Risk mitigation of genetically modified bacteria and plants designed for bioremediation

While the possible advantages of bioremediation and phytoremediation, by both recombinant microbes and plants, have been extensively reviewed, the biosafety concerns have been less extensively treated. This article reviews the possible risks associated with the use of recombinant bacteria and plants for bioremediation, with particular emphasis on ways in which molecular genetics could contribute to risk mitigation. For example, genetic techniques exist that permit the site-specific excision of unnecessary DNA, so that only the transgenes of interest remain. Other mechanisms exist whereby the recombinant plants or bacteria contain conditional suicide genes that may be activated under certain conditions. These methods act to prevent the spread and survival of the transgenic bacteria or plants in the environment, and to prevent horizontal gene flow to wild or cultivated relatives. Ways in which these genetic technologies may be applied to risk mitigation in bioremediation and phytoremediation are discussed.     

Expression analysis in response to low temperature stress in blood oranges: implication of the flavonoid biosynthetic pathway

This minireview explores the environmental bioremediation mediated by genetically engineered (GE) bacteria and it also highlights the limitations and challenges associated with the release of engineered bacteria in field conditions. Application of GE bacteria based remediation of various heavy metal pollutants is in the forefront due to eco-friendly and lesser health hazards compared to physico-chemical based strategies, which are less eco-friendly and hazardous to human health. A combination of microbiological and ecological knowledge, biochemical mechanisms and field engineering designs would be an essential element for successful in situ bioremediation of heavy metal contaminated sites using engineered bacteria. Critical research questions pertaining to the development and implementation of GE bacteria for enhanced bioremediation have been identified and poised for possible future research. Genetic engineering of indigenous microflora, well adapted to local environmental conditions, may offer more efficient bioremediation of contaminated sites and making the bioremediation more viable and eco-friendly technology. However, many challenges are to be addressed concerning the release of genetically engineered bacteria in field conditions. There are possible risks associated with the use of GE bacteria in field condition, with particular emphasis on ways in which molecular genetics could contribute to the risk mitigation. Both environmental as well as public health concerns need to be addressed by the molecular biologists. Although bioremediation of heavy metals by using the genetically engineered bacteria has been extensively reviewed in the past also, but the bio-safety assessment and factors of genetic pollution have been never the less ignored.     

Endophyte-assisted phytoremediation: mechanisms and current application strategies for soil mixed pollutants

Abstract

Phytoremediation uses plants and associated microbes to remove pollutants from the environment and is considered a promising bioremediation method. Compared with well-described single contaminant treatments, the number of studies reporting phytoremediation of soil mixed pollutants has increased recently. Endophytes, including bacteria and fungi, exhibit beneficial traits for the promotion of plant growth, stress alleviation, and biodegradation. Moreover, endophytes either directly or indirectly assist host plants to survive high concentrations of organic and inorganic pollutants in the soil. Endophytic microorganisms can also regulate the plant metabolism in different ways, exhibiting a variety of physiological characteristics. This review summarizes the taxa and physiological properties of endophytic microorganisms that may participate in the detoxification of contaminant mixtures. Furthermore, potential biomolecules that may enhance endophyte mediated phytoremediation are discussed. The practical applications of pollutant-degrading endophytes and current strategies for applying this valuable bio-resource to soil phytoremediation are summarized.     

有机磷生物修复研究进展

目前,有机磷的生物修复还主要是微生物修复。但是植物修复更具优越性,因其花费更少、对环境更安全。然而植物对生长条件的要求相对较高,修复效率较低,应用还非常有限。本文综述了有机磷微生物修复和植物修复的研究进展,总结了已知的有机磷降解酶及其生物来源。结果表明,植物材料的筛选、土壤与OPs作用机理的研究、植物耐受和消除OPs的基因组学研究、植物-微生物联合降解体系的建立以及降解酶的植物根系分泌系统的利用是提高有机磷植物修复效率的重要途径。     

The use of transgenic plants in the bioremediation of soils contaminated with trace elements

The use of plants to clean-up soils contaminated with trace elements could provide a cheap and sustainable technology for bioremediation. Field trials suggested that the rate of contaminant removal using conventional plants and growth conditions is insufficient. The introduction of novel traits into high biomass plants in a transgenic approach is a promising strategy for the development of effective phytoremediation technologies. This has been exemplified by generating plants able to convert organic and ionic forms of mercury into the less toxic, volatile, elemental mercury, a trait that occurs naturally only in some bacteria and not at all in plants. The engineering of a phytoremediator plant requires the optimization of a number of processes, including trace element mobilization in the soil, uptake into the root, detoxification and allocation within the plant. A number of transgenic plants have been generated in an attempt to modify the tolerance, uptake or homeostasis of trace elements. The phenotypes of these plants provide important insights for the improvement of engineering strategies. A better understanding, both of micronutrient acquisition and homeostasis, and of the genetic, biochemical and physiological basis of metal hyperaccumulation in plants, will be of key importance for the success of phytoremediation.     

