutants and the diversity of microbiota. Daily average concentrations of six common air pollutants were obtained from China National Environmental Monitoring Centre. The PAHs exposure levels were evaluated by external and internal exposure detection methods, including monitoring atmospheric PAHs and urinary hydroxyl-polycyclic aromatic hydrocarbon (OH-PAH) metabolite levels. We analyzed the diversity of environmental and commensal bacterial communities with 16S rRNA gene sequencing and performed functional enrichment with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Correlation analysis and logistic regression modeling were conducted to evaluate the relationship of PAHs levels with air pollutants and microbial diversity. Correlation analysis found that the concentrations of atmospheric PAHs were significantly positively correlated with those of PM10, NO2, and SO2. There also was a positive correlation between the abundance of the genus Micrococcus (Actinobacteria) and high molecular weight PAHs, and Bacillus, such as genera and low molecular weight PAHs in the atmosphere. Logistic regression showed that the level of urinary 1-OHPyrene was associated with childhood asthma after sex and age adjustment. The level of urinary 1-OHPyrene was significantly positively correlated with that of PM2.5 and PM10. In addition, the level of 1-OHPyrene was positively correlated with oral Prevotella-7 abundance. Functional enrichment analysis demonstrated that PAHs exposure may disturb signaling pathways by the imbalance of commensal microbiota, such as purine metabolism, pyrimidine metabolites, lipid metabolism, and one carbon pool by folate, which may contribute to public health issues. Our results confirmed that atmospheric PAHs and urinary 1-OHPyrene were correlated with part of six common air pollutants and indicated that PAHs pollution may alter both environmental and commensal microbiota communities associated with health-related problems. The potential health and environmental impacts of PAHs should be further explored.
Background: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml – 5 mL), and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and Propidium Monoazide.
Results: In relation to urine sample volume, ³ 3.0 mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data, and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for core metabolic functions and environmental chemical metabolism. We identified long chain alkane utilization in two of the urine MAGs. Long chain alkanes are common pollutants that result from industrial combustion processes and end up in urine.
Conclusions: This is the first study, to our knowledge, to demonstrate environmental chemical degradation potential in urine microbes through genome-resolved metagenomics. These findings provide guidelines for studying the urobiome in relation to sample volume and host depletion, and lay the foundation for future evaluation of urobiome function in relation to health and disease.
Petroleum-derived substances, like industrial oils and grease, are ubiquitous in our daily lives. Comprised of petroleum hydrocarbons (PH), these substances can come into contact with our skin, potentially causing molecular disruptions and contributing to the development of chronic disease. In this pilot study, we employed mass spectrometry-based untargeted metabolomics and 16S rRNA gene sequencing analyses to explore these effects. Superficial skin samples were collected from subjects with and without chronic dermal exposure to PH at two anatomical sites: the fingers (referred to as the hand) and arms (serving as an inter-subject variability control). Exposed hands exhibited higher bacterial diversity (Shannon and Simpson indices) and an enrichment of petroleum-degrading bacteria (ODB), including Dietzia, Paracoccus, and Kocuria. Functional prediction suggested enriched pathways associated with PH degradation in exposed hands vs. non-exposed hands, while no differences were observed when comparing the arms. Furthermore, carboxylic acids, glycerophospholipids, organooxygen compounds, phenol ethers, among others, were found to be more abundant in exposed hands. We observed positive correlations among multiple ODB and xenobiotics, suggesting a chemical remodeling of the skin favorable for ODB thriving. Overall, our study offers insights into the complex dysregulation of bacterial communities and the chemical milieu induced by chronic dermal exposure to PH.
Background: Viruses play an essential role in the human skin microbiome under healthy and diseased conditions. We previously reported that exposure to polycyclic aromatic hydrocarbons (PAHs) led to the differentiation of bacteria samples from the cheeks of 124 Chinese women into two cutotypes with distinct taxonomic and functional compositions. In addition, we found that women with a high level of PAH exposure exhibited skin dryness and hyperpigmentation. However, the characteristics of viruses associated with these cutotypes are not well understood. In this study, we employed bulk metagenomic sequencing to investigate the diversity and functions of skin viromes and the virus–host interactions of the two cutotypes.
Results: The viruses associated with the two cutotypes had distinct diversities, compositions, functions, and lifestyles. Moreover, virus–host interactions were substantially increased by high levels of PAH exposure, especially when the hosts were potential pathogens. Under high- PAH exposure conditions, the viruses were enriched in xenobiotic degradation functions, and there was evidence suggesting that the insertion of bacteriophage-encoded auxiliary metabolic genes into hosts aids biodegradation. Furthermore, under low-PAH exposure conditions, virus– host interactions followed the “Piggyback-the-Winner” model, with Cutibacterium strains being “winners,” whereas under high-PAH exposure conditions, the interactions followed the “Piggyback-the-Persistent” model, with the biodegradation bacteria being “persistent.”
Conclusion: Our findings demonstrate that PAHs not only influence skin bacteria but also impact the composition of skin viruses and their interactions with skin bacteria, which may influence skin health. A detailed understanding of the roles played by viruses on skin exposed to air pollutants would aid the development of strategies to harness the potential of viruses to prevent undesirable skin conditions.
This chapter discusses the importance of air pollution in human health, outlining its relationship with cutaneous tegument and in particular with early aging, atopic dermatitis, urticaria, acne, melasma, and skin cancer. Aspects of epidemiology and physiopathology of such associations are discussed. Preventive medical interventions are proposed to improve the population’s quality of life.KeywordsAir pollutionFree radicalsSkin barrierMicrofloraDermatosesSkinEarly agingAtopic dermatitisUrticariaAcneMelasmaSkin cancer
Understanding the interaction of plants and microbes during rhizodegradation of organic contaminants is critical for developing effective bioremediation technologies. Plant secretes about 20% of their fixed carbons from photosynthesis into their root zone in the forms of sugar, amino acids, phenolics, flavonoids, and many other compounds. These chemical cocktails of plant metabolites, also known as root exudates, provide a viable nutrient source for soil microbial communities where nutrient availability is known to be limited. In general, contaminant concentration in the environment is inversely correlated to the concentration of plant root exudates. There are higher microbial biomass and contaminant transformation rate as root exudates promote microbial growth and catabolic activities. Due to this evidence, environmental scientists sought to figure out the suitable plant-microbe pairs that show the highest remediation capability suited to the specific organic contaminants.
