Fungal metabolism of polycyclic aromatic hydrocarbons: past, present and future applications in bioremediation

This article examines the importance of non-ligninolytic and ligninolytic fungi in the bioremediation of polycyclic aromatic hydrocarbon contaminated wastes. The research from the initial studies in Dave Gibson’s laboratory to the present are discussed. Received 10 August 1997/ Accepted in revised form 15 August 1997     

Alicycliphilus: current knowledge and potential for bioremediation of xenobiotics

Alicycliphilus is a promising candidate for participating in the development of novel xenobiotics bioremediation processes. Members of the Alicycliphilus genus are environmental bacteria mostly found in polluted sites such as landfills and contaminated watercourses, and in sewage sludges from wastewater treatment plants. They exhibit a versatile metabolism and the ability to use oxygen, nitrate and chlorate as terminal electron acceptors, which allow them to biodegrade xenobiotics under oxic or anoxic conditions. Pure cultures of Alicycliphilus strains are able to biodegrade some pollutants such as industrial solvents (acetone, cyclohexanol and N-methylpyrrolidone), aromatic hydrocarbons (benzene, toluene and anthracene), as well as polyurethane varnishes and foams, and they can even transform Cr(VI) to Cr(III). In addition, Alicycliphilus has also been identified in bacterial communities involved in wastewater treatment plants for denitrification, and the degradation of emerging pollutants such as triclosan, nonylphenol, N-heterocyclic aromatic compounds (indole and quinoline), and antibiotics (tetracycline and oxytetracycline). This work summarizes the current knowledge on the Alicycliphilus genus, describing its different metabolic characteristics, focusing on its xenobiotic biodegradation abilities and examining the distinct pathways and molecular bases that sustain them. We also discuss the progress made in genetic manipulation and ‘omics’ analyses, as well as Alicycliphilus participation in novel bioremediation strategies.     

细菌对环境污染物的趋化性及其在生物修复中的作用

细菌对有机化合物的降解能力是一种利用碳源和能源的优势,这种能力可以用来设计安全、有效和无二次污染的污染物的生物修复系统。趋化性是细菌适应外界化学环境变化而作出的行为反应,是一种寻找碳源和能源的优势。细菌的趋化性能够增强细菌在自然环境中的降解污染物的效果,细菌的趋化性与降解性之间的关系研究已经成为热点。介绍了细菌的趋化性的基本概念和趋化信号转导的机制,重点讨论了细菌对环境污染化合物的趋化性,从基因水平揭示了趋化性与降解性之间的紧密联系,认为趋化性可以有效地促进降解性细菌对污染物的生物修复作用。     

土壤与水体有机污染的生物修复及其应用研究进展

系统论述了土壤、水有机污染物的主要来源、特点、有机污染生物修复的概念、应用范围、成功实例与研究进展等,特别是对于泄漏石油污染的生物成功降解方法、效果,土壤中易爆炸物如ＴＮＴ、废水中有机污染的有效降解等,评价了生物修复所具有突出优势,对有机、无机污染物降解过程中植物、微生物筛选、基因修饰、分子克隆与转基因植物方面近年来所取得的惊人成果与突破性进展,无疑正激励着人们开拓更大的应用范围。预计不久的将来,更多具有环境净化与生物修复功能的商业性综合技术与高效性工程生物将投入应用。     

Fungal deterioration of melon seeds stored in jute sacks and polyethylene bags in Ago-Iwoye,southwestern Nigeria

Laboratory studies were carried out in the Department of Biological Sciences, Ogun State University, Ago-Iwoye, southwestern Nigeria, to determine the extent of fungal deterioration of melon seeds stored in two types of storage bags viz; jute and polyethylene bags. Melon seeds of varieties Tc139 and V2 were stored in jute and polyethylene bags under ambient conditions using the 2 × 2 factorial design (variety vs type of bag) for 12 months. The moisture content (mc), incidence of visible mouldiness (ivm) and germinability of the stored seeds were determined monthly. The mc of Tc139 ranged from 6.1 to 6.7% in jute and 6.2 to 6.5% in polyethylene bags. The ivm which was initially 2.1% increased to 10.7% and 5.5% in jute and polyethylene bags respectively, after 12 months in storage. The germination percentage decreased from 96.3% to 28.7% and 45.3% in jute and polyethylene bags, respectively. The mc of V2 stored in jute and polyethylene bags varied from 5.9 to 6.4%, and 5.8 to 6.2%, respectively. The ivm increased from 1.8% before storage to 8.9% and 4.8% in jute and polyethylene bags, respectively, after 12 months. The percentage seed germination declined from 98.0%to 37.3% in jute and 48.7% in polyethylene bags after 12 months. Decreased incidence of field fungi namely: Alternaria, Botryodiplodia theobromae, Cladosporium, Fusarium and Macrophomina phaseolina was accompanied by simultaneous increase in storage fungi viz: Aspergillus, Penicillium, and Rhizopus with prolonged storage. This revised version was published online in June 2006 with corrections to the Cover Date.     

