Detoxification of hydroxylated polychlorobiphenyls by Sphingomonas sp. strain N-9 isolated from forest soil

Integrated transcriptomics and metabolomics analyses reveal the aerobic biodegradation and molecular mechanisms of 2,3',4,4',5-pentachlorodiphenyl (PCB 118) in Methylorubrum sp. ZY-1

2,3',4,4',5-pentachlorodiphenyl (PCB 118), a highly representative PCB congener, has been frequently detected in various environments, garnering much attention across the scientific community. The degradation of highly chlorinated PCBs by aerobic microorganisms is challenging due to their hydrophobicity and persistence. Herein, the biodegradation and adaptation mechanisms of Methylorubrum sp. ZY-1 to PCB 118 were comprehensively investigated using an integrative approach that combined degradation performance, product identification, metabolomic and transcriptomic analyses. The results indicated that the highest degradation efficiency of 0.5 mg L-1 PCB 118 reached 75.66% after seven days of inoculation when the bacteria dosage was 1.0 g L-1 at pH 7.0. A total of eleven products were identified during the degradation process, including low chlorinated PCBs, hydroxylated PCBs, and ring-opening products, suggesting that strain ZY-1 degraded PCB 118 through dechlorination, hydroxylation, and ring-opening pathways. Metabolomic analysis demonstrated that the energy supply and redox metabolism of strain ZY-1 was disturbed with exposure to PCB 118. To counteract this environmental stress, strain ZY-1 adjusted both the fatty acid synthesis and purine metabolism. The analysis of transcriptomics disclosed that multiple intracellular and extracellular oxidoreductases (e.g., monooxygenase, alpha/beta hydrolase and cytochrome P450) participated in the degradation of PCB 118. Besides, active efflux of PCB 118 and its degradation intermediates mediated by multiple transporters (e.g., MFS transporter and ABC transporter ATP-binding protein) might enhance bacterial resistance against these substances. These discoveries provided the inaugural insights into the biotransformation of strain ZY-1 to PCB 118 stress, illustrating its potential in the remediation of contaminated environments.

Bioremediation of PBDEs and heavy metals co-contaminated soil in e-waste dismantling sites by Pseudomonas plecoglossicida assisted with biochar

Biochar-assisted microbial remediation has been proposed as a promising strategy to eliminate environmental pollutants. However, studies on this strategy used in the remediation of persistent organic pollutants and heavy metals co-contaminated soil are lacking, and the effect of the combined incorporation of biochar and inoculant on the assembly, functions, and microbial interactions of soil microbiomes are unclear. Here, we studied 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) degradation and heavy metal immobilization by and biochar-based bacterial inoculant (BC/PP) in an e-waste contaminated soil, and corresponding microbial regulation mechanisms. Results showed that BC/PP addition was more effective in reducing Cu and Pb availability and degrading BDE-47 than inoculant alone. Notably, BC/PP facilitated bound-residue formation of BDE-47, reducing the ecological risk of residual BDE-47. Meanwhile, microbial carbon metabolism and enzyme activities (related to C-, N-, and P- cycles) were enhanced in soil amended with BC/PP. Importantly, biochar played a crucial role in inoculant colonization, community assembly processes, and microbiome multifunction. In the presence of biochar, positive interactions in co-occurrence networks of the bacterial community were more frequent, and higher network stability and more keystone taxa were observed (including potential degraders). These findings provide a promising strategy for decontaminating complex-polluted environments and recovering soil ecological functions.

Oxidative dehalogenation and mineralization of polychlorinated biphenyls by a resuscitated strain Streptococcus sp. SPC0

Most functional microorganisms cannot be cultivated due to entering a viable but non-culturable (VBNC) state, which limits the characterization and application of polychlorinated biphenyl (PCB)-degrading strains. Resuscitating VBNC bacteria could provide huge candidates for obtaining high-efficient PCB degraders. However, limited studies have focused on the ability of resuscitated strains for PCBs degradation. In the present study, whole-genome analysis of a resuscitated strain SPC0, and its performances in degradation of three prevalent PCB congeners (PCBs 18, 52 and 77) were investigated. The results indicate that the strain SPC0 belonged to the genus Streptococcus, possessed the degradation potential for aromatic xenobiotics. The SPC0 could effectively degrade PCBs 18 and 52, but exhibited lower degradation efficiency of PCB 77. Degradation of PCBs 18 and 52 could be fitted well by zero-order model, whereas the fittest model for PCB 77 degradation was pseudo second-order kinetics. The bph genes expression, chloride ions release and degradation metabolites identification, suggest that SPC0 possessed the capability of oxidative dehalogenation and mineralization of PCBs. Interestingly, SPC0 can degrade PCBs via the bph-encoded biphenyl pathway, and further mineralize metabolite dichlorobenzoate via protocatechuate pathway. This study is the first to show that a strain belonging to genus Streptococcus possessed PCB-degrading capability, which uncovered the powerful potential of resuscitated strains for bioremediation of PCB-contaminated sites.