Benzopyrene is a high molecular weight polycyclic aromatic hydrocarbon with highly recalcitrant and develops carcinogenic effects. CsrA is a conserved regulatory protein, which controls the translation and stability of its target transcripts, having negative or positive effects depending on the target mRNAs. It is known that Bacillus licheniformis M2-7 has the ability to grow and survive in concentrations of hydrocarbons as benzopyrene, which prompted in part by CsrA, as it occurs in the presence of gasoline. However, there are a few studies that reveal the genes involved in that process. In order to know the involved genes in the Bacillus licheniformis M2-7 degradation pathway, the plasmid pCAT-sp containing a mutation in the catE gen was constructed and used to transform B. licheniformis M2-7 and generate the CAT1 strain. We determined the capacity of the mutant B. licheniformis (CAT1) to grow in the presence of glucose and benzopyrene as a carbon source. We observed that CAT1 strain presented an increase in growth in the presence of glucose, but a statistically considerable decrease in the presence of benzopyrene with respect to the wild strain M2-7. Also we demonstrated that the Csr system regulates its expression positively since it was observed that the expression of the gene in the mutant strain LYA12 (M2-7 csrA :: Sp, SpR ) decreased considerably with respect to the wild strain. This allowed to characterize the metabolic pathway that Bacillus licheniformis M2-7 implements in the presence of benzopyrene.
Benzo[a]pyrene is a polycyclic aromatic hydrocarbon (PAH) having a high molecular weight. Benzo[a]pyrene and other PAHs are induces severe acute or chronic human health hazards and are extremely carcinogenic, mutagenic, immunotoxic, and teratogenic. Microorganisms play a crucial part in the degradation of benzo[a]pyrene from polluted environments. Such micro-organisms synthesize monooxygenase and di-oxygenase enzymes that proceed with the aerobic or anaerobic catabolic degradations of benzo[a]pyrene. Bioaugmentation, biomineralization, and biostimulation methods can be used for the decontamination of benzo[a]pyrene from hydrocarbon contaminated sites. In this review paper, we thoroughly explained the impacts of benzo[a]pyrene pollution on human health and the environment. Further, this study also described various pathways regarding the bio-degradation of benzo[a]pyrene and also an updated overview of future prospects of benzo[a]pyrene biodegradation.
Micrococcus yunnanensis TT9 was isolated from the forehead of human skin. This strain can grow on Triton X-100. We report the complete whole-genome sequence of this strain, which has one chromosome of 2,470,932 bp (73.0% G+C content) with 2,151 coding sequences.
Polycyclic aromatic hydrocarbons (PAHs) are widespread persistent contaminants that enter the environment from both natural and anthropogenic sources. The principal role of PAHs in environmental degradation is played by biological systems. The most important among these are plants and microorganisms, which have a flexible metabolism and unique mechanisms of pollutant detoxification. This review discusses the uptake, translocation, accumulation, and biochemical transformation of PAHs in plants, PAH effects on rhizosphere microbial communities, and pathways for the microbial degradation of these compounds. Special attention is given to plant growth promoting rhizobacteria, which are closely associated with plants, and to plant microbial cooperation for the biodegradation of PAHs. The review concludes with a discussion of the microbe-assisted phytoremediation of PAHs.
The skin plays an important role in human health by providing barrier protection against environmental stressors. In addition to human skin cells, the cutaneous barrier is also home to a network of organisms that have co‐evolved with humans, referred to as the cutaneous microbiome. This network has been demonstrated to play an active role in skin health and the manifestation of cutaneous disease. Here, we review how a warming world and its attendant changes in climatic variables, including temperature, humidity, ultraviolet radiation, and air pollution, influence the cutaneous microbiome and, in turn, skin health. Studies indicate that the cutaneous microbiome is affected by these factors, and these changes may influence the epidemiology and severity of cutaneous disorders including atopic dermatitis, acne vulgaris, psoriasis, and skin cancer. Further investigation into how the cutaneous microbiome changes in response to climate change and subsequently influences skin disease is needed to better anticipate future dermatologic needs and potentially generate novel therapeutic solutions in response.
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants that are harmful products of incomplete combustion of organic matter. PAH and their derivatives possess toxic, carcinogenic, and mutagenic effects in nearly all living organisms, which are further enhanced due to bioaccumulation and biomagnification. Thus, their detrimental effects generated the need for their mitigation in a sustainable manner. Among various remediation strategies, microbial remediation is increasingly gaining interest as economically justified and effective cleanup approach, because many microbial species use PAH as their energy source. These microbes possess various PAH degrading genes such as ndoB, nidA, pdoB, nahAc, and cytochrome P450, which also make them perfect tools for genetic engineering. Bacterial species such as Pseudomonas, Comamonas, Mycobacterium, Rhodococcus, and Sphingomonas may aerobically or anaerobically use various metabolic pathways to degrade PAH. Both ligninolytic and non‐ligninolytic fungi are well known for either co‐metabolizing or completely metabolizing PAH. Moreover, some algal and microalgal species such as Scenedesmus acutus, Selanastum capricornutum, and Ankistrodesmus braunii have the ability to either transform or co‐metabolize PAH. Microbial remediation depends on various factors such as microbial activity, bioavailability of PAH, and environmental factors such as pH, temperature, nutrients, oxygen, and humidity. We review the remediation strategies of PAH through diverse degradation pathways by various bacterial, fungal, and algal species. Moreover, we provide an insight of genes and enzymes involved in these processes in order to explore genetic engineering approaches for effective and sustainable degradation of PAH.
The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.
La dermatite de contact allergique (DCA) est une réaction exacerbée du système immunitaire cutané vis-à-vis d’un allergène de contact. La prévalence de la DCA étant de 20 % au sein de la population mondiale, il est important d’identifier les composés allergisants. Différentes réglementations européennes, telles que le règlement REACh ou la directive cosmétique, interdisent l’utilisation de test sur l’animal. C’est dans ce contexte que différentes méthodes alternatives ont été développées pour évaluer la sensibilisation cutanée. La stratégie actuelle d’évaluation du potentiel sensibilisant consiste à réaliser un ensemble de tests alternatifs, chacun mimant un évènement clé du mécanisme : l’hapténisation, l’activation des kératinocytes ou des cellules dendritiques.Cependant, ces tests utilisent principalement des monocultures et ne prennent donc pas en compte les interactions cellulaires qui peuvent avoir lieu in vivo. De plus, les évaluations de la pénétration et du métabolisme cutanés sont négligées dans les tests développés.Afin de mimer la fine orchestration des événements intervenant lors de la sensibilisation cutanée, nous proposons un modèle d’épiderme humain reconstruit (RhE) co-cultivé avec la lignée cellulaire THP-1, servant de substitut aux cellules dendritiques. Nous avons caractérisé, et étudié la pertinence de ce modèle à l’aide de molécules chimiques de référence. Ce travail a permis l’identification de biomarqueurs, tels que CD54, IL-8 et CCL3, spécifiques à l’évaluation in vitro de la sensibilisation cutanée des xénobiotiques.
