Characterization of the molecular degradation mechanism of diphenyl ethers by Cupriavidus sp. WS

Discovery of diphenyl ether-degrading Streptomyces strains by direct screening based on ether bond-cleaving activity

Diphenyl ethers (DEs), which are widely used in the agricultural and chemical industries, have become hazardous contaminants in the environment. Although several DE-degrading bacteria have been reported, discovering new types of such microorganisms could enhance understanding of the degradation mechanism in the environment. In this study, we used a direct screening method based on detection of ether bond-cleaving activity to screen for microorganisms that degrade 4,4'-dihydroxydiphenyl ether (DHDE) as a model DE. Microorganisms isolated from soil samples were incubated with DHDE, and strains producing hydroquinone via ether bond cleavage were selected using hydroquinone-sensitive Rhodanine reagent. This screening procedure resulted in the isolation of 3 bacteria and 2 fungi that transform DHDE. Interestingly, all of the isolated bacteria belonged to one genus, Streptomyces. To our knowledge, these are the first microorganisms of the genus Streptomyces shown to degrade a DE. Streptomyces sp. TUS-ST3 exhibited high and stable DHDE-degrading activity. HPLC, LC-MS, and GC-MS analyses revealed that strain TUS-ST3 converts DHDE to its hydroxylated analogue and generates hydroquinone as an ether bond-cleavage product. Strain TUS-ST3 also transformed DEs other than DHDE. In addition, glucose-grown TUS-ST3 cells began to transform DHDE after incubation with this compound for 12 h, and produced 75 μM hydroquinone in 72 h. These activities of streptomycetes may play an important role in DE degradation in the environment. We also report the whole genome sequence of strain TUS-ST3.

The interaction mechanisms of co-existing polybrominated diphenyl ethers and engineered nanoparticles in environmental waters: A critical review

This review focuses on the occurrence and interactions of engineered nanoparticles (ENPs) and brominated flame retardants (BFRs) such as polybrominated diphenyl ethers (PBDEs) in water systems and the generation of highly complex compounds in the environment. The release of ENPs and BFRs (e.g. PBDEs) to aquatic environments during their usage and disposal are summarised together with their key interaction mechanisms. The major interaction mechanisms including electrostatic, van der Waals, hydrophobic, molecular bridging and steric, hydrogen and π-bonding, cation bridging and ligand exchange were identified. The presence of ENPs could influence the fate and behaviour of PBDEs through the interactions as well as induced reactions under certain conditions which increases the formation of complex compounds. The interaction leads to alteration of behaviour for PBDEs and their toxic effects to ecological receptors. The intermingled compound (ENPs-BFRs) would show different behaviour from the parental ENPs or BFRs, which are currently lack of investigation. This review provided insights on the interactions of ENPs and BFRs in artificial, environmental water systems and wastewater treatment plants (WWTPs), which are important for a comprehensive risk assessment.

Aerobic Degradation Characteristics and Mechanism of Decabromodiphenyl Ether (BDE-209) Using Complex Bacteria Communities

Complex bacteria communities that comprised Brevibacillus sp. (M1) and Achromobacter sp. (M2) with effective abilities of degrading decabromodiphenyl ether (BDE-209) were investigated for their degradation characteristics and mechanisms under aerobic conditions. The experimental results indicated that 88.4% of 10 mg L^-1 BDE-209 could be degraded after incubation for 120 h under the optimum conditions of pH 7.0, 30 °C and 15% of the inoculation volume, and the addition ratio of two bacterial suspensions was 1:1. Based on the identification of BDE-209 degradation products via liquid chromatography-mass spectrometry (LC-MS) analysis, the biodegradation pathway of BDE-209 was proposed. The debromination, hydroxylation, deprotonation, breakage of ether bonds and ring-opening processes were included in the degradation process. Furthermore, intracellular enzymes had the greatest contribution to BDE-209 biodegradation, and the inhibition of piperyl butoxide (PB) for BDE-209 degradation revealed that the cytochrome P450 (CYP) enzyme was likely the key enzyme during BDE-209 degradation by bacteria M (1+2). Our study provided alternative ideas for the microbial degradation of BDE-209 by aerobic complex bacteria communities in a water system.

