Analysis of PCBs degradation abilities of biphenyl dioxygenase derived from Enterobacter sp. LY402 by molecular simulation

The uptake and degradation of polychlorinated biphenyls in constructed wetlands planted with Myriophyllum aquaticum

The unregulated dismantling and improper disposal of electronic waste lead to severe soil contamination by polychlorinated biphenyls (PCBs). Constructed wetlands (CWs) play an important role in PCBs removal as a result of the co-existence of anaerobic and aerobic conditions. However, the effects and mechanisms of different PCBs concentrations in soils on plant uptake and PCBs degradation within CWs are unclear. We evaluated the uptake and degradation of PCBs at different concentrations by Myriophyllum aquaticum (Vell.) Verdc. Planting significantly increased PCBs removal by 8.70% (p < 0.05) in soils with 1500 and 2500 μg/kg PCBs, whereas no significant effect was observed at 500 and 1000 μg/kg. PCBs levels did not significantly affect plant growth and PCBs accumulation. The contribution of plant uptake to PCBs removal was only 0.10-0.12%, indicating that microbial degradation was the dominant pathway for PCBs removal after planting with M. aquaticum. In the treatments with PCBs ≥ 1500 μg/kg, M. aquaticum increased the microbial population, altered the microbial community structure and enriched PCB-degrading bacteria. Functional prediction revealed that microbes in M. aquaticum rhizosphere secreted more peroxidase and glycosyltransferase than non-plant control, which were likely involved in PCBs metabolism.

Cyclic and linear siloxane contamination in sediment and invertebrates around a thermal power plant in Korea: Source impact, distribution, seasonal variation, and potential for bioaccumulation

Siloxanes have been commonly used as additives in a variety of industrial and consumer products. Media and government investigations have revealed that defoamers containing siloxanes are used in the effluent of thermal power plants in Korea. However, investigations of the source impact of siloxane contamination from the discharge of thermal power plants into coastal environments are scarce. In this study, sediment and invertebrates were collected around a thermal power plant to assess source impact, seasonal variation, and a potential for bioaccumulation. Although siloxanes were detectable in sediment and invertebrates, the spatial distribution and composition (which differed between the siloxanes found in sediment and invertebrates and those in defoamer used in the plant) suggest they were likely transported by long-distance migration as well as the discharge of thermal power plant. Seasonal differences might affect sedimentary contamination and the bioaccumulation potential of siloxanes. Specifically, octamethylcyclotetrasiloxane (D4) may have limited adsorption capacity and potential for long-distance migration, as its contribution in sediment far from the coastline was greater than that of decamethylcyclopentasiloxane (D5) and dodecamethylcyclohexasiloxane (D6). However, higher D5 accumulation in invertebrates, and D5 has a potential bioaccumulation. A molecular docking analysis showed that the binding affinity between D5 and the cytochrome enzyme in invertebrates was weaker than that with other siloxanes, which could lead to higher D5 accumulation in invertebrates.

Congener-specificity, dioxygenation dependency and association with enzyme binding for biodegradation of polybrominated diphenyl ethers by typical aerobic bacteria: Experimental and theoretical studies

Polybrominated diphenyl ethers (PBDEs) are a group of organic pollutants that have attracted much concerns of scientific community over the ubiquitous distribution, chemical persistence and toxicological risks in the environment. Though a great number of aerobic bacteria have been isolated for the rapid removal of PBDEs, the knowledge about biodegradation characteristics and mechanism is less provided yet. Herein, the congener-specificity of aerobic biodegradation of PBDEs by typical bacteria, i.e. B. xenovorans LB400 was identified with the different biodegradation kinetics, of which the changes were largely hinged on the bromination pattern. The more bromination isomerically at ortho-sites other than meta-sites or the single bromination at one of aromatic rings might always exert the positive effect. The biodegradation of PBDEs should be thermodynamically constrained to some extent because the calculated Gibbs free energy changes of initial dioxygenation by quantum chemical method increased with the increase of bromination. Within the transition state theory, the high correlativity between the apparent biodegradation rates and Gibbs free energy changes implied the predominance and rate-limiting character of initial dioxygenation, while the regioselectivity of dioxygenation at the ortho/meta-sites was also manifested for the more negative charge population. The molecular binding with the active domain of dioxygenase BphA1 in aerobe was firstly investigated using docking approach. As significantly illustrated with the positive relationship, the higher binding affinity with BphA1 should probably signify the more rapid biodegradation. Besides the edge-on π-π stacking of PBDEs with F227 or Y277 and π-cation formulation with histidines (H233, H239) in BphA1, the reticular hydrophobic contacts appeared as the major force to underpin the high binding affinity and rapid biodegradation of PBDEs. Overall, the experimental and theoretical results would not only help understand the aerobic biodegradation mechanism, but facilitate enhancing applicability or strategy development of engineering bacteria for bioremediation of PBDEs in the environment.

