药物类新污染物的微生物降解机制研究进展

环境微生物作为自然界中主要的分解者蕴含着丰富的遗传和代谢多样性,在有机污染物降解中发挥着重要作用。药物被持续不断地释放到环境中,其环境暴露、环境风险和对人体健康的潜在影响已得到广泛关注。研究药物在环境中的微生物降解过程对于药物的环境命运、药物的环境风险评估和药物污染去除技术的开发等具有重要价值。本文重点综述了目前环境中常检出药物的微生物降解途径及其分子机理,总结了目前药物微生物降解研究领域的进展,最后探讨了药物的微生物降解领域未来的研究趋势。     

The organization of the microbial biodegradation network from a systems-biology perspective

Microbial biodegradation of environmental pollutants is a field of growing importance because of its potential use in bioremediation and biocatalysis. We have studied the characteristics of the global biodegradation network that is brought about by all the known chemical reactions that are implicated in this process, regardless of their microbial hosts. This combination produces an efficient and integrated suprametabolism, with properties similar to those that define metabolic networks in single organisms. The characteristics of this network support an evolutionary scenario in which the reactions evolved outwards from the central metabolism. The properties of the global biodegradation network have implications for predicting the fate of current and future environmental pollutants.     

Engineering bacteria for bioremediation

The treatment of environmental pollution by microorganisms is a promising technology. Various genetic approaches have been developed and used to optimize the enzymes, metabolic pathways and organisms relevant for biodegradation. New information on the metabolic routes and bottlenecks of degradation is still accumulating, enlarging the available toolbox. With molecular methods allowing the characterization of microbial community structure and activities, the performance of microorganisms under in situ conditions and in concert with the indigenous microflora will become predictable.     

Biocatalytic degradation of pollutants

Microbial reactions play key roles in biocatalysis and biodegradation. The recent genome sequencing of environmentally relevant bacteria has revealed previously unsuspected metabolic potential that could be exploited for useful purposes. For example, oxygenases and other biodegradative enzymes are benign catalysts that can be used for the production of industrially useful compounds. In conjunction with their biodegradative capacities, bacterial chemotaxis towards pollutants might contribute to the ability of bacteria to compete with other organisms in the environment and to be efficient agents for bioremediation. In addition to the bacterial biomineralization of organic pollutants, certain bacteria are also capable of immobilizing toxic heavy metals in contaminated aquifers, further illustrating the potential of microorganisms for the removal of pollutants.     

Dynamic changes in microbial community structure and function in phenol-degrading microcosms inoculated with cells from a contaminated aquifer

Contamination of aquifers by organic pollutants threatens groundwater supplies and the environment. In situ biodegradation of organic pollutants by microbial communities is important for the remediation of contaminated sites, but our understanding of the relationship between microbial development and pollutant biodegradation is poor. A particular challenge is understanding the in situ status of microorganisms attached to solid surfaces, but not accessible via conventional sampling of groundwater. We have developed novel flow-through microcosms and examined dynamic changes in microbial community structure and function in a phenol-degrading system. Inoculation of these microcosms with a complex microbial community from a plume in a phenol-contaminated aquifer led to the initial establishment of a population dominated by a few species, most attached to the solid substratum. Initially, phenol biodegradation was incomplete, but as the microbial community structure became more complex, phenol biodegradation was more extensive and complete. These results were replicated between independent microcosms, indicating a deterministic succession of species. This work demonstrates the importance of examining community dynamics when assessing the potential for microbial biodegradation of organic pollutants. It provides a novel system in which such measurements can be made readily and reproducibly to study the temporal development and spatial succession of microbial communities during biodegradation of organic pollutants at interfaces within such environments.     

Interspecific interactions in mixed microbial cultures in a biodegradation perspective

In recent works, microbial consortia consisting of various bacteria and fungi exhibited a biodegradation performance superior to single microbial strains. A highly efficient biodegradation of synthetic dyes, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and other organic pollutants can be achieved by mixed microbial cultures that combine degradative enzyme activities inherent to individual consortium members. This review summarizes biodegradation results obtained with defined microbial cocultures and real microbial consortia. The necessity of using a proper strategy for the microbial consortium development and optimization was clearly demonstrated. Molecular genetic and proteomic techniques have revolutionized the study of microbial communities, and techniques such as the denaturing gradient gel electrophoresis, rRNA sequencing, and metaproteomics have been used to identify consortium members and to study microbial population dynamics. These analyses could help to further enhance and optimize the natural activities of mixed microbial cultures.     

