Advances and perspective in bioremediation of polychlorinated biphenyl-contaminated soils

Microbial and chemically induced reductive dechlorination of polychlorinated biphenyls in the environment

Polychlorinated biphenyls (PCBs) are persistent organic pollutants and are emitted during e-waste activities. Once they enter into the environment, PCBs could pose toxic effects to environmental compartments and public health. Reductive dechlorination offers a sustainable solution to manage the PCBs-contaminated environment. Under anaerobic conditions, reductive dechlorination of PCBs occurs, and PCBs congeners serve as potential electron acceptors which stimulate the growth of PCBs-dechlorinating microorganisms. In this review, microbial and chemically induced reductive dechlorination was summarized. During anaerobic conditions, highly chlorinated PCBs undergo reductive dechlorination and are converted into less chlorinated PCBs. The mechanisms involved in reductive dechlorination are mainly attacks on meta and/or para chlorines of PCBs mixtures in a contaminated environment and ortho dechlorination of PCBs. Based on methods, PCBs removal efficiency was as chemical > biological. Activated carbon (90%) showed more treatment efficiency than bacterial (84%). The review suggested that microbial remediation is a slow process; however, efficiency could be enhanced after amendments. Different microorganisms appear to be responsible for different dechlorination activities and the occurrence of various dehalogenation routes. However, PCBs dechlorination rate, extent, and route are influenced by pH, temperature, availability of carbon sources, and the presence or absence of H2 or competing electron acceptors and other electron donors.

Linking industrial emissions and dietary exposure to human burdens of polychlorinated naphthalenes

Relationships between toxic pollutant emissions during industrial processes and toxic pollutant dietary intakes and adverse health burdens have not yet been quantitatively clarified. Polychlorinated naphthalenes (PCNs) are typical industrial pollutants that are carcinogenic and of increasing concern. In this study, we established an interpretable machine learning model for quantifying the contributions of industrial emissions and dietary intakes of PCNs to health effects. We used the SHapley Additive exPlanations model to achieve individualized interpretability, enabling us to evaluate the specific contributions of individual feature values towards PCNs concentration levels. A strong relationship between PCN dietary intake and body burden was found using a robust large-scale PCN diet survey database for China containing the results of the analyses of 17,280 dietary samples and 4480 breast milk samples. Industrial emissions and dietary intake contributed 12 % and 52 %, respectively, of the PCN burden in breast milk. The model quantified the contributions of food consumption and industrial emissions to PCN exposure, which will be useful for performing accurate health risk assessments and developing reduction strategies of PCNs.

Investigating PCB degradation by indigenous fungal strains isolated from the transformer oil-contaminated site: degradation kinetics, Bayesian network, artificial neural networks, QSAR with DFT, molecular docking, and molecular dynamics simulation

The widespread prevalence of polychlorinated biphenyls (PCBs) in the environment has raised major concerns due to the associated risks to human health, wildlife, and ecological systems. Here, we investigated the degradation kinetics, Bayesian network (BN), quantitative structure-activity relationship-density functional theory (QSAR-DFT), artificial neural network (ANN), molecular docking (MD), and molecular dynamics stimulation (MS) of PCB biodegradation, i.e., PCB-10, PCB-28, PCB-52, PCB-138, PCB-153, and PCB-180 in the soil system using fungi isolated from the transformer oil-contaminated sites. Results revealed that the efficacy of PCB biodegradation best fits the first-order kinetics (R2 ≥ 0.93). The consortium treatment (29.44-74.49%) exhibited more efficient degradation of PCBs than those of Aspergillus tamarii sp. MN69 (27.09-71.25%), Corynespora cassiicola sp. MN69 (23.76-57.37%), and Corynespora cassiicola sp. MN70 (23.09-54.98%). 3'-Methoxy-2, 4, 4'-trichloro-biphenyl as an intermediate derivative was detected in the fungal consortium treatment. The BN analysis predicted that the biodegradation efficiency of PCBs ranged from 11.6 to 72.9%. The ANN approach showed the importance of chemical descriptors in decreasing order, i.e., LUMO > MW > IP > polarity no. > no. of chlorine > Wiener index > Zagreb index > HOMU > Pogliani index > APE in PCB removal. Furthermore, the QSAR-DFT model between the chemical descriptors and rate constant (log K) exhibited a high fit and good robustness of R2 = 99.12% in predicting ability. The MD and MS analyses showed the lowest binding energy through normal mode analysis (NMA), implying stability in the interactions of the docked complexes. These findings provide crucial insights for devising strategies focused on natural attenuation, holding substantial potential for mitigating PCB contamination within the environment.

The bioremediation of the typical persistent organic pollutants (POPs) by microalgae-bacteria consortia: A systematic review

With industrialisation and the rapidly growing agricultural demand, many organic compounds have been leaked into the environment, causing serious damage to the biosphere. Persistent organic pollutants (POPs) are a type of toxic chemicals that are resistant to degradation through normal chemical, biological or photolytic approaches. With their stable chemical structures, POPs can be accumulated in the environment, and transported through wind and water, causing global environmental issues. Many researches have been conducted to remediate POPs contamination using various kinds of biological methods, and significant results have been seen. Microalgae-bacteria consortium is a newly developed concept for biological technology in contamination treatment, with the synergetic effects between microalgae and bacteria, their potential for pollutants degradation can be further released. In this review, two types of POPs (polychlorinated biphenyls and polycyclic aromatic hydrocarbons) are selected as the targeted pollutants to give a systematic analysis of the biodegradation through microalgae and bacteria, including the species selection, the identification of dominant enzymes, as well as the real application performance of the consortia. In the end, some outlooks and suggestions are given to further guide the development of applying microalgae-bacteria consortia in remediating POPs contamination. In general, the coculturing of microalgae and bacteria is a novel and efficient way to fulfil the advanced treatment of POPs in soil or liquid phase, and both monooxygenase and dioxygenase belonging to oxygenase play a vital role in the biodegradation of PCBs and PAHs. This review provides a general guide in the future investigation of biological treatment of POPs.

Modeled Pathways and Fluxes of PCB Dechlorination by Redox Potentials

Dechlorination is one of the main processes for the natural degradation of polychlorinated biphenyls (PCBs) in an anaerobic environment. However, PCB dechlorination pathways and products vary with PCB congeners, types of functional dechlorinating bacteria, and environmental conditions. The present study develops a novel model for determining dechlorination pathways and fluxes by tracking redox potential variability, transforming the complex dechlorination process into a stepwise sequence. The redox potential is calculated via the Gibbs free energy of formation, PCB concentrations in reactants and products, and environmental conditions. Thus, the continuous change in the PCB congener composition can be tracked during dechlorination processes. The new model is assessed against four measurements from several published studies on PCB dechlorination. The simulation errors in all four measurements are calculated between 2.67 and 35.1% under minimum (n = 0) and maximum (n = 34) numbers of co-eluters, respectively. The dechlorination fluxes for para-dechlorination pathways dominate PCB dechlorination in all measurements. Furthermore, the model also considers multiple-step dechlorination pathways containing intermediate PCB congeners absent in both the reactants and the products. The present study indicates that redox potential might be an appropriate indicator for predicting PCB dechlorination pathways and fluxes even without prior knowledge of the functional dechlorinating bacteria.