Rapid industrialization has led to the generation of large number of pollutants that are dumped into the environment posing serious health concerns. Bioremediation is a reliable and eco‐friendly technique that utilizes diverse metabolic activitises of microorganisms to transform a broad range of pollutants into harmless products. The energy and carbon produced during the metabolism of pollutants are utilized by the microbes for their growth. A wide range of microorganisms with degradation potential have been isolated and characterized from different sites of contamination. Microbes carry genes for diverse metabolic processes such as oxidation, immobilization, transformation, or nitration for degradation of different types of pollutants. Complete degradation of the compounds depends on the interaction between the microbes, substrates, and the environmental conditions. Considering the increase in production of waste, current research aims to integrate the multi‐omics and system biology approaches to generate recombinant strains of microbes in order to expedite the process of bioremediation.
Activities of gut microbiomes are often overlooked in assessments of ecotoxicological effects of environmental contaminants. Effects of the polycyclic aromatic hydrocarbon, benzo[a]pyrene (BaP) on active gut microbiomes of juvenile fathead minnows (Pimephales promelas) were investigated. Fish were exposed for two weeks, to concentrations of 0, 1, 10, 100, or 1000 μg BaP g⁻¹ in the diet. The active gut microbiome was characterized using 16S rRNA metabarcoding, to determine its response to dietary exposure of BaP. BaP reduced alpha-diversity at the greatest exposure concentrations. Additionally, exposure to BaP altered community composition of active microbiome and resulted in differential proportion of taxa associated with hydrocarbon degradation and fish health. Neighborhood selection networks of active microbiomes were not reduced with greater concentrations of BaP, which suggests ecological resistance and/or resilience of gut microbiota. The active gut microbiome had a similar overall biodiversity as that of the genomic gut microbiota, but had a distinct composition from that of 16s rDNA profile. The responses of alpha- and beta-diversities of the active microbiome to BaP exposure were consistent with that of genomic microbiomes. Normalized activity of microbiome via the ratio of rRNA to rDNA abundance revealed rare taxa that became active or dormant due to exposure to BaP. These differences highlight the need to assess both 16S rDNA and rRNA metabarcoding to fully derive bacterial compositional changes resulting from exposure to contaminants.
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment. They are highly toxigenic and carcinogenic. Probiotic bacteria isolated from fermented foods were tested to check their ability to degrade and/or detoxify PAHs. Five probiotic bacteria with distinct morphologies were isolated from a mixture of 26 fermented foods co-cultured with benzo(a)pyrene (BaP) containing Bushnell Haas minimal broth. Among them, B. velezensis (PMC10) significantly reduced the abundance of BaP in the broth. PMC10 completely degraded BaP presented at a lower concentration in broth culture. B. velezensis also showed a clear zone of degradation on BaP coated Bushnell Haas agar plate. Gene expression profiling showed significant increases of PAH-ring hydroxylating dioxygenases and 4-hydroxybenzoate 3-monooxygenase genes in B. velezensis in response to BaP treatment. Besides, both live and heat-killed B. velezensis removed BaP and naphthalene (Nap) from phosphate buffer solution. Live B. velezensis did not show any cytotoxicity to macrophage or human dermal fibroblast cells. Live-cell and cell-free supernatant of B. velezensis showed potential anti-inflammatory effects. Cell-free supernatant and extract of B. velezensis also showed free radical scavenging effects. These results highlight the prospective of B. velezensis for the biodegradation and removal of toxic PAHs from the human body. The biodegradation of BaP might be regulated by ring-hydroxylating dioxygenase initiated metabolic pathway.
The skin is our frontier with the exterior environment and is naturally exposed of an innumerous variety of chemical, physical and biological agents, which complete set is named as exposome. The relation of the exposome with the microbial community of the skin is a new field of interest of the science. This article aim to present a review of the scientific knowledge published in the literature about the relation of the two major skin exposome agents, solar radiation and pollution, and the skin microbiome.
The chapter gave an insight into the biodegradation roles of microbes existing within the extreme environment of polycyclic aromatic hydrocarbon - degraded sites.
Polycyclic Aromatic Hydrocarbons (PAHs) are widespread pollutants in various ecosystems. These pollutants are of great concern due to their potential toxicity, mutagenicity and carcinogenicity as well as recalcitrance in the environment due to their hydrophobicity. United States Environment Protection Agency (USEPA) has enlisted 16 of PAHs as priority pollutants that must be disposed. Physicochemical properties of PAHs and their classification according to carcinogenicity as determined by specific agencies have been recorded. Treatment of PAHs by physicochemical methods are expensive and having limited efficiency. So, obligatory development of alternative technology for in situ application must be created. Microbial degradation of PAHs represent the major mechanism responsible for cleaning up of the environment and recovery of PAHs contaminated sites. The main goal of this review is to provide an outline of bacterial degradation pathways of PAHs catabolism. A number of bacterial genera that metabolize PAHs have been isolated (Alcaligenesspp. Bordetellaspp. Bacillusspp. Rhodococcusspp. Pseudomonas spp. and Mycobacteriumspp.). This review includes the catabolic pathway of the Low Molecular Weight-Polycyclic Aromatic Hydrocarbons (LMW-PAHs) and High Molecular Weight-Polycyclic Aromatic Hydrocarbons (HMW-PAHs) by different bacterial isolates and strains. Also the catabolic enzymes (Monooxygenases and diooxygenases) involved in bacterial catabolic pathways has received a considerable attention for better understanding of the catabolic pathways. Application of bacterial strains in treatments of Refinery Waste Water of Petroleum (RWP) have been taken in consideration to facilitate the development of new treatment methods to enhance PAHs bioremediation as a sole compound or in a mixtures in polluted ecosystems.
Dioxins and dioxin-like compounds comprise a group of chemicals including polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF), as well as certain dioxin-like polychlorinated biphenyls (dl-PCB), and potentially others. They act via a common mechanism, stimulation of aryl hydrocarbon receptor (AH receptor, AHR), a vital transcription factor in cells. There are very high differences in potency among these compounds, i.e. in the ability to stimulate the receptor. This leads to ten thousand fold or higher differences in doses causing similar toxic effects. Most of these compounds are eliminated very slowly in the environment, animals, or humans, which makes them persistent. They are much more soluble in fat than in water, and therefore they tend to accumulate in lipid or fatty tissues, and concentrate along the food web (bioaccumulation and biomagnification).
PCDD/PCDFs are formed mostly as side products in burning processes, but PCBs were oils manufactured for many purposes. Because of toxicity and persistence, dioxin-like compounds have been regulated strictly since 1980s, and their levels in the environment and animals have decreased by an order of magnitude or more. Therefore the effects on wildlife have clearly decreased, and even populations at the top of the food web such as fish-eating birds or seals have recovered after serious effects on their reproductive capacity and developmental effects in their young especially in 1970s and 1980s. This does not exclude the possibility of some remaining effects.
In humans the intake is mostly from food of animal sources, but because our diet is much more diverse than that of such hallmark animals as white-tailed eagles or seals, the concentrations never increased to similar levels. However, during 1970s and 1980s effects were probably also seen in humans, including developmental effects in teeth, sexual organs, and the development of immune systems.
