Microbiological methods for the cleanup of soil and ground water contaminated with halogenated organic compounds

There is growing interest in the enhancement of microbial degradative activities as a means of bringing about the in situ cleanup of contaminated soils and ground water. The halogenated organic compounds are likely to be prime targets for such biotechnological processes because of their widespread utilisation and the biodegradability of many of the most commonly used compounds. The aim of this review is to consider the potential for microbiological cleanup of haloorganic-contaminated sites. The technologies available involve the provision of suitable environmental conditions to facilitate maximum biodegradation rates either in the subsurface or in on-site bioreactors. Methodologies include the supply of inorganic nutrients, the supply of oxygen gas, the addition of degradative microbial inocula and the introduction of co-metabolic substrates. The potential efficiencies and limitations of the methods are critically discussed from a microbiological viewpoint with respect to substrate degradability and population responses to supplementation.     

The environment,microbes and bioremediation: microbial activities modulated by the environment

Microorganisms in nature are largely responsible for the biodegradation and removal of toxic and non-toxic chemicals. Many organisms are also known to have specific ecological niches for proliferation and colonization. The nature of the environment dictates to a large extent the biodegradability of synthetic compounds by modulating the evolutionary processes in microorganisms for new degradative genes. Similarly, environmental factors often determine the extent of microbial gene expression by activating or repressing specific gene or sets of genes through a sensory signal transduction process. Understanding how the environment modulates microbial activity is critical for successful bioremediative applications.     

Molecular basis of biodegradation of chloroaromatic compounds

Chlorinated aromatic hydrocarbons are widely used in industry and agriculture, and comprise the bulk of environmental pollutants. Although simple aromatic compounds are biodegradable by a variety of degradative pathways, their halogenated counterparts are more resistant to bacterial attack and often necessitate evolution of novel pathways. An understanding of such evolutionary processes is essential for developing genetically improved strains capable of mineralizing highly chlorinated compounds. This article provides an overview of the genetic aspects of dissimilation of chloroaromatic compounds and discusses the potential of gene manipulation to promote enhanced evolution of the degradative pathways.     

Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances

Poly- and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today’s society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called ‘forever chemicals’ due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.     

Metabolic diversity in bacterial degradation of aromatic compounds

Aromatic compounds pose a major threat to the environment, being mutagenic, carcinogenic, and recalcitrant. Microbes, however, have evolved the ability to utilize these highly reduced and recalcitrant compounds as a potential source of carbon and energy. Aerobic degradation of aromatics is initiated by oxidizing the aromatic ring, making them more susceptible to cleavage by ring-cleaving dioxygenases. A preponderance of aromatic degradation genes on plasmids, transposons, and integrative genetic elements (and their shuffling through horizontal gene transfer) have lead to the evolution of novel aromatic degradative pathways. This enables the microorganisms to utilize a multitude of aromatics via common routes of degradation leading to metabolic diversity. In this review, we emphasize the exquisiteness and relevance of bacterial degradation of aromatics, interlinked degradative pathways, genetic and metabolic regulation, carbon source preference, and biosurfactant production. We have also explored the avenue of metagenomics, which opens doors to a plethora of uncultured and uncharted microbial genetics and metabolism that can be used effectively for bioremediation.     

Biodegradation of halogenated organic compounds.

