Bacterial diversity and reductive dehalogenase redundancy in a 1,2-dichloroethane-degrading bacterial consortium enriched from a contaminated aquifer

Background  

Bacteria possess a reservoir of metabolic functionalities ready to be exploited for multiple purposes. The use of microorganisms to clean up xenobiotics from polluted ecosystems (e.g. soil and water) represents an eco-sustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and accurate strategies for monitoring and identification of bacteria and catabolic genes involved in the degradation of xenobiotics, key processes to follow up the activities in situ.     

Recent developments in biodegradation of industrial pollutants by white rot fungi and their enzyme system

Increasing discharge and improper management of liquid and solid industrial wastes have created a great concern among industrialists and the scientific community over their economic treatment and safe disposal. White rot fungi (WRF) are versatile and robust organisms having enormous potential for oxidative bioremediation of a variety of toxic chemical pollutants due to high tolerance to toxic substances in the environment. WRF are capable of mineralizing a wide variety of toxic xenobiotics due to non-specific nature of their extracellular lignin mineralizing enzymes (LMEs). In recent years, a lot of work has been done on the development and optimization of bioremediation processes using WRF, with emphasis on the study of their enzyme systems involved in biodegradation of industrial pollutants. Many new strains have been identified and their LMEs isolated, purified and characterized. In this review, we have tried to cover the latest developments on enzyme systems of WRF, their low molecular mass mediators and their potential use for bioremediation of industrial pollutants.     

Biodegradation of nitroaromatics and other nitrogen-containing xenobiotics

Nitroaromatic compounds constitute a major class of widely distributed environmental contaminants. Compounds like nitrobenzene, nitrotoluenes, nitrophenols, nitrobenzoates and nitrate esters are of considerable industrial importance. They are frequently used as pesticides, explosives, dyes, and in the manufacture of polymers and pharmaceuticals. Many nitroaromatic compounds and their conversion products have been shown to have toxic or mutagenic properties. Most of them are biodegradable in nature by various microorganisms. However, most contaminated environments have combinations of nitroaromatic compounds present, which complicates the bioremediation efforts. During the last 10 years, research on the biodegradation of nitroaromatic compounds has yielded a wealth of information on the microbiological, biochemical and genetic aspects of the process. New metabolic pathways have been discovered and genes and enzymes responsible for key transformation reactions have been identified and characterized. Knowledge and advances in pathway engineering have helped further understanding of the nature of nitroaromatic biodegradation and the development of bioremediation solutions. In this paper, an overview of recent developments on the biodegradation of nitrogen-containing xenobiotics is presented.     

Marine bacteria: potential candidates for enhanced bioremediation

Bacteria are widespread in nature as they can adapt to any extreme environmental conditions and perform various physiological activities. Marine environments are one of the most adverse environments owing to their varying nature of temperature, pH, salinity, sea surface temperature, currents, precipitation regimes and wind patterns. Due to the constant variation of environmental conditions, the microorganisms present in that environment are more suitably adapted to the adverse conditions, hence, possessing complex characteristic features of adaptation. Therefore, the bacteria isolated from the marine environments are supposed to be better utilized in bioremediation of heavy metals, hydrocarbon and many other recalcitrant compounds and xenobiotics through biofilm formation and production of extracellular polymeric substances. Many marine bacteria have been reported to have bioremediation potential. The advantage of using marine bacteria for bioremediation in situ is the direct use of organisms in any adverse conditions without any genetic manipulation. This review emphasizes the utilization of marine bacteria in the field of bioremediation and understanding the mechanism behind acquiring the characteristic feature of adaptive responses.     

Phytoremediation--a novel and promising approach for environmental clean-up

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 ofphytochelatin 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.     