A Pilot Study on the Concentration, Distribution and Bioaccumulation of Polybrominated Diphenyl Ethers (PBDEs) in Tissues and Organs of Grassland Sheep

Polybrominated diphenyl ether (PBDE) concentrations in various tissues and organs of grassland sheep from Inner Mongolia, China, were determined. The abilities of PBDEs binding to ovine serum albumin (OSA) and Cytochrome P450 enzyme (CYP3A24) were assessed by fluorescence spectroscopy and molecular docking simulations. The PBDE concentrations in the sheep tissue and organ samples were 33.4-167 pg/g dw. The distribution of PBDEs in sheep organs and tissues is affected not only by the function of organs and tissues, but also by the characteristics of PBDEs. Adipose tissue tends to bioaccumulate more-brominated BDEs (BDE-154, -153, and -183), but muscle tissues and visceral organs mainly bioaccumulate less-brominated BDEs. The distribution of PBDEs in visceral organs is mainly affected by the transport of ovine serum albumin (OSA) and the metabolism of CYP3A24 enzyme. The distribution of PBDEs in adipose tissue and brain is mainly affected by their logK_OW.

Degradability of commercial mixtures of polychlorobiphenyls by three Rhodococcus strains

Biodegradative characteristics were investigated for the commercially available mixtures of polychlorinated biphenyls (PCBs) Trikhlorbifenil and Sovol degraded by the Rhodococcus wratislaviensis КT112-7, Rhodococcus wratislaviensis CH628 and Rhodococcus ruber P25 strains isolated from the natural habitats. For bioutilization of the Trikhlorbifenil, all three strains were found to have a high biodegrading potential: the complete destruction was achieved in 10-14 days. For the mixture Sovol, the bioutilization parameters were found to be of lower values: the degradation of the PCBs congeners was 96-98% after 14 days. For the tested polychlorobiphenyl mixtures, the structural specificities of congeners are discussed, the genes encoding monooxygenases are revealed, and explanation is given to the differences in biodegradative characteristics of the Rhodococcus strains towards di-, tri-, tetra-, penta-, hexa- and heptachlorobiphenyls. The presented data are highly relevant for environmental remediation of objects polluted with the extremely hazardous polychlorobiphenyls.

PAEs Derivatives' Design for Insulation: Integrated In-Silico Methods, Functional Assessment and Environmentally Friendly Molecular Modification

As a common substance in production and life, phthalic acid esters (PAEs), the main component of plastics, have brought more and more serious problems to the environment. This study normalized the insulation, toxicity, and bioconcentration data of 13 PAEs to eliminate the dimensional coefficients of each index, and then used the comprehensive index method to calculate the comprehensive effect value of PAEs with three properties. The comprehensive effect value was used as the data source to construct the 3D-QSAR model of PAE molecular comprehensive effect. The DAP was selected as the target molecule, the distribution of each force field in the three-dimensional equipotential map was analyzed, and 30 molecular modification schemes were created. The constructed single-effect models of insulation, toxicity, and bioconcentration of PAEs and the scoring function module of DS software were used to evaluate the stability and environmental friendliness of PAE derivative molecules. Four PAE derivatives were screened for increased comprehensive effects, enhanced insulation, and reduced toxicity and bioconcentration. By calculating the binding energy of the target molecule and the derivative molecule with the degrading enzyme under different applied electric fields, it was found that the binding energy of DAP-1-NO2-2-CH2C6H5 decreases more than DAP does when there is an applied electric field, indicating that the degradation ability of degrading enzymes on PAE derivative molecules is reduced, which indirectly proves that the insulation is enhanced. The innovation of this paper lies in the insulation, toxicity, and bioenrichment data of PAEs being processed by mathematical method for the first time, and PAEs with high insulation, low toxicity, and low bioconcentration were designed by building a comprehensive model.