Both scientists and administrative bodies debate at the moment about the importance of remaining risks. This is very important, because the AH receptors seem to be physiologically important regulators of growth and development of organs, immunological development, food intake and hunger, and in addition regulate enzymes protecting us from many chemicals. Thus a certain level of activation is needed, although inappropriate stimulation of the receptor is harmful. This dualism emphasizes the importance of benefit versus risk analysis. As a whole, regulating the emissions to the environment is still highly important, but one should be very cautious in limiting consumption of important and otherwise healthy food items and e.g. breast feeding.
Distinct toxic effects of high doses of dioxins in humans have been clearly demonstrated by frank poisonings and the highest occupational exposures. Hallmark effects have been skin lesions called chloracne, various developmental effects of children, and a slightly increased risk of total cancer rate. The highest dioxin levels have been ten thousand fold higher than those seen in the general population today.
A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.
The 97-megabase genomic sequence of the nematode Caenorhabditis elegans reveals over 19,000 genes. More than 40 percent of the predicted protein products find significant matches in other organisms.
There is a variety of repeated sequences, both local and dispersed. The distinctive distribution of some repeats and highly
conserved genes provides evidence for a regional organization of the chromosomes.
Comamonas testosteroni T-2 was grown in salts medium containing intermediates of the established, inducible degradative pathway(s) for 4-toluenesulphonate/4-toluenecarboxylate. The specific activity or, if appropriate, the specific expression of pathway enzymes or their components was constant throughout growth and decreased only slowly in the stationary phase. It was found that the 4-toluenesulphonate methyl-monooxygenase system and 4-sulphobenzyl alcohol dehydrogenase (with 4-sulphobenzaldehyde dehydrogenase) were always co-induced, with similar ratios of their activities during growth with 4-toluenesulphonate 4-toluenecarboxylate and 4-sulphobenzoate. We presume these enzymes to be co-expressed from one regulatory unit. The ratio of activities of the terephthalate 1,2-dioxygenase system to those of (1R,2S)-dihydroxy-1,4-dicarboxy-3,5-cyclohexadiene dehydrogenase was also constant, and present only during growth with 4-toluenecarboxylate or terephthalate. We presume these two enzymes to be co-expressed from a different regulatory unit. The oxygenase component of 4-sulphobenzoate 3,4-dioxygenase (PSBDOS) was expressed at high levels in most growth conditions examined, the exception being with 4-toluenecarboxylate as carbon source. However, no expression of a specific reductase activity linked to synthesis of the oxygenase of PSBDOS could be detected. The PSBDOS was thus active in vivo solely under conditions where the 4-toluenesulphonate methyl-monooxygenase system was also present, whose reductase is active with the oxygenase of the 4-sulphobenzoate 3,4-dioxygenase system in vitro, and, apparently, in vivo. The synthesis of PSBDOS is thus under the control of a third regulatory unit.
The unprecedented population increase and industrial development during the twentieth century has increased conventional solid and liquid waste pollutants to critical levels as well as produced a range of previously unknown strange synthetic chemicals for which society was unprepared. Increasing pollution of the environment by xenobiotic compounds has provoked the need for understanding the impact of toxic compounds on microbial populations, the catabolic degradation pathway of xenobiotics and upgrade in bioremediation processes. Adaptation of native microbial community to xenobiotic substrates is thus crucial for any mineralization to occur in polluted environment. Enzymes which catalyze the biodegradation of xenobiotics are often produced by induction process and this subsequently determine the acclimation time to xenobiotic substrates. Microbial degraders are adapted to xenobiotic substrates via various genetic mechanisms that subsequently determine the evolution of functional degradative pathways. The ultimate goal of these genetic mechanisms is to creating novel genetic combinations in microorganisms that facilitates mineralization of xenobiotics. Moreover, recent development of high-throughput molecular techniques such as polymerase chain reaction (PCR), microarrays and metagenomic libraries have helped to uncover issues of genetic diversity among environmentally relevant microorganisms as well as identification of new functional genes which would enhance pollution abatement management in the twenty-first century.
Carbon-limited aerobic batch enrichment cultures were grown and 17 bacteria able to degrade orthanilic acid (2-aminobenzenesulphonic acid), sulphanilic acid, sulphonamide, 4-sulphobenzoic acid, and benzene-, toluene- and phenolsulphonic acids were isolated. The organisms could each use one to three of the substances. Strain O-1, a Pseudomonas sp., which utilized three of these compounds, was studied in detail. A complete mass balance was obtained for the growth of the organism in medium containing, for example, orthanilic acid, and a specific growth rate of 0.1 h-1 was observed. Cell extracts desulphonated six aromatic sulphonates. The enzyme(s) was soluble and was not syntesized in succinate-grown cells. Enzyme activity [about 40 μkat (kg protein)-1] was dependent on the presence of catalytic amounts of NAD(P)H.
Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, S(max), and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, ("τ"), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ's greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome.
Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/ or http://www.kegg.jp/) is a database resource that integrates genomic, chemical and systemic functional information. In particular, gene catalogs
from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism and the ecosystem.
Major efforts have been undertaken to manually create a knowledge base for such systemic functions by capturing and organizing
experimental knowledge in computable forms; namely, in the forms of KEGG pathway maps, BRITE functional hierarchies and KEGG
modules. Continuous efforts have also been made to develop and improve the cross-species annotation procedure for linking
genomes to the molecular networks through the KEGG Orthology system. Here we report KEGG Mapper, a collection of tools for
KEGG PATHWAY, BRITE and MODULE mapping, enabling integration and interpretation of large-scale data sets. We also report a
variant of the KEGG mapping procedure to extend the knowledge base, where different types of data and knowledge, such as disease
genes and drug targets, are integrated as part of the KEGG molecular networks. Finally, we describe recent enhancements to
the KEGG content, especially the incorporation of disease and drug information used in practice and in society, to support
translational bioinformatics.
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.
To examine the inhalation exposure of cooks at night markets in Taiwan to PAHs and to estimate the corresponding potential human health risks posed by the inhalation of carcinogenic PAHs.
Eight-hour personal air samples collecting particle-bound PAHs and XAD-2 retaining PAHs in the gas phase were taken by personal PM(2.5) cyclones with cooks carrying the sampler on the shoulder while cooking at selected food stalls at four night markets in Taipei, and the concentrations of 16 priority PAHs in both particulates and air were measured with GC/MS.
The total identified PAHs in both gas and PM(2.5) phases exposed by cooks during cook hours ranged from 233,995 to 44,166 ng m(-3). Total exposed PAHs in cooks, as well as the percentage of PAHs in PM(2.5), were the highest at the barbecue stall F3. The fractions of gaseous PAHs (97%) in the four food stalls were consistently higher than the fractions of particulate PAHs (3%). The diagnostic ratios of PAHs fell within the range of those found in other studies related to cooking. At all typical food stalls in night markets except for F2, the excess lifetime cancer risk (ELCR) of cooks are beyond the acceptable target risk range of 10(-6) to 10(-4) for occupational workers set by USEPA.