Under explored roles of microbial ligninolytic enzymes in aerobic polychlorinated biphenyl transformation

Polychlorinated biphenyls (PCBs) are persistent organic pollutants in the environment that are responsible for many adverse health effects. Bioremediation appears to be a healthy and cost-effective alternative for remediating PCB-contaminated environments. While some microbial species have been observed to be capable of transforming PCBs, only two different microbial pathways (rdh and bph pathways) have been described to be involved in PCB transformations. Ligninolytic enzymes have been observed or are under suspicion in some microbial PCB transformations. However, the role of these promising PCB-transforming enzymes, which are produced by fungi and some aerobic bacteria, is still unclear. The present review describes their role by identifying microbial PCB-transforming species and their reported ligninolytic enzymes whether proven or suspected to be involved in PCB transformations. There are several lines of evidence that ligninolytic enzymes are responsible for PCB transformations such as (1) the ability of purified laccases from Myceliophthora thermophila, Pycnoporus cinnabarinus, Trametes versicolor, Cladosporium sp, and Coprinus cumatus to transform hydroxy-PCBs; (2) the increased production of laccases and peroxidases by many fungi in the presence of PCBs; and (3) the enhanced PCB transformation by Pseudomonas stutzeri and Sinorhizobium meliloti NM after the addition of ligninolytic enzyme enhancers. However, if the involvement of ligninolytic enzymes in PCB transformation is clearly demonstrated in some fungal species, it does not seem to be implicated in all microbial species suggesting other still unknown metabolic pathways involved in PCB transformation and different from the bph and rdh pathways. Therefore, PCB transformation may involve several metabolic pathways, some involving ligninolytic enzymes, bph or rdh genes, and some still unknown, depending on the microbial species. In addition, current knowledge does not fully clarify the role of ligninolytic enzymes in PCB oxidation and dechlorination. Therefore, further studies focusing on purified ligninolytic enzymes are needed to clearly elucidate their role in PCB transformation.

Strategy for Remediation of Polychlorinated Biphenyls-Contaminated Soil Through Redox Management Based on Electronegativity of the Contaminants

Literature review reveals that Persistent Organic Pollutants (POPs), such as polychlorinated biphenyls (PCBs), are electron deficient compounds due to the presence of highly electronegative groups. Hence, they are more amenable to anaerobic biodegradation rather than oxidative metabolism. However, the studies on PCBs bioremediation are more inclined towards aerobic treatment. Besides, the past studies are mainly centered on screening and application of PCB-degrading microorganisms. In our opinion the degradative capacity is already present in the native microflora, and choice of electron donor is of paramount importance for faster reductive metabolism of PCBs. In this study, the use of methanol as electron donor with cow dung as the general microbial inoculum resulted in high specific rate of degradation (0.0542-0.0637 /day) for high-chlorinated biphenyls. The % removal of PCBs ranged between 67.7 and 71.7%. It may be the first study on the application of methanol as a cheap electron donor for PCBs biodegradation without bioaugmentation with specifically selected microorganisms.

Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy)

Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.

Exploring the role of microbes for the management of persistent organic pollutants

Persistent organic pollutants (POPs) are chemicals which have been persisting in the environment for many years due to their longer half-lives. POPs have gained attention over the last few decades due to the unsustainable management of chemicals which led to their widespread and massive contamination of biota from different strata and environments. Due to the widespread distribution, bio-accumulation and toxic behavior, POPs have become a risk for organisms and environment. Therefore, a focus is required to eliminate these chemicals from the environment or transform into non-toxic forms. Among the available techniques for the removal of POPs, most of them are inefficient or incur high operational costs. As an alternative to this, microbial bioremediation of POPs such as pesticides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pharmaceuticals and personal care products is much more efficient and cost-effective. Additionally, bacteria play a vital role in the biotransformation and solubilization of POPs, which reduces their toxicity. This review specifies the Stockholm Convention that evaluates the risk profile for the management of existing as well as emerging POPs. The sources, types and persistence of POPs along with the comparison of conventional elimination and bioremediation methods of POPs are discussed comprehensively. This study demonstrates the existing bioremediation techniques of POPs and summaries the potential of microbes which serve as enhanced, cost-effective, and eco-friendly approach for POPs elimination.

Prokaryotic, Microeukaryotic, and Fungal Composition in a Long-Term Polychlorinated Biphenyl-Contaminated Brownfield

Polychlorinated biphenyls (PCBs) are recognized as persistent organic pollutants and accumulate in organisms, soils, waters, and sediments, causing major health and ecological perturbations. Literature reported PCB bio-transformation by fungi and bacteria in vitro, but data about the in situ impact of those compounds on microbial communities remained scarce while being useful to guide biotransformation assays. The present work investigated for the first time microbial diversity from the three-domains-of-life in a long-term contaminated brownfield (a former factory land). Soil samples were ranked according to their PCB concentrations, and a significant increase in abundance was shown according to increased concentrations. Microbial communities structure showed a segregation from the least to the most PCB-polluted samples. Among the identified microorganisms, Bacteria belonging to Gammaproteobacteria class, as well as Fungi affiliated to Saccharomycetes class or Pleurotaceae family, including some species known to transform some PCBs were abundantly retrieved in the highly polluted soil samples.

Eichhornia crassipes biochar aided pollutants sorption competence of multi-metal tolerant fungi species on South Pennar river

The number of studies about the use of efficient techniques to treat contaminated water bodies has increased in recent years. The use of bioremediation method for the reduction of contaminants from aqueous system is receiving a lot of attention. Thus, this study was designed to assess the Eichhornia crassipes biochar amended pollutants sorption competence of multi-metal tolerant Aspergillus flavus on South Pennar River. The physicochemical characteristics declared that the, half of the parameters (turbidity, TDS, BOD, COD, Ca, Mg, Fe, free NH3, Cl-, and F-) of South Pennar River were beyond the permissible limits. Furthermore, the lab-scale bioremediation investigation with different treatment groups (group I, II, and III) revealed that the group III (E. crassipes biochar and A. flavus mycelial biomass) showed considerable remediation efficiency on South Pennar River water in 10 days of treatment. The metals adsorbed on the surface of E. crassipes biochar and A. flavus mycelial biomass was also affirmed by SEM analysis. Hence such findings, E. crassipes biochar amended A. flavus mycelial biomass could be a sustainable method of remediating contaminated South Pennar River water.

Role of Microbes in the degradation of organic semivolatile compounds in polar ecosystems: A review

The Arctic and the Antarctic Continent correspond to two eco-regions with extreme climatic conditions. These regions are exposed to the presence of contaminants resulting from human activity (local and global), which, in turn, represent a challenge for life forms in these environments. Anthropogenic pollution by semi-volatile organic compounds (SVOCs) in polar ecosystems has been documented since the 1960s. Currently, various studies have shown the presence of SVOCs and their bioaccumulation and biomagnification in the polar regions with negative effects on biodiversity and the ecosystem. Although the production and use of these compounds has been regulated, their persistence continues to threaten biodiversity and the ecosystem. Here, we summarize the current literature regarding microbes and SVOCs in polar regions and pose that bioremediation by native microorganisms is a feasible strategy to mitigate the presence of SVOCs. Our systematic review revealed that microbial communities in polar environments represent a wide reservoir of biodiversity adapted to extreme conditions, found both in terrestrial and aquatic environments, freely or in association with vegetation. Microorganisms adapted to these environments have the potential for biodegradation of SVOCs through a variety of genes encoding enzymes with the capacity to metabolize SVOCs. We suggest that a comprehensive approach at the molecular and ecological level is required to mitigate SVOCs presence in these regions. This is especially patent when considering that SVOCs degrade at slow rates and possess the ability to accumulate in polar ecosystems. The implications of SVOC degradation are relevant for the preservation of polar ecosystems with consequences at a global level.