In this review we discuss the degradation of chlorinated hydrocarbons by microorganisms, emphasizing the physiological, biochemical, and genetic basis of the biodegradation of aliphatic, aromatic, and polycyclic compounds. Many environmentally important xenobiotics are halogenated, especially chlorinated. These compounds are manufactured and used as pesticides, plasticizers, paint and printing-ink components, adhesives, flame retardants, hydraulic and heat transfer fluids, refrigerants, solvents, additives for cutting oils, and textile auxiliaries. The hazardous chemicals enter the environment through production, commercial application, and waste. As a result of bioaccumulation in the food chain and groundwater contamination, they pose public health problems because many of them are toxic, mutagenic, or carcinogenic. Although synthetic chemicals are usually recalcitrant to biodegradation, microorganisms have evolved an extensive range of enzymes, pathways, and control mechanisms that are responsible for catabolism of a wide variety of such compounds. Thus, such biological degradation can be exploited to alleviate environmental pollution problems. The pathways by which a given compound is degraded are determined by the physical, chemical, and microbiological aspects of a particular environment. By understanding the genetic basis of catabolism of xenobiotics, it is possible to improve the efficacy of naturally occurring microorganisms or construct new microorganisms capable of degrading pollutants in soil and aquatic environments more efficiently. Recently a number of genes whose enzyme products have a broader substrate specificity for the degradation of aromatic compounds have been cloned and attempts have been made to construct gene cassettes or synthetic operons comprising these degradative genes. Such gene cassettes or operons can be transferred into suitable microbial hosts for extending and custom designing the pathways for rapid degradation of recalcitrant compounds. Recent developments in designing recombinant microorganisms and hybrid metabolic pathways are discussed.     

Detection and quantification of degradative genes in soils contaminated by toluene

Abstract: A method based on the polymerase chain reaction (PCR) was developed for a rapid and specific detection of toluene degradative genes in soil. The xylE gene coding for catechol 2,3-dioxygenase was chosen as a target gene. The detection threshold was evaluated in microcosms using a sterilized standard soil inoculated with various amounts of a degradative strain of Pseudomonas putida (mX). The extracted DNA was used as a template to amplify the xylE gene. PCR followed by hybridization with an internal probe allowed us to detect 10² bacteria per g of soil. In polluted soils, quantification of target DNA by competitive PCR was compared with enumeration of degradative microflora. This molecular method appeared to be rapid, sensitive and more suitable than the microbiological approach to estimate the biodegradative potential of a polluted soil.     

Degradation of Phenol Compounds by Microbial Communities of the Amur Estuary

The microbiological transformation of various phenol compounds and their origin in the mixing zone of the Amur Estuary is considered. The results of the model experiments on the decomposition and transformation of phenol compounds by microbial communities and bacteria are reported. Self-depuration of the Amur Estuary depends on the mechanisms of the transformation of aromatic compounds in the presence of cosubstrates, the enzymatic activity of microbial communities, and the temperature. In winter, the ecological risk of pollution by aromatic compounds increases.     

重金属与农药污染的农业土壤脱毒过程研究进展

农业土壤环境自身脱毒过程是极其复杂的生态化学过程,对于土壤健康质量的维持和改善具有重要意义。然而,一直以来,人们对污染物的致毒过程研究得较多,对农业土壤自身脱毒能力及机制未给予足够重视。本文就农业土壤环境中,重金属与农药污染物的吸附脱毒、非生物降解(水解、光解)脱毒、微生物降解脱毒、土壤酶学脱毒、根际环境中的降解和转化脱毒以及植物富集固定进行了综述,并分析了各脱毒过程中所涉及到的反应机理。     

水体沉积物中微生物厌氧呼吸耦合多环芳烃降解的研究进展

多环芳烃(Polycyclic aromatic hydrocarbons,PAHs)是一种具有致癌、致畸、致突变的持久性有机污染物。本文在分析国内外主要水体沉积物中PAHs污染状况的基础上,综述了近几年有关厌氧水体沉积物中微生物以硝酸盐、Fe(III)以及硫酸盐为电子受体进行呼吸耦合PAHs降解的研究概况。此外,还总结了基于微生物的PAHs降解基因组、蛋白质组、代谢组以及菌群水平上互作网络的研究进展,以期为进一步加速PAHs污染水体沉积物原位生物修复提供科学理论参考。     

Phylogenetic diversity of microbial communities in real drinking water distribution systems

Microbial regrowth in drinking water distribution systems (DWDS) is a major concern in the water supply industry. Detailed knowledge of the microbial community in DWDS will be of great importance for assessing the microbiological risks of drinking water. The spatial heterogeneity of microbial community structures in the bulk waters of a large real DWDS was investigated using 16S rRNA clone library analysis. The results indicate that high residual chlorine in drinking water could not control microbial regrowth in DWDS. The bacterial communities in the bulk waters were spatially heterogenic, mainly composed of Alphaproteobacteria and Betaproteobacteria (or Cyanobacteria). Microorganisms from the genera Acinetobacter, Sphingomonas and Gemella were detected, implying there is microbiological risk from drinking water. This work provides new insight into microbial ecology in DWDS.     