The PAHs measured in the night markets originated from combustion due to food cooking. The control of gaseous PAH emissions would be more important than the fractions of particulate PAH emissions. Occupational exposure to cooking emissions in Taiwanese workers at night markets is of health concern. Thus, effective protective measures are therefore suggested to minimize cooks' exposure to such emissions, such as wearing mask of activated carbon, evacuating the exhaust into water tank with bio-surfactant to improve PAH removal, installing effective mechanical exhaust vacuum or building high exhaust fume hood above cooking ovens.
The Close and Personal Biome
Fortunately, our skin is readily accessible for ecological studies of the microbial communities that influence health and disease states. Grice et al. (p. 1190 ) present a metagenomic survey of body sites from 10 healthy human individuals sampled over time. Although, altogether 18 phyla were discovered, only a few predominated. The most diverse communities were found on the forearm and the least behind the ear, but between people the microorganisms living behind the knees, in the elbow, and behind the ear were most similar. This finding might have some bearing on the common occurrence of atopic dermatitis in these zones, although no similar relationship was discerned between skin microbial flora and psoriasis.
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
A Beijerinckia strain designated strain B1 was shown to oxidize benz[a]anthracene after induction with biphenyl, m-xylene, and salicylate. Biotransformation experiments showed that after 14 h a maximum of 56% of the benz[a]anthracene was converted to an isomeric mixture of three o-hydroxypolyaromatic acids. Nuclear magnetic resonance and mass spectral analyses led to the identification of the major metabolite as 1-hydroxy-2-anthranoic acid. Two minor metabolites were also isolated and identified as 2-hydroxy-3-phenanthroic acid and 3-hydroxy-2-phenanthroic acid. Mineralization experiments with [12-14C]benz[a]anthracene led to the formation of 14CO2. These results show that the hydroxy acids can be further oxidized and that at least two rings of the benz[a]anthracene molecule can be degraded.
We examined the degradation of biphenyl and the commercial polychlorinated biphenyl (PCB) mixture Aroclor 1221 by indigenous Arctic soil microorganisms to assess both the response of the soil microflora to PCB pollution and the potential of the microflora for bioremediation. In soil slurries, Arctic soil microflora and temperate-soil microflora had similar potentials to mineralize [14C]biphenyl. Mineralization began sooner and was more extensive in slurries of PCB-contaminated Arctic soils than in slurries of uncontaminated Arctic soils. The maximum mineralization rates at 30 and 7 degrees C were typically 1.2 to 1.4 and 0.52 to 1.0 mg of biphenyl g of dry soil-1 day-1, respectively. Slurries of PCB-contaminated Arctic soils degraded Aroclor 1221 more extensively at 30 degrees C (71 to 76% removal) than at 7 degrees C (14 to 40% removal). We isolated from Arctic soils organisms that were capable of psychrotolerant (growing at 7 to 30 degrees C) or psychrophilic (growing at 7 to 15 degrees C) growth on biphenyl. Two psychrotolerant isolates extensively degraded Aroclor 1221 at 7 degrees C (54 to 60% removal). The soil microflora and psychrotolerant isolates degraded all mono-, most di-, and some trichlorobiphenyl congeners. The results suggest that PCB pollution selected for biphenyl-mineralizing microorganisms in Arctic soils. While low temperatures severely limited Aroclor 1221 removal in slurries of Arctic soils, results with pure cultures suggest that more effective PCB biodegradation is possible under appropriate conditions.
Interest in the biodegradation mechanisms and environ- mental fate of polycyclic aromatic hydrocarbons (PAHs) is prompted by their ubiquitous distribution and their potentially deleterious effects on human health. PAHs constitute a large and diverse class of organic compounds and are generally de- scribed as molecules which consist of three or more fused aromatic rings in various structural configurations (5). The biodegradation of PAHs by microorganisms is the subject of many excellent reviews (references 16, 17, 18, 30, 88, and 92, for example), and the biodegradation of PAHs composed of three rings is well documented. In the last decade, research pertaining specifically to the bacterial biodegradation of PAHs composed of more than three rings has been advanced signif- icantly. The bacterial biodegradation of PAHs with more than three rings, which are often referred to in the biodegradation literature as high-molecular-weight (HMW) PAHs, is the sub- ject of this minireview. cases, PAH genotoxicity also increases with size, up to at least four or five fused benzene rings (17). The relationship between PAH environmental persistence and increasing numbers of benzene rings is consistent with the results of various studies correlating environmental biodegradation rates and PAH mol- ecule size (2, 8, 40, 45). For example, reported half-lives in soil and sediment of the three-ring phenanthrene molecule may range from 16 to 126 days while for the five-ring molecule BaP
The catabolic IncP1β plasmid pTSA from Comamonas testosteroni T-2 was mapped by subtractive analysis of restriction digests, by sequencing outwards from the tsaoperon (toluenesulfonate degradation), and by generating overlapping, long-distance-PCR amplification products. The plasmid
was estimated to comprise 72 ± 4 kb. The tsa region was found to be a composite transposon flanked by two IS1071 elements. A cryptic tsa operon was also present in the tsa transposon. Those backbone genes and regions which we sequenced were in the same order as the corresponding genes in resistance
plasmid R751, and identities of about 99% were observed. Enrichment cultures with samples from four continents were done to
obtain organisms able to utilizep-toluenesulfonate as the sole source of carbon and energy for aerobic growth. Most (15) of the 16 cultures (13 of them isolates)
were obtained from contaminated sites and were attributed to three metabolic groups, depending on their metabolism ofp-toluenesulfonate. The largest group contained thetsa transposon, usually (six of seven isolates) with negligible differences in sequence from strain T-2.