Hydroxylated Polychlorinated Biphenyls Are Emerging Legacy Pollutants in Contaminated Sediments

We measured the concentrations of 837 hydroxylated polychlorinated biphenyls (OH-PCBs, in 275 chromatographic peaks) and 209 polychlorinated biphenyls (PCBs, in 174 chromatographic peaks) in sediments from New Bedford Harbor in Massachusetts, Altavista wastewater lagoon in Virginia, and the Indiana Harbor and Ship Canal in Indiana, USA and in the original commercial PCB mixtures Aroclors 1016, 1242, 1248, and 1254. We used the correlation between homologues and the peak responses to quantify the full suite of OH-PCBs including those without authentic standards available. We found that OH-PCB levels are approximately 0.4% of the PCB levels in sediments and less than 0.0025% in Aroclors. The OH-PCB congener distributions of sediments are different from those of Aroclors and are different according to sites. We also identified a previously unknown compound, 4-OH-PCB52, which together with 4'-OH-PCB18 made up almost 30% of the OH-PCBs in New Bedford Harbor sediments but less than 1.2% in the Aroclors and 3.3% in any other sediments. This indicates site-specific environmental transformations of PCBs to OH-PCBs. We conclude that the majority of OH-PCBs in these sediments are generated in the environment. Our findings suggest that these toxic breakdown products of PCBs are prevalent in PCB-contaminated sediments and present an emerging concern for humans and ecosystems.

Enhanced bioremediation of 2,3',4,4',5-pentachlorodiphenyl by consortium GYB1 immobilized on sodium alginate-biochar

2,3',4,4',5-pentachlorodiphenyl (PCB 118), a dioxin-like PCB, is often detected in the environment and is difficult to be aerobically biodegraded. In this study, a novel polychlorinated biphenyl degrading consortium GYB1 that can metabolize PCB 118 was successfully obtained by acclimatization process. To enhance the application performance of free bacterial cells, consortium GYB1 was immobilized with sodium alginate and biochar to prepare SC-GYB1 beads. Orthogonal experiments indicated that the optimal composition of the beads (0.2 g) was 2.0% sodium alginate (SA) content, 2.0% wet weight of cells and 1.5% biochar content, which can degrade 50.50% PCB 118 in 5 d. Immobilization shortened the degradation half-life of 1 mg/L PCB 118 by consortium GYB1 from 8.14 d to 3.79 d and made the beads more robust to respond to environmental stress. The SC-GYB1 beads could even keep considerable PCB degradation ability under 200 mg/L Cd²⁺ stress. According to 16S rRNA gene analysis, Pseudomonas and Stenotrophomonas played the dominant role in consortium GYB1. And embedding obviously altered the community structure and the key bacterial genera during the PCB removal process. Therefore, the immobilization of bacteria consortium by sodium alginate-biochar enhanced the biodegradation of PCB 118, which will provide new insights into functional microorganisms' actual application for PCB restoration.

The inhibitory mechanism of natural soil colloids on the biodegradation of polychlorinated biphenyls by a degrading bacterium

In spite of extensive studies of soil model components, the role of natural soil colloids in the biodegradation of organic pollutants remain poorly understood. Accordingly, the present study selected Mollisol colloids (MCs) and Ultisol colloids (UCs) to investigate their effects on the biodegradation of 3, 3', 4, 4'-tetrachlorobiphenyl (PCB77) by Bradyrhizobium diazoefficiens USDA 110. Results demonstrated that both natural soil colloids significantly decreased the biodegradation of PCB77, which partly resulted from the significant decrease in the bioaccessibility of PCB77. Furthermore, the activity of Bradyrhizobium diazoefficiens USDA 110 was remarkably inhibited under the exposure to the two types of soil colloids, which was mainly ascribed to the inhibition of cell reproduction but not the lethal effect of reactive oxygen species. The calculated results from Ex-DLVO theory further indicated that the repulsion between UCs and biodegrading bacteria retarded the effective contact of cells with adsorbed PCB77 from UCs, resulting in the decline of the rate of cell reproduction. In general, the inhibition of MCs was limited to PCB77 bioaccessibility, whereas the negative effect of UCs was controlled by PCB77 bioaccessibility and the effective contact of cells with colloids. This study could provide implication for the enhancement of microbial remediation in contaminated soil.