Engineering plants for the phytodetoxification of explosives

Summary  Widespread contaimination of the environment by explosives resulting from the manufacture, disposal and testing of munitions is becoming a matter of increasing concern. Most explosives are considered to be a major hazard to biological systems due to their toxic and mutagenic effects. Interest on the bioremediation of land contaminated with explosives has recently been focused on phytoremediation. Unfortunately., whilst plants have many advantages for the remediation of contaminated land and water, they lack the catabolic versatility which enables microorganisms to mineralize such a wide diversity of xenobiotic compounds. This raised the interesting question as to whether the impressive biodegradative capabilities of soil bacteria could be combined with the high biomass and stability of plants to yield an optimal system for in situ bioremediation of explosive residues in soil. Our investigation into the degradation of explosive residues by soil bacteria resulted in the isolation of Enterobacter cloacae PB2, which is capable of utilizing nitrate ester explosives such as pentaerythritol tetranitrate (PETN) and nitroglycerin as the sole source of nitrogen for growth. We have successfully introduced PETN reductase, the enzyme initiating explosive degradation in this organism, into plants to create transgenic plants that degrade explosives. Since the bacterial degradative pathways for many classes of organic pollutant have been elucidated, this may be a generally applicable method of achieving bioremediation of contaminated soil in the environment.     

A comprehensive overview of elements in bioremediation

Sustainable development requires the development and promotion of environmental management and a constant search for green technologies to treat a wide range of aquatic and terrestrial habitats contaminated by increasing anthropogenic activities. Bioremediation is an increasingly popular alternative to conventional methods for treating waste compounds and media with the possibility to degrade contaminants using natural microbial activity mediated by different consortia of microbial strains. Many studies about bioremediation have been reported and the scientific literature has revealed the progressive emergence of various bioremediation techniques. In this review, we discuss the various in situ and ex situ bioremediation techniques and elaborate on the anaerobic digestion technology, phytoremediation, hyperaccumulation, composting and biosorption for their effectiveness in the biotreatment, stabilization and eventually overall remediation of contaminated strata and environments. The review ends with a note on the recent advances genetic engineering and nanotechnology have had in improving bioremediation. Case studies have also been extensively revisited to support the discussions on biosorption of heavy metals, gene probes used in molecular diagnostics, bioremediation studies of contaminants in vadose soils, bioremediation of oil contaminated soils, bioremediation of contaminants from mining sites, air sparging, slurry phase bioremediation, phytoremediation studies for pollutants and heavy metal hyperaccumulators, and vermicomposting.     

Rhizoremediation: a beneficial plant-microbe interaction

Worldwide, contamination of soil and ground water is a severe problem. The negative effects of pollutants on the environment and on human health are diverse and depend on the nature of the pollution. The search for alternative methods for excavation and incineration to clean polluted sites resulted in the application of bioremediation techniques. In this review, we describe some generally accepted bioremediation tools and subsequently focus on the combination of two approaches, phytoremediation and bioaugmentation, resulting in rhizoremediation. During rhizoremediation, exudates derived from the plant can help to stimulate the survival and action of bacteria, which subsequently results in a more efficient degradation of pollutants. The root system of plants can help to spread bacteria through soil and help to penetrate otherwise impermeable soil layers. The inoculation of pollutant-degrading bacteria on plant seed can be an important additive to improve the efficiency of phytoremediation or bioaugmentation.     

金属结合蛋白基因及其在清除重金属污染中的应用

一些微生物和植物由于对毒性金属具有独特的抗性机制,使得利用它们来清除日益严重的环境污染已发展成为一种十分有效的技术——生物修复。研究表明,不同的金属结合蛋白（如MT 和PC）,在生物忍耐和降解过量重金属毒性机制中起重要作用。愈来愈多的MT 和PC基因被克隆,并已成功地应用于生物遗传转化,这些转基因生物在清除重金属污染方面已显示出潜在的应用价值。 Abstract:Heavy metal pollution has become a global environmental hazard.The use of microorganisms and plants for the decontamination of heavy metals is recognized as a low lost and high efficiency method for cleaning up metal contamination.It shows that various metal-binding proteins such as metallothioneins (MTs) or phytochelatines (PCs) play an important role in defense systems and detoxification to heavy metals in organisms.Many genes of MTs and PCs have been cloned and utilized successfully in genetically modified bacteria and plants for increasing remediation capacity.These transgenic organisms have been displayed a great potential in bioremediation and phytoremediation of heavy metals.     