Polycyclic aromatic hydrocarbons (PAHs) are formed upon incomplete combustion of organic matter. Due to the abundant use of fossil energy sources, PAHs are readily detectable as ubiquitous contaminants in the environment. The great interest in this group of chemicals originated on the observation in animal tumor models that some member compounds possessed strong carcinogenic activity in skin, lung, breast, and other organs. Epidemiological meta-analyses confirmed that heavy exposures to mixtures of PAHs entail a substantial risk to develop cancer in certain organs. No matter what kind of source, humans are always exposed to mixtures of PAH with different degrees of biological activity. From all hydrocarbons detectable in the human environment the most intensively studied example benzo[. a]pyrene (B[. a]P) has been traditionally used as an indicator for carcinogenic PAHs.About four decades ago it was proposed that there is a significant positive correlation between the binding to DNA and the biological potency of carcinogenic PAHs. In more recent years it became clear that vicinal diol-epoxides of PAHs that contain the epoxy moiety in a sterically crowded bay or fjord region are the actual DNA-binding metabolites that mediate the biological effects associated with their parent structures. Hence, PAHs would not be carcinogenic if they were not stereoselectively metabolized by cytochrome P450-dependent monooxygenases (CYPs). The DNA adduct level at a given time point is an integrated product of PAH's toxicokinetic and toxicodynamic behavior, including metabolic activation and detoxification prior to covalent binding, as well as the effectiveness of the repair of those DNA lesions that have been formed. Covalent PAH-DNA adducts are fixed as mutations if left to error-prone excision repair, misrepair, or replication errors during early S phase. If such somatic mutations occur in proto-oncogenes (e.g., K-. Ras) and/or tumor suppressor genes (e.g., TP53), they can contribute to the aggravation of neoplastic growth through the processes of tumor promotion and progression.Given the chemical complexity of most environmental matrices, it seems difficult, if not impossible, to uncover causative relationships between certain forms of human cancer and the exposure to particular carcinogenic PAHs though. Nevertheless, molecular epidemiology has been able to point to the role of individual compounds and to extract their contribution from the overall biological response on environmental mixtures. One of the most well worked-out examples is the crucial role of B[. a]P in the etiology of human lung cancer based on its presence in cigarette smoke. Its important role in tumor initiation is supported by several lines of evidence such as (1) increased levels of PAH activating CYP enzymes in lung cancer patients compared to controls, (2) a correlation between pulmonary levels of activating CYP enzymes and bulky B[. a]P-DNA adduct levels in human lung tissue from cancer patients, (3) increased levels of B[. a]P-DNA adducts in lung tissue of smokers compared to nonsmokers, and (4) the coincidence of mutational hotspots at certain codons of K-. Ras or TP53 and B[. a]P-DNA adduct hotspots as the preceding lesions found at the same sites.
Interest in the biodegradation mechanisms and environmental fate of polycyclic aromatic hydrocarbons (PAHs) is motivated by their ubiquitous distribution, their low bioavailability and high persistence in soil, and their potentially deleterious effect on human health. Due to high hydrophobicity and solid-water distribution ratios, PAHs tend to interact with non-aqueous phases and soil organic matter and, as a consequence, become potentially unavailable for microbial degradation since bacteria are known to degrade chemicals only when they are dissolved in water. As the aqueous solubility of PAHs decreases almost logarithmically with increasing molecular mass, high-molecular weight PAHs ranging in size from five to seven rings are of special environmental concern. Whereas several reviews have focussed on metabolic and ecological aspects of PAH degradation, this review discusses the microbial PAH-degradation with special emphasis on both biological and physico-chemical factors influencing the biodegradation of poorly available PAHs.
The kinetics of polycyclic aromatic hydrocarbons (PAH) elimination from a contaminated sludge were determined in bioreactors under different conditions: continuously oxic, anoxic, and anoxic/oxic oscillations. The dynamics of metabolically active bacterial communities and their involvement in PAH degradation were followed by T-RFLP targeting 16S rRNA and ring hydroxylating dioxygenase (RHD) transcripts, respectively. PAH degradation was related to toxicity elimination using an aryl hydrocarbon receptor-responsive reporter cell line. Oxygen supply was identified as the main factor affecting the structure of bacterial communities and PAH removal. PAH-degrading bacterial communities were stable throughout the experiment in all conditions according to the presence of RHD transcripts, indicating that bacterial communities were well adapted to the presence of pollutants. Oxic and anoxic/oxic oscillating conditions showed similar levels of PAH removal at the end of the experiment despite several anoxic periods in oscillating conditions. These results highlight the role of dioxygenase activity after oxygen addition. Nevertheless, the higher toxicity elimination observed under oxic conditions suggests that some metabolites or other unidentified active compounds persisted under oscillating and anoxic conditions. Our results emphasize the importance of using complementary biological, chemical and toxicological approaches to implement efficient bioremediation strategies.
Aromatics of a C15C30 mineral oil fraction, the “batching oil” used for producing jute fabrics, were analyzed for estimating the toxicity of oil transferred from jute bags to foods. Group-type pre-separation according to ring systems occurred on a LC NH2 column with pentane and small additions of methanol as eluent. LC fractions were characterized by LC-GC-MS and quantitated by LC-GC-FID. The oil contained 23% aromatics and 1% “polars”; some 99.5% of the aromatics were alkylated.
High molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) increase in hydrophobicity with increases in their molecular weight and ring angularity. Microbial strategies to deal with PAH hydrophobicity include biofilm formation, enzyme induction, and biosurfactants, the effect of which is variable on PAH metabolism depending on the surfactant type and concentration, substrate, and microbial strain(s). Aerobic HMW PAH metabolism proceeds via mineralization, partial degradation, and cometabolic transformations. Generally, bacteria and nonlignolytic fungi metabolize PAHs via initial PAH ring oxidation by dioxygenases to form cis-dihydrodiols, which are transformed to catechol compounds by dehydrogenases and other mono- and dioxygenases to substituted catechol and noncatechol compounds, all ortho- or metacleaved and further oxidized to simpler compounds. However, lignolytic fungi form quinones and acids to CO2. This review discusses the pathways for HMW PAH microbial metabolism. © 2008 Wiley Periodicals, Inc.
Recycled paper and board used in food packaging materials (boxes, paper bags) often cause migration of mineral oil into food
at levels which are unacceptable according to present toxicological assessments. When foods in recycled board are densely
packed into larger boxes or onto pallets, most of the hydrocarbons up to n-C20 may migrate into the packed food within a few weeks, those up to n-C28 at a decreasing rate. Unprinted recycled board contained 300–1,000mg/kg mineral oil <n-C28. The main sources are the inks used for printing newspapers: newspapers contained roughly 3,000mg/kg mineral oil <n-C28. These mineral oils fall into classes for which JECFA established a tolerable daily intake of 0.01mg/kg body weight. Using
standard assumptions for calculating specific migration limits, a maximum tolerable concentration in food of 0.6mg/kg is
derived. This evaluation assumes highly refined white oils, whereas the oils found in recycled board are of technical quality
and contain 15–25% aromatic compounds, predominantly with 1–3 aromatic rings, as shown by comprehensive GC×GC. This finding precipitates authorities into a dilemma: recycling is supported for the sustainable use of materials, but
on the basis of present toxicological assessments the migration is often far beyond acceptable.
Polycyclic aromatic hydrocarbons, the products of the incomplete combustion of fossil fuels, are ubiquitous in nature. Some of these chemicals are of environmental concern because of their genotoxic and carcinogenic potential and their persistence in the environment. Over the last few decades, many investigators have focused on the biodegradation of these pollutants. Bioremediation technologies have been developed to clean up contaminated soils. A better understanding of the metabolism, enzyme mechanisms, and genetics of polycyclic aromatic hydrocarbon degrading microorganisms is critical for the optimization of these bioremediation processes.
