Transgenic plants to improve rhizoremediation of polychlorinated biphenyls (PCBs)

Potential Environmental Risk Characteristics of PCB Transformation Products in the Environmental Medium

The complementary construction of polychlorinated biphenyl (PCB) phytotoxicity and the biotoxicity 3D-QSAR model, combined with the constructed PCB environmental risk characterization model, was carried out to evaluate the persistent organic pollutant (POP) properties (toxicity (phytotoxicity and biotoxicity), bioconcentration, migration, and persistence) of PCBs and their corresponding transformation products (phytodegradation, microbial degradation, biometabolism, and photodegradation). The transformation path with a significant increase in environmental risks was analyzed. Some environmentally friendly PCB derivatives, exhibiting a good modification effect, and their parent molecules were selected as precursor molecules. Their transformation processes were simulated and evaluated for assessing the environmental risks. Some transformation products displayed increased environmental risks. The environmental risks of plant degradation products of the PCBs in the environmental media showed the maximum risk, indicating that the potential risks of the transformation products of the PCBs and their environmentally friendly derivatives could not be neglected. It is essential to further improve the ability of plants to degrade their transformation products. The improvement of some degradation products for environmentally friendly PCB derivatives indicates that the theoretical modification of a single environmental feature cannot completely control the potential environmental risks of molecules. In addition, this method can be used to analyze and evaluate environmentally friendly PCB derivatives to avoid and reduce the potential environmental and human health risks caused by environmentally friendly PCB derivatives.

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.

Advances and perspective in bioremediation of polychlorinated biphenyl-contaminated soils

In recent years, microbial degradation and bioremediation approaches of polychlorinated biphenyls (PCBs) have been studied extensively considering their toxicity, carcinogenicity and persistency potential in the environment. In this direction, different catabolic enzymes have been identified and reported for biodegradation of different PCB congeners along with optimization of biological processes. A genome analysis of PCB-degrading bacteria has led in an improved understanding of their metabolic potential and adaptation to stressful conditions. However, many stones in this area are left unturned. For example, the role and diversity of uncultivable microbes in PCB degradation are still not fully understood. Improved knowledge and understanding on this front will open up new avenues for improved bioremediation technologies which will bring economic, environmental and societal benefits. This article highlights on recent advances in bioremediation of PCBs in soil. It is demonstrated that bioremediation is the most effective and innovative technology which includes biostimulation, bioaugmentation, phytoremediation and rhizoremediation and acts as a model solution for pollution abatement. More recently, transgenic plants and genetically modified microorganisms have proved to be revolutionary in the bioremediation of PCBs. Additionally, other important aspects such as pretreatment using chemical/physical agents for enhanced biodegradation are also addressed. Efforts have been made to identify challenges, research gaps and necessary approaches which in future, can be harnessed for successful use of bioremediation under field conditions. Emphases have been given on the quality/efficiency of bioremediation technology and its related cost which determines its ultimate acceptability.

Phytoremediation: State-of-the-art and a key role for the plant microbiome in future trends and research prospects

Phytoremediation is increasingly adopted as a more sustainable approach for soil remediation. However, significant advances in efficiency are still necessary to attain higher levels of environmental and economic sustainability. Current interventions do not always give the expected outcomes in field settings due to an incomplete understanding of the multicomponent biological interactions. New advances in -omics are gradually implemented for studying microbial communities of polluted land in situ. This opens new perspectives for the discovery of biodegradative strains and provides us new ways of interfering with microbial communities to enhance bioremediation rates. This review presents retrospectives and future perspectives for plant microbiome studies relevant to phytoremediation, as well as some knowledge gaps in this promising research field. The implementation of phytoremediation in soil clean-up management systems is discussed, and an overview of the promoting factors that determine the growth of the phytoremediation market is given. Continuous growth is expected since elimination of contaminants from the environment is demanded. The evolution of scientific thought from a reductionist view to a more holistic approach will boost phytoremediation as an efficient and reliable phytotechnology. It is anticipated that phytoremediation will prove the most promising for organic contaminant degradation and bioenergy crop production on marginal land.

Theoretical investigation on proton transfer mechanism of extradiol dioxygenase

The formation mechanism of alkyl(hydro)peroxo species is performed via two parallel pathways.