A comprehensive review on the potential of microbial enzymes in multipollutant bioremediation: Mechanisms, challenges, and future prospects

Industrialization and other human activity represent significant environmental hazards. Toxic contaminants can harm a comprehensive platform of living organisms in their particular environments. Bioremediation is an effective remediation process in which harmful pollutants are eliminated from the environment using microorganisms or their enzymes. Microorganisms in the environment often create a variety of enzymes that can eliminate hazardous contaminants by using them as a substrate for development and growth. Through their catalytic reaction mechanism, microbial enzymes may degrade and eliminate harmful environmental pollutants and transform them into non-toxic forms. The principal types of microbial enzymes which can degrade most hazardous environmental contaminants include hydrolases, lipases, oxidoreductases, oxygenases, and laccases. Several immobilizations, genetic engineering strategies, and nanotechnology applications have been developed to improve enzyme performance and reduce pollution removal process costs. Until now, the practically applicable microbial enzymes from various microbial sources and their ability to degrade multipollutant effectively or transformation potential and mechanisms are unknown. Hence, more research and further studies are required. Additionally, there is a gap in the suitable approaches considering toxic multipollutants bioremediation using enzymatic applications. This review focused on the enzymatic elimination of harmful contaminants in the environment, such as dyes, polyaromatic hydrocarbons, plastics, heavy metals, and pesticides. Recent trends and future growth for effectively removing harmful contaminants by enzymatic degradation are also thoroughly discussed.

Myco- and phyco-remediation of polychlorinated biphenyls in the environment: a review

Polychlorinated biphenyls (PCBs) are toxic organic compounds and pose serious threats to environment and public health. PCBs still exist in different environments such as air, water, soil, and sediments even on ban. This review summarizes the phyco- and myco-remediation technologies developed to detoxify the PCB-polluted sites. It was found that algae mostly use bioaccumulation to biodegradation strategies to reclaim the environment. As bio-accumulator, Ulva rigida C. Agardh has been best at 25 ng/g dry wt to remove PCBs. Evidently, Anabaena PD-1 is the only known PCB degrading alga and efficiently degrade Aroclor 1254 and dioxin-like PCBs up to 84.4% and 37.4% to 68.4%, respectively. The review suggested that factors such as choice of algal strains, response of microalgae, biomass, the rate of growth, and cost-effective cultivation conditions significantly influence the remediation of PCBs. Furthermore, the Anabaena sp. linA gene of Pseudomonas paucimobilis Holmes UT26 showed enhanced efficiency. Pleurotus ostreatus (Jacq.) P. Kumm is the most efficient PCB degrading fungus, degrading up to 98.4% and 99.6% of PCB in complex and mineral media, respectively. Combine metabolic activities of bacteria and yeast led to the higher detoxification of PCBs. Fungi-algae consortia would be a promising approach in remediation of PCBs. A critical analysis on potentials and limits of PCB treatment through fungal and algal biosystems have been reviewed, and thus, new insights have emerged for possible bioremediation, bioaccumulation, and biodegradation of PCBs.

Bacterial Degradation of PCB 70 and its Hydroxy Derivatives is an Environmentally Friendly Way to Destroy Pops

One of the problems of our time is the environmentally safe destruction of polychlorinated biphenyls (PCBs) and their hydroxylated derivatives. The aim of the study was to investigate the features and prospects of the decomposition of PCB 70 (2,5,3’,4’-tetrachlorobiphenyl) and hydroxylated chlorobiphenyls derived from it by Rhodococcus wratislaviensis strain CH628. As a result of the application of methods of periodic cultivation, gas chromatography and light spectrometry, it was found that the efficiency of destruction of PCB 70 1 g of cells of strain CH628 was 90 mg PCB/day, and the same indicator for a mixture consisting of hydroxy derivatives obtained from PCB 70 was 56 mg PCB/day. It was shown that the strain uses all components of the mixture of hydroxy-PCB 70 as a growth substrate, but with different degradation rates. When cultivated in a mineral medium with PCB 70 or a mixture of hydroxy-PCB 70, strain CH628 forms biofilms. The analysis of the obtained results shows that the use of the Rhodococcus wratislaviensis CH628 strain will make it possible to develop a technology for the environmentally safe destruction of PCB 70 and hydroxy-PCBs derived from it.

Enhanced rhizoremediation of polychlorinated biphenyls by resuscitation-promoting factor stimulation linked to plant growth promotion and response of functional microbial populations

Rhizoremediation is acknowledged as a green technology for removing polychlorinated biphenyls (PCBs) in soil. However, rhizoremediation is limited because most soil microorganisms enter into a viable but non-culturable (VBNC) state under PCBs stress. This work was to study the effect of resuscitation-promoting factor (Rpf) on rhizoremediation efficiency of PCBs in alfalfa and rhizosphere microbiological communities. Results suggested that Rpf promoted alfalfa growth in PCB-contaminated soil by improving antioxidant enzymes and detoxification metabolites in alfalfa. After 40 d Rpf treatment, removal rate for five selected PCBs significantly increased by 0.5-2.2 times. Rpf enhanced relative abundances of bphA and bphC responsible for degrading PCBs, and enzymatic activities of metabolizing exogenous compounds in rhizosphere soil. High-throughput sequencing showed that Rpf did not change the dominant microbial population at phyla and genera levels, but caused variation of the bacterial community structures. The promoting function of Rpf was linked to the shift of various key populations having different functions depending on Rpf concentrations. Pseudomonas and Rhizobium spp. enrichment might stimulate PCB degradation and Streptomyces and Bacillus spp. primarily contributed to alfalfa growth. Predicted functions in rhizosphere soil bacterial community indicated Rpf facilitated soil nutrient cycling and environmental adaptation. This study indicated that Rpf was an active additive for strengthening rhizoremediation efficiency of PCB-contaminated soil and enhancing their in-situ remediation.

Emerging bio-dispersant and bioremediation technologies as environmentally friendly management responses toward marine oil spill: A comprehensive review

Marine oil spills emanating from wells, pipelines, freighters, tankers, and storage facilities draw public attention and necessitate quick and environmentally friendly response measures. It is sometimes feasible to contain the oil with booms and collect it with skimmers or burn it, but this is impracticable in many circumstances, and all that can be done without causing further environmental damage is adopting natural attenuation, particularly through microbial biodegradation. Biodegradation can be aided by carefully supplying biologically accessible nitrogen and phosphorus to alleviate some of the microbial growth constraints at the shoreline. This review discussed the characteristics of oil spills, origin, ecotoxicology, health impact of marine oils spills, and responses, including the variety of remedies and responses to oil spills using biological techniques. The different bioremediation and bio-dispersant treatment technologies are then described, with a focus on the use of green surfactants and their advances, benefits/drawbacks. These technologies were thoroughly explained, with a timeline of research and recent studies. Finally, the hurdles that persist as a result of spills are explored, as well as the measures that must be taken and the potential for the development of existing treatment technologies, all of which must be linked to the application of integrated procedures.

E-waste scenario in South-Asia: an emerging risk to environment and public health

Over the past decade, e-waste generation has been accelerated in the world as never before, particularly South-Asia is confronted with an enormous risk of e-waste intensification owing to both locally generated and internationally imported. There has been a gradual increase of e-waste generated in South-Asia and in 2019, 4,057 Kilo tons (kt) of e-waste was generated, which is about 16% of the Asian region. Though there is an urgent requirement to rectify the catastrophic accumulation of e-waste and for its effective eco-friendly management, inadequate legal implementation and poor enforcement, lack of awareness, weak formal e-waste collection and recycling process allow for escalating problems associated with e-waste, particularly towards the environmental and public health concern. Under these circumstances, this paper has been written by reviewing the available research findings, since 2000 to find out the current scenario of South-Asia. Unfortunately, the problem is also not seen as a hot topic to address by the researchers, there are only 106 research studies conducted in South-Asia. Out of that, a considerable number of studies were conducted only in India (54%), Bangladesh (23%), and Pakistan (16%). Sri Lanka, Nepal, and Bhutan shared the rest. As a matter of fact, many more studies are needed on environmental and human health effects, legal implementations, awareness and novel managerial strategies etc. to assist policymakers and other relevant authorities in making their decisions. Similarly, rather than facing threats alone, fighting against as a region would be ideal, which also helps to restrict intra movement of e-waste among the South-Asian countries.