A model for phthalic acid esters' biodegradability and biotoxicity multi-effect pharmacophore and its application in molecular modification

The objective of this study was to investigate 13 phthalic acid esters (PAEs) with medium or long straight-alkyl-chain, branching or unsaturated side chains, because their structural characteristics make them difficult to biodegrade or highly toxic. A biodegradability and biotoxicity multi-effect pharmacophore model was built using comprehensive evaluation method. The results suggested that introducing hydrophobic groups to the side chains of the PAEs could improve the molecules' biodegradability and biotoxicity effects simultaneously. Thus, 40 target PAE (HEHP, DNOP, DUP) derivatives were designed. Two environmentally friendly PAE derivatives (HEHP-Anthryl and HEHP-Naphthyl) were screened via the test of environmental friendliness and functionality. In addition, the biodegradation and biotoxicity of derivatives were found to have improved as a result of the change in van der Waals forces between molecules and their corresponding proteins. Moreover, the environmental safety of the screened PAE derivatives was confirmed by predicting the toxicity of their intermediates and calculating the energy barrier values for biodegradation and metabolic pathways. This study could provide theoretical guidance for the practical development of environmentally friendly plasticizer.

Structure and diversity of native bacterial communities in soils contaminated with polychlorinated biphenyls

Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) are a group of high-risk synthetic substances for human and environmental health. Currently, the study of sites contaminated by the spillage of equipment PCBs containing have been considered targeted areas for the study of bacterial communities with potential for PCBs degradation. There in isolation of bacterial strains is vital for use in biodegradable processes, such as bacterial bioaugmentation, which accelerates the development of phenomena such as natural attenuation of contaminated sites. The objective of this study was to assess biodiversity of bacteria contained in anthropogenic contaminated soils (H_S and H_P) with PCBs compared to a control sample without contaminant and the modified forest (F) and agricultural (A) soil in the laboratory with 100 mg L⁻¹ PCB. For the analysis of 16S rRNA genes amplified from DNA extracted from the soils evaluated, the latest generation of Illumina Miseq and Sanger sequencing for the cultivable strains were detected. The bacteria identified as the most abundant bacterial phyla for H_S and H_P soil was Proteobacteria (56.7%) and Firmicutes (22.9%), which decreased in F and A soils. The most abundant bacterial genera were Burkholderia, Bacillus, Acinetobacter, Comamonas and Cupriavidus. Several species identified in this study, such as Bacillus cereus, Burkholderia cepacia, Comamonas testosteroni and Acinetobacter pittii have been reported as PCBs degraders. Finally, by means of a principal component analysis (PCA), a correlation between the physical and chemical characteristics of the soils in relation to the relative abundances of the bacteria identified was obtained. The C/N ratio was directly related to the control soil (without contaminant), while SOM maintained a relationship with F and A soils and the bacterial abundances were directly related to Hs and Hp soils due to the presence of aroclor 1260. Bacteria with the ability to tolerate high concentrations of this pollutant are considered for future use in biostimulation and bioaugmentation processes in contaminated soils.

Understanding the role of bacterial cellular adsorption, accumulation and bioavailability regulation by biosurfactant in affecting biodegradation efficacy of polybrominated diphenyl ethers

Microbiological degradation is often considered as an important strategy to reduce the risks of polybrominated diphenyl ethers (PBDEs), which are environmentally widespread and harmful to human health and wildlife. With the well-identified aerobic bacteria, i.e. B. xenovorans LB400, the biodegradation of 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) occurred efficiently in conformity to the first-order kinetics and showed the strong dependence on initial concentration of pollutant and bioavailability regulation by biosurfactant. The mild increase of initial concentration of BDE-47 would enhance biodegradation whereas the excessive increase failed due to the oxidative stress or cytotoxicity to bacteria. Rather than the bacterial extracellular adsorption that was bioactively-mediated in thermodynamics, the intracellular accumulations at different time gradients showed the negative correlation with biodegradation efficiency of BDE-47. The spontaneous biodegradation of pollutant should be sourced from the gradual reduction of intracellular accumulation. Though the improved bioavailability of BDE-47 by sucrose fatty acid ester (SFAE) hardly altered the extracellular adsorption, the bacterial intracellular accumulation was indicated to increase continuously with used amount of biosurfactant and then decrease for the cellular morphological damage, and interestingly it appeared to be temporary reservoir for prompt delivery to biodegradation in light of the opposite variation tendency with time.

