乙醇合成途径的计算机重构

目的:用计算机重构乙醇合成途径,为合成生物燃料乙醇提供理论依据。方法:利用KEGG反应、化合物数据提取反应等式,过滤掉42个通用代谢物参与的反应,然后利用剩下的反应构建反应矩阵;利用广度优先搜索算法在反应矩阵中搜索生成乙醇的代谢途径。结果:计算机重构了23 108条乙醇合成途径,以大肠杆菌作为产乙醇基因工程菌为例,通过限制改构菌整合的关键酶数目,分别得到了78条以酒精O-乙酰基转移酶为关键酶的乙醇合成通路和89条以丙酮酸脱羧酶和乙醇脱氢酶为关键酶的乙醇合成通路,并构建了相应的乙醇合成网络图,标注每个反应的酶及编码该酶的基因。结论:通过计算机方法重构了多种乙醇合成途径,可以为利用微生物工业化生产乙醇提供理论依据。     

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。     

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。     

海洋石油降解微生物及其降解机理

微生物修复作为一种新型环保的生物修复技术,已成为海洋石油污染生物修复的核心技术。对海洋石油降解微生物的种类即细菌、蓝藻、真菌以及藻类进行了总结,对微生物对石油烃的降解途径与降解机理进行了综述。微生物降解烷烃的过程包括末端氧化、烷基氢过氧化物以及环己烷降解3种形式。微生物对芳香烃的降解是通过芳香烃被氧化酶氧化导致苯环开环来实现的。微生物对多环芳烃的降解是在单加氧酶或双加氧酶的催化作用下被最终降解为二氧化碳和水而被分解。并对影响石油烃降解微生物的因素包括温度、营养物质等因素进行了分析。     

微生物降解石油污染物机制研究进展

石油污染是当前紧迫的水环境问题,研究石油污染物降解机制有助于探索石油污染修复技术路径。重点介绍了微生物降解石油污染物过程中的微生物种类、降解机制和反应机理,即具有代表性的细菌、真菌和藻类,石油烃的有氧降解(链烷烃、环烷烃和芳香烃)和厌氧降解(脱氢羟基化、延胡索酸盐加成)。并对微生物降解石油组分的影响因素进行了讨论,具体包括:烃类结构(支链多结构越复杂,越难降解)、微生物种类(混合菌的生化降解能力更强)、环境因子(pH、温度、盐度、含氧量和营养物质),进一步指出了生物修复技术应用于石油污染修复治理研究中的优缺点。此外,还对现有微生物降解技术的应用做了简要概述,归纳总结现有研究中存在的问题,尝试性的提出了今后生物降解石油污染物的研究重点,即生物降解石油的机制还需进一步明确,并重点分析了生物电化学方法在降解去除石油污染物方面可行性。综述石油烃生物降解机制和反应机理,以期为生物修复水体石油污染提供参考和借鉴作用。     

不动杆菌属(Acinetobacter)细菌降解石油烃的研究进展

不动杆菌属细菌分布广泛,作为重要的石油烃降解者,在乳化和降解石油烃、降低石油烃生物毒性等方面有重要作用。本文概述了不动杆菌属细菌对烷烃、芳香烃等石油烃组分的降解,总结了该属细菌中已发现的烷烃氧化酶和芳香烃氧化酶,综述了该属细菌所分泌的表面活性剂的类型和乳化机理,讨论了固定化对该属细菌降解石油烃的影响,展望了该属细菌降解石油烃的应用前景。基于此,作者认为探索不动杆菌属细菌降解石油烃的详细机理和途径、发现关键酶、寻找遗传工具、构建基因工程菌、发掘环境友好的固定化材料,应是未来的研究重点及热点。     

低温微生物修复石油烃类污染土壤研究进展

耐冷菌、嗜冷菌等低温微生物广泛存在于极地、高山以及高纬度等土壤环境中,是石油烃类污染物在低温条件下降解与转化的重要微生物资源.利用低温微生物的独特优势,石油污染土壤的低温生物修复技术的研究成为当前热点领域.本文系统综述了低温石油烃降解菌的分类及冷适机制,低温微生物对不同类型石油烃组分的降解特征和降解机理,低温环境中接种降解菌、添加营养物质和表面活性剂等强化技术在石油污染土壤中生物修复的应用.以及微生物分子生物学技术在低温微生物降解石油烃的研究现状,为拓展我国石油污染土壤生物修复技术提供参考.     