Promotion of the biodegradation of phenanthrene adsorbed on microplastics by the functional bacterial consortium QY1 in the presence of humic acid: Bioavailability and toxicity evaluation

The adsorption of hydrophobic organic compounds (HOCs) by microplastics (MPs) has attracted great attention in recent years. However, the ultimate environmental fate of the HOCs sorbed on MPs (HOCs-MPs) is poorly understood. In this work, we investigated the potential influence of the biotransformation process on the environmental fate of phenanthrene (PHE, a model HOC) sorbed on MPs (PHE-MPs) under the existence of humic acid (HA, the main ingredient of dissolved organic matter (DOM)) in the aquatic environment. The results indicated that the adsorption behavior of PHE on MPs decreased its bioavailability and thus inhibited its biotransformation efficiency. However, HA significantly promoted the biodegradation rate and percentage of PHE-MPs. This was probably because HA improved the desorption of PHE from MPs, which promoted the acquisition of PHE by bacteria from the aqueous phase. Further, HA dramatically increased the bacterial community diversity and richness and altered the community composition. The richness of some PHE-degrading bacteria, such as Methylobacillus and Sphingomonas, significantly increased, which may also be an important factor for promoting PHE biodegradation. Molecular ecological network analysis implied that HA enhanced the modularity and complexity of bacterial interaction networks, which was beneficial to maintaining the functional stability of the consortium QY1. Besides, HA decreased the cytotoxicity of functional microbes induced by HOCs-MPs. This work broadens our knowledge of the environmental fate of HOCs-MPs and interactions of MPs, HOCs, DOMs and functional microbial consortiums in aqueous environments.

Biostimulation and Bioaugmentation of Soils Contaminated with Decachlorobiphenyl (PCB-209) Using Native Bacterial Strains Individually and in Consortia

Historically, microorganisms have proven to be efficient alternatives for the removal of PCBs, since these contaminants continue to be a major problem for human health and the environment. In this work, the removal of decachlorobiphenyl (PCB-209) was evaluated using native bacterial strains individually and in consortia through biostimulation and bioaugmentation processes. Bacillus sp. DCB13, Staphylococcus sp. DCB28, and Acinetobacter sp. DCB104 were biostimulated in a minimal medium that initially contained biphenyl and later PCB-209 for adaptation as a carbon source. The removal potential of PCB-209 by bacterial strains was evaluated in a bioaugmentation process under aerobic conditions. Using a completely randomized design, ten different treatments were evaluated. Finally, the bacterial growth (CFU/g of soil) and the chemical characteristics of the bioaugmented soil were determined, as was the content of PCB-209 removed by gas chromatography–mass spectrometry. Strains DCB13, DCB28, and DCB104 showed cell growth (>3.4 × 105 CFU/mL) during 120 h of biostimulation, with a marked difference between treatments with biphenyl compared with those where PCB-209 was added. Strains DCB13 and DCB104 (3.4 × 105 CFU/mL and 2.0 × 106 CFU/mL, respectively) grew better with PCB-209, while DCB28 grew better with biphenyl (4.5 × 106 CFU/mL). In bioaugmented soils contaminated with PCB-209, the strains showed maximum growth when inoculated in a consortium (>2.0 × 104 CFU/g). The results showe that the range of the bacterial elimination of PCB-209 in the treatments was from 9.58 to 17.33 mg/kg. The highest elimination potential of PCB-209 was obtained when the bacterial strains were inoculated in a consortium. These findings open a wide perspective for the use of native bacteria for the cleaning and restoration of soils contaminated by toxic chemicals.

Elucidating the biodegradation pathway and catabolic genes of benzophenone-3 in Rhodococcus sp. S2-17

A new bacterium, Rhodococcus sp. S2-17, which could completely degrade an emerging organic pollutant, benzophenone-3 (BP-3), was isolated from contaminated sediment through an enrichment procedure, and its BP-3 catabolic pathway and genes were identified through metabolic intermediate and transcriptomic analyses and biochemical and genetic studies. Metabolic intermediate analysis suggested that strain S2-17 may degrade BP-3 using a catabolic pathway progressing via the intermediates BP-1, 2,4,5-trihydroxy-benzophenone, 3-hydroxy-4-benzoyl-2,4-hexadienedioic acid, 4-benzoyl-3-oxoadipic acid, 3-oxoadipic acid, and benzoic acid. A putative BP-3 catabolic gene cluster including cytochrome P450, flavin-dependent oxidoreductase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, and α/β hydrolase genes was identified through genomic and transcriptomic analyses. Genes encoding the cytochrome P450 complex that demethylates BP-3 to BP-1 were functionally verified through protein expression, and the functions of the other genes were also verified through knockout mutant construction and intermediate analysis. This study suggested that strain S2-17 might have acquired the ability to catabolize BP-3 by recruiting the cytochrome P450 complex and α/β hydrolase, which hydrolyzes 4-benzoyl-3-oxoadipic acid to benzoic acid and 3-oxoadipic acid, genes, providing insights into the recruitment of genes of for the catabolism of emerging organic pollutants.

The impact of pollutant as selection pressure on conjugative transfer of dioxin-catabolic plasmids harbored by Rhodococcus sp. strain p52

Plasmid-mediated bioaugmentation has potential application in the cleanup of recalcitrant environmental pollutants. In this study, we examined the influence of various contaminants (in different categories or different amounts) as a selection pressure on the spread of catabolic plasmids within an activated sludge bacteria community bioaugmented with Rhodococcus sp. strain p52 harboring pDF01 and pDF02. The distinguishable genera of transconjugants were isolated under the stresses of phenanthrene, dibenzothiophene, and dibenzo-p-dioxin. The three contaminants exerted different degrees of influence on the activated sludge bacteria bearing the catabolic plasmids. The relatively high ratios of transconjugant-bearing catabolic plasmids were detected in the reactor fed with dibenzo-p-dioxin. As dibenzo-p-dioxin from 10 to 80 mg/L was fed into the reactors, the ratios of transconjugant-bearing catabolic plasmids increased. Additionally, levels of ROS and extracellular LDH of activated sludge bacteria in the contaminants-fed reactors increased, comparing with that in the control reactor, indicating that the contaminants exerted toxicity which promoted the cell membrane permeability of the activated sludge bacteria. Our study provides a characterization of the recalcitrant contaminants as a selection pressure that can modulate catabolic plasmid transfer during genetic bioaugmentation for the removal of contaminants.

Sinorhizobium meliloti AS A PERSPECTIVE OBJECT FOR MODERN BIOTECHNOLOGY

Sinorhizobium meliloti is a Gram-negative soil nitrogen-fixing bacterium that increases the yield of legumes. There is information in the literature about the complete genome sequence of this bacterium, in addition, the polysaccharide composition of the biofilm, which is actively involved in nitrogen fixation, has been studied. The well-known nucleotide sequence, as well as the genetic and biochemical features of S. meliloti make this organism an ideal model for biotechnological research. The purpose of this work was to analyze the current data provided in the literature on the symbiotic interaction of Sinorhizobium meliloti with the host plant, and to characterize the main directions of the use of this bacterium in agriculture, bioremediation and medicine.