Optimization of soil physical and chemical conditions for the bioremediation of creosote-contaminated soil

Mispah type soil (FAO : Lithosol) contaminated with >250 000 mg kg^-1 creosote was collected from the yard of a creosote treatment plant. The soils carbon, nitrogen and phosphorus contents were determined. Due to creosote contamination, thecarbon content of the soil was found to be 130,000 mg C kg^-1. This concentration was found to greatly affect the nitrogen content (0.08%). The phosphorus content was less affected (4.5%). It was estimated that a nutrient amendment to bring the soil to a C : N 10 : 1 would be adequate to stimulate microbial growth and creosote degradation. The soil was amended with a range of C : N ratios below and above the estimated ratio. In one of the treatments, the phosphorus content was amended. Sterile and natural controls were also set up. The soil was incubated at 30 °C on a rotaryshaker at 150 rpm in the dark for six weeks. Water content was maintained at 70% field capacity. The lowest nitrogen supplementation (C : N = 25 : 1) was more effective in enhancing microbial growth (3.12E + 05) and creosote removal (68.7%) from the soil. Additional phosphorus was not very effective in enhancing the growth of microorganisms and removal of creosote. The highest nitrogen supplementation(C : N = 5 : 1) did not enhance microbial growth and creosote removal.A relationship between mass loss and creosote removal was also observed. Phenolics and lower molecular mass polycyclic aromatic hydrocarbons (PAHs) were observed to be more susceptible to microbial degradation than higher molecular mass compounds. Nutrient concentration, moisture content and pH were thus observed to play very significant roles in the utilization of creosote in soil. These results are being used for the development of a bioremediation technology for the remediation of creosote contaminated soils in a treatment plant in South Africa.     

Intrinsic bioremediation in a solvent-contaminated alluvial groundwater

An industrial site contaminated with a mixture of volatile organic compounds in its subsurface differed from previously reported locations in that the contamination consisted of a mixture of chlorinated, brominated, and non-halogenated aromatic and aliphatic solvents in an alluvial aquifer. The source area was adjacent to a river. Of the contaminants present in the aquifer, benzene, toluene, and chlorobenzene (BTC) were of primary concern. Studies of the physical, chemical, and microbiological characteristics of site groundwater were conducted. The studies concentrated on BTC, but also addressed the fate of the other aquifer VOCs. Gas chromatographic analyses performed on laboratory microcosms demonstrated that subsurface microorganisms were capable of BTC degradation. Mineralization of BTC was demonstrated by the release of ¹⁴CO₂ from radiolabelled BTC. In the field, distribution patterns of nutrients and electron acceptors were consistent with expression of in situ microbial metabolic activity: methane, conductivity, salinity and o-phosphate concentrations were all positively correlated with contaminant concentration; while oxidation-reduction potential, nitrate, dissolved oxygen and sulfate concentrations were negatively correlated. Total aerobes, aerotolerant anaerobes, BTC-specific degraders, and acridine orange direct microscopic microorganism counts were strongly and positively correlated with field contaminant concentrations. The relative concentrations of benzene and toluene were lower away from the core of the plume compared to the less readily metabolized compound, chlorobenzene. Hydrodynamic modeling of electron-acceptor depletion conservatively estimated that 450 kg of contaminant have been removed from the subsurface yearly. Models lacking a biodegradation term predicted that 360 kg of contaminant would reach the river annually, which would result in measurable contaminant concentrations. River surveillance, however, has only rarely detected these compounds in the sediment and then only at trace concentrations. Thus, the combination of field modeling, laboratory studies, and site surveillance data confirm that significant in situ biodegradation of the contaminants has occurred. These studies establish the presence of intrinsic bioremediation of groundwater contaminants in this unusual industrial site subsurface habitat. Received 01 December 1995/ Accepted in revised form 27 July 1996     

