scholarly journals Characterization of Novel Polycyclic Aromatic Hydrocarbon Dioxygenases from the Bacterial Metagenomic DNA of a Contaminated Soil

2014 ◽  
Vol 80 (21) ◽  
pp. 6591-6600 ◽  
Author(s):  
Angelina Chemerys ◽  
Eric Pelletier ◽  
Corinne Cruaud ◽  
Florence Martin ◽  
Fabien Violet ◽  
...  
Keyword(s):  
Aromatic Hydrocarbons ◽  
Current Knowledge ◽  
Pollutant Removal ◽  
Metagenomic Data ◽  
Metabolic Potential ◽  
Metagenomic Dna ◽  
Metagenomic Sequence ◽  
Soil Dna ◽  
Content Type ◽  
Polycyclic Aromatic

ABSTRACTRing-hydroxylating dioxygenases (RHDs) play a crucial role in the biodegradation of a range of aromatic hydrocarbons found on polluted sites, including polycyclic aromatic hydrocarbons (PAHs). Current knowledge on RHDs comes essentially from studies on culturable bacterial strains, while compelling evidence indicates that pollutant removal is mostly achieved by uncultured species. In this study, a combination of DNA-SIP labeling and metagenomic sequence analysis was implemented to investigate the metabolic potential of main PAH degraders on a polluted site. Followingin situlabeling using [13C]phenanthrene, the labeled metagenomic DNA was isolated from soil and subjected to shotgun sequencing. Most annotated sequences were predicted to belong toBetaproteobacteria, especiallyRhodocyclaceaeandBurkholderiales, which is consistent with previous findings showing that main PAH degraders on this site were affiliated to these taxa. Based on metagenomic data, four RHD gene sets were amplified and cloned from soil DNA. For each set, PCR yielded multiple amplicons with sequences differing by up to 321 nucleotides (17%), reflecting the great genetic diversity prevailing in soil. RHDs were successfully overexpressed inEscherichia coli, but full activity required the coexpression of two electron carrier genes, also cloned from soil DNA. Remarkably, two RHDs exhibited much higher activity when associated with electron carriers from a sphingomonad. The four RHDs showed markedly different preferences for two- and three-ring PAHs but were poorly active on four-ring PAHs. Three RHDs preferentially hydroxylated phenanthrene on the C-1 and C-2 positions rather than on the C-3 and C-4 positions, suggesting that degradation occurred through an alternate pathway.

scholarly journals Complete Genome Sequence of Pseudomonas putida BS3701, a Promising Polycyclic Aromatic Hydrocarbon-Degrading Strain for Bioremediation Technologies

2020 ◽  
Vol 9 (40) ◽  
Author(s):  
Andrey Filonov ◽  
Yanina Delegan ◽  
Irina Puntus ◽  
Leonid Valentovich ◽  
Artur Akhremchuk ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Pseudomonas Putida ◽  
Russian Federation ◽  
Aromatic Hydrocarbons ◽  
Complete Genome Sequence ◽  
Circular Chromosome ◽  
Content Type ◽  
Polycyclic Aromatic

ABSTRACT The strain Pseudomonas putida BS3701 was isolated from soil contaminated with coke by-product waste (Moscow Region, Russian Federation). It is capable of degrading crude oil and polycyclic aromatic hydrocarbons (PAHs). The P. putida BS3701 genome consists of a 6,337,358-bp circular chromosome and two circular plasmids (pBS1141 with 107,388 bp and pBS1142 with 54,501 bp).

Effect of fatty acid on the formation of polycyclic aromatic hydrocarbons (PAHs) and the proposed formation mechanism during electric roasting

2019 ◽  
Vol 121 (12) ◽  
pp. 3193-3207
Author(s):  
Congcong Liu ◽  
Chong Wang ◽  
Keping Ye ◽  
Yun Bai ◽  
Xiaobo Yu ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Fatty Acid ◽  
Carbon Atom ◽  
Formation Mechanism ◽  
Aromatic Hydrocarbons ◽  
Meat Products ◽  
Content Type ◽  
Animal Fats ◽  
Animal Fat ◽  
Polycyclic Aromatic