Unraveling metabolic flexibility of rhodococci in PCB transformation

Even though the genetic attributes suggest presence of multiple degradation pathways, most of rhodococci are known to transform PCBs only via regular biphenyl (bph) pathway. Using GC-MS analysis, we monitored products formed during transformation of 2,4,4'-trichlorobiphenyl (PCB-28), 2,2',5,5'-tetrachlorobiphenyl (PCB-52) and 2,4,3'-trichlorobiphenyl (PCB-25) by previously characterized PCB-degrading rhodococci Z6, T6, R2, and Z57, with the aim to explore their metabolic pleiotropy in PCB transformations. A striking number of different transformation products (TPs) carrying a phenyl ring as a substituent, both those generated as a part of the bph pathway and an array of unexpected TPs, implied a curious transformation ability. We hypothesized that studied rhodococcal isolates, besides the regular one, use at least two alternative pathways for PCB transformation, including the pathway leading to acetophenone formation (via 3,4 (4,5) dioxygenase attack on the molecule), and a third sideway pathway that includes stepwise oxidative decarboxylation of the aliphatic side chain of the 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate. Structure of the identified chlorinated benzoic acids and acetophenones allowed us to hypothesize that the first two pathways were the outcome of a ring-hydroxylating dioxygenase with the ability to attack both the 2,3 (5,6) and the 3,4 (4,5) positions of the biphenyl ring as well as dechlorination activity at both, -ortho and -para positions. We propose that several TPs produced by the bph pathway could have caused the triggering of the third sideway pathway. In conclusion, this study proposed ability of rhodococci to use different strategies in PCB transformation, which allows them to circumvent potential negative aspect of TPs on the overall transformation pathway.

Molecular Characterization of Fungal Biodiversity in Long-Term Polychlorinated Biphenyl-Contaminated Soils

Polychlorinated biphenyls (PCBs) belong to the organic pollutants that are toxic to humans and harmful to environments. Numerous studies dealing with the impact of PCBs on soil microorganisms have focused on bacterial communities. The effects of PCBs on fungal communities in three different PCB-polluted soils from former industrial sites were investigated using high-throughput sequencing of the internal transcribed spacer 1 region. Significant differences in fungal alpha diversity were observed mainly due to soil physico-chemical properties. PCBs only influenced the richness of the fungal communities by increasing it. Fungal composition was rather strongly influenced by both PCBs and soil properties, resulting in different communities associated with each soil. Sixteen Ascomycota species were present in all three soils, including Stachybotrys chartarum, Fusarium oxysporum, Penicillium canescens, Penicillium chrysogenum,Penicillium citrosulfuratum and Penicillium brevicompactum, which are usually found in PCB-polluted soils, and Fusarium solani, Penicillium canescens, Penicillium citrosulfuratum and Penicillium chrysogenum, which are known PCB degraders. This study demonstrated that PCBs influence the richness and the composition of fungal communities. Their influence, associated with that of soil physico-chemical properties, led to distinct fungal communities, but with sixteen species common to the three soils which could be considered as ubiquitous species in PCB-polluted soils.

Bioremediation strategies with biochar for polychlorinated biphenyls (PCBs)-contaminated soils: A review

Polychlorinated biphenyls (PCBs) are hazardous organic contaminants threatening human health and environmental safety due to their toxicity and carcinogenicity. Biochar (BC) is an eco-friendly carbonaceous material that can extensively be utilized for the remediation of PCBs-contaminated soils. In the last decade, many studies reported that BC is beneficial for soil quality enhancement and agricultural productivity based on its physicochemical characteristics. In this review, the potential of BC application in PCBs-contaminated soils is elaborated as biological strategies (e.g., bioremediation and phytoremediation) and specific mechanisms are also comprehensively demonstrated. Further, the synergy effects of BC application on PCBs-contaminated soils are discussed, in view of eco-friendly, beneficial, and productive aspects.

Keystone taxa shared between earthworm gut and soil indigenous microbial communities collaboratively resist chlordane stress

Chlordane is an organochlorine pesticide that is applied extensively. Residual concentrations that remain in soils after application are highly toxic to soil organisms, particularly affecting the earthworm gut and indigenous soil microorganisms. However, response mechanisms of the earthworm gut and indigenous soil microorganism communities to chlordane exposure are not well known. In this study, earthworms (Metaphire guillelmi) were exposed to chlordane-contaminated soils to investigate their response mechanisms over a gradient of chlordane toxicity. Results from high-throughput sequencing and network analysis showed that the bacterial composition in the earthworm gut varied more significantly than that in indigenous soil microbial communities under different concentrations of chlordane stress (2.3-60.8 mg kg^-1; p < 0.05). However, keystone species of Flavobacterium, Candidatus Nitrososphaera, and Acinetobacter remained stable in both the earthworm gut and bacterial communities despite varying degrees of chlordane exposure, and their relative abundance was slightly higher in the low-concentration treatment group (T1, T2) than in the high-concentration treatment group (T3, T4). Additionally, network analysis demonstrated that the average value of the mean degree of centrality, closeness centrality, and eigenvector centrality of all keystone species screened by four methods (MetagenomeSeq, LEfSe, OPLS-DA, Random Forest) were 161.3, 0.5, and 0.63, respectively, and that these were significantly higher (p < 0.05) than values for non-keystone species (84.9, 0.4, and 0.2, respectively). Keystone species had greater network connectivity and a stronger capacity to degrade pesticides and transform carbon and nitrogen than non-keystone species. The keystone species, which were closely related to the microbial community in soil indigenous flora and earthworm intestinal flora, could resist chlordane stress and undertake pesticide degradation. These results have increased understanding of the role of the earthworm gut and indigenous soil bacteria in resisting chlordane stress and sustaining microbial equilibrium in soil.

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits

PREMISE

Within a broader study on leaf fossilization in freshwater environments, a long-term study on the development and microbiome composition of biofilms on the foliage of aquatic plants has been initiated to understand how microbes and biofilms contribute to leaf decay and preservation. Here, water lily leaves are employed as a study model to investigate the relationship between bacterial microbiomes, biodegradation, and fossilization. We compare four DNA extraction kits to reduce biases in interpretation and to identify the most suitable kit for the extraction of DNA from bacteria associated with biofilms on decaying water lily leaves for 16S rRNA amplicon analysis.

METHODS

We extracted surface-associated DNA from Nymphaea leaves in early stages of decay at two water depth levels using four commercially available kits to identify the most suitable protocol for bacterial extraction, applying a mock microbial community standard to enable a reliable comparison of the kits.

RESULTS

Kit 4, the FastDNA Spin Kit for Soil, resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition.

DISCUSSION

The success of Kit 4 may be attributed to its use of bead beating with a homogenizer, which was more efficient in the lysis of Gram-positive bacteria than the manual vortexing protocols used by the other kits. Our results show that microbial composition on leaves during early decay remains comparable and may change only in later stages of decomposition.

Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus

Polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs), that can be detected in a variety of environments including the human body, adversely affecting global health. Bioremediation is an emerging field for the detoxification and removal of environmental pollutants, with novel biocatalysts appropriate for this task being in high demand. In this study, a biobank of novel fungal strains isolated as symbionts of marine invertebrates was screened for their ability to remove 2,4,5-trichlorobiphenyl (PCB29). The most efficient strains were studied further for their ability to express laccase activity, the most commonly associated extracellular activity involved in the removal of aromatic pollutants and encoded in fungi by the enzymatic class of multicopper oxidases (MCOs). The strain expressing the highest laccase activity, Cladosporium sp. TM138-S3, was cultivated in the presence of copper ions in a 12 L bioreactor and two enzymes exhibiting laccase activity were isolated from the culture broth through ion-exchange chromatography. The two enzymes, Lac1 and Lac2, were biochemically characterized and showed similar characteristics, although an improved ability to remove PCB29 (up to 71.2%) was observed for Lac2 in the presence of mediators. In parallel, we performed RNAseq of the strain growing in presence and absence of PCB29 and reconstructed its transcriptome assembly. Functional annotation allowed identifying the MCO repertoire of the fungus, consisting of 13 enzymes. Phylogenetic analysis of Ascomycete MCOs further allowed classifying these enzymes, revealing the diversity of laccase activities in Cladosporium sp. TM138-S3.

Assessment of Perceptions and Cancer Risks of Workers at a Polychlorinated Biphenyl-Contaminated Hotspot in Ethiopia

BACKGROUND

Polychlorinated biphenyls (PCBs) are synthetic and persistent toxic chemicals with a high potential to bioaccumulate in human tissue. There is no existing literature on workers' perceptions and occupational cancer risk due to exposure to PCBs in Ethiopia.

OBJECTIVES

The aim of the present study was to assess workers' perceptions of occupational health and safety measures of PCB management and to evaluate the cancer risk posed by PCBs to workers handling these chemicals in Ethiopia.

METHODS

A total of 264 questionnaires were administered to workers at the study area to obtain information about PCB management. A mathematical model adopted from the United States Environmental Protection Agency (USEPA) was used to assess the potential cancer risk of people working in PCB-contaminated areas.

RESULTS

The results showed that the majority of the workers had little knowledge of safe PCB management practices. Furthermore, 82.6% had not received training on chemical management and occupational health and safety protocols. The association between respondents' responses on the impact of PCBs to the use of personal protective equipment was statistically significant (p <0.005). Accidental ingestion, dermal contact and inhalation exposure pathways were considered in assessing the cancer risk of people working in these areas. The estimated cancer risk for PCBs via dermal contact was higher than for the accidental ingestion and inhalation pathways. The health risk associated with dermal contact was 73.8-times higher than the inhalation exposure route. Workers at the oil tanker and oil barrel area and swampy site are at higher risk of cancer via dermal contact at the 95th centile (879 and 2316 workers per million due to PCB exposure, respectively). However, there is very low cancer risk at the staff residence and garden area via the inhalation route.

CONCLUSIONS

Training programs would help improve the knowledge of workers in the area of occupational health and safety of chemical handling. Further studies on PCBs in the exposed workers will provide information on their blood sera PCB levels and consequently identify potential health impacts.

PARTICIPANT CONSENT

Obtained.

ETHICS APPROVAL

Ethics approval was obtained from the Research Ethics Review Committee of Adama Hospital Medical College, Adama, Ethiopia.

COMPETING INTERESTS

The authors declare no competing financial interests.

Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges

Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces, and Trichoderma. Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.

Potentiality of Native Ascomycete Strains in Bioremediation of Highly Polychlorinated Biphenyl Contaminated Soils

Polychlorinated biphenyls (PCBs) are organic pollutants that are harmful to environment and toxic to humans. Numerous studies, based on basidiomycete strains, have reported unsatisfactory results in the mycoremediation of PCB-contaminated soils mainly due to the non-telluric origin of these strains. The abilities of a five-Ascomycete-strain consortium in the mycoremediation of PCB-polluted soils and its performance to restore their sound functioning were investigated using mesocosm experiments associated with chromatography gas analysis and enzymatic activity assays. With the soil H containing 850 ppm PCB from which the strains had been isolated, a significant PCB depletion of 29% after three months of treatment was obtained. This led to an important decrease of PCBs from 850 to 604 ppm. With the soil L containing 36 ppm PCB, biodegradation did not occur. In both soils, the fungal biomass quantified by the ergosterol assay, did not increase at the end of the treatment. Biodegradation evidenced in the soil H resulted in a significantly improved stoichiometry of N and P acquiring enzymatic activities. This unprecedented study demonstrates that the native Ascomycetes display remarkable properties for remediation and restoration of functioning of the soil they originated from paving the way for greater consideration of these strains in mycoremediation.

Microbial and enzymatic degradation of PCBs from e-waste-contaminated sites: a review

Electronic waste is termed as e-waste and on recycling it produces environmental pollution. Among these e-waste pollutants, polychlorinated biphenyls (PCBs) are significantly important due to ubiquitous, organic in nature and serious health and environmental hazards. PCBs are used in different electrical equipment such as in transformers and capacitors for the purposes of exchange of heat and hydraulic fluids. Bioremediation is a reassuring technology for the elimination of the PCBs from the environment. In spite of their chemical stability, there are several microbes which can bio-transform or mineralize the PCBs aerobically or anaerobically. In this review paper, our objective was to summarize the information regarding PCB-degrading enzymes and microbes. The review suggested that the most proficient PCB degraders during anaerobic condition are Dehalobacter, Dehalococcoides, and Desulfitobacterium and in aerobic condition are Burkholderia, Achromobacter, Comamonas, Ralstonia, Pseudomonas, Bacillus, and Alcaligenes etc., showing the broadest substrate among bacterial strains. Enzymes found in soil such as dehydrogenases and fluorescein diacetate (FDA) esterases have the capability to breakdown PCBs. Biphenyl upper pathway involves four enzymes: dehydrogenase (bphB), multicomponent dioxygenase (bphA, E, F, and G), second dioxygenase (bphC), hydrolase, and (bphD). Biphenyl dioxygenase is considered as the foremost enzyme used for aerobic degradation of PCBs in metabolic pathway. It has been proved that several micro-organisms are responsible for the PCB metabolization. The review provides novel strategies for e-waste-contaminated soil management.

Microbial Polyethylene Terephthalate Hydrolases: Current and Future Perspectives

Plastic has rapidly transformed our world, with many aspects of human life now relying on a variety of plastic materials. Biological plastic degradation, which employs microorganisms and their degradative enzymes, has emerged as one way to address the unforeseen consequences of the waste streams that have resulted from mass plastic production. The focus of this review is microbial hydrolase enzymes which have been found to act on polyethylene terephthalate (PET) plastic. The best characterized examples are discussed together with the use of genomic and protein engineering technologies to obtain PET hydrolase enzymes for different applications. In addition, the obstacles which are currently limiting the development of efficient PET bioprocessing are presented. By continuing to study the possible mechanisms and the structural elements of key enzymes involved in microbial PET hydrolysis, and by assessing the ability of PET hydrolase enzymes to work under practical conditions, this research will help inform large-scale waste management operations. Finally, the contribution of microbial PET hydrolases in creating a potential circular PET economy will be explored. This review combines the current knowledge on enzymatic PET processing with proposed strategies for optimization and use, to help clarify the next steps in addressing pollution by PET and other plastics.