Assessment of crude oil degradation efficiency of newly isolated actinobacteria reveals untapped bioremediation potentials

Bioremediation is gaining favorable attention as a more economical and environmentally friendly technique for the remediation of crude oil hydrocarbons. This makes the search for crude oil–degrading microbes very crucial. In this study, the isolation and identification of actinobacteria in soil samples from a selected crude oil spill site were carried out. Eighteen isolates from different soil depths (20–120 cm) were screened for their ability to grow on crude oil–based medium (COBM). Actinomyces naeslundii, Actinomyces viscosus, Actinomyces israelii, Actinomyces meyeri, and Nocardia formicae from a 20 cm soil depth exhibited higher growth profiles on COBM than on glucose-based medium (GBM). A. viscosus and A. isrealii exhibited 5- and 3-fold increase in growth over GBM and were selected for biodegradation studies. Growth kinetics and residual crude oil were used to measure the degradation efficiency of A. viscosus and A. israeli over varying crude oil concentrations. Surprisingly, A. viscosus and A. isrealii achieved 98% degradation of 10 g/L crude oil in 12 days and 97% degradation of 30, 50, and 75 g/L in 16 and 18 days, respectively. Specific activity of total peroxidase was assayed over the biodegradation period. Peroxidase activity increased with degradation efficiency of A. viscosus and A. isrealii, suggesting that peroxidases play a key role in the crude oil biodegradation process. The unique tolerance exhibited by A. viscosus and A. israelii to crude oil and high crude oil degradation efficiencies indicate their promising potential for bioremediation applications.     

聚乙烯塑料生物降解研究进展

聚乙烯(polyethylene,PE)塑料是全球通用合成树脂中产量最丰富的品种,也是最难降解的塑料之一,其在环境中大量积累已造成严重的生态污染。传统的垃圾填埋、堆肥和焚烧处理技术难以满足生态环境的保护要求,生物降解是解决塑料污染问题的一种生态友好、成本低廉、前景可期的方法。本文对PE塑料的化学结构、降解微生物的种类、降解酶和代谢途径等方面进行了综述,结合国内外PE塑料生物降解的前沿和热点问题,建议重点开展高效降解菌株筛选、人工合成菌群构建、降解酶的挖掘与改造等方面的研究,为PE塑料生物降解研究提供路径选择和理论借鉴。     

Biodegradation of trinitrotoluene (TNT) by indigenous microorganisms from TNT-contaminated soil,and their application in TNT bioremediation

Soil and groundwater contaminated by munitions compounds is a crucial issue in environmental protection. Trinitrotoluene (TNT) is highly toxic and carcinogenic; therefore, the control and remediation of TNT contamination is a critical environmental issue. In this study, the authors characterized the indigenous microbial isolates from a TNT-contaminated site and evaluated their activity in TNT biodegradation. The bacteria Achromobacter sp. BC09 and Citrobacter sp. YC4 isolated from TNT-contaminated soil by enrichment culture with TNT as the sole carbon and nitrogen source (strain BC09) and as the sole nitrogen but not carbon source (strain YC4) were studied for their use in TNT bioremediation. The efficacy of degradation of TNT by indigenous microorganisms in contaminated soil without any modification was insufficient in the laboratory-scale pilot experiments. The addition of strains BC09 and YC4 to the contaminated soil did not significantly accelerate the degradation rate. However, the addition of an additional carbon source (e.g., 0.25% sucrose) could significantly increase the bioremediation efficiency (ca. decrease of 200 ppm for 10 days). Overall, the results suggested that biostimulation was more efficient as compared with bioaugmentation. Nevertheless, the combination of biostimulation and bioaugmentation using these indigenous isolates is still a feasible approach for the development of bioremediation of TNT pollution.     