Enhanced tolerance and remediation to mixed contaminates of PCBs and 2,4-DCP by transgenic alfalfa plants expressing the 2,3-dihydroxybiphenyl-1,2-dioxygenase

Polychlorinated biphenyls (PCBs) and 2,4-dichlorophenol (2,4-DCP) generally led to mixed contamination of soils as a result of commercial and agricultural activities. Their accumulation in the environment poses great risks to human and animal health. Therefore, the effective strategies for disposal of these pollutants are urgently needed. In this study, genetic engineering to enhance PCBs/2,4-DCP phytoremediation is a focus. We cloned the 2,3-dihydroxybiphenyl-1,2-dioxygenase (BphC.B) from a soil metagenomic library, which is the key enzyme of aerobic catabolism of a variety of aromatic compounds, and then it was expressed in alfalfa driven by CaMV 35S promoter using Agrobacterium-mediated transformation. Transgenic line BB11 was selected out through PCR, Western blot analysis and enzyme activity assays. Its disposal and tolerance to both PCBs and 2,4-DCP were examined. The tolerance capability of transgenic line BB11 towards complex contaminants of PCBs/2,4-DCP significantly increased compared with non-transgenic plants. Strong dissipation of PCBs and high removal efficiency of 2,4-DCP were exhibited in a short time. It was confirmed expressing BphC.B would be a feasible strategy to help achieving phytoremediation in mixed contaminated soils with PCBs and 2,4-DCP.

Expression of Arabidopsis acyl-CoA-binding proteins AtACBP1 and AtACBP4 confers Pb(II) accumulation in Brassica juncea roots

In Arabidopsis thaliana, the expression of two genes encoding acyl-CoA-binding proteins (ACBPs) AtACBP1 and AtACBP4, were observed to be induced by lead [Pb(II)] in shoots and roots in qRT-PCR analyses. Quantitative GUS (β-glucuronidase) activity assays confirmed induction of AtACBP1pro::GUS by Pb(II). Electrophoretic mobility shift assays (EMSAs) revealed that Pas elements in the 5'-flanking region of AtACBP1 were responsive to Pb(II) treatment. AtACBP1 and AtACBP4 were further compared in Pb(II) uptake using Brassica juncea, a potential candidate for phytoremediation given its rapid growth, large roots, high biomass and good capacity to accumulate heavy metals. Results from atomic absorption analyses on transgenic B. juncea expressing AtACBP1 or AtACBP4 indicated Pb(II) accumulation in roots. Subsequent Pb(II)-tracing assays demonstrated Pb(II) accumulation in the cytosol of root tips and vascular tissues of transgenic B. juncea AtACBP1-overexpressors (OXs) and AtACBP4-OXs and transgenic Arabidopsis AtACBP1-OXs. Transgenic Arabidopsis AtACBP1-OXs sequestered Pb(II) in the trichomes and displayed tolerance to hydrogen peroxide (H2 O2 ) treatment. In addition, AtACBP1 and AtACBP4 were H2 O2 -induced in the roots of wild-type Arabidopsis, while lipid hydroperoxide (LOOH) measurements of B. juncea AtACBP1-OX and AtACBP4-OX roots suggested that AtACBP1 and AtACBP4 can protect lipids against Pb(II)-induced lipid peroxidation.

Metabolism of (14)C-labeled polychlorinated biphenyl congeners by wheat cell suspension cultures

The metabolism of [UL-(14)C]-2,2',5,5'-tetrachlorobiphenyl ((14)C-PCB-52), [UL-(14)C]-2,2',4,4',5,5'-hexachlorobiphenyl ((14)C-PCB-153, and a congeneric mixture of [UL-(14)C]-labeled polychlorinated biphenyls ((14)C-PCB-Mix) was studied in cell suspension cultures of wheat (Triticum aestivum L. cv. 'Heines Koga II'). About 50% of applied (14)C-PCB-52 (20 μg/assay) was transformed during 96 h of incubation. While 7.6% on non-extractable residues emerged, turnover of (14)C-PCB-52 was mainly due to soluble polar metabolites. These were subjected to chemical glycoside cleavage. In the resulting hydrolysate, four aglycons were identified by GC-EIMS, namely four tetrachloro-hydroxy-biphenyl isomers (C6H6Cl4O, M(+·) at m/z = 306, 308, 310 and 312), and one trichloro-hydroxy-biphenyl (C6H7Cl3O, M(+·) at m/z = 272, 274 and 276). Number and character of hydroxylated products pointed to cytochromes P450 as enzymatic catalysts of hydroxylation. (14)C-PCB-153 was metabolized by wheat to minor degree if at all. Due to GC-EIMS analysis, of (14)C-PCB-Mix consisted of biphenyl, one mono-, four di-, seven tri-, eleven tetra-, and four pentachlorobiphenyls besides traces of further mono- and hexachlorobiphenyls. Among these were PCB-28, PCB-52, PCB 101, and PCB-118 (identified by seven key congeners standard). The mixture resembled industrial products Clophen A30 or Aroclor 1016. Metabolic turnover of applied (14)C-PCB-Mix (15 μg/assay) was 30% after 96 h; 8.4% of non-extractable residues emerged. Using DDE (p,p'-dichlorodiphenyl-dichloroethylene) as internal standard it was demonstrated that biphenyl, one monochloro-, two dichloro-, and one trichlorobiphenyl were completely metabolized to polar products. Partial metabolization occurred with one di-, five tri-, and four tetrachlorobiphenyls. Two tri-, four tetra-, and all pentachlorbiphenyls proved to be stable. Due to strong interference by matrix, evaluation of three congeners was not possible. In addition to wheat, results of similar experiments with cell cultures of other species are briefly mentioned.