石油烃污染土壤的生物修复

从中原油田污染土壤中通过实验室驯化培养分离到一组能以中原原油为碳源的快速生长的石油烃降解菌.用该组降解菌接种原油污染土壤,研究其原位生物联合修复实验,接种降解菌的各区分别种植大豆、施有机肥料、施有机肥料和锯末,与空白试样作对比.经过120d的联合修复,各区石油降解菌的总数(lgcfu/g)由接种时的5.25分别变为7.79、4.96、5.15、4.67.石油烃降解率分别达到89.4%、72.5%、76.7%、49.2%.表明分离的该组石油烃降解菌是一组高效降解菌且其与植物联合修复石油污染土壤能显著提高修复效果.     

石油中长链烷烃微生物降解及分子机制研究进展

中长链烷烃是石油烃中的重要组成部分,由于其疏水性强、黏度大、化学活性低、难降解,是地下原油黏度大、石油采收率低、泄漏后长期污染生态环境的重要原因,因此成为提高石油采收率和石油污染环境治理中的重要降解目标。微生物降解中长链烷烃作为一种新型高效的绿色技术日益受到重视。本文总结了微生物降解中长链烷烃的间期适应与转运过程,与转运过程相关的膜蛋白,微生物好氧与厌氧降解的代谢途径,以及好氧降解过程中的基因调控机制,并对微生物降解中长链烷烃的研究方向提出了展望,以期为后续的相关研究工作提供参考。     

长链烷烃降解菌的降解特性

对长链烷烃降解菌的降解能力和摄取模式进行了研究。评价14株烃降解菌利用中长链烃生长的能力,发现只有少数烃降解菌能够获得良好生长,其中Mycobacterium fortuitum514,Pseudomonas aeruginosa1785和Pseudomonas marginata766等3株菌能够高效降解C20到C33的长链烷烃。辛烷不能支持这些长链烷烃降解菌的生长,说明其烃氧化酶与Pseudomonas oleovorans的OCT质粒编码的单氧酶不同。此外,M.fortuitum不产胞外表面活性剂,而P.aeruginosa和P.marginata则是表面活性剂产生菌,然而三者在以烃为碳源生长时均显示出很高的细胞表面疏水性。根据生长现象分析3株菌采用了不同的烷烃摄取模式。     

Microbial communities in oil-contaminated seawater

Although diverse bacteria capable of degrading petroleum hydrocarbons have been isolated and characterized, the vast majority of hydrocarbon-degrading bacteria, including anaerobes, could remain undiscovered, as a large fraction of bacteria inhabiting marine environments are uncultivable. Using culture-independent rRNA approaches, changes in the structure of microbial communities have been analyzed in marine environments contaminated by a real oil spill and in micro- or mesocosms that mimic such environments. Alcanivorax and Cycloclasticus of the gamma-Proteobacteria were identified as two key organisms with major roles in the degradation of petroleum hydrocarbons. Alcanivorax is responsible for alkane biodegradation, whereas Cycloclasticus degrades various aromatic hydrocarbons. This information will be useful to develop in situ bioremediation strategies for the clean-up of marine oil spills.     

不同类型原油污染土壤生物修复技术研究

对不同类型原油污染土壤在实用规模的预制床上采用堆制技术进行生物修复 .通过投加肥料、菌剂、控制水分和pH ,可使微生物获得较好的生态环境 .当稀油、高凝油、特稠油和稠油污染的土壤中原油总量为 2 5 .8～ 77.2 g·kg-1土时 ,经过近 2个月的运行 ,石油总量的去除率可达 38.37%～ 5 6 .74 % .石油中芳烃、沥青和胶质混合物是制约石油快速降解的主要因素 .在处理过程中筛选出石油降解的优势菌株 ,其中有 6株真菌、6株细菌和 1株放线菌 .研究结果为石油污染土壤异位生物修复技术实用化提供了理论依据 .     

二硝基苯胺类除草剂微生物降解研究进展

二硝基苯胺类除草剂是一类广谱、高效且广泛使用的除草剂,微生物的降解代谢作用是其在环境中消解的最主要因素。分离筛选除草剂的高效降解菌株、分析其降解途径并阐明其微生物降解机制,可为除草剂残留污染的微生物降解修复提供理论依据和优良的降解菌株、降解基因和酶资源。本文简述了二硝基苯胺类除草剂的微生物降解菌株、降解代谢途径和降解基因/酶的研究进展,为进一步研究该类除草剂的微生物降解及其污染生物修复提供理论依据和资源。     