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.     

Rhizosphere microflora of plants used for the phytoremediation of bitumen-contaminated soil

The microbial communities and their degradative potential in rhizospheres of alfalfa (Medicago sativa) and reed (Phragmites australis) and in unplanted soil in response to bitumen contamination of soil were studied in pot experiments. According to the results of fluorescence microscopy, over a period of 27 months, bitumen contamination of soil reduced the total number of microorganisms more significantly (by 75%) in unplanted than in rhizosphere soil (by 42% and 7% for reed and alfalfa, respectively) and had various effects on some important physiological groups of microorganisms such as actinomycetes as well as nitrogen-fixing, nitrifying, denitrifying, ammonifying, phosphate-solubilizing, sulphur-oxidizing, cellulolytic and hydrocarbon-degrading microorganisms. The changes in the physiological structure of the microbial community under bitumen contamination were found to hinge on not merely the presence of plants but also their type. It was noted that the rhizosphere microflora of alfalfa was less inhibited by hydrocarbon pollution and had a higher degradative potential than the rhizosphere microflora of reed.     

Adaptive responses and cellular behaviour of biphenyl-degrading bacteria toward polychlorinated biphenyls

Polychlorinated biphenyls (PCBs) are one of the most widely distributed classes of chlorinated chemicals in the environment. For cleanup of large areas of PCB-contaminated environments, bioremediation seems to be a promising approach. However, the multitude of PCB congeners, their low bioavailability and high toxicity are important factors that affect the cleanup progression. Elucidating how the PCB-degrading microorganisms involved in the process adapt to and deal with the stressing conditions caused by this class of compounds may help to improve the bioremediation process. Also specific physiological characteristics of biphenyl-utilizing bacteria involved in the degradation of PCBs may enhance their availability to these compounds and therefore contribute to a better microbial mineralization. This review will focus in the stress responses caused in aerobic biphenyl-utilizing bacteria by PCBs and its metabolic intermediates and will also analyze bacterial properties such as motility and chemotaxis, adherence to solid surfaces, biosurfactant production and biofilm development, all properties found to enhance bacteria-pollutant interaction.     

Plant--rhizosphere-microflora association during phytoremediation of PAH-contaminated soil

The capability of plants to promote the microbial degradation of pollutants in rhizosphere soil is a principal mechanism of phytoremediation of PAH-contaminated soil. The formation of a specific rhizosphere microbocenosis with a high degradative potential toward contaminants is largely determined by plant species. The comparative PAH-degradation in unplanted soil and in soil planted with reed (Phragmites australis) and alfalfa (Medicago sativa) was studied in pot experiments during 2 years. Both alfalfa and reed successfully remediated contaminated soil by degrading 74.5 and 68.7% of PAHs, respectively. The study of the rhizosphere, rhizoplane, and unplanted-soil microflora in experimental pots showed that alfalfa stimulated the rhizosphere microflora of PAH-contaminated soil more effectively than did reed. Alfalfa clearly enhanced both the total number of microorganisms (1.3 times, according to fluorescence microscopy data) and the rate of the PAH-degrading population (almost seven times, according to plate counting). The degradative potential of its rhizosphere microflora toward PAHs was higher than the degradative activity of the reed rhizosphere. This study provides relevant information for the successful application of alfalfa to phytoremediate PAH-contaminated soil.     