Prospects for using combined engineered bacterial enzymes and plant systems to rhizoremediate polychlorinated biphenyls

The fate of polychlorinated biphenyls (PCBs) in soil is driven by a combination of interacting biological processes. Several investigations have brought evidence that the rhizosphere provides a remarkable ecological niche to enhance the PCB degradation process by rhizobacteria. The bacterial oxidative enzymes involved in PCB degradation have been investigated extensively and novel engineered enzymes exhibiting enhanced catalytic activities toward more persistent PCBs have been described. Furthermore, recent studies suggest that approaches involving processes based on plant-microbe associations are very promising to remediate PCB-contaminated sites. In this review emphasis will be placed on the current state of knowledge regarding the strategies that are proposed to engineer the enzymes of the PCB-degrading bacterial oxidative pathway and to design PCB-degrading plant-microbe systems to remediate PCB-contaminated soil.

Metabolites of 2,2'-dichlorobiphenyl and 2,6-dichlorobiphenyl in hairy root culture of black nightshade Solanum nigrum SNC-9O

The hairy root culture of black nightshade (Solanum nigrum) SNC-9O was exposed to 2,2'-dichlorobiphenyl (PCB 4) and 2,6-dichlorobiphenyl (PCB 10) to follow the metabolites produced. The analytical standards of 4-hydroxy-2,2'-dichlorobiphenyl, 5'-hydroxy-2,2'-dichlorobiphenyl, 4-hydroxy-2,6-dichlorobiphenyl, 2-hydroxy-2',6'-dichlorobiphenyl, 3-hydroxy-2',6'-dichlorobiphenyl and 4-hydroxy-2',6'-dichlorobiphenyl have been synthesized. Hydroxy-metabolites of both PCB 4 and PCB 10 were present in the biomass. These appeared mainly as conjugates rather than as free hydroxy-PCBs, both maintained in plant cells. The concentrations of non-conjugated hydroxy-PCBs ranged between 0.9 and 35.2 μg kg(-1) of biomass fresh weight and the concentration of the conjugated ones ranged between 2.0 and 113.0 μg kg(-1) depending on the position of hydroxyl. The para- position of biphenyl (4 or 4') seems to be preferred for hydroxylation. Methoxy-PCBs and hydroxy-methoxy-PCBs have also been identified in plant cells. Hydroxyl in the meta-position (3, 3', 5 or 5') appears to be preferred for methylation in hydroxy-PCBs. Hydroxy-methoxy-PCBs have occurred in the conjugated form as well.

Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation

Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.

Phylogenetic analysis reveals the surprising diversity of an oxygenase class

As metalloenzymes capable of transforming a broad range of substrates with high stereo- and regio-specificity, the multicomponent Rieske oxygenases (ROs) have been studied in bacterial systems for applications in bioremediation and industrial biocatalysis. These studies include genetic and biochemical investigations, determination of enzyme structure, phylogenetic analysis, and enzyme classification. Although RO terminal oxygenase components (RO-Os) share a conserved domain structure, their sequences are highly divergent and present significant challenges for identification and classification. Herein, we present the first global phylogenetic analysis of a broad range of RO-Os from diverse taxonomic groups. We employed objective, structure-based criteria to significantly reduce the inclusion of erroneously aligned sequences in the analysis. Our findings reveal that RO biochemical studies to date have been largely concentrated in an unexpectedly narrow portion of the RO-O sequence landscape. Additionally, our analysis demonstrates the existence two distinct groups of RO-O sequences. Finally, the sequence diversity recognized in this study necessitates a new RO-O classification scheme. We therefore propose a P450-like naming system. Our results reveal a diversity of sequence and potential catalytic functionality that has been wholly unappreciated in the RO literature. This study also demonstrates that many commonly used bioinformatic tools may not be sufficient to analyze the vast amount of data available in current databases. These findings facilitate the expanded exploration of RO catalytic capabilities in both biological and technological contexts and increase the potential for practical exploitation of their activities.