Over the past 30 years, research on the microbial degradation of polycyclic aromatic hydrocarbons (PAHs) has resulted in the isolation of numerous genera of bacteria, fungi and algae capable of degrading low molecular weight PAHs (compounds containing three or less fused benzene rings). High molecular weight PAHs (compounds containing four or more fused benzene rings) are generally recalcitrant to microbial attack, although some fungi and algae are capable of transforming these compounds. Until recently, only a few genera of bacteria have been isolated with the ability to utilise four-ring PAHs as sole carbon and energy sources while cometabolism of five-ring compounds has been reported. The focuss of this review is on the high molecular weight PAH benzo[a]pyrene (BaP). There is concern about the presence of BaP in the environment because of its carcinogenicity, teratogenicity and toxicity. BaP has been observed to accumulate in marine organisms and plants which could indirectly cause human exposure through food consumption. This review provides an outline of the occurrence of BaP in the environment and the ability of bacteria, fungi and algae to degrade the compound, including pathways for BaP degradation by these organisms. In addition, approaches for improving microbial degradation of BaP are discussed.
The bacteria responsible for the degradation of naphthalene, phenanthrene, pyrene, fluoranthene or benz[a]anthracene in a polycyclic aromatic hydrocarbon (PAH)-contaminated soil were investigated by DNA-based stable-isotope probing (SIP). Clone libraries of 16S rRNA genes were generated from the (13) C-enriched ('heavy') DNA recovered from each SIP experiment, and quantitative PCR primers targeting the 16S rRNA gene were developed to measure the abundances of many of the SIP-identified sequences. Clone libraries from the SIP experiments with naphthalene, phenanthrene and fluoranthene primarily contained sequences related to bacteria previously associated with the degradation of those compounds. However, Pigmentiphaga-related sequences were newly associated with naphthalene and phenanthrene degradation, and sequences from a group of uncultivated γ-Proteobacteria known as Pyrene Group 2 were newly associated with fluoranthene and benz[a]anthracene degradation. Pyrene Group 2-related sequences were the only sequences recovered from the clone library generated from SIP with pyrene, and they were 82% of the sequences recovered from the clone library generated from SIP with benz[a]anthracene. In time-course experiments with each substrate in unlabelled form, the abundance of each of the measured groups increased in response to the corresponding substrate. These results provide a comprehensive description of the microbial ecology of a PAH-contaminated soil as it relates to the biodegradation of PAHs from two to four rings, and they underscore that bacteria in Pyrene Group 2 are well-suited for the degradation of four-ring PAHs.
In many of the DNA-based stable-isotope probing (SIP) studies published to date in which soil communities were investigated, a single DNA extraction was performed on the soil sample, usually using a commercial DNA extraction kit, prior to recovering the (13)C-labeled (heavy) DNA by density-gradient ultracentrifugation. Recent evidence suggests, however, that a single extraction of a soil sample may not lead to representative recovery of DNA from all of the organisms in the sample. To determine whether multiple DNA extractions would affect the DNA yield, the eubacterial 16S rRNA gene copy number, or the identification of anthracene-degrading bacteria, we performed seven successive DNA extractions on the same aliquot of contaminated soil either untreated or enriched with [U-(13)C]anthracene. Multiple extractions were necessary to maximize the DNA yield and 16S rRNA gene copy number from both untreated and anthracene-enriched soil samples. Sequences within the order Sphingomonadales, but unrelated to any previously described genus, dominated the 16S rRNA gene clone libraries derived from (13)C-enriched DNA and were designated "anthracene group 1." Sequences clustering with Variovorax spp., which were also highly represented, and sequences related to the genus Pigmentiphaga were newly associated with anthracene degradation. The bacterial groups collectively identified across all seven extracts were all recovered in the first extract, although quantitative PCR analysis of SIP-identified groups revealed quantitative differences in extraction patterns. These results suggest that performing multiple DNA extractions on soil samples improves the extractable DNA yield and the number of quantifiable eubacterial 16S rRNA gene copies but have little qualitative effect on the identification of the bacterial groups associated with the degradation of a given carbon source by SIP.
Fungi possess the biochemical and ecological capacity to degrade environmental organic chemicals and to decrease the risk associated with metals, metalloids and radionuclides, either by chemical modification or by influencing chemical bioavailability. Furthermore, the ability of these fungi to form extended mycelial networks, the low specificity of their catabolic enzymes and their independence from using pollutants as a growth substrate make these fungi well suited for bioremediation processes. However, despite dominating the living biomass in soil and being abundant in aqueous systems, fungi have not been exploited for the bioremediation of such environments. In this Review, we describe the metabolic and ecological features that make fungi suited for use in bioremediation and waste treatment processes, and discuss their potential for applications on the basis of these strengths.
In previous work, only one culture (strain TA12) from a pristine site was reported to utilize the xenobiotic compound p-toluenesulfonate (TSA) as a sole source of carbon and energy for aerobic growth. 'Strain TA12' has now been recognized as a community of three bacteria: Achromobacter xylosoxidans TA12-A, Ensifer adhaerens TA12-B and Pseudomonas nitroreducens TA12-C. Achromobacter xylosoxidans TA12-A and E. adhaerens TA12-B were identified as the TSA degraders. These two organisms contain several tsa genes from the Tntsa cluster described previously in Comamonas testosteroni T-2 and use the tsa pathway. Apparently, due to vitamin auxotrophy, the growth of the pure cultures with TSA was markedly slower than the growth of the community with TSA. The third bacterium (P. nitroreducens) TA12-C is, then, a provider of essential vitamins for the TSA degraders and occurs at a low frequency.
Most antibiotic resistance mechanisms are associated with a fitness cost that is typically
observed as a reduced bacterial growth rate. The magnitude of this cost is the main
biological parameter that influences the rate of development of resistance, the stability of
the resistance and the rate at which the resistance might decrease if antibiotic use were
reduced. These findings suggest that the fitness costs of resistance will allow susceptible
bacteria to outcompete resistant bacteria if the selective pressure from antibiotics is
reduced. Unfortunately, the available data suggest that the rate of reversibility will be
slow at the community level. Here, we review the factors that influence the fitness costs of
antibiotic resistance, the ways by which bacteria can reduce these costs and the possibility
of exploiting them.
Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from
which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution
of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions. We found
that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high,
whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than
the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota,
although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome
changes cause or prevent disease.