Bioremediation of copper in sediments from a constructed wetland ex situ with the novel bacterium Cupriavidus basilensis SRS

The H-02 constructed wetland was designed to remove metals (primarily copper and zinc) to treat building process water and storm water runoff from multiple sources associated with the Tritium Facility at the DOE-Savannah River Site, Aiken, SC. The concentration of Cu and Zn in the sediments has increased over the lifetime of the wetland and is a concern. A bioremediation option was investigated at the laboratory scale utilizing a newly isolated bacterium of the copper metabolizing genus Cupriavidus isolated from Tim's Branch Creek, a second-order stream that eventually serves as a tributary to the Savannah River, contaminated with uranium and other metals including copper, nickel, and mercury. Cupriavidus basilensis SRS is a rod-shaped, gram-negative bacterium which has been shown to have predatory tendencies. The isolate displayed resistance to the antibiotics ofloxacin, tetracycline, ciprofloxacin, select fungi, as well as Cu²⁺ and Zn²⁺. Subsequent ribosomal sequencing demonstrated a 100% confidence for placement in the genus Cupriavidus and a 99.014% match to the C. basilensis type strain. When H-02 wetland samples were inoculated with Cupriavidus basilensis SRS samples showed significant (p < 0.05) decrease in Cu²⁺ concentrations and variability in Zn²⁺ concentrations. Over the 72-h incubation there were no significant changes in the inoculate densities (10⁶-10⁸ cells/ML) indicating Cupriavidus basilensis SRS resiliency in this environment. This research expands our understanding of the Cupriavidus genus and demonstrates the potential for Cupriavidus basilensis SRS to bioremediate sites impacted with heavy metals, most notably copper.

Low dose of fire retardant, 2,2',4,4'-tetrabromodiphenyl ether (BDE47), stimulates the proliferation and differentiation of progenitor Leydig cells of male rats during prepuberty

2,2',4,4'-Tetrabromodiphenyl ether (BDE47), a flame retardant, is extensively distributed in the food chain. However, whether BDE47 affects Leydig cell development during prepuberty remains unclear. BDE47 was daily gavaged to 21-day-old Sprague-Dawley male rats with 0 (corn oil), 0.1, 0.2, and 0.4 mg/kg for 14 days. BDE47 did not affect the body weight or testis weight of rats. It significantly increased serum testosterone level at 0.4 mg/kg, but decreased luteinizing hormone (LH) level without affecting estradiol level. BDE47 induced Leydig cell hyperplasia (the number of CYP11A1-positive Leydig cells increased), and up-regulated the expression of Scarb1, Star, Hsd11b1, Pcna, and Ccnd1 in the testis. BDE47 significantly reduced p53 and p21 levels but increased CCND1 level. It also markedly increased the phosphorylation of AKT1, AKT2, ERK1/2, and CREB. BDE47 significantly up-regulated the expression of Scarb1, Star, and Hsd11b1 and stimulated androgen production by immature Leydig cells from rats under basal, LH, and 8Br-cAMP stimulated conditions at 100 nM in vitro. In conclusion, BDE47 increased Leydig cell number and up-regulated the expression of Scarb1 and Star, thereby leading to increased testosterone synthesis.

Isolation and characterization of 2-butoxyethanol degrading bacterial strains

A total of 11 bacterial strains capable of completely degrading 2-butoxyethanol (2-BE) were isolated from forest soil, a biotrickling filter, a bioscrubber, and activated sludge, and identified by 16S rRNA gene sequence analysis. Eight of these strains belong to the genus Pseudomonas; the remaining three strains are Hydrogenophaga pseudoflava BOE3, Gordonia terrae BOE5, and Cupriavidus oxalaticus BOE300. In addition to 2-BE, all isolated strains were able to grow on 2-ethoxyethanol and 2-propoxyethanol, ethanol, n-hexanol, ethyl acetate, 2-butoxyacetic acid (2-BAA), glyoxylic acid, and n-butanol. Apart from the only gram-positive strain isolated, BOE5, none of the strains were able to grow on the nonpolar ethers diethyl ether, di-n-butyl ether, n-butyl vinyl ether, and dibenzyl ether, as well as on 1-butoxy-2-propanol. Strains H. pseudoflava BOE3 and two of the isolated pseudomonads, Pseudomonas putida BOE100 and P. vancouverensis BOE200, were studied in more detail. The maximum growth rates of strains BOE3, BOE100, and BOE200 at 30 °C were 0.204 h-1 at 4 mM, 0.645 h-1 at 5 mM, and 0.395 h-1 at 6 mM 2-BE, respectively. 2-BAA, n-butanol, and butanoic acid were detected as potential metabolites during the degradation of 2-BE. These findings indicate that the degradation of 2-BE by the isolated gram-negative strains proceeds via oxidation to 2-BAA with subsequent cleavage of the ether bond yielding glyoxylate and n-butanol. Since Gordonia terrae BOE5 was the only strain able to degrade nonpolar ethers like diethyl ether, the degradation pathway of 2-BE may be different for this strain.