Secretion and folding of human growth hormone in Escherichia coli

Abstract

Phytoremediation is the use of plants for the treatment of environmental pollution, including chlorinated organics. although conceptually very attractive, removal and biodegradation of chlorinated pollutants by plants is a rather slow and inefficient process resulting in incomplete treatment and potential release of toxic metabolites into the environment. In order to overcome inherent limitations of plant metabolic capabilities, plants have been genetically modified, following a strategy similar to the development of transgenic crops: genes from bacteria, fungi, and mammals involved in the metabolism of organic contaminants, such as cytochrome p-450 and glutathione substrate catabolic genes, natural or engineered, for the simultaneous remediation of a range of pollutants, such as usually found in contaminated sites, e.g., chlorinated solvent, metals, and nitroaromatics. In addition, biodegradation of many xenobiotics are catalyzed by similar, broad-substrate enzymes, such as cytochrome P-450 monoxygenases, glutathione S-transferases, and fungal peroxidases, that can potentially be used for the treatment of multiple pollutants. Moreover, the introduction of multiple transgenes involved in different phases of the metabolism of xenobiotics in plants, i.e., uptake by roots and the different phases of the green liver model, would allow enhancing both the removal and metabolism of several toxic compounds and could therefore help overcome a major limitation inherent to phytoremediation, i.e., the threat that accumulated toxic compounds would volatilize or otherwise contaminate the food chain. An important barrier to the application of transgenic plants for bioremediation in the field is associated with the true or perceived risk of horizontal gene transfer to related wild or cultivated plants. Therefore, it is likely that the next generation of transgenic plants will involve systems preventing such a transfer, for instance by the introduction of transgenes into chloroplastic DNA or the use of conditional lethality genes (Davison, 2005). Since bacteria naturally exchange plasmids via conjugation, endophytes that gain genes involved in pollutant degradation might not be considered ‘genetically modified’ and may be subject to fewer restrictions in usage.     

Use of Genetically Engineered Microorganisms (GEMs) for the Bioremediation of Contaminants

ABSTRACT

This paper presents a critical review of the literature on the application of genetically engineered microorganisms (GEMs) in bioremediation. The important aspects of using GEMs in bioremediation, such as development of novel strains with desirable properties through pathway construction and the modification of enzyme specificity and affinity, are discussed in detail. Particular attention is given to the genetic engineering of bacteria using bacterial hemoglobin (VHb) for the treatment of aromatic organic compounds under hypoxic conditions. The application of VHb technology may advance treatment of contaminated sites, where oxygen availability limits the growth of aerobic bioremediating bacteria, as well as the functioning of oxygenases required for mineralization of many organic pollutants. Despite the many advantages of GEMs, there are still concerns that their introduction into polluted sites to enhance bioremediation may have adverse environmental effects, such as gene transfer. The extent of horizontal gene transfer from GEMs in the environment, compared to that of native organisms including benefits regarding bacterial bioremediation that may occur as a result of such transfer, is discussed. Recent advances in tracking methods and containment strategies for GEMs, including several biological systems that have been developed to detect the fate of GEMs in the environment, are also summarized in this review. Critical research questions pertaining to the development and implementation of GEMs for enhanced bioremediation have been identified and posed for possible future research.     

Harnessing plant-bacteria-fungi interactions to improve plant growth and degradation of organic pollutants

Exploiting the potential of bacteria in phytoremediation for the removal of organic and inorganic pollutants from soils and (ground)water holds great promise. Besides bacteria, mycorrhizal fungi and free-living saprotrophs are well known for their strong degradative capacities and plant growth promotion effects, which makes them of high interest for use in different bioremediation strategies. To further increase the efficiency and successes of phytoremediation, interactions between plants and their associated microorganisms, both bacteria and fungi, should be further investigated, in addition to the close interactions between bacteria and fungi. Benefitting from an increased understanding of microbial community structure and assembly allows us to better understand how the holobiont can be modified to improve pollutant degradation and plant growth. In this review, we present an overview of insights in plant-bacteria-fungi interactions and the opportunities of exploiting these tripartite interactions to enhance the effectiveness of phytoremediation of organic pollutants.     