Recent developments in microbial biotransformation and biodegradation of dioxins

Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs), commonly known as dioxins (PCDD/Fs), are toxic environmental pollutants formed from various sources. Elimination of these pollutants from the environment is a difficult task due to their persistent and ubiquitous nature. Removal of dioxins by biological degradation (biodegradation) is considered a feasible method as an alternative to other expensive physicochemical approaches. Biodegradation of dioxins has been extensively studied in several microorganisms, and details concerning biodiversity, biodegradation, biochemistry and molecular biology of this process have accumulated during the last three decades. There are several microbial mechanisms responsible for biodegradation of dioxins, including oxidative degradation by dioxygenase-containing aerobic bacteria, bacterial and fungal cytochrome P-450, fungal lignolytic enzymes, reductive dechlorination by anaerobic bacteria, and direct ether ring cleavage by fungi containing etherase-like enzymes. Many attempts have been made to bioremediate PCDD/Fs using this basic knowledge of microbial dioxin degradation. This review emphasizes the present knowledge and recent advancements in the microbial biotransformation, biodegradation and bioremediation of dioxins.     

Cometabolic degradation of organic wastewater micropollutants by activated sludge and sludge-inherent microorganisms

Municipal wastewaters contain a multitude of organic trace pollutants. Often, their biodegradability by activated sludge microorganisms is decisive for their elimination during wastewater treatment. Since the amounts of micropollutants seem too low to serve as growth substrate, cometabolism is supposed to be the dominating biodegradation process. Nevertheless, as many biodegradation studies were performed without the intention to discriminate between metabolic and cometabolic processes, the specific contribution of the latter to substance transformations is often not clarified. This minireview summarizes current knowledge about the cometabolic degradation of organic trace pollutants by activated sludge and sludge-inherent microorganisms. Due to their relevance for communal wastewater contamination, the focus is laid on pharmaceuticals, personal care products, antibiotics, estrogens, and nonylphenols. Wherever possible, reference is made to the molecular process level, i.e., cometabolic pathways, involved enzymes, and formed transformation products. Particular cometabolic capabilities of different activated sludge consortia and various microbial species are highlighted. Process conditions favoring cometabolic activities are emphasized. Finally, knowledge gaps are identified, and research perspectives are outlined.     

石油烃生物降解过程的研究进展

石油烃污染物属于难降解混合物,生物修复已经成为石油烃污染环境的主要修复方法。文中简述了微生物对石油烃的间期适应过程和转运过程,并通过对部分典型石油烃成分的微生物降解机理和代谢路径的梳理和综述,阐释了石油烃生物降解过程中的菌株、基因、代谢路径等研究进展。此外,利用基因工程和代谢工程等手段,可对野生型石油烃降解菌进行改造,进一步提升其对石油烃污染环境的生物修复能力。最后,从石油烃降解菌的代谢途径改造、人工混菌体系的设计构建等角度,结合合成生物学和代谢工程的手段,提出了对石油烃降解的研究展望,以期提升对石油烃污染物的生物修复效果。     

Enhancement of metal bioremediation by use of microbial surfactants

Metal pollution all around the globe, especially in the mining and plating areas of the world, has been found to have grave consequences. An excellent option for enhanced metal contaminated site bioremediation is the use of microbial products viz. microbial surfactants and extracellular polymers which would increase the efficiency of metal reducing/sequestering organisms for field bioremediation. Important here is the advantage of such compounds at metal and organic compound co-contaminated site since microorganisms have long been found to produce surface-active compounds when grown on hydrocarbons. Other options capable of proving efficient enhancers include exploiting the chemotactic potential and biofilm forming ability of the relevant microorganisms. Chemotaxis towards environmental pollutants has excellent potential to enhance the biodegradation of many contaminants and biofilm offers them a better survival niche even in the presence of high levels of toxic compounds.     