AM真菌对重金属污染土壤生物修复的应用与机理

土壤重金属污染威胁人类健康和整个生态系统,而高效、低耗、安全的生物修复技术显示出了极大的应用潜力,特别是利用植物-微生物共生体增强生物修复效应的应用.丛枝菌根(Arbuscular Mycorrhizae,AM)真菌是一类广泛分布于土壤生态系统中的有益微生物,能与90％以上的陆生高等植物形成共生体.研究发现,AM真菌能够增强宿主植物对土壤中重金属胁迫的耐受性.当前,利用AM真菌开展重金属污染土壤的生物修复已经引起环境学家和生态学家的广泛关注.基于此,围绕AM真菌在重金属污染土壤生物修复作用中的最新研究进展,从物理性防御体系的形成、对植物生理代谢的调控、生化拮抗物质的产生、基因表达的调控等角度探究AM真菌在重金属污染土壤生物修复中的作用机理,以期为利用AM真菌开展重金属污染的生物修复提供理论依据,并对本领域未来的发展和应用前景进行了展望.     

Assessment of in-situ bioremediation at a refinery waste-contaminated site and an aviation gasoline contaminated site

A combination of geochemical, microbiological and isotopic methods were used to evaluate in-situ bioremediation of petroleum hydrocarbons at one site contaminated with refinery waste and a second site contaminated with aviation gasoline at Alameda Point, California. At each site, geochemical and microbiological characteristics from four locations in the contaminated zone were compared to those from two uncontaminated background locations. At both sites, the geochemical indicators of in-situbiodegradation includeddepleted soil gas and groundwater oxygen, elevated groundwater alkalinity, and elevated soil gas carbon dioxide and methane in the contaminated zone relative to the background. Radiocarbon content of methane and carbon dioxide measured in soil gas at both sites indicated that they were derived from hydrocarbon contaminant degradation. Direct microscopy of soil core samples using cell wall stains and activity stains, revealed elevated microbial numbers and enhanced microbial activities in contaminated areas relative to background areas, corroborating geochemical findings. While microbial plate counts and microcosm studies using soil core samples provided laboratory evidence for the presence of some microbial activity and contaminant degradation abilities, they did not correlate well with either contaminant location, geochemical, isotopic, or direct microscopy data.     

聚对苯二甲酸乙二醇酯生物降解的研究进展

塑料广泛存在于人类的日常生活中,在给人们生活带来便利的同时,大量塑料废物也给环境带来很大压力。聚对苯二甲酸乙二醇酯(polyethylene terephthalate, PET)是一种以石油为原料的高分子热塑性材料,因其具有耐用、透明度高、重量轻等特性,已成为世界上使用最广泛的塑料之一。由于PET具有结构复杂以及难降解的特性,可在自然界中长期存在,不仅对全球生态环境造成严重的污染,而且已经威胁到人类健康。如何对PET废弃物进行降解已成为全球的难题之一,相较于物理法和化学法,生物降解法是目前处理PET废弃物最为绿色环保的方法。本文分别介绍了微生物和生物酶对PET生物降解的研究现状、PET的生物降解途径、PET生物降解机制以及PET降解酶的分子改造等方面的研究,并对如何实现PET的高效降解、寻找和改造可降解高结晶度PET的微生物或酶进行展望,为PET的生物降解微生物或酶的有效开发应用提供理论依据。     

Effects of Fungal Bioaugmentation and Cyclodextrin Amendment on Fluorene Degradation in Soil Slurry

This study assesses the potential of fungal bioaugmentation and the effect of maltosyl-cyclodextrin amendment, as an approach to accelerate fluorene biodegradation in soil slurries. 47 fungal strains isolated from a contaminated site were tested in the biodegradation of fluorene. Results showed the greater efficiency of "adaptated" fungi isolated from contaminated soil vs. reference strains belonging to the collection of the laboratory. These assays allowed us to select the most efficient strain, Absidia cylindrospora, which was used in a bioaugmentation process. In the presence of Absidia cylindrospora, more than 90% of the fluorene was removed in 288 h while 576 h were necessary in the absence of fungal bioaugmentation. Maltosyl-cyclodextrin, a branched-cyclodextrin was chosen in order to optimize fluorene bioavailability and biodegradation in soil slurries. The results of this study indicate that Absidia cylindrospora and maltosyl-cyclodextrin could be used successfully in bioremediation systems.     