Arbuscular Mycorrhizae Effects on Heavy Metal Uptake by Corn

Maximizing uptake of soil-borne metals into plants is important for successful phytoremediation. Arbuscular mycorrhizae (AM) have been shown previously by our group to sequester metals in the roots of plants and prevent translocation to the shoot. If AM colonization of roots can be reduced, it may be possible to increase metal uptake into plants, thus increasing the efficiency of phytoremediation. The fungicide Benomy® was applied to a Pb-contaminated soil and seeded to corn (Zea mays). Because soil pH affects metal solubility, two pHs were also examined. Colonization of roots by AM was significantly decreased by application of Benomyl to soil, but only at the higher soil pH. Benomyl increased the concentration of several elements, including Pb, in shoots. However, the total Pb content in the shoot decreased due to the reduced shoot weight associated with Benomyl application.

     

Suitability of aromatic plants for phytoremediation of heavy metal contaminated areas: a review

Abstract

This review briefly elucidates the research undertaken and benefits of using aromatic plants for remediation of heavy metal polluted sites. A sustainable approach to mitigate heavy metal contamination of environment is need of the hour. Phytoremediation has emerged to be one of the most preferable choices for combating the metal pollution problem. Aromatic plants can be used for remediation of contaminated sites as they are non-food crops thus minimizing the risk of food chain contamination. Most promising aromatic plants for phytoremediation of heavy metal contaminated sites have been identified from families – Poaceae, Lamiaceae, Asteraceae, and Geraniaceae. They act as potential phytostabilisers, hyper accumulators, bio-monitors, and facultative metallophytes. Being high value economic crops, monetary benefits can be obtained by growing them in tainted areas instead of food crops. It has been observed that heavy metal stress enhances the essential oil percentage of certain aromatic crops. Research conducted on some major aromatic plants in this context has been highlighted in the present review which suggests that aromatic plants hold a great potential for phytoremediation. It has been reported that essential oil from aromatic crops is not contaminated by heavy metals significantly. Thus, aromatic plants are emerging as an ideal candidate for phytoremediation.

Highlights

? Aromatic plants hold a great potential for phytoremediation of heavy metal contaminated sites.

? Being high value economic crops, monetary benefits can be obtained by growing them in contaminated areas instead of food crops.

? Research done on some major aromatic plants in this context has been highlighted in the present review.     

Phytoremediation—A Novel and Promising Approach for Environmental Clean-up

ABSTRACT

Phytoremediation is an eco friendly approach for remediation of contaminated soil and water using plants. Phytoremediation is comprised of two components, one by the root colonizing microbes and the other by plants themselves, which degrade the toxic compounds to further non-toxic metabolites. Various compounds, viz. organic compounds, xenobiotics, pesticides and heavy metals, are among the contaminants that can be effectively remediated by plants. Plant cell cultures, hairy roots and algae have been studied for their ability to degrade a number of contaminants. They exhibit various enzymatic activities for degradation of xenobiotics, viz. dehalogenation, denitrification leading to breakdown of complex compounds to simple and non-toxic products. Plants and algae also have the ability to hyper accumulate various heavy metals by the action of phytochelatins and metallothioneins forming complexes with heavy metals and translocate them into vacuoles. Molecular cloning and expression of heavy metal accumulator genes and xenobiotic degrading enzyme coding genes resulted in enhanced remediation rates, which will be helpful in making the process for large-scale application to remediate vast areas of contaminated soils. A few companies worldwide are also working on this aspect of bioremediation, mainly by transgenic plants to replace expensive physical or chemical remediation techniques. Selection and testing multiple hyperaccumulator plants, protein engineering of phytochelatin and membrane transporter genes and their expression would enhance the rate of phytoremediation, making this process a successful one for bioremediation of environmental contamination. Recent years have seen major investments in the R&D, which have also resulted in competition of filing patents by several companies for economic gains. The details of science & technology related to phytoremediation have been discussed with a focus on future trends and prospects of global relevance.     

Endophytic microorganisms—promising applications in bioremediation of greenhouse gases

Bioremediation is a technique that uses microbial metabolism to remove pollutants. Various techniques and strategies of bioremediation (e.g., phytoremediation enhanced by endophytic microorganisms, rhizoremediation) can mainly be used to remove hazardous waste from the biosphere. During the last decade, this specific technique has emerged as a potential cleanup tool only for metal pollutants. This situation has changed recently as a possibility has appeared for bioremediation of other pollutants, for instance, volatile organic compounds, crude oils, and radionuclides. The mechanisms of bioremediation depend on the mobility, solubility, degradability, and bioavailability of contaminants. Biodegradation of pollutions is associated with microbial growth and metabolism, i.e., factors that have an impact on the process. Moreover, these factors have a great influence on degradation. As a result, recognition of natural microbial processes is indispensable for understanding the mechanisms of effective bioremediation. In this review, we have emphasized the occurrence of endophytic microorganisms and colonization of plants by endophytes. In addition, the role of enhanced bioremediation by endophytic bacteria and especially of phytoremediation is presented.     