白腐菌的研究进展及其在重金属修复中的展望

白腐菌是一类特殊的丝状真菌,能降解多种污染物质,具有广谱、彻底、高效、无专一性的 特点,在生物修复中有广阔的应用前景。综述了白腐菌的分类、酶系、降解机理以及应用于有机 物污染的研究现状,特别介绍了白腐菌在重金属污染的生物修复的应用进展情况,包括白腐菌吸 附重金属的原理、在重金属污染的废水中的研究应用现状及在修复重金属污染土壤中需考虑的 因素。同时展望了白腐菌在重金属污染及复合污染的生物修复中的应用前景。     

Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics

Increasing pollution of water and soils by xenobiotic compounds has led in the last few decades to an acute need for understanding the impact of toxic compounds on microbial populations, the catabolic degradation pathways of xenobiotics and the set-up and improvement of bioremediation processes. Recent advances in molecular techniques, including high-throughput approaches such as microarrays and metagenomics, have opened up new perspectives and pointed towards new opportunities in pollution abatement and environmental management. Compared with traditional molecular techniques dependent on the isolation of pure cultures in the laboratory, microarrays and metagenomics allow specific environmental questions to be answered by exploring and using the phenomenal resources of uncultivable and uncharacterized micro-organisms. This paper reviews the current potential of microarrays and metagenomics to investigate the genetic diversity of environmentally relevant micro-organisms and identify new functional genes involved in the catabolism of xenobiotics.     

Mechanisms Prevalent during Bioremediation of Wastewaters from the Pulp and Paper Industry

Bioremediation of wastewaters represents an important treatment methodology, especially when examined against the backdrop of ever-stricter legislation that is evolving in order to regulate effluent release into the environment. It has been reported that bioremediation specifically holds promise in solving environmental problems. Crucial questions surrounding the treatment of effluents include: efficiency of the process, economic feasibility, legal requirements, and the mechanisms involved in the remediation process. Of all these issues mentioned, the last requires special attention. This paper investigates these matters and focuses on techniques that are currently employed to determine the efficiency of bioremediation and mechanisms involved therein. The physiological significance of biosorption is also examined, as this subject has not been fully addressed in previous publications.     

Mechanisms prevalent during bioremediation of wastewaters from the pulp and paper industry

Bioremediation of wastewaters represents an important treatment methodology, especially when examined against the backdrop of ever-stricter legislation that is evolving in order to regulate effluent release into the environment. It has been reported that bioremediation specifically holds promise in solving environmental problems. Crucial questions surrounding the treatment of effluents include: efficiency of the process, economic feasibility, legal requirements, and the mechanisms involved in the remediation process. Of all these issues mentioned, the last requires special attention. This paper investigates these matters and focuses on techniques that are currently employed to determine the efficiency of bioremediation and mechanisms involved therein. The physiological significance of biosorption is also examined, as this subject has not been fully addressed in previous publications.     

固态发酵技术在资源环境中的应用

发酵工程是生物技术的瓶颈,固态发酵作为发酵工程一个重要的部分,在资源环境应用研究方面取得了重要进展,主要表现在生物燃料,生物农药,生物转化,生物解毒及生物修复等领域,解决了能源危机,治理环境污染等问题,综述了近几年固态发酵技术在资源环境领域应用中一些重要的发展。     

Bioremediation through microbes: systems biology and metabolic engineering approach

Today, environmental pollution is a serious problem, and bioremediation can play an important role in cleaning contaminated sites. Remediation strategies, such as chemical and physical approaches, are not enough to mitigate pollution problems because of the continuous generation of novel recalcitrant pollutants due to anthropogenic activities. Bioremediation using microbes is an eco-friendly and socially acceptable alternative to conventional remediation approaches. Many microbes with a bioremediation potential have been isolated and characterized but, in many cases, cannot completely degrade the targeted pollutant or are ineffective in situations with mixed wastes. This review envisages advances in systems biology (SB), which enables the analysis of microbial behavior at a community level under different environmental stresses. By applying a SB approach, crucial preliminary information can be obtained for metabolic engineering (ME) of microbes for their enhanced bioremediation capabilities. This review also highlights the integrated SB and ME tools and techniques for bioremediation purposes.     

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.     