石油污染生态系统中细菌群落结构及其代谢机制研究进展

石油化工产品的不合理处置与泄漏导致石油及其衍生物大量释放到环境中,由此造成的环境污染问题日益严重,石油污染已成为全球性公害之一。微生物修复技术凭借其成本低、环境友好等优势,广泛应用于石油污染的治理。大量研究表明功能微生物群落在石油污染生态系统的修复体系中发挥了重要的作用。其中,细菌是最主要、最活跃的石油降解微生物。然而,在原位/异位生物修复过程中,存在功能菌群在污染体系中难维持、易失调及石油烃降解途径不明晰等问题。因此,本文总结了石油污染自然生态系统和微宇宙实验体系中的细菌群落结构、石油烃代谢机制及相关功能基因,并对微生物法处理石油污染的未来研究方向提出展望,为石油污染场地生物修复方案的制定提供理论参考。     

Assessment of the horizontal transfer of functional genes as a suitable approach for evaluation of the bioremediation potential of petroleum-contaminated sites: a mini-review

Petroleum sludge contains recalcitrant residuals. These compounds because of being toxic to humans and other organism are of the major concerns. Therefore, petroleum sludge should be safely disposed. Physicochemical methods which are used by this sector are mostly expensive and need complex devices. Bioremediation methods because of being eco-friendly and cost-effective overcome most of the limitations of physicochemical treatments. Microbial strains capable to degrade petroleum hydrocarbons are practically present in all soils and sediments and their population density increases in contact with contaminants. Bacterial strains cannot degrade alone all kinds of petroleum hydrocarbons, rather microbial consortium should collaborate with each other for degradation of petroleum hydrocarbon mixtures. Horizontal transfer of functional genes between bacteria plays an important role in increasing the metabolic potential of the microbial community. Therefore, selecting a suitable degrading gene and tracking its horizontal transfer would be a useful approach to evaluate the bioremediation process and to assess the bioremediation potential of contaminated sites.     

Microbial community dynamics during assays of harbour oil spill bioremediation: a microscale simulation study

AIMS: Microcosm experiments simulating an oil spill event were performed to evaluate the response of the natural microbial community structure of Messina harbour seawater following the accidental load of petroleum. METHODS AND RESULTS: An experimental harbour seawater microcosm, supplemented with nutrients and crude oil, was monitored above 15 days in comparison with unpolluted ones (control microcosms). Bacterial cells were counted with a Live/Dead BacLight viability kit; leucine aminopeptidase, beta-glucosidase, alkaline phosphatase, lipase and esterase enzymes were measured using fluorogenic substrates. The microbial community dynamic was monitored by isolation of total RNA, RT-PCR amplification of 16S rRNA, cloning and sequencing. Oil addition stimulated an increase of the total bacterial abundance, leucine aminopeptidase and phosphatase activity rates, as well as a change in the community structure. This suggested a prompt response of micro-organisms to the load of petroleum hydrocarbons. CONCLUSIONS: The present study on the viability, specific composition and metabolic characteristics of the microbial community allows a more precise assessment of oil pollution. Both structural and functional parameters offer interesting perspectives as indicators to monitor changes caused by petroleum hydrocarbons. SIGNIFICANCE AND IMPACT OF THE STUDY: A better knowledge of microbial structural successions at oil-polluted sites is essential for environmental bioremediation. Data obtained in microcosm studies improve our understanding of natural processes occurring during oil spills.     

Biodegradation of petroleum hydrocarbons in estuarine sediments: metal influence

In this work, the potential effect of metals, such as Cd, Cu and Pb, on the biodegradation of petroleum hydrocarbons in estuarine sediments was investigated under laboratory conditions. Sandy and muddy non-vegetated sediments were collected in the Lima River estuary (NW Portugal) and spiked with crude oil and each of the metals. Spiked sediments were left in the dark under constant shaking for 15 days, after which crude oil biodegradation was evaluated. To estimate microbial abundance, total cell counts were obtained by DAPI staining and microbial community structure was characterized by ARISA. Culturable hydrocarbon degraders were determined using a modified most probable number protocol. Total petroleum hydrocarbons concentrations were analysed by Fourier Transform Infrared Spectroscopy after their extraction by sonication, and metal contents were determined by atomic absorption spectrometry. The results obtained showed that microbial communities had the potential to degrade petroleum hydrocarbons, with a maximum of 32 % degradation obtained for sandy sediments. Both crude oil and metals changed the microbial community structure, being the higher effect observed for Cu. Also, among the studied metals, only Cu displayed measurable deleterious effect on the hydrocarbons degradation process, as shown by a decrease in the hydrocarbon degrading microorganisms abundance and in the hydrocarbon degradation rates. Both degradation potential and metal influence varied with sediment characteristics probably due to differences in contaminant bioavailability, a feature that should be taken into account in developing bioremediation strategies for co-contaminated estuarine sites.