Proteomic mechanism of decabromodiphenyl ether (BDE-209) biodegradation by Microbacterium Y2 and its potential in remediation of BDE-209 contaminated water-sediment system

The investigation of BDE-209 degradation by Microbacterium Y2 under different condition was conducted. Cell membrane permeability, cell surface hydrophobicity (CSH), membrane potential (MP) and reactive oxygen species (ROS) production were altered under BDE-209 stress. Eleven debrominated congeners were identified, suggesting that BDE-209 biodegradation by Microbacterium Y2 was dominantly a successive debromination process. Proteome analysis showed that the overexpression of haloacid dehalogenases, glutathione S-transferases (GSTs) and ATP-binding cassette (ABC) transporters might occupy important roles in BDE-209 biotransformation. Meanwhile, heat shock proteins (HSPs), ribonuclease E, oligoribonuclease (Orn) and ribosomal protein were activated to counter the BDE-209 toxicity. The up-regulated pyruvate dehydrogenase E1 component beta subunit and dihydrolipoamide dehydrogenase suggested that the pyruvate metabolism pathway was activated. Bioaugmentation of BDE-209 polluted water-sediments system with Microbacterium Y2 could efficiently improve BDE-209 removal. The detection of total 16S rRNA genes in treatment system suggested that Microbacterium (25.6 %), Luteimonas (14.3 %), Methylovorus (12.6 %), Hyphomicrobium (9.2 %) were the dominant genera and PICRUSt results further revealed that the diminution of BDE-209 was owed to cooperation between the introduced bacteria and aboriginal ones.

Fouling Microbial Communities on Plastics Compared with Wood and Steel: Are They Substrate- or Location-Specific?

Although marine biofouling has been widely studied on different substrates, information on biofouling on plastics in the Arabian Gulf is limited. Substrate- and location-specific effects were investigated by comparing the microbial communities developed on polyethylene terephthalate (PET) and polyethylene (PE) with those on steel and wood, at two locations in the Sea of Oman. Total biomass was lower on PET and PE than on steel and wood. PET had the highest bacterial abundance at both locations, whereas chlorophyll a concentrations did not vary between substrates. MiSeq 16S ribosomal RNA sequencing revealed comparable operational taxonomic unit (OTU) richness on all substrates at one location but lower numbers on PET and PE at the other location. Non-metric multidimensional scaling (NMDS) showed distinct clusters of the bacterial communities based on substrate (analysis of similarity (ANOSIM), R = 0.45-0.97, p < 0.03) and location (ANOSIM, R = 0.56, p < 0.0001). The bacterial genera Microcystis and Hydrogenophaga and the diatoms Licmophora and Mastogloia were specifically detected on plastics. Desulfovibrio and Pseudomonas spp. exhibited their highest abundance on steel and Corynebacterium spp. on wood. Scanning electron microscopy (SEM) revealed fissure formation on PET and PE, indicating physical degradation. The presence of free radicals on PET and carbonyl bonds (C=O) on PE, as revealed by Fourier transform infrared (FTIR) spectroscopy, indicated abiotic degradation while hydroxyl groups and spectral peaks for proteins and polysaccharides on PE indicated biotic degradation. We conclude that fouling microbial communities are not only substrate-specific but also location-specific and microbes developing on plastics could potentially contribute to their degradation in the marine environment.