Influence of biochar and compost on phytoremediation of oil-contaminated soil

The use of pyrolyzed carbon, biochar, as a soil amendment is of potential interest for improving phytoremediation of soil that has been contaminated by petroleum hydrocarbons. To examine this question, the research reported here compared the effects of biochar, plants (mesquite tree seedlings), compost and combinations of these treatments on the rate of biodegradation of oil in a contaminated soil and the population size of oil-degrading bacteria. The presence of mesquite plants significantly enhanced oil degradation in all treatments except when biochar was used as the sole amendment without compost. The greatest extent of oil degradation was achieved in soil planted with mesquite and amended with compost (44% of the light hydrocarbon fraction). Most probable number assays showed that biochar generally reduced the population size of the oil-degrading community. The results of this study suggest that biochar addition to petroleum-contaminated soils does not improve the rate of bioremediation. In contrast, the use of plants and compost additions to soil are confirmed as important bioremediation technologies.     

Phytoremediation of toxic trace elements in soil and water

Toxic heavy metals and metalloids, such as cadmium, lead, mercury, arsenic, and selenium, are constantly released into the environment. There is an urgent need to develop low-cost, effective, and sustainable methods for their removal or detoxification. Plant-based approaches, such as phytoremediation, are relatively inexpensive since they are performed in situ and are solar-driven. In this review, we discuss specific advances in plant-based approaches for the remediation of contaminated water and soil. Dilute concentrations of trace element contaminants can be removed from large volumes of wastewater by constructed wetlands. We discuss the potential of constructed wetlands for use in remediating agricultural drainage water and industrial effluent, as well as concerns over their potential ecotoxicity. In upland ecosystems, plants may be used to accumulate metals/metalloids in their harvestable biomass (phytoextraction). Plants can also convert and release certain metals/metalloids in a volatile form (phytovolatilization). We discuss how genetic engineering has been used to develop plants with enhanced efficiencies for phytoextraction and phytovolatilization. For example, metal-hyperaccumulating plants and microbes with unique abilities to tolerate, accumulate, and detoxify metals and metalloids represent an important reservoir of unique genes that could be transferred to fast-growing plant species for enhanced phytoremediation. There is also a need to develop new strategies to improve the acceptability of using genetically engineered plants for phytoremediation.

     

Using soil bacteria to facilitate phytoremediation

In the past twenty years or so, researchers have endeavored to utilize plants to facilitate the removal of both organic and inorganic contaminants from the environment, especially from soil. These phytoremediation approaches have come a long way in a short time. However, the majority of this work has been done under more controlled laboratory conditions and not in the field. As an adjunct to various phytoremediation strategies and as part of an effort to make this technology more efficacious, a number of scientists have begun to explore the possibility of using various soil bacteria together with plants. These bacteria include biodegradative bacteria, plant growth-promoting bacteria and bacteria that facilitate phytoremediation by other means. An overview of bacterially assisted phytoremediation is provided here for both organic and metallic contaminants, with the intent of providing some insight into how these bacteria aid phytoremediation so that future field studies might be facilitated.     

Phytoremediation of Light Crude Oil by Maize (Zea mays L.) Bio-Augmented with Plant Growth Promoting Bacteria

The aim of this study was to evaluate the converged effect of maize and plant growth promoting bacteria on degradation of petroleum hydrocarbons under axenic conditions. Artificially spiked sand with 10 g kg^?1 light crude oil was planted with maize alone and in combination with eight bacterial isolates having plant growth promotion and bioremediation potential to observe the dissipation of petroleum hydrocarbons. Results showed remarkable suppression of maize growth and biomass production due to phytotoxicity of the crude oil contamination. However, bio-augmentation of plants with bacteria having ACC-deaminase activity significantly compensated the reduction in plant growth compared to uninoculated plants. The results revealed that plants bio-augmented with PM32Y exhibited significant increase in root length (75%), plant height (74%), and biomass (67%) as compared to uninoculated plants after 60 days of planting. The same bacterium in convergence with maize caused 43% degradation of petroleum hydrocarbons as compared to the unplanted and uninoculated control. Amplification, sequencing and phylogenetic analysis of 16S rRNA gene sequence identified PM32Y bacterium as Bacillus subtilis strain. It is concluded that bio-augmentation of plants with plant growth promoting bacteria having bioremediation potential and ACC-deaminase activity can successfully be used in phytoremediation of petroleum hydrocarbons.