Plant exudates promote PCB degradation by a rhodococcal rhizobacteria

Rhodococcus erythropolis U23A is a polychlorinated biphenyl (PCB)-degrading bacterium isolated from the rhizosphere of plants grown on a PCB-contaminated soil. Strain U23A bphA exhibited 99% identity with bphA1 of Rhodococcus globerulus P6. We grew Arabidopsis thaliana in a hydroponic axenic system, collected, and concentrated the plant secondary metabolite-containing root exudates. Strain U23A exhibited a chemotactic response toward these root exudates. In a root colonizing assay, the number of cells of strain U23A associated to the plant roots (5.7 × 10⁵ CFU g⁻¹) was greater than the number remaining in the surrounding sand (4.5 × 10⁴ CFU g⁻¹). Furthermore, the exudates could support the growth of strain U23A. In a resting cell suspension assay, cells grown in a minimal medium containing Arabidopsis root exudates as sole growth substrate were able to metabolize 2,3,4'- and 2,3',4-trichlorobiphenyl. However, no significant degradation of any of congeners was observed for control cells grown on Luria-Bertani medium. Although strain U23A was unable to grow on any of the flavonoids identified in root exudates, biphenyl-induced cells metabolized flavanone, one of the major root exudate components. In addition, when used as co-substrate with sodium acetate, flavanone was as efficient as biphenyl to induce the biphenyl catabolic pathway of strain U23A. Together, these data provide supporting evidence that some rhodococci can live in soil in close association with plant roots and that root exudates can support their growth and trigger their PCB-degrading ability. This suggests that, like the flagellated Gram-negative bacteria, non-flagellated rhodococci may also play a key role in the degradation of persistent pollutants.

[Advance in bioremediation of polychlorinated biphenyls]

As one of the persistent organic pollutants, polychlorinated biphenyls are harmful to the environment and humans. Biodegradation is the most potential way to remove PCBs. Biodegradation can mainly be divided into microbial degradation, phytoremediation, plant and microbial combined remediation. Here, we introduced isolation of the PCBs-degrading strains, cloning and modification of the related degradation genes. Additionally, on the other hand, the natural remediation of plant, plant and microbial combined remediation, plant transgenic remediation were described.

Cloning the bacterial bphC gene into Nicotiana tabacum to improve the efficiency of phytoremediation of polychlorinated biphenyls

The aim of this work was to construct transgenic plants with increased capabilities to degrade organic pollutants, such as polychlorinated biphenyls. The environmentally important gene of bacterial dioxygenase, the bphC gene, was chosen to clone into a plant of Nicotiana tabacum. The chosen bphC gene encodes 2,3-dihydroxybiphenyl-1,2-dioxygenase, which cleaves the aromatic ring of dihydroxybiphenyl, and we cloned it in fusion with the gene for β-glucuronidase (GUS), luciferase (LUC) or with a histidine tail. Several genetic constructs were designed and prepared and the possible expression of desired proteins in tobacco plants was studied by transient expression. We used genetic constructs successfully expressing dioxygenase's genes we used for preparation of transgenic tobacco plants by agrobacterial infection. The presence of transgenic DNA , mRNA and protein was determined in parental and the first filial generation of transgenic plants with the bphC gene. Properties of prepared transgenic plants will be further studied.

Phytoremediation of polychlorinated biphenyls: new trends and promises

Transgenic plants and associated bacteria constitute a new generation of genetically modified organisms for efficient and environment-friendly treatment of soil and water contaminated with polychlorinated biphenyls (PCBs). This review focuses on recent advances in phytoremediation for the treatment of PCBs, including the development of transgenic plants and associated bacteria. Phytoremediation, or the use of higher plants for rehabilitation of soil and groundwater, is a promising strategy for cost-effective treatment of sites contaminated by toxic compounds, including PCBs. Plants can help mitigate environmental pollution by PCBs through a range of mechanisms: besides uptake from soil (phytoextraction), plants are capable of enzymatic transformation of PCBs (phytotransformation); by releasing a variety of secondary metabolites, plants also enhance the microbial activity in the root zone, improving biodegradation of PCBs (rhizoremediation). However, because of their hydrophobicity and chemical stability, PCBs are only slowly taken up and degraded by plants and associated bacteria, resulting in incomplete treatment and potential release of toxic metabolites into the environment. Moreover, naturally occurring plant-associated bacteria may not possess the enzymatic machinery necessary for PCB degradation. To overcome these limitations, bacterial genes involved in the metabolism of PCBs, such as biphenyl dioxygenases, have been introduced into higher plants, following a strategy similar to the development of transgenic crops. Similarly, bacteria have been genetically modified that exhibit improved biodegradation capabilities and are able to maintain stable relationships with plants. Transgenic plants and associated bacteria bring hope for a broader and more efficient application of phytoremediation for the treatment of PCBs.