Biodegradation of decabromodiphenyl ether (BDE-209) using a novel microbial consortium GY1: Cells viability, pathway, toxicity assessment, and microbial function prediction

GY1, a novel microbial consortium with efficient ability to degrade decabromodiphenyl ether (BDE-209) has been isolated and the sequencing analysis has been conducted. The results revealed that Hyphomicrobium, Pseudomonas, Aminobacter, Sphingopyxis, Chryseobacterium, Bacillus, Pseudaminobacter, Stenotrophomonas, Sphingobacterium and Microbacterium were the dominant genera, and the function genes involved in BDE-209 conversion were predicted by PICRUSt. When BDE-209 concentration increased from 0.5 to 10mg/L, its degradation efficiency declined from 57.2% to 22.3%. Various kinds of debrominated metabolites were detected during the biodegradation process, including BDE-208, BDE-207, BDE-206, BDE-205, BDE-190, BDE-181, BDE-155, BDE-154, BDE-99, BDE-47, BDE-17 and BDE-7. Also, the proportion of necrotic cells was observed during GY1 mediated degradation of BDE-209 to reveal the changes of cells viability under BDE-209 stress. Subsequent analysis showed that the reaction of BDE-209 with GY1 was a detoxification process and bioaugmentation with GY1 effectively enhanced BDE-209 degradation in actual water and water-sediment system.

4-Bromodiphenyl ether delays pubertal Leydig cell development in rats

Polybrominated diphenyl ethers are a class of brominated flame retardants that are potential endocrine disruptors. 4-Bromodiphenyl ether (BDE-3) is the most abundant photodegradation product of higher polybrominated diphenyl ethers. However, whether BDE-3 affects Leydig cell development during puberty is still unknown. The objective of this study was to explore effects of BDE-3 on the pubertal development of rat Leydig cells. Male Sprague Dawley rats (35 days of age) were gavaged daily with BDE-3 (0, 50, 100, and 200 mg/kg body weight/day) for 21 days. BDE-3 decreased serum testosterone levels (1.099 ± 0.412 ng/ml at a dose of 200 mg/kg BDE-3 when compared to the control level (2.402 ± 0.184 ng/ml, mean ± S.E.). BDE-3 decreased Leydig cell size and cytoplasmic size at a dose of 200 mg/kg, decreased Lhcgr, Star, Dhh, and Sox9 mRNA levels at ≥ 100 mg/kg and Scarb1, Cyp11a1, Hsd17b3, and Fshr at 200 mg/kg. BED-3 also decreased the phosphorylation of AKT1, AKT2, ERK1/2, and AMPK at 100 or 200 mg/kg. BDE-3 in vitro induced ROS generation, inhibited androgen production, down-regulated Lhcgr, Scarb1, Star, Cyp11a1, Hsd3b1, Srd5a1, and Akr1c14 expression in immature Leydig cells after 24-h treatment. In conclusion, the current study indicates that BDE-3 disrupts Leydig cell development via suppressing AKT, ERK1/2, and AMPK phosphorylation and inducing ROS generation.

Bacterial Biodegradation of 4-Monohalogenated Diphenyl Ethers in One-Substrate and Co-Metabolic Systems

The use of diphenyl ether (DE) and its 4-monohalogenated derivatives (4-HDE) as flame retardants, solvents, and substrates in biocide production significantly increases the risk of ecosystem contamination. Their removal is important from the point of view of environmental protection. The aim of this study was to evaluate the degradation processes of DE and 4-HDE by enzymes of the environmental bacterial strains under one-substrate and co-metabolic conditions. The study is focused on the biodegradation of DE and 4-HDE, the enzymatic activity of microbial strains, and the cell surface properties after contact with compounds. The results show that the highest biodegradation (96%) was observed for 4-chlorodiphenyl ether in co-metabolic culture with P. fluorescens B01. Moreover, the activity of 1,2-dioxygenase during degradation of 4-monohalogenated diphenyl ethers was higher than that of 2,3-dioxygenase for each strain tested. The presence of a co-substrate provoked changes in dioxygenase activity, resulting in the increased activity of 1,2-dioxygenase. Moreover, the addition of phenol as a co-substrate allowed for increased biodegradation of the diphenyl ethers and noticeable modification of the cell surface hydrophobicity during the process. All observations within the study performed have led to a deeper understanding of the contaminants’ biodegradation processes catalyzed by environmental bacteria.