Biodegradation of trichlorobiphenyls and their hydroxylated derivatives by Rhodococcus-strains

A possibility of using a complex approach is considered to explain features of biodestruction of polychlorinated biphenyls (PCBs), which are known to be persistent organic pollutants. The approach comprises the following main stages: (i) chemical modification of chloroarenes by hydroxylation and (ii) bacterial degradation of the hydroxylated derivatives. This approach is applicable to individual trichlorobiphenyls (PCB 29, PCB 30) and to a widespread mixture Trikhlorbifenil (analog of Aroclor 1242 and Delor 103). As bacterial strain destructors, the Rhodococcus-strains (КТ112-7, СН628, P25) were used. It was established that the main metabolites of microbial biodegradation of both polychlorobiphenyls and their hydroxy derivatives are polychloro- and hydroxy(polychloro)benzoic acids, which allows an assumption to be made about possible further biodegradation of these compounds down to the products of the base exchange reaction in a cell: water, carbon dioxide and chlorine compounds. The study discusses the effect that the structure of PCBs congeners causes on the conversion by hydroxylation, on the biodegradation rate of both PCBs and their hydroxy derivatives, and on the metabolite formation levels.

Enhancement of polychlorinated biphenyl biodegradation by resuscitation promoting factor (Rpf) and Rpf-responsive bacterial community

The activities of indigenous bacterial communities in polychlorinated biphenyls (PCBs) contaminated environments is closely related to the efficiency of bioremediation processes. Using resuscitation promoting factor (Rpf) from Micrococcus luteus is a promising method for resuscitation and stimulation of functional bacterial populations under stressful conditions. This study aims to use the Rpf to accelerate the biodegradation of Aroclor 1242, and explore putative PCB degraders which were resuscitated by Rpf addition. The Rpf-responsive bacterial populations were investigated using culture-dependent and culture-independent approaches, respectively. The results confirm that Rpf was capable of enhancing PCB degradation of enriched cultures from PCB-contaminated soils, and improving the activities of cultures with low tolerance to PCBs. High-throughput 16S rRNA analysis displays that the Rpf greatly altered the composition and abundance of bacterial populations in the phylum Proteobacteria. Identification of the resuscitated strains further suggests that the Rpf-responsive population was mostly represented by Sphingomonas and Pseudomonas, which are most likely the key PCB-degraders for enhanced biodegradation of PCBs.

Biodegradability of hydroxylated derivatives of commercial polychlorobiphenyls mixtures by Rhodococcus-strains

For the first time, investigations are is carried out for the interactions of hydroxylated polychlorobiphenyls (HO-PCBs) mixtures, which were obtained from PCBs commercially available under the trade name Sovol, with the Rhodococcus (R.) strains. It is established that the HO-PCBs mixtures containing basic products within the range of 83.2-95.8% cause a toxic effect on the growth of R. wratislaviensis KT112-7, R. wratislaviensis CH628, R. ruber P25 strains. The inhibitory concentration (IC50) was varied within the range of 30-490 mg/l. For the first time, it is found that the bacterial strains can use HO-PCBs as a source of carbon with no co-substrate added. The strains are shown to degrade 95.5-100% of the HO-PCBs mixtures at a concentration of 0.1 g/l during 14 days. It is demonstrated that HO-PCBs degrading occurs following the classical bacterial pathway of transforming biphenyl/PCB. However, the HO-PCBs metabolites, which are substituted benzoic acids, are not the final products of the transformation and are subjected to further degrading by the strains. Therefore, the R. wratislaviensis KT112-7, R. wratislaviensis CH628, and R. ruber P25 strains are shown to degrade the HO-PCBs mixtures efficiently and are found to be stable to their toxic action.

Recent advances in the biodegradation of polychlorinated biphenyls

Polychlorinated biphenyls (PCBs) are typical lasting organic pollutants. Persistence and recalcitrance to biodegradation of PCBs have hampered the transformation of PCB congeners from the environment. Biological transformation of polychlorinated biphenyls could take place through anaerobic dechlorination, aerobic microbial degradation, and a combination of transformation of anaerobic dechlorination and aerobic degradation. Under anaerobic conditions, microbial dechlorination is an important degradation mode for PCBs, especially high-chlorinated congeners. The low-chlorinated compounds formed after reductive dechlorination could be further aerobically degraded and completely mineralized. This paper reviews the recent advances in biological degradation of PCBs, introduces the functional bacteria and enzymes involved in the anaerobic and aerobic degradation of PCBs, and discusses the synergistic action of anaerobic reduction and aerobic degradation. In addition, the different ways to the microbial remediation of PCBs-contaminated environments are discussed. This review provides a theoretical foundation and practical basis to use PCBs-degrading microorganisms for bioremediation.