A polyphenol-rich cranberry extract protects against endogenous exposure to persistent organic pollutants during weight loss in mice

The dramatic rise in the global occurrence of obesity and associated diseases calls for new strategies to promote weight loss. However, while the beneficial effects of weight loss are well known, rapid loss of fat mass can also lead to the endogenous release of liposoluble molecules with potential harmful effects, such as persistent organic pollutants (POP). The aim of this study was to evaluate the impact of a polyphenol-rich cranberry extract (CE) on POP release and their potential deleterious effects during weight loss of obese mice. C57BL/6 J mice were fed an obesogenic diet with or without a mixture of POP for 12 weeks and then changed to a low-fat diet to induce weight loss and endogenous POP release. The POP-exposed mice were then separated in two groups during weight loss, receiving either CE or the vehicle. Unexpectedly, despite the higher fat loss in the CE-treated group, the circulating levels of POP were not enhanced in these mice. Moreover, glucose homeostasis was further improved during CE-induced weight loss, as revealed by lower fasting glycemia and improved glucose tolerance as compared to vehicle-treated mice. Interestingly, the CE extract also induced changes in the gut microbiota after weight loss in POP-exposed mice, including blooming of Parvibacter, a member of the Coriobacteriaceae family which has been predicted to play a role in xenobiotic metabolism. Our data thus suggests that the gut microbiota can be targeted by polyphenol-rich extracts to protect from increased POP exposure and their detrimental metabolic effects during rapid weight loss.

Bioremediation of typical chlorinated hydrocarbons by microbial reductive dechlorination and its key players: A review

Chlorinated hydrocarbon contamination in soils and groundwater has a severe negative impact on the human health. Microbial reductive dechlorination is a major degradation pathway of chlorinated hydrocarbon in anaerobic subsurface environments, has been extensively studied. Recent progress on the diversity of the reductive dechlorinators and the key enzymes of chlororespiration has been well reviewed. Here, we present a thorough overview of the studies related to bioremediation of chloroethenes and polychlorinated biphenyls based on enhanced in situ reductive dechlorination. The major part of this review is to provide an up-to-date summary of functional microorganisms which are either detected during in situ biostimulation or applied in bioaugmentation strategies. The applied biostimulants and corresponding reductive dechlorination products are also summarized and the future research needs are finally discussed.

Evaluation of bioremediation strategies for treating recalcitrant halo-organic pollutants in soil environments

The aim of this study was to investigate the bioremediation potential of polychlorinated biphenyls (PCBs) in soil, mimicking three strategies: (a) mycoaugmentation: by the addition of Trametes sanguinea and Pleurotus sajor-caju co-cultures immobilized on sugarcane bagasse; (b) biostimulation: by supplementation of sugarcane bagasse; and (c) natural attenuation: no amendments. The experiments were done in microcosms using Ultisol soil. Remediation effectiveness was assessed based on pollutants content, soil characteristics, and ecotoxicological tests. Biostimulation and mycoaugmentation demonstrated the highest PCBs-removal (approx. 90%) with a significant toxicity reduction at 90 d. The studied strains were able to survive during the incubation period in non-sterilized soil. Laccase, manganese-peroxidase and endoxylanase activities increased significantly in co-cultures after 60 d. Sugarcane bagasse demonstrated to be not only a suitable support for fungal immobilization but also an efficient substrate for fungal colonization of PCBs-contaminated soils. Mycoaugmentation and biostimulation with sugarcane bagasse improved oxidable organic matter and phosphorous contents as well as dehydrogenase activity in soil. Therefore, biostimulation with sugarcane bagasse and mycoaugmentation applying dual white-rot fungal cultures constitute two efficient bioremediation alternatives to restore PCBs-contaminated soils.

Engineering Burkholderia xenovorans LB400 BphA through Site-Directed Mutagenesis at Position 283

Biphenyl dioxygenase (BPDO), which is a Rieske-type oxygenase (RO), catalyzes the initial dioxygenation of biphenyl and some polychlorinated biphenyls (PCBs). In order to enhance the degradation ability of BPDO in terms of a broader substrate range, the BphAE_S283M, BphAE_p4-S283M, and BphAE_RR41-S283M variants were created from the parent enzymes BphAE_LB400, BphAE_p4, and BphAE_RR41, respectively, by a substitution at one residue, Ser283Met. The results of steady-state kinetic parameters show that for biphenyl, the k _cat/K_m values of BphAE_S283M, BphAE_p4-S283M, and BphAE_RR41-S283M were significantly increased compared to those of their parent enzymes. Meanwhile, we determined the steady-state kinetics of BphAEs toward highly chlorinated biphenyls. The results suggested that the Ser283Met substitution enhanced the catalytic activity of BphAEs toward 2,3',4,4'-tetrachlorobiphenyl (2,3',4,4'-CB), 2,2',6,6'-tetrachlorobiphenyl (2,2',6,6'-CB), and 2,3',4,4',5-pentachlorobiphenyl (2,3',4,4',5-CB). We compared the catalytic reactions of BphAE_LB400 and its variants toward 2,2'-dichlorobiphenyl (2,2'-CB), 2,5-dichlorobiphenyl (2,5-CB), and 2,6-dichlorobiphenyl (2,6-CB). The biochemical data indicate that the Ser283Met substitution alters the orientation of the substrate inside the catalytic site and, thereby, its site of hydroxylation, and this was confirmed by docking experiments. We also assessed the substrate ranges of BphAE_LB400 and its variants with degradation activity. BphAE_S283M and BphAE_p4-S283M were clearly improved in oxidizing some of the 3-6-chlorinated biphenyls, which are generally very poorly oxidized by most dioxygenases. Collectively, the present work showed a significant effect of mutation Ser283Met on substrate specificity/regiospecificity in BPDO. These will certainly be meaningful elements for understanding the effect of the residue corresponding to position 283 in other Rieske oxygenase enzymes.IMPORTANCE The segment from positions 280 to 283 in BphAEs is located at the entrance of the catalytic pocket, and it shows variation in conformation. In previous works, results have suggested but never proved that residue Ser283 of BphAE_LB400 might play a role in substrate specificity. In the present paper, we found that the Ser283Met substitution significantly increased the specificity of the reaction of BphAE toward biphenyl, 2,3',4,4'-CB, 2,2',6,6'-CB, and 2,3',4,4',5-CB. Meanwhile, the Ser283Met substitution altered the regiospecificity of BphAE toward 2,2'-dichlorobiphenyl and 2,6-dichlorobiphenyl. Additionally, this substitution extended the range of PCBs metabolized by the mutated BphAE. BphAE_S283M and BphAE_p4-S283M were clearly improved in oxidizing some of the more highly chlorinated biphenyls (3 to 6 chlorines), which are generally very poorly oxidized by most dioxygenases. We used modeled and docked enzymes to identify some of the structural features that explain the new properties of the mutant enzymes. Altogether, the results of this study provide better insights into the mechanisms by which BPDO evolves to change and/or expand its substrate range and its regiospecificity.

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.

Establishing the relationship between molecular biomarkers and biotransformation rates: Extension of knowledge for dechlorination of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs)

Anaerobic reductive treatment technologies offer cost-effective and large-scale treatment of chlorinated compounds, including polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The information about the degradation rates of these compounds in natural settings is critical but difficult to obtain because of slow degradation processes. Establishing a relationship between biotransformation rate and abundance of biomarkers is one of the most critical challenges faced by the bioremediation industry. When solved for a given contaminant, it may result in significant cost savings because of serving as a basis for action. In the current review, we have summarized the studies highlighting the use of biomarkers, particularly DNA and RNA, as a proxy for reductive dechlorination of chlorinated ethenes. As the use of biomarkers for predicting biotransformation rates has not yet been executed for PCDD/Fs, we propose the extension of the same knowledge for dioxins, where slow degradation rates further necessitate the need for developing the biomarker-rate relationship. For this, we have first retrieved and calculated the bioremediation rates of different PCDD/Fs and then highlighted the key sequences that can be used as potential biomarkers. We have also discussed the implications and hurdles in developing such a relationship. Improvements in current techniques and collaboration with some other fields, such as biokinetic modeling, can improve the predictive capability of the biomarkers so that they can be used for effectively predicting biotransformation rates of dioxins and related compounds. In the future, a valid and established relationship between biomarkers and biotransformation rates of dioxin may result in significant cost savings, whilst also serving as a basis for action.

Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology

Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.

Assessment of Biodegradation Efficiency of Polychlorinated Biphenyls (PCBs) and Petroleum Hydrocarbons (TPH) in Soil Using Three Individual Bacterial Strains and Their Mixed Culture

Biodegradation is one of the most effective and profitable methods for the elimination of toxic polychlorinated biphenyls (PCBs) and total petroleum hydrocarbons (TPH) from the environment. In this study, aerobic degradation of the mentioned pollutants by bacterial strains Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN129, and Rhodococcus sp. IN306 and mixed culture M1 developed based on those strains at 1:1:1 ratio was analyzed. The effectiveness of individual strains and of the mixed culture was assessed based on carried out respirometric tests and chromatographic analyses. The Rhodococcus sp. IN306 turned out most effective in terms of 18 PCB congeners biodegradation (54.4%). The biodegradation index was decreasing with an increasing number of chlorine atoms in a molecule. Instead, the Mycolicobacterium frederiksbergense IN53 was the best TPH degrader (37.2%). In a sterile soil, contaminated with PCBs and TPH, the highest biodegradation effectiveness was obtained using inoculation with mixed culture M1, which allowed to reduce both the PCBs (51.8%) and TPH (34.6%) content. The PCBs and TPH biodegradation capacity of the defined mixed culture M1 was verified ex-situ with prism method in a non-sterile soil polluted with aged petroleum hydrocarbons (TPH) and spent transformer oil (PCBs). After inoculation with mixed culture M1, the PCBs were reduced during 6 months by 84.5% and TPH by 70.8% as well as soil toxicity was decreased.

Microcosm Experiment to Assess the Capacity of a Poplar Clone to Grow in a PCB-Contaminated Soil

Polychlorinated byphenyls (PCBs) are a class of Persistent Organic Pollutants extremely hard to remove from soil. The use of plants to promote the degradation of PCBs, thanks to synergic interactions between roots and the natural soil microorganisms in the rhizosphere, has been proved to constitute an effective and environmentally friendly remediation technique. Preliminary microcosm experiments were conducted in a greenhouse for 12 months to evaluate the capacity of the Monviso hybrid poplar clone, a model plant for phytoremediation, to grow in a low quality and PCB-contaminated soil in order to assess if this clone could be subsequently used in a field experiment. For this purpose, three different soil conditions (Microbiologically Active, Pre-sterilized and Hypoxic soils) were set up in order to assess the capacity of this clone to grow in the polluted soil in these different conditions and support the soil microbial community activity. The growth and physiology (chlorophyll content, chlorophyll fluorescence, ascorbate, phenolic compounds and flavonoid contents) of the poplar were determined. Moreover, chemical analyses were performed to assess the concentrations of PCB indicators in soil and plant roots. Finally, the microbial community was evaluated in terms of total abundance and activity under the different experimental conditions. Results showed that the poplar clone was able to grow efficiently in the contaminated soil and to promote microbial transformations of PCBs. Plants grown in the hypoxic condition promoted the formation of a higher number of higher-chlorinated PCBs and accumulated lower PCBs in their roots. However, plants in this condition showed a higher stress level than the other microcosms, producing higher amounts of phenolic, flavonoid and ascorbate contents, as a defence mechanism.

Degradation Mechanism of 4-Chlorobiphenyl by Consortium of Pseudomonas sp. Strain CB-3 and Comamonas sp. Strain CD-2

Polychlorinated biphenyls (PCBs) are types of lasting environmental pollutants which are widely used in various industries. 4-chlorobiphenyl (4CBP) is a PCB which is harmful to the environment as well as humans. Two strains, CB-3 and CD-2, were isolated from the polluted soil of a chemical factory and could completely degrade 50 mg/L 4CBP within 12 h by co-culture. The consortium comprising strains CB-3 and CD-2 was effective in the degradation of 4CBP. 4CBP was degraded initially by strain CB-3 to accumulate 4-chlorobenzoate (4CBA) and further oxidised by strain CD-2. Based on 16S rRNA gene sequence analysis and phenotypic typing, strain CB-3 and strain CD-2 were identified as Pseudomonas sp. and Comamonas sp., respectively. The substrate spectra experiment showed that strain CB-3 could degrade PCBs with no more than three chlorine atoms. A gene cluster of biphenyl metabolism was found in the genome of strain CB-3. Besides, a dechlorination gene cluster and a gene cluster of protocatechuate (PCA) metabolic were found in the genome of strain CD-2. These gene clusters are supposed to be involved in 4CBP degradation. The ability of strains CB-3 and CD-2 to degrade 4CBP in soil was assessed by soil experiment, and 4CBP at the initial concentration of 10 mg/kg was 80.5% removed within 15 days.

Biological enrichment prediction of polychlorinated biphenyls and novel molecular design based on 3D-QSAR/HQSAR associated with molecule docking

Based on the experimental data of octanol-water partition coefficients (Kow, represents bioaccumulation) for 13 polychlorinated biphenyl (PCB) congeners, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to establish 3D-QSAR models, combined with the hologram quantitative structure-activity relationship (HQSAR), the substitution sites (mono-substituted and bis-substituted) and substituent groups (electron-withdrawing hydrophobic groups) that significantly affect the octanol-water partition coefficients values of PCBs were identified, a total of 63 monosubstituted and bis-substituted were identified. Compared with using 3D-QSAR model alone, the coupling of 3D-QSAR and HQSAR models greatly increased the number of newly designed bis-substituted molecules, and the logKow reduction in newly designed bis-substituted molecules was larger than that of monosubstituted molecules. This was established to predict the Kow values of 196 additional PCBs and carry out a modification of target molecular PCB-207 to lower its Kow (biological enrichment) significantly, simultaneously maintaining the flame retardancy and insulativity after calculation by using Gaussian09. Simultaneously, molecular docking could further screen out three more environmental friendly low biological enrichment newly designed PCB-207 molecules (5-methyl-PCB-207, 5-amino-PCB-207, and 4-amino-5-ethyl-PCB-207).

Metabolic adaptation of fungal strains in response to contamination by polychlorinated biphenyls

Polychlorinated biphenyls (PCBs) represent a large group of recalcitrant environmental pollutants. Up to now, many studies have focused on bioremediation of PCBs by fungal strains; however, the mechanisms of adaptation of these strains towards PCBs remain unknown despite their importance in developing effective bioremediation processes. We studied five species, each consisting of two strains isolated either from PCB-polluted or PCB-unpolluted substrates (control strains). We investigated their responses to PCB contamination by studying their tolerance to PCBs, their ability to reduce these pollutants, and their expression level of Laccase genes. In Thermothelomyces thermophila, Thermothelomyces heterothallica, Thermoascus crustaceus, and Fusarium solani, all the studied strains showed a similar tolerance and PCB degradation regardless of their origin. In Schizophyllum commune, while both strains showed similar resistance to PCBs, i.e., PCBs and their degradation products presented no toxicity for these strains, the rate of PCB degradation of the strain from a PCB-polluted environment was significantly slightly higher. The PCB degradation did not correlate with the expression level of genes encoding Laccases. These results demonstrate that the tolerance and PCB degradation by the fungal strains, which did not involve Laccase genes, required different adaptation systems which seem to be constitutive or rapidly inducible by PCB according to the fungal species.