Biphenyl-Metabolizing Microbial Community and a Functional Operon Revealed in E-Waste-Contaminated Soil

Primitive electronic waste (e-waste) recycling activities release massive amounts of persistent organic pollutants (POPs) and heavy metals into surrounding soils, posing a major threat to the ecosystem and human health. Microbes capable of metabolizing POPs play important roles in POPs remediation in soils, but their phylotypes and functions remain unclear. Polychlorinated biphenyls (PCBs), one of the main pollutants in e-waste contaminated soils, have drawn increasing attention due to their high persistence, toxicity, and bioaccumulation. In the present study, we employed the culture-independent method of DNA stable-isotope probing to identify active biphenyl and PCB degraders in e-waste-contaminated soil. A total of 19 rare operational taxonomic units and three dominant bacterial genera ( Ralstonia, Cupriavidus, and uncultured bacterium DA101) were enriched in the ¹³C heavy DNA fraction, confirming their functions in PCBs metabolism. Additionally, a 13.8 kb bph operon was amplified, containing a bphA gene labeled by ¹³C that was concentrated in the heavy DNA fraction. The tetranucleotide signature characteristics of the bph operon suggest that it originated from Ralstonia. The bph operon may be shared by horizontal gene transfer because it contains a transposon gene and is found in various bacterial species. This study gives us a deeper understanding of PCB-degrading mechanisms and provides a potential resource for the bioremediation of PCBs-contaminated soils.

Biodegradation of 3-methyldiphenylether (MDE) by Hydrogenophaga atypical strain QY7-2 and cloning of the methy-oxidation gene mdeABCD

3-Methyldiphenylether (MDE) is an important alkyl-substituted diphenyl ether compound that is widely used as an intermediate in the synthesis of pyrethroid insecticides. An efficient MDE-degrading strain QY7-2, identified as Hydrogenophaga atypical, was isolated from activated sludge for the first time. Strain QY7-2 can utilize MDE as the sole carbon and energy source and completely mineralize MDE. The degradation pathway of MDE was proposed in the strain through metabolites identification. A gene cluster involving in methy-oxidation of MDE was cloned from QY7-2 and expressed in Escherichia coli BL21 (DE3), and the products were purified by SDS-PAGE. The specific activities of the recombinant enzymes MdeAB, MdeC and MdeD were 113.8 ± 3.5, 274.5 ± 6.2 and 673.4 ± 8.7 nmol min⁻¹ mg⁻¹, respectively. These results provide the biochemical and genetic foundation of microbial degradation pathway of MDE and benefit the bioremediation of MDE-contaminated environments.

Isolation of bacterial strains able to degrade biphenyl, diphenyl ether and the heat transfer fluid used in thermo-solar plants

Thermo-solar plants use eutectic mixtures of diphenyl ether (DE) and biphenyl (BP) as heat transfer fluid (HTF). Potential losses of HTF may contaminate soils and bioremediation is an attractive tool for its treatment. DE- or BP-degrading bacteria are known, but up to now bacteria able to degrade HTF mixture have not been described. Here, five bacterial strains which are able to grow with HTF or its separate components DE and BP as sole carbon sources have been isolated, either from soils exposed to HTF or from rhizospheric soils of plants growing near a thermo-solar plant. The organisms were identified by 16S rRNA gene sequencing as Achromobacter piechaudii strain BioC1, Pseudomonas plecoglossicida strain 6.1, Pseudomonas aeruginosa strains HBD1 and HBD3, and Pseudomonas oleovorans strain HBD2. Activity of 2,3-dihydroxybiphenyl dioxygenase (BphC), a key enzyme of the biphenyl upper degradation pathway, was detected in all isolates. Pseudomonas strains almost completely degraded 2000ppm HTF after 5-day culture, and even tolerated and grew in the presence of 150,000ppm HTF, being suitable candidates for in situ soil bioremediation. Degradation of both components of HTF is of particular interest since in the DE-degrader Sphingomonas sp. SS3, growth on DE or benzoate was strongly inhibited by addition of BP.