Purpose The purpose of this paper is to elucidate the influences of the animal fat and fatty acid type on the formation of polycyclic aromatic hydrocarbons (PAHs) and to propose a formation mechanism of PAHs in fat during electric roasting, which is a method of non-direct-contact-flame heating. Design/methodology/approach The effects of animal fats and model fat on the formation of PAHs were valued on the basis of the ultra high-performance liquid chromatography data. The corresponding products of the FAME pyrolysis were detected by TG-FTIR. The proposal formation mechanism of PAHs was based on the summary of the literature. Findings Contrary to the International Agency for Research on Cancer, DF had higher risk with 280.53 ng/g of concentration after being roasted than the others animal fats of red meat in terms of PAHs formation. This research also ensured the importance of fat on PAHs formation, the concentration of PAHs in pure fats was higher after being electric roasted than that in meat patties and juice which made from corresponding animal fat. What is more, during pure animal fats and meat products being processed, less PAHs formed in the fat with lower extent of unsaturation and lower content of linolenate. In the same way, methyl linolenate demonstrated the significant increasement to PAHs formation compared to the other fatty acids. And, the number of carbon atom and the extent of unsaturation in fatty acid affects the formation of PAHs during roasting. The detection of alkene and alkane allows to propose a formation mechanism of PAHs during model fat being heated. Further study is required to elucidate the confirm moleculars during the formation of PAHs. Originality/value This work studied the effect of the carbon atom number and the unsaturation extent of fats and model fats on the formation of PAHs. This work also assure the important of alkene and alkane on the pyrolysis of model fats. This study also researched the formation and distribution of PAHs in pure fats and meat products after being heated.

scholarly journals Biofilm and Planktonic Bacterial and Fungal Communities Transforming High-Molecular-Weight Polycyclic Aromatic Hydrocarbons

2016 ◽  
Vol 82 (8) ◽  
pp. 2288-2299 ◽  
Author(s):  
Benjamin D. Folwell ◽  
Terry J. McGenity ◽  
Corinne Whitby
Keyword(s):  
Molecular Weight ◽  
Polycyclic Aromatic Hydrocarbons ◽  
High Molecular Weight ◽  
Community Composition ◽  
Aromatic Hydrocarbons ◽  
Fungal Community ◽  
Bacterial Species ◽  
Bacterial Community Composition ◽  
Content Type ◽  
Polycyclic Aromatic

ABSTRACTHigh-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs) are natural components of fossil fuels that are carcinogenic and persistent in the environment, particularly in oil sands process-affected water (OSPW). Their hydrophobicity and tendency to adsorb to organic matter result in low bioavailability and high recalcitrance to degradation. Despite the importance of microbes for environmental remediation, little is known about those involved in HMW-PAH transformations. Here, we investigated the transformation of HMW-PAHs using samples of OSPW and compared the bacterial and fungal community compositions attached to hydrophobic filters and in suspension. It was anticipated that the hydrophobic filters with sorbed HMW-PAHs would select for microbes that specialize in adhesion. Over 33 days, more pyrene was removed (75% ± 11.7%) than the five-ring PAHs benzo[a]pyrene (44% ± 13.6%) and benzo[b]fluoranthene (41% ± 12.6%). For both bacteria and fungi, the addition of PAHs led to a shift in community composition, but thereafter the major factor determining the fungal community composition was whether it was in the planktonic phase or attached to filters. In contrast, the major determinant of the bacterial community composition was the nature of the PAH serving as the carbon source. The main bacteria enriched by HMW-PAHs werePseudomonas,Bacillus, andMicrobacteriumspecies. This report demonstrates that OSPW harbors microbial communities with the capacity to transform HMW-PAHs. Furthermore, the provision of suitable surfaces that encourage PAH sorption and microbial adhesion select for different fungal and bacterial species with the potential for HMW-PAH degradation.

scholarly journals Occurrence and Phylogenetic Diversity of Sphingomonas Strains in Soils Contaminated with Polycyclic Aromatic Hydrocarbons

2004 ◽  
Vol 70 (4) ◽  
pp. 1944-1955 ◽  
Author(s):  
Natalie M. E. J. Leys ◽  
Annemie Ryngaert ◽  
Leen Bastiaens ◽  
Willy Verstraete ◽  
Eva M. Top ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Aromatic Hydrocarbons ◽  
Contaminated Soils ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Soil Dna ◽  
Detection Techniques ◽  
Polycyclic Aromatic