Bacterial metabolism of polychlorinated biphenyls

Microbial metabolism is responsible for the removal of persistent organic pollutants including PCBs from the environment. Anaerobic dehalogenation of highly chlorinated congeners in aquatic sediments is an important process, and recent evidence has indicated that Dehalococcoides and related organisms are predominantly responsible for this process. Such anaerobic dehalogenation generates lower chlorinated congeners which are easily degraded aerobically by enzymes of the biphenyl upper pathway (bph). Initial biphenyl 2,3-dioxygenases are generally considered the key enzymes of this pathway which determine substrate range and extent of PCB degradation. These enzymes have been subject to different protein evolution strategies, and subsequent enzymes have been considered as crucial for metabolism. Significant advances have been made regarding the mechanistic understanding of these enzymes, which has also included elucidation of the function of BphK glutathione transferase. So far, the genomes of two important PCB-metabolizing organisms, namely Burkholderia xenovorans strain LB400 and Rhodococcus sp. strain RHA1, have been sequenced, with the rational to better understand their overall physiology and evolution. Genomic and proteomic analysis also allowed a better evaluation of PCB toxicity. Like all bph gene clusters which have been characterized in detail, particularly in strains LB400 and RHA1, these genes were localized on mobile genetic elements endowing single strains and microbial communities with a high flexibility and adaptability. However, studies show that our knowledge on enzymes and genes involved in PCB metabolism is still rather fragmentary and that the diversity of bacterial strategies is highly underestimated. Overall, metabolism of biphenyl and PCBs should not be regarded as a simple linear pathway, but as a complex interplay between different catabolic gene modules.     

微生物降解石油烃的功能基因研究进展

微生物对石油烃的降解在自然衰减去除土壤和地下水石油烃污染的过程中发挥了重要作用。微生物通过其产生的一系列酶来利用和降解这类有机污染物,其中,编码关键降解酶的基因称为功能基因。功能基因可作为生物标志物用于分析环境中石油烃降解基因的多样性。因此,研究石油降解功能基因是分析土著微生物群落多样性、评价自然衰减潜力与构建基因工程菌的重要基础。本文主要介绍了烷烃和芳香烃在有氧和无氧条件下的微生物降解途径,重点总结了烷烃和芳香烃降解的主要功能基因及其作用,包括参与羟化作用的单加氧酶和双加氧酶基因、延胡索酸加成反应的琥珀酸合酶基因以及中心中间产物的降解酶基因等。     

Mining enzymes from extreme environments

Current advances in metagenomics have revolutionized the research in fields of microbial ecology and biotechnology, enabling not only a glimpse into the uncultured microbial population and mechanistic understanding of possible biogeochemical cycles and lifestyles of extreme organisms but also the high-throughput discovery of new enzymes for industrial bioconversions. Nowadays, the genetic and enzymatic differences across the gradients from 'neutral and pristine' to 'extreme and polluted' environments are well documented. Yet, extremophilic organisms are possibly the least well understood because our ability to study and understand their metabolic potential has been hampered by our inability to isolate pure cultures. There are at least two obstacles for reaping the fruit of the microbial diversity of extremophiles: first, in spite of the recent progress in development of new culturing techniques most extremophiles cannot be cultured using traditional culturing technologies; and second, the problem of the very low biomass densities often occurs under the conditions hostile for life, which often do not yield enough DNA and reduces the effectiveness of cloning.     

Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches

Biodegradation can achieve complete and cost-effective elimination of aromatic pollutants through harnessing diverse microbial metabolic processes. Aromatics biodegradation plays an important role in environmental cleanup and has been extensively studied since the inception of biodegradation. These studies, however, are diverse and scattered; there is an imperative need to consolidate, summarize, and review the current status of aromatics biodegradation. The first part of this review briefly discusses the catabolic mechanisms and describes the current status of aromatics biodegradation. Emphasis is placed on monocyclic, polycyclic, and chlorinated aromatic hydrocarbons because they are the most prevalent aromatic contaminants in the environment. Among monocyclic aromatic hydrocarbons, benzene, toluene, ethylbenzene, and xylene; phenylacetic acid; and structurally related aromatic compounds are highlighted. In addition, biofilms and their applications in biodegradation of aromatic compounds are briefly discussed. In recent years, various biomolecular approaches have been applied to design and understand microorganisms for enhanced biodegradation. In the second part of this review, biomolecular approaches, their applications in aromatics biodegradation, and associated biosafety issues are discussed. Particular attention is given to the applications of metabolic engineering, protein engineering, and “omics” technologies in aromatics biodegradation.     

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.     