PAHs are aromatic hydrocarbons with two or more fused benzene rings with natural as well as anthropogenic sources. They are widely distributed environmental contaminants that have detrimental biological effects, toxicity, mutagenecity and carcinogenicity. Due to their ubiquitous occurrence, recalcitrance, bioaccumulation potential and carcinogenic activity, the PAHs have gathered significant environmental concern. Although PAH may undergo adsorption, volatilization, photolysis, and chemical degradation, microbial degradation is the major degradation process. PAH degradation depends on the environmental conditions, number and type of the microorganisms, nature and chemical structure of the chemical compound being degraded. They are biodegraded/biotransformed into less complex metabolites, and through mineralization into inorganic minerals, H(2)O, CO(2) (aerobic) or CH(4) (anaerobic) and rate of biodegradation depends on pH, temperature, oxygen, microbial population, degree of acclimation, accessibility of nutrients, chemical structure of the compound, cellular transport properties, and chemical partitioning in growth medium. A number of bacterial species are known to degrade PAHs and most of them are isolated from contaminated soil or sediments. Pseudomonas aeruginosa, Pseudomons fluoresens, Mycobacterium spp., Haemophilus spp., Rhodococcus spp., Paenibacillus spp. are some of the commonly studied PAH-degrading bacteria. Lignolytic fungi too have the property of PAH degradation. Phanerochaete chrysosporium, Bjerkandera adusta, and Pleurotus ostreatus are the common PAH-degrading fungi. Enzymes involved in the degradation of PAHs are oxygenase, dehydrogenase and lignolytic enzymes. Fungal lignolytic enzymes are lignin peroxidase, laccase, and manganese peroxidase. They are extracellular and catalyze radical formation by oxidation to destabilize bonds in a molecule. The biodegradation of PAHs has been observed under both aerobic and anaerobic conditions and the rate can be enhanced by physical/chemical pretreatment of contaminated soil. Addition of biosurfactant-producing bacteria and light oils can increase the bioavailability of PAHs and metabolic potential of the bacterial community. The supplementation of contaminated soils with compost materials can also enhance biodegradation without long-term accumulation of extractable polar and more available intermediates. Wetlands, too, have found an application in PAH removal from wastewater. The intensive biological activities in such an ecosystem lead to a high rate of autotrophic and heterotrophic processes. Aquatic weeds Typha spp. and Scirpus lacustris have been used in horizontal-vertical macrophyte based wetlands to treat PAHs. An integrated approach of physical, chemical, and biological degradation may be adopted to get synergistically enhanced removal rates and to treat/remediate the contaminated sites in an ecologically favorable process.
Biotransformation is essential to convert lipophilic chemicals to water-soluble and readily excretable metabolites. Formally, biotransformation reactions are classified into phase I and phase II reactions. Phase I reactions represent the introduction of functional groups, whereas phase II reactions are conjugations of such functional groups with endogenous, polar products. Biotransformation also plays an essential role in the toxicity of many chemicals due to the metabolic formation of toxic metabolites. These may be classified as stable but toxic products, reactive electrophiles, radicals, and reactive oxygen metabolites. The interaction of toxic products formed by biotransformation reactions with cellular macromolecules initiates the sequences resulting in cellular damage, cell death and toxicity.
Polycyclic aromatic hydrocarbons (PAHs) are widespread in various ecosystems and are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Because of their hydrophobic nature, most PAHs bind to particulates in soil and sediments, rendering them less available for biological uptake. Microbial degradation represents the major mechanism responsible for the ecological recovery of PAH-contaminated sites. The goal of this review is to provide an outline of the current knowledge of microbial PAH catabolism. In the past decade, the genetic regulation of the pathway involved in naphthalene degradation by different gram-negative and gram-positive bacteria was studied in great detail. Based on both genomic and proteomic data, a deeper understanding of some high-molecular-weight PAH degradation pathways in bacteria was provided. The ability of nonligninolytic and ligninolytic fungi to transform or metabolize PAH pollutants has received considerable attention, and the biochemical principles underlying the degradation of PAHs were examined. In addition, this review summarizes the information known about the biochemical processes that determine the fate of the individual components of PAH mixtures in polluted ecosystems. A deeper understanding of the microorganism-mediated mechanisms of catalysis of PAHs will facilitate the development of new methods to enhance the bioremediation of PAH-contaminated sites.
A mutant strain of Beijerinckia, after growth with succinate plus biphenyl, contains an enzyme system that oxidizes benzo
[a] pyrene and benzo [a] anthracene to mixtures of vicinal dihydrodiols. The major dihydrodiol formed from benzo [a] pyrene
was identified as cis-9, 10-dihydroxy-9, 10-dihydrobenzo [a] pyrene by comparison with a synthetic sample. Benzo [a] anthracene
was metabolized to four dihydrodiols, the major isomer being cis-1, 2-dihydroxy-1, 2-dihydroxy-1, 2-dihydrobenzo [a] anthracene.
Naphthalene biodegradation was investigated in microcosms containing sediment and water collected from three ecosystems which varied in past exposure to anthropogenic and petrogenic chemicals. Mineralization half-lives for naphthalene in microcosms ranged from 2.4 weeks in sediment chronically exposed to petroleum hydrocarbons to 4.4 weeks in sediment from a pristine environment. Microbiological analysis of sediments indicated that hydrocarbon-utilizing microbial populations also varied among ecosystems and were 5 to 12 times greater in sediment after chronic petrogenic chemical exposure than in sediment from an uncontaminated ecosystem. Sediment from an ecosystem exposed to agricultural chemicals had a mineralization half-life of 3.2 weeks for naphthalene and showed about a 30-fold increase in heterotrophic bacterial populations in comparison to uncontaminated sediments, but only a 2- to 3-fold increase in hydrocarbon-degrading bacteria. Analysis of organic solvent-extractable residues from the microcosms by high-pressure liquid chromatography detected polar metabolites which accounted for 1 to 3% of the total radioactivity. Purification of these residues by thin-layer chromatography and further analysis by gas chromatography-mass spectrometry indicated that cis-1,2-dihydroxy-1,2-dihydronaphthalene, 1-naphthol, salicylic acid, and catechol were metabolites of naphthalene. These results provide useful estimates for the rates of naphthalene mineralization in different natural ecosystems and on the degradative pathway for microbial metabolism of naphthalene in freshwater and estuarine environments.
We investigated the potential biodegradation of polycyclic aromatic hydrocarbons (PAHs) by an aerobic mixed culture utilizing phenanthrene as its carbon source. Following a 3-5 h post-treatment lag phase, complete degradation of 5 mg/l phenanthrene occurred within 28 h (optimal conditions determined as 30 degrees C and pH 7.0). Phenanthrene degradation was enhanced by the individual addition of yeast extract, acetate, glucose or pyruvate. Results show that the higher the phenanthrene concentration, the slower the degradation rate. While the mixed culture was also capable of efficiently degrading pyrene and acenaphthene, it failed to degrade anthracene and fluorene. In samples containing a mixture of the five PAHs, treatment with the aerobic culture increased degradation rates for fluorene and anthracene and decreased degradation rates for acenaphthene, phenanthrene and pyrene. Finally, it was observed that when nonionic surfactants were present at levels above critical micelle concentrations (CMCs), phenanthrene degradation was completely inhibited by the addition of Brij 30 and Brij 35, and delayed by the addition of Triton X100 and Triton N101.