Microbial extracellular polymeric substances: central elements in heavy metal bioremediation

Extracellular polymeric substances (EPS) of microbial origin are a complex mixture of biopolymers comprising polysaccharides, proteins, nucleic acids, uronic acids, humic substances, lipids, etc. Bacterial secretions, shedding of cell surface materials, cell lysates and adsorption of organic constituents from the environment result in EPS formation in a wide variety of free-living bacteria as well as microbial aggregates like biofilms, bioflocs and biogranules. Irrespective of origin, EPS may be loosely attached to the cell surface or bacteria may be embedded in EPS. Compositional variation exists amongst EPS extracted from pure bacterial cultures and heterogeneous microbial communities which are regulated by the organic and inorganic constituents of the microenvironment. Functionally, EPS aid in cell-to-cell aggregation, adhesion to substratum, formation of flocs, protection from dessication and resistance to harmful exogenous materials. In addition, exopolymers serve as biosorbing agents by accumulating nutrients from the surrounding environment and also play a crucial role in biosorption of heavy metals. Being polyanionic in nature, EPS forms complexes with metal cations resulting in metal immobilization within the exopolymeric matrix. These complexes generally result from electrostatic interactions between the metal ligands and negatively charged components of biopolymers. Moreover, enzymatic activities in EPS also assist detoxification of heavy metals by transformation and subsequent precipitation in the polymeric mass. Although the core mechanism for metal binding and / or transformation using microbial exopolymer remains identical, the existence and complexity of EPS from pure bacterial cultures, biofilms, biogranules and activated sludge systems differ significantly, which in turn affects the EPS-metal interactions. This paper presents the features of EPS from various sources with a view to establish their role as central elements in bioremediation of heavy metals.     

Fungi as a toolbox for sustainable bioremediation of pesticides in soil and water

Pesticides can help reduce yield losses caused by pests, pathogens, and weeds, but their overuse causes serious environmental pollution. They are persistent in the environment and are biomagnified through the food chain, becoming a serious health hazard for humankind. Bioremediation, where microbes are used to degrade pesticides in situ, is a useful technology. This review summarizes data on the fungi involved in the biodegradation of chemical pesticides and their application in soil and water bioremediation. Indications for future studies in this field are given.     

Development of a standard bacterial consortium for laboratory efficacy testing of commercial freshwater oil spill bioremediation agents

Six crude oil-degrading bacterial strains isolated from different soil and water environments were combined to create a defined consortium for use in standardized efficacy testing of commercial oil spill bioremediation agents (OSBA). The isolates were cryopreserved in individual aliquots at pre-determined cell densities, stored at −70°C, and thawed for use as standardized inocula as needed. Aliquots were prepared with precision (typically within 10% of the mean) ensuring reproducible inoculation. Five of the six strains displayed no appreciable loss of viability during cryopreservation exceeding 2.5 years, and five isolates demonstrated stable hydrocarbon-degrading phenotypes during inoculum preparation and storage. When resuscitated, the defined consortium reproducibly biodegraded Alberta Sweet Mixed Blend crude oil (typically ± 7% of the mean of triplicate cultures), as determined by quantitative gas chromatography–mass spectrometry of various analyte classes. Reproducible biodegradation was observed within a batch of inoculum in trials spanning 2.5 years, and among three batches of inoculum prepared more than 2 years apart. Biodegradation was comparable after incubation for 28 days at 10°C or 14 days at 22°C, illustrating the temperature tolerance of the bacterial consortium. The results support the use of the synthetic consortium as a reproducible, predictable inoculum to achieve standardized efficacy tests for evaluating commercial OSBA. Received 31 August 1998/ Accepted in revised form 30 November 1998     

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.     

土壤有效硅对大豆生长发育和生理功能的影响

人工调节土壤有效硅含量及盆栽试验,研究土壤有效硅对大豆生长发育和生理功能的影响.结果表明,土壤有效硅含量在55.1～202.8mg·kg^-1范围内,随着土壤有效硅含量的提高,大豆种子萌发过程中蛋白酶和脂肪酶活性升高,淀粉酶活性无显著变化,呼吸速率加快,种子活力升高,萌发速度加快,种子萌发率无显著变化;幼苗生长过程中叶片叶绿素含量无显著变化,光合速率加快,根系活力、硝酸还原酶活力升高,蒸腾强度减弱,水分利用效率和叶含水量升高,抗旱保水能力提高.大豆幼苗含硅量与土壤有效硅含量呈线性正相关趋势(r=0.994).土壤有效硅含量大于202.8mg·kg^-1,生理功能不再显著变化,说明土壤中的硅被大豆吸收后,改善了大豆萌发种子和幼苗的生理功能,使种子萌发和幼苗生长加快.