ABSTRACT Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 104 CFU g of soil−1. The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.

scholarly journals Croceicoccus naphthovorans sp. nov., a polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing bacterium isolated from marine biofilm, and emended description of the genus Croceicoccus

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1531-1536 ◽  
Author(s):  
Yili Huang ◽  
Yanhua Zeng ◽  
Hao Feng ◽  
Yuehong Wu ◽  
Xuewei Xu
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Type Species ◽  
Minor Amount ◽  
Content Type ◽  
Acylhomoserine Lactone ◽  
Link Type ◽  
Marine Biofilm ◽  
The Family ◽  
Polycyclic Aromatic

A polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing marine bacterium, designated strain PQ-2T, was isolated from marine biofilm collected from a boat shell at a harbour of Zhoushan island in Zhejiang Province, PR China. Strain PQ-2T is Gram-stain-negative, yellow-pigmented, non-motile and short rod-shaped. Optimal growth of strain PQ-2T was observed at 32 °C, at pH 7.0 and in 2 % (w/v) NaCl. The 16S rRNA gene sequence of strain PQ-2T showed highest similarity to Croceicoccus marinus E4A9T (96.3 %) followed by Novosphingobium malaysiense MUSC 273T (95.6 %) and Altererythrobacter marinus H32T (95.6 %). Phylogenetic analysis with all species of the family Erythrobacteraceae with validly published names revealed that strain PQ-2T formed a phyletic line with Croceicoccus marinus E4A9T that was distinct from other members of the family Erythrobacteraceae . The sole respiratory quinone was ubiquinone 10 (Q-10). The predominant fatty acids were C18 : 1ω7c, C17 : 1ω6c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content was 61.7 mol%. In the polar lipid profile, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one unidentified phospholipid and one sphingoglycolipid were the major compounds; and another sphingoglycolipid was present in a minor amount. Based on the genotypic and phenotypic data, strain PQ-2T represents a novel species of the genus Croceicoccus , for which the name Croceicoccus naphthovorans sp. nov. is proposed. The type strain is PQ-2T ( = CGMCC 1.12805T = NBRC 110381T). In addition, emended descriptions for the genus Croceicoccus and the species C. marinus are given.

scholarly journals Polycyclic Aromatic Hydrocarbons in Foods: Biological Effects, Legislation, Occurrence, Analytical Methods, and Strategies to Reduce their Formation

2021 ◽  
Vol 22 (11) ◽  
pp. 6010
Author(s):  
Geni Sampaio ◽  
Glória Guizellini ◽  
Simone da Silva ◽  
Adriana de Almeida ◽  
Ana Pinaffi-Langley ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Analytical Methods ◽  
Current Knowledge ◽  
Biological Effects ◽  
Food Products ◽  
Hydrogen Molecules ◽  
Processing Strategies ◽  
Contaminated Food ◽  
Polycyclic Aromatic

Polycyclic aromatic hydrocarbons (PAHs) are chemical compounds comprised of carbon and hydrogen molecules in a cyclic arrangement. PAHs are associated with risks to human health, especially carcinogenesis. One form of exposure to these compounds is through ingestion of contaminated food, which can occur during preparation and processing involving high temperatures (e.g., grilling, smoking, toasting, roasting, and frying) as well as through PAHs present in the soil, air, and water (i.e., environmental pollution). Differently from changes caused by microbiological characteristics and lipid oxidation, consumers cannot sensorially perceive PAH contamination in food products, thereby hindering their ability to reject these foods. Herein, the occurrence and biological effects of PAHs were comprehensively explored, as well as analytical methods to monitor their levels, legislations, and strategies to reduce their generation in food products. This review updates the current knowledge and addresses recent regulation changes concerning the widespread PAHs contamination in several types of food, often surpassing the concentration limits deemed acceptable by current legislations. Therefore, effective measures involving different food processing strategies are needed to prevent and reduce PAHs contamination, thereby decreasing human exposure and detrimental health effects. Furthermore, gaps in literature have been addressed to provide a basis for future studies.

scholarly journals Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic GenusCaldicellulosiruptorby Genomic, Pangenomic, and Metagenomic Analyses