我国污染土壤生物修复技术的发展及现状

本文简要回顾了近30年来我国污染土壤生物修复技术的发展过程,主要包括生物修复技术在我国的发展阶段、生物修复的4大类型及其所适用对象与范围、生物修复用菌株的筛选与特性研究、活性菌株(菌剂)在典型污染土壤中的应用及其效果等,并针对土壤污染和生物修复技术的发展现状,简要讨论了未来生物修复技术的发展。     

Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed and relocated in the environment as a result of the incomplete combustion of organic matter. Many PAHs and their epoxides are highly toxic, mutagenic and/or carcinogenic to microorganisms as well as to higher systems including humans. Although various physicochemical methods have been used to remove these compounds from our environment, they have many limitations. Xenobiotic-degrading microorganisms have tremendous potential for bioremediation but new modifications are required to make such microorganisms effective and efficient in removing these compounds, which were once thought to be recalcitrant. Metabolic engineering might help to improve the efficiency of degradation of toxic compounds by microorganisms. However, efficiency of naturally occurring microorganisms for field bioremediation could be significantly improved by optimizing certain factors such as bioavailability, adsorption and mass transfer. Chemotaxis could also have an important role in enhancing biodegradation of pollutants. Here, we discuss the problems of PAH pollution and PAH degradation, and relevant bioremediation efforts.     

Conceptualizing "suicidal genetically engineered microorganisms" for bioremediation applications

Use of genetically modified microorganisms (GEMs) for pollution abatement has been limited because of risks associated with their release in the environment. Recent developments in the area of recombinant DNA technologies have paved the way for conceptualizing "suicidal genetically engineered microorganisms" (S-GEMS) to minimize such anticipated hazards and to achieve efficient and safer bioremediation of contaminated sites. Our strategy of designing a novel S-GEM is based on the knowledge of killer-anti-killer gene(s) that would be susceptible to programmed cell death after detoxification of any given contaminated site(s).     

Tolerance to Various Toxicants by Marine Bacteria Highly Resistant to Mercury

Bacteria highly resistant to mercury isolated from seawater and sediment samples were tested for growth in the presence of different heavy metals, pesticides, phenol, formaldehyde, formic acid, and trichloroethane to investigate their potential for growth in the presence of a variety of toxic xenobiotics. We hypothesized that bacteria resistant to high concentrations of mercury would have potential capacities to tolerate or possibly degrade a variety of toxic materials and thus would be important in environmental pollution bioremediation. The mercury-resistant bacteria were found to belong to Pseudomonas, Proteus, Xanthomonas, Alteromonas, Aeromonas, and Enterobacteriaceae. All these environmental bacterial strains tolerant to mercury used in this study were capable of growth at a far higher concentration (50 ppm) of mercury than previously reported. Likewise, their ability to grow in the presence of toxic xenobiotics, either singly or in combination, was superior to that of bacteria incapable of growth in media containing 5 ppm mercury. Plasmid-curing assays done in this study ascertained that resistance to mercury antibiotics, and toxic xenobiotics is mediated by chromosomally borne genes and/or transposable elements rather than by plasmids.     

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.     

Degradation of BTEX by anaerobic bacteria: physiology and application

Pollution of the environment with aromatic hydrocarbons, such as benzene, toluene, ethylbenzene and xylene (so-called BTEX) is often observed. The cleanup of these toxic compounds has gained much attention in the last decades. In situ bioremediation of aromatic hydrocarbons contaminated soils and groundwater by naturally occurring microorganisms or microorganisms that are introduced is possible. Anaerobic bioremediation is an attractive technology as these compounds are often present in the anoxic zones of the environment. The bottleneck in the application of anaerobic techniques is the lack of knowledge about the anaerobic biodegradation of benzene and the bacteria involved in anaerobic benzene degradation. Here, we review the existing knowledge on the degradation of benzene and other aromatic hydrocarbons by anaerobic bacteria, in particular the physiology and application, including results on the (per)chlorate stimulated degradation of these compounds, which is an interesting new alternative option for bioremediation.