Phyto/rhizoremediation studies using long-term PCB-contaminated soil

PURPOSE

Polychlorinated biphenyls (PCBs) represent a large group of recalcitrant environmental pollutants, differing in the number of chlorine atoms bound to biphenyl ring. Due to their excellent technological properties, PCBs were used as heat-transfer media, for filling transformers and condensers, as paint additives, etc. With increasing knowledge of their toxicity, transfer to food chains and accumulation in living organisms, their production ended in most countries in the 1970s and in 1984 in the former Czechoslovakia. But even a quarter of century after the PCB production ceased, from contaminated areas, the volatile PCBs evaporate and contaminate much larger areas even at very distant parts of the world. For this reason, PCBs still represent a global problem. The main method of PCB removal from contaminated environment is at present the expensive incineration at high temperatures. With the aim of finding effective alternative approaches, we are studying biological methods for PCB removal from the environment. In this paper, we summarise 10 years of studies using long-term PCB-contaminated soil from a dumpsite in South Bohemia, targeted for the use of plants (phytoremediation) and their cooperation with microorganisms in the root zone (rhizoremediation).

MATERIALS AND METHODS

Long-term contaminated soil from Lhenice dumpsite, more than hundred kilograms of homogenised material, was used in microcosms (pots and buckets), and field plots were established at the site. Tested plants include among others tobacco, black nightshade, horseradish, alfalfa and willow. Aseptic plant cell and tissue cultures were from the collection of the IOCB. Microorganisms were our own isolates. The paper summarises experiments done between 1998 and 2008 with real contaminated soil, both vegetated and non-vegetated. PCB analysis was performed by GC-ECD, metabolic products identified mostly using 2D-GC/MS-MS and synthetic standards, whereas molecular methods included quantitative PCR and sequencing.

RESULTS

The soil was used both for preparation of field plots at the site and for greenhouse and laboratory tests in microcosms. The results include analyses of changes in PCB content in untreated and vegetated soil, PCB uptake and distribution in different parts of various plant species, analysis of products formed, identification and characterisation of cultivable and non-cultivable bacteria both in rhizosphere and in bulk soil. Different treatments and amendments were also tested. Experiments in real contaminated soil were accompanied by in vitro experiments using aseptic cultures of plant biomass, genetically modified (GM) plants and bacteria, to allow identification of players responsible for PCB metabolisation in soil. The time-span of the experiments allows extrapolating some of the results and drawing conclusions concerning the effectivity of exploitation of various plant species and treatments to remove PCBs from soils.

DISCUSSION

The approach using plants proved to represent a viable alternative to costly incineration of PCB-contaminated soils. The recent studies using molecular methods show that plants are responsible for the composition of consortia of microorganisms present in their root zone, including those with ability to degrade the chlorinated aromatic compounds.

CONCLUSIONS

In addition to uptake, accumulation and partial metabolisation of PCBs by plants, compounds produced by plants allow survival of microorganisms even in poor soils, serve as carbon and energy source, and can even induce the degradation pathways of different xenobiotics. Thus, the choice of proper plant species is crucial for effective cleaning of different polluted sites. Our study shows how the efficiency of PCB removal is dependent on the plant used.

RECOMMENDATIONS AND PERSPECTIVES

The use of plants in biological remediation of different organic xenobiotics proved to be a useful approach. Further improvement can be expected by application of specifically tailored GM plants and use of selective conditions ensuring high remediation potential based on optimal composition of the soil microbial consortia designed for the needs of given site.

Plant-associated bacterial degradation of toxic organic compounds in soil

A number of toxic synthetic organic compounds can contaminate environmental soil through either local (e.g., industrial) or diffuse (e.g., agricultural) contamination. Increased levels of these toxic organic compounds in the environment have been associated with human health risks including cancer. Plant-associated bacteria, such as endophytic bacteria (non-pathogenic bacteria that occur naturally in plants) and rhizospheric bacteria (bacteria that live on and near the roots of plants), have been shown to contribute to biodegradation of toxic organic compounds in contaminated soil and could have potential for improving phytoremediation. Endophytic and rhizospheric bacterial degradation of toxic organic compounds (either naturally occurring or genetically enhanced) in contaminated soil in the environment could have positive implications for human health worldwide and is the subject of this review.