合成生物学在环境修复中的应用

环境问题是21世纪人类面临的最严重的挑战。随着现代工农业飞速发展,生态环境日益恶化,难降解污染物如新兴污染物逐渐显现,已成为制约社会经济可持续发展的重要因素。微生物具有强大的环境修复能力,但是其进化速度远不及新兴污染物出现的速度,亟需应用合成生物学的技术来解决这一难题。在充分认识难降解有机污染物微生物降解(途径)特性的基础上,利用我国丰富的微生物与基因资源,运用合成生物学的手段,定向设计和改造现有降解菌株,构建能够降解一种或多种污染物的工程菌株;同时针对复合型污染,如废水等,在建立典型有机污染物代谢、调控和抗逆相关基因元件的模块库基础上,引入人工菌群等策略,对生物系统进行理性设计和组装,构建典型环境污染物的高效降解菌群,可有效促进我国新兴污染物微生物分解代谢的研究,为环境修复的工程应用提供技术支持。     

基于电活性微生物的芳香烃类污染物转化机制研究进展

芳香烃类化合物(aromatic hydrocarbon compounds)是一类基于苯环结构的有机物,广泛分布在自然环境中,难以自然降解、易被生物积累,且有很大的环境危害性。生物法是有机化合物转化降解的主流工艺,而电活性微生物(electroactive microorganisms, EAM)因其独特的胞外电子传递(extracellular electron transfer, EET)能力和生理代谢模式在芳香烃类化合物污染修复领域具有巨大的应用潜力。电活性微生物可以通过还原脱卤、脱硝与氧化开环过程相结合的方式,最终实现芳香烃类污染物的降解矿化。本文重点综述了电活性微生物降解芳香烃类污染物过程中主要还原/氧化反应机理,归纳了电活性微生物高效还原脱卤、脱硝的关键酶活、代谢途径及转化机理,分析了不同含氧条件下电活性微生物开环方式及降解代谢途径,并通过调控微生物胞外聚合物与添加导电材料等途径来提升电活性微生物的胞外电子传递过程,总结了电极电位、电极材料、电解液性质及温度等环境因子对芳香烃类化合物降解的影响,探讨了芳香烃类污染物的强化生物降解策略的可行性。最后,展望了电活性微生物降解技...     

Biodegradation: gaining insight through proteomics

Biodegradation, a generic term used to describe methodologies to affect cleanup of environmental pollutants, has come up as an improved substitute for ineffective and expensive physico-chemical remediation methods. However, lack of information about the factors controlling the growth and metabolism of microorganisms in the polluted environment often limits its implementation. Recent advances in the understanding of biogeochemical processes and genomics have opened up new perspectives towards new opportunities of pollution abatement. High throughput genomic techniques have revolutionized the remediation process leading to breakthroughs in characterizing proteomes, metabolomes and phenotypes for organisms, communities and populations. These new techniques have allowed us to address longstanding questions regarding the molecular mechanisms that may control the mineralization processes and have an in-depth understanding of microbial community structure and stress responses. In order to explore insights of biodegradation this article discusses ways in which proteomics may be able to meet challenges in biodegradation.     

多环芳烃污染土壤微生物修复研究进展

多环芳烃是我国土壤环境质量标准中要求严格管控的一类持久性有机污染物,利用微生物技术修复有机污染土壤具有绿色、经济等突出特点,应用前景广泛。目前多学科的协同发展和新技术的研究应用,为多环芳烃土壤微生物转化机制与污染生态过程等方面带来了新的认识,同时对修复技术的实际应用与调控提供了新的思考方向。本文以多环芳烃污染土壤微生物修复为主体,从污染土壤微生物修复应用技术、多环芳烃微生物降解特征、土壤体系污染物归趋规律与微生物作用及土壤污染微生物群落响应与研究技术等方面进行综合评述,并针对现存应用技术瓶颈和理论空白作进一步思考和展望。     

Bioaugmentation of soils by increasing microbial richness: missing links

It is generally assumed that increased microbial diversity corresponds to increased catabolic potential and, hence, to better removal of metabolites and pollutants. Yet, microbial diversity, more specifically richness of species in environmental samples and sites, is difficult to assess. It is proposed to interpret this diversity more in the framework of Pareto's law, i.e. 20% of the species govern 80% of the energy flux of the ecosystem. Ecological studies should attempt to delineate the main energy fluxes and that group of species playing quantitative key roles in the system. Consequently, bioaugmentation should aim at the rearrangement of the group of organisms dominantly involved in the overall energy flux, so that specific catabolic traits necessary for the clean up of pollutants are part of that active group. For soil ecosystems, the capacity of plant roots as creators of physical and chemical discontinuity should be used more strategically to bring about such rearrangements. Overall, this paper identifies a number of ecological concepts, such as the Pareto law, the Gompertz model and plant community-induced microbial competence, which may, given careful underpinning, open new perspectives for microbial ecology and biodegradation.