Enrichment and identification of polycyclic aromatic compound-degrading bacteria enriched from sediment samples

The degradation of polycyclic aromatic compounds (PACs) has been widely studied. Knowledge of the degradation of PACs by microbial populations can be utilized in the remediation of contaminated sites. To isolate and identify PAC-degrading bacteria for potential use in future bioremediation programmes, we established a series of PAC enrichments under the same experimental conditions from a single sediment sample taken from a highly polluted estuarine site. Enrichment cultures were established using the pollutants: anthracene, phenanthrene and dibenzothiophene as a sole carbon source. The shift in microbial community structure on each of these carbon sources was monitored by analysis of a time series of samples from each culture using 16S rRNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Significantly, our findings demonstrate that shifts in the constituent species within each degradative community are directly attributable to enrichment with different PACs. Subsequently, we characterized the microorganisms comprising the degradative communities within each enrichment using 16S rRNA sequence data. Our findings demonstrate that the ability to degrade PACs is present in five divisions of the Proteobacteria and Actinobacteria. By determining the precise identity of the PAC-degrading bacterial species isolated from a single sediment sample, and by comparing our findings with previously published research, we demonstrate how bacteria with similar PAC degrading capabilities and 16S rRNA signatures are found in similarly polluted environments in geographically very distant locations, e.g., China, Italy, Japan and Hawaii. Such a finding suggests that geographical barriers do not limit the distribution of key PAC-degrading bacteria; this finding is in accordance with the Baas-Becking hypothesis “everything is everywhere; the environment selects” and may have significant consequences for the global distribution of PAC-degrading bacteria and their use in bioremediation.     

Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges

Natural products isolated from sponges are an important source of new biologically active compounds. However, the development of these compounds into drugs has been held back by the difficulties in achieving a sustainable supply of these often-complex molecules for pre-clinical and clinical development. Increasing evidence implicates microbial symbionts as the source of many of these biologically active compounds, but the vast majority of the sponge microbial community remain uncultured. Metagenomics offers a biotechnological solution to this supply problem. Metagenomes of sponge microbial communities have been shown to contain genes and gene clusters typical for the biosynthesis of biologically active natural products. Heterologous expression approaches have also led to the isolation of secondary metabolism gene clusters from uncultured microbial symbionts of marine invertebrates and from soil metagenomic libraries. Combining a metagenomic approach with heterologous expression holds much promise for the sustainable exploitation of the chemical diversity present in the sponge microbial community.     

The convention on Biological Diversity: Some implications for microbiology and microbial culture collections

The coming into force of the Convention on Biological Diversity has led to a series of discussions aiming to clarify its implementation. A number of uncertainties exist at the microbial level and there is a lack of awareness of the role played by microorganisms in ecosystem function. There is moreover a great lack of knowledge about the number of species of microorganisms that exist, their distribution, stability in the environment and intricate interactive roles. Conservation and use of biological material for sustainable environmental management are major issues. Specialist microbiological input into the debate is required to ensure that provisions made for national programmes are appropriate and practicable at the microbiological level. The Articles of the Convention of special relevance to microbiologists are listed and discussed. The role of microbial culture collections within the framework of the Convention is considered. The difficulties and uncertainties of conservation and study of microorganisms in their habitat (in situ) increase the need forex situ conservation in microbial culture collections. The World Federation for Culture Collections plays a coordinating role with regard to expertise, information, training and the management and operation of microbial resource centres. It has the potential for providing a special interest Clearing House Mechanism for the support of the Convention.     

Rains, drains and active strains: towards online assessment of wastewater bacterial communities

Wastewater treatment is one of the largest scale and arguably the most commercially important biotechnological process in the world. Bacterial breakdown of waste materials facilitates the safe disposal of effluents into receiving water bodies. Given this significance, research has focused on identifying the keystone species on which efficient treatment is based. However, unravelling the microbial diversity within such systems has proven difficult. This is highlighted by our lack of detailed knowledge of the microbial interactions within these complex populations, limiting our ability to fully exploit bacterial degradative abilities. Even with the incorporation of new emerging molecular techniques, there have been no investigations linking genetic sequence to microbial function and successful treatment operation. To reach this goal, researchers need the ability to identify, enumerate and monitor the metabolic functions of subpopulations within these complex bacterial communities. Flow cytometry (FCM) combined with fluorescence-based molecular identification techniques provides a method for such studies. Moreover, single-cell sorting provides a unique opportunity to identify and remove individual cells of interest. Laboratory culture of sorted cells is often possible and permits the use of more traditional microbiological techniques to backup molecular investigations. Utilising this approach will advance our understanding of wastewater treatment processes and help maintain and enhance plant operation to improve efficiency.