Study on the biodegradation of persistent organic pollutants (POPs)

The use of organochlorine pesticides, such as dichlorodiphenyltrichloroethane (DDT) and benzene hexachloride (BHC), have contributed substantially to the increase and stable supply of food production post-World War II. However, they have also become a major source of pollution on a global scale due to their persistence in the environment, high bioconcentration, toxicity, and their long-distance mobility. Although the use and production of these pesticides were banned over 45 years ago, they still present a risk to human health and ecosystems, and pose a threat to food safety. These pesticides were designated as persistent organic pollutants (POPs) by the Stockholm Convention in 2001, which urged the industry to reduce or eliminate them globally. The authors of this study have been involved in the research and development of bioaugmentation soil remediation technology to reduce the risk of environmental and crop contamination originating from POPs. In this paper, these studies are summarized, from basic studies (1, 2, 3) to an applied study (4), as follows: (1) use of the soil-charcoal perfusion method to explore POP-degrading bacteria, (2) bacteriological characteristics, metabolic pathways and dechlorination genes of the hexaclorobenzene (HCB)-mineralizing bacterial strain PD653, (3) characteristics and metabolic pathways of the dieldrin-degrading bacterial strain KSF27, and (4) application of these degrading bacteria for remediation of POPs-contaminated soil.

Aerobic degradation of 3,3',4,4'-tetrachlorobiphenyl by a resuscitated strain Castellaniella sp. SPC4: Kinetics model and pathway for biodegradation

Resuscitated strains which were obtained by addition of resuscitation promoting factor (Rpf) could provide a vast majority of microbial source for obtaining highly efficient polychlorinated biphenyl (PCB)-degrading bacteria. In this study, the Castellaniella sp. strain SPC4 which was resuscitated by Rpf addition showed the highest efficiency in degradation of 3,3',4,4'-tetrachlorobiphenyl (PCB 77) among the resuscitated and non-resuscitated isolates. Further investigations on the PCB 77 degradation capability of the resuscitated strain SPC4 showed that SPC4 could efficiently degrade PCB 77 with maximum degradation rate (q_max) of 0.066/h at about 20 mg/L of PCB 77. The maximum growth rate on PCB 77 was 2.663 × 10⁷ CFU/(mL·h) (0.024/h). The most suitable model of Edward demonstrated that the SPC4 could achieve q_max of 0.9315/h, with substrate-affinity of 11.33 mg/L and substrate-inhibition constants of 11.41 mg/L. Meanwhile, the presence of bphA gene expression and chlorine ions release, together with the identification of metabolites, confirmed that the bph-encoded biphenyl pathway was involved in PCB 77 mineralization by SPC4. This report is the first to demonstrate aerobic degradation of PCB 77 by the resuscitated strain Castellaniella sp. SPC4, indicating excellent potential for PCB bioremediation.

Metabolic enhancement of 2,3',4,4',5-pentachlorobiphenyl (CB118) using cytochrome P450 monooxygenase isolated from soil bacterium under the presence of perfluorocarboxylic acids (PFCAs) and the structural basis of its metabolism

2,3',4,4',5-Pentachlorobiphenyl (CB118) is one of the most abundant polychlorinated biphenyl (PCB) congeners in the environment, and perfluoroalkyl acids, including perfluorocarboxylic acids (PFCAs), are widely distributed in the environment. Although CB118 and perfluoroalkyl acids are present in all humans and biota, effects in the metabolic fate of CB118 leading to toxicity change are unclear. P450BM3, which is isolated from the soil bacterium Bacillus megaterium, metabolized CB118 to three different hydroxylated pentachlorobiphenyls (M1-M3). M2 was identified as 4'-OH-2,3',4,5,5'-pentachlorobiphenyl. These reactions were promoted by the presence of PFCAs, and perfluorooctanoic acid (PFCA-C8) was the most effective for accelerating these reactions among PFCAs with different carbon chain length. The production rate of M2 was accelerated by 25-times using PFCA-C8. Furthermore, the docking models of P450BM3 with CB118 and PFCAs revealed that the conformational changes of the substrate-binding cavity of P450BM3 after binding of PFCAs to P450BM3 were important for selective production of CB118 metabolites. This study leads to the clarification of the different metabolic fates of PCBs under complex contamination with PFCAs.