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Laura L. Lee ◽  
Sara E. Blumer-Schuette ◽  
Javier A. Izquierdo ◽  
Jeffrey V. Zurawski ◽  
Andrew J. Loder ◽  
...  
Keyword(s):  
Microcrystalline Cellulose ◽  
Plant Biomass ◽  
Thermophilic Bacteria ◽  
Cellulose Degradation ◽  
Glycoside Hydrolases ◽  
Metagenomic Data ◽  
Lignocellulose Degradation ◽  
Sequence Information ◽  
Metagenomic Sequence ◽  
Content Type

ABSTRACTMetagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilicCaldicellulosiruptor. The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species,Caldicellulosiruptorsp. strain Rt8.B8 (renamed hereCaldicellulosiruptor morganii),Thermoanaerobacter cellulolyticusstrain NA10 (renamed hereCaldicellulosiruptor naganoensis), andCaldicellulosiruptorsp. strain Wai35.B1 (renamed hereCaldicellulosiruptor danielii), degraded Avicel and lignocellulose (switchgrass).C. morganiiwas more efficient thanCaldicellulosiruptor besciiin this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that ofCaldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter,Fervidobacterium,Caloramator, andClostridium). One enrichment, containing 89.8%Caldicellulosiruptorand 9.7%Caloramator, had a capacity for switchgrass solubilization comparable to that ofC. bescii. These results refine the known biodiversity ofCaldicellulosiruptorand indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes.IMPORTANCEThe genusCaldicellulosiruptorcontains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.

scholarly journals Discovery of Significant Emission of Halogenated Polycyclic Aromatic Hydrocarbons From Secondary Zinc Smelting

2021 ◽  
Author(s):  
Yuanping Yang ◽  
Lili Yang ◽  
Guorui Liu ◽  
Minghui Zheng ◽  
Qiuting Yang ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Current Knowledge ◽  
Copper Smelting ◽  
Source Control ◽  
Formation Mechanisms ◽  
Secondary Aluminum ◽  
Zinc Smelting ◽  
Polycyclic Aromatic ◽  
Stack Gas

Abstract Chlorinated and brominated polycyclic aromatic hydrocarbons (Cl/Br-PAHs) are persistent organic pollutants, and controlling their adverse effects requires the identification of their sources. However, current knowledge on the formations of Cl/Br-PAHs is far insufficient for source control, much less on their formation mechanisms. In this field study, we firstly discovered secondary zinc smelting as a significant source of Cl/Br-PAHs. The mean concentration of Cl/Br-PAHs emitted in stack gas from secondary zinc smelting was 9,553 ng/m3, exceeding concentrations from other metal smelting sources by one or two orders of magnitude. Cl/Br-PAHs with fewer rings were the dominant congeners in stack gas from secondary zinc smelting and secondary copper smelting. However, emissions from secondary aluminum smelting were dominated by congeners with more rings. The differences in congener profiles were attributable to the catalytic effects of metal compounds during smelting activities. Zinc oxide and copper oxide dominantly catalyzed dehydrogenation reactions, contributing to the formation of intermediate radicals and subsequent dimerization to Cl/Br-PAHs with fewer rings. Aluminum oxide induced alkylation reactions and accelerated ring growth, resulting in the formation of Cl-PAHs with more rings. The newly proposed mechanisms can successfully explain the emission characteristics of Cl/Br-PAHs during smelting activities and the higher concentrations of Cl/Br-PAHs from secondary zinc smelting, which should be useful in targeted source control.

scholarly journals Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH DegraderCycloclasticussp. Strain P1

2018 ◽  
Vol 84 (21) ◽  
Author(s):  
Wanpeng Wang ◽  
Lin Wang ◽  
Zongze Shao
Keyword(s):  
Metabolic Network ◽  
Aromatic Hydrocarbons ◽  
Gene Clusters ◽  
Degradation Pathway ◽  
Degradation Pathways ◽  
Marine Environments ◽  
Content Type ◽  
Pah Degradation ◽  
Polycyclic Aromatic ◽  
Pah Metabolism

ABSTRACTBacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments,Cycloclasticusis one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs byCycloclasticus.Cycloclasticussp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome ofCycloclasticussp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated inCycloclasticussp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway forCycloclasticus.Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism inCycloclasticus.IMPORTANCEPAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability.Cycloclasticusis an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed inCycloclasticus. This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence ofCycloclasticusin oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.

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