Microbial transformation of chiral organohalides: Distribution, microorganisms and mechanisms

Chiral organohalides including dichlorodiphenyltrichloroethane (DDT), Hexabromocyclododecane (HBCD) and polychlorinated biphenyls (PCBs) raise a significant concern in the environmental occurrence, fate and ecotoxicology due to their enantioselective biological effects. This review provides a state-of-the-art overview on enantioselective microbial transformation of the chiral organohalides. We firstly summarized worldwide field assessments of chiral organohalides in a variety of environmental matrices, which suggested the pivotal role of microorganisms in enantioselective transformation of chiral organohalides. Then, laboratory studies provided experimental evidences to further link enantioselective attenuation of chiral organohalides to specific functional microorganisms and enzymes, revealing mechanistic insights into the enantioselective microbial transformation processes. Particularly, a few amino acid residues in the functional enzymes could play a key role in mediating the enantioselectivity at the molecular level. Finally, major challenges and further developments toward an in-depth understanding of the enantioselective microbial transformation of chiral organohalides are identified and discussed.

Intracellular toxicity exerted by PCBs and role of VBNC bacterial strains in biodegradation

Polychlorinated biphenyls (PCBs) are xenobiotic compounds that persists in the environment for long-term, though its productivity is banned. Abatement of the pollutants have become laborious due to it's recalcitrant nature in the environment leading to toxic effects in humans and other living beings. Biphenyl degrading bacteria co-metabolically degrade low chlorinated PCBs using the active metabolic pathway. bph operon possess different genetic arrangements in gram positive and gram negative bacteria. The binding ability of the genes and the active sites were determined by PCB docking studies. The active site of bphA gene with conserved amino acid residues determines the substrate specificity and biodegradability. Accumulation of toxic intermediates alters cellular behaviour, biomass production and downturn the metabolic activity. Several bacteria in the environment attain unculturable state which is viable and metabolically active but not cultivable (VBNC). Resuscitation-promoting factor (Rpf) and Rpf homologous protein retrieve the culturability of the so far uncultured bacteria. Recovery of this adaptive mechanism against various physical and chemical stressors make a headway in understanding the functionality of both environmental and medically important unculturable bacteria. Thus, this paper review about the general aspects of PCBs, cellular toxicity exerted by PCBs, role of unculturable bacterial strains in biodegradation, genes involved and degradation pathways. It is suggested to extrapolate the research findings on extracellular organic matters produced in culture supernatant of VBNC thus transforming VBNC to culturable state.

Relationship between the binding free energy and PCBs' migration, persistence, toxicity and bioaccumulation using a combination of the molecular docking method and 3D-QSAR

The molecular docking method was used to calculate the binding free energies between biphenyl dioxygenase and 209 polychlorinated biphenyl (PCB) congeners. The relationships between the calculated binding free energies and migration (octanol-air partition coefficients, KOA), persistence (half-life, t1/2), toxicity (half maximal inhibitory concentration, IC50), and bioaccumulation (bioconcentration factor, BCF) values for the PCBs were used to gain insight into the degradation of PCBs in the presence of biphenyl dioxygenase. The relationships between the calculated binding free energies and the molecular weights, KOA, BCF, and t1/2 values for the PCBs were statistically significant (P < 0.01), whereas the relationship between the calculated binding free energies and the IC50 for the PCBs was not statistically significant (P > 0.05). The electrostatic field, derived from three-dimensional quantitative structure-activity relationship studies, was a primary factor governing the binding free energy, which agreed with literature findings for KOA, t1/2, and BCF. Comparative molecular field analysis and comparative molecular similarity indices analysis contour maps showed that the binding free energies, KOA, t1/2, and BCF values for the PCBs decreased simultaneously when substituents with electropositive groups at the 3-position or electronegative groups at the 3'-position were introduced. This indicated the binding free energy was correlated with the persistent organic pollutant characteristics of PCBs. Furthermore, low binding free energies improved the degradation of the PCBs and simultaneously decreased the KOA, t1/2, and BCF values, thereby reducing the persistent organic pollutant characteristics of PCBs in the environment. These results are expected to be beneficial in providing a theoretical foundation for further elucidation of the degradation and molecular modification of PCBs.