Effect of lower chlorinated hydroxylated-polychlorobiphenyls on development of PC12 cells

Hydroxylated polychlorobiphenyls (OH-PCBs) are major metabolites of PCBs that are widely distributed in the environment. While the effects of penta- to hepta-chlorinated OH-PCBs on neuronal differentiation have been widely reported, those of lower chlorinated OH-PCBs have not been extensively studied. To investigate the effects of lower chlorinated OH-PCBs on neuronal development, we studied the effects of mono- to hexa-chlorinated OH-PCBs on PC12 cells. Morphological changes were examined using an automatic system IN Cell Analyzer. Seventeen of the 20 OH-PCBs investigated promoted neuronal elongation in an OH-PCB concentration-dependent manner, while three OH-PCB congeners suppressed neuronal elongation based on Dunnett's analysis. In particular, the top five OH-PCBs (4OH-PCB2, 4'OH-PCB3, 4'OH-PCB25, 4'OH-PCB68, and 4'OH-PCB159), which have hydroxyl groups at the para-position and chlorine substitutions at the 2, 4, or 3' positions, significantly promoted neuronal elongation. Moreover, these neuronal elongations were suppressed by U0126, and phosphorylation of extracellular signal-regulated kinase (ERK) 1/2 was observed in PC12 cells treated with 4OH-PCB2, 4'OH-PCB25, and 4'OH-PCB159. Taken together, our results indicate that the effect of OH-PCB on neuronal development is not dependent on the number of chlorine groups but on the chemical structure, and the mitogen-activated kinase kinase (MEK)-ERK1/2 signaling pathway is involved in this process.

Effect of copper on the translocation and transformation of polychlorinated biphenyls in rice

Contamination of organic pollutants in the environment is usually accompanied by heavy metals. However, a little information on the influences of heavy metals on the uptake, translocation and transformation of organic pollutants in plants is available. In this study, ten-day hydroponic exposure was conducted to explore the influence of copper (Cu) on the bioaccumulation and biotransformation of polychlorinated biphenyls (PCBs) in intact young rice (Oryza sativa L.). Low dose of Cu (≤100 μmol/L) increased the accumulation of CB-61 in rice plants, while excess concentrations of Cu (>100 μmol/L) inhibited uptake and translocation of CB-61. Effect of Cu on the uptake of CB-61 was attributed to the Cu-triggered damage to the roots of rice plants. The presence of a moderate dose of Cu (50 μmol/L) enhanced the formation of hydroxylated polychlorinated biphenyls (OH-PCBs) and methoxylated polychlorinated biphenyls (MeO-PCBs), whereas excess concentrations of Cu (250 μmol/L) inhibited the metabolism of CB-61. The effect of Cu on the interconversion between 4'-OH-CB-61 and 4'-MeO-CB-61 was also concentration dependent: the biotransformation was promoted by a moderate concentration of Cu but inhibited by excess concentrations of Cu. The activities of Cytochrome P450 (CYP450) and S-adenosyl-l-methionine (SAM)-dependent methyltransferase in the roots of rice plants exposed to Cu and CB-61 or its derivatives were consistent with the pattern and trend of the metabolites observed in rice roots. These results could provide valuable insights into the interactions and combined effects of PCBs and heavy metals in plants.

Degradation of chlorpyrifos by an endophytic bacterium of the Sphingomonas genus (strain HJY) isolated from Chinese chives (Allium tuberosum)

The degradation of chlorpyrifos (CP) by an endophytic bacterial strain (HJY) isolated from Chinese chives (Allium tuberosum Rottl. ex Spreng) was investigated. Strain HJY was identified as Sphingomonas sp. based on morphological, physiological, and biochemical tests and a 16S rDNA sequence analysis. Approximately 96% of 20 mg L^-1 CP was degraded by strain HJY over 15 days in liquid minimal salts medium (MSM). The CP degradation rate could also be increased by glucose supplementation. The optimal conditions for the removal of 20 mg L^-1 CP by strain HJY in MSM were 2% inoculum density, pH 6.0, and 30-35°C. The CP degradation rate constant and half-life were 0.2136 ± 0.0063 d^-1 and 3.2451 ± 0.0975 d, respectively, under these conditions, but were raised to 0.7961 ± 0.1925 d^-1 and 0.8707 ± 0.3079 d with 1% glucose supplementation. The detection of metabolic products and screening for degrading genes indicated that O,O-diethyl O-3,5,6-trichloropyridinol was the major degradation product from CP, while it was likely that some functional genes were undetected and the mechanism responsible for CP degradation by strain HJY remained unknown. Strain HJY is potentially useful for the reduction of CP residues in Chinese chives and may be used for the in situ phytoremediation of CP.