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。     

瘤胃微生物对纤维素的降解及其应用

瘤胃微生物主要包括细菌、真菌和原生动物。其中,瘤胃细菌和瘤胃真菌能分泌纤维素酶,对纤维素有较强的降解能力,主要介绍了瘤胃微生物对纤维素的降解作用及其广阔的应用前景。     

多环芳烃微生物降解基因的研究进展

多环芳烃(PAHs)是环境中普遍存在的一类有机污染物,微生物的降解是PAHs去除的主要途径。近年来,有关PAHs微生物降解途径和代谢产物的研究已有很多报道。小分子PAHs一般可以直接被微生物降解,而大分子PAHs则需要微生物以共代谢的方式降解。在过去20年中,微生物降解PAHs的基因相继被发现,各种基因在调控PAHs降解过程中的功能也越来越清晰。本文概述了PAHs微生物降解基因方面的研究进展,详细介绍了微生物对萘、菲的降解基因,最后对PAHs微生物降解基因的应用前景进行了展望。     

二噁英的生物降解及其机理

利用微生物降解二噁英是一种具有广阔前景的治理二噁英污染的方法。近年来利用微生物降解二噁英已经引起众多研究者的重视,国外在这方面的研究已取得了一定成果。介绍了能降解二噁英的微生物种类及其所能降解的二噁英类型,对近年来提出的微生物降解(包括氧化降解和还原降解)的可能途径,中间产物及其降解效果进行了综述。并对土壤在被污染后如何进行生物修复等方面进行了探讨。     

微生物对环境中难降解有机污染物共代谢作用

对微生物共代谢途径的概念、机理、类型进行了综述,详细介绍了微生物共代谢作用在去除难降解有机污染物过程中所起到的重要作用,并对微生物共代谢作用降解有机污染物的关键因素及其应用价值做出分析。     

萘的微生物降解研究进展

萘是一类具有严重"三致"效应(致癌、致畸、致突变)的多环芳烃类有机化合物,严重威胁人类健康。萘的微生物降解由于具有操作简单、经济实用及不产生二次污染等优点,近年来成为治理萘污染的主要手段之一。对不同环境中筛选的萘降解菌的系统生物学分类、培养条件对萘微生物降解效率的影响、萘的微生物降解途径、关键基因和酶及其实际应用方面进行了综述,指出了目前萘微生物降解研究领域存在的问题,并对未来的研究方向做出了展望。     

多环芳烃(PAHs)微生物降解的原位表征方法

多环芳烃(polycyclic aromatic hydrocarbons,PAHs)是一类在环境中广泛存在的持久性有机污染物,微生物降解是去除环境中多环芳烃污染的主要途径。传统的有关PAHs微生物降解的研究主要依靠分离培养技术,难以准确认识PAHs微生物降解的原位过程及机制。近年来发展起来的原位表征方法可以在基因及单细胞水平研究PAHs在复杂环境中的微生物降解过程,能够原位表征具有PAHs降解功能的微生物及其功能基因和代谢活性,是阐明PAHs原位降解过程及分子机制的强有力的手段。该文综述了宏基因组技术(meta-genomics)、稳定同位素探针技术(stable isotope probe,SIP)、荧光原位杂交技术(fluorescence in situ hybridization,FISH)、拉曼光谱技术(Raman spectra)以及二次离子质谱技术(secondary ion mass spectrometry,SIMS)等原位表征技术在PAHs微生物降解研究领域的应用及其存在的问题和发展趋势等。PAHs微生物降解过程及机制的原位表征将为缓解与修复PAHs污染提供科学基础。     

微生物对三苯基甲烷类染料脱色的研究进展

三苯基甲烷染料广泛应用于纺织印染、医药、生物染色、造纸、皮革、食品及化妆品等领域, 常见的有作为抗菌剂的孔雀石绿和结晶紫等。由于其特殊的化学结构, 在环境中较稳定且难以降解脱色, 因此其生物脱色降解的研究可为印染废水处理和染料污染环境的生物修复提供理论依据。本文从细菌、放线菌、真菌及藻类等微生物对三苯基甲烷类染料降解脱色研究新进展做综述。通过分析不同微生物脱色三苯基甲烷类染料的中间产物来探讨其降解机理和降解途径, 同时论及功能酶的分离纯化、酶学特性及其编码基因的克隆表达新进展, 并分别从基础理论和应用两方面对微生物降解三苯基甲烷类染料未来的研究方向进行了展望。     

油藏微生物及其压力适应机制

目前我国油田开发主要处于高含水后期,微生物驱提高石油采收率技术(MEOR)以低成本、环境友好等独特的优势引起了石油工业界的重视。实际上,经过半个多世纪的发展,MEOR已经成为提高采收率的重要前沿技术。高压是油藏的主要环境特征,在影响油藏微生物生存与活性等方面具有重要作用。本文从油藏及其微生物的主要特征、微生物对高压环境的适应机制以及高压下微生物降解烃的代谢特征等方面进行了综述。介绍了对油藏微生物资源、群落结构、微生物在油水相中分布的认识,微生物乳化原油机制,以及微生物在油藏厌氧环境中协同代谢、受温度和压力影响的特点,并列举了MEOR的矿场应用。在高压适应机制上,微生物主要通过改变和调整细胞膜结构、增加胞内脂质组分和表达胞内特殊酶等作用来实现对压力的适应;在高压下烃降解微生物代谢速率低于常压,而且耐压菌和嗜压菌具有不同的烃降解效率。     

微生物法降解木质素的研究进展

生物质是代替石化资源生产能源和化学品的关键资源,木质素作为植物细胞壁的主要成分已经在很多行业中得到了广泛的应用。然而,由于木质素结构复杂且难以降解,成为生物质资源利用的最大障碍,因此,去除或者降解木质素是利用细胞壁中其他成分的关键步骤。许多行业使用有害化学物质降解木质素,严重危害了生态环境,自然界中木质素经常被包括真菌和细菌在内的微生物降解,因此,研究微生物降解木质素的机制为解决这一问题提供了可能性。本文讨论了木质素的化学组成成分,重点讨论了自然界降解木质素的微生物种类及其降解机制,包括各种真菌和细菌的木质素降解活性,描述了由各种微生物特别是白腐真菌、褐腐真菌和细菌产生的木质素降解酶,并展望了今后木质素生物降解的研究和应用的可能方向。     

The potential of cloud point system as a novel two-phase partitioning system for biotransformation

Although the extractive biotransformation in two-phase partitioning systems have been studied extensively, such as the water–organic solvent two-phase system, the aqueous two-phase system, the reverse micelle system, and the room temperature ionic liquid, etc., this has not yet resulted in a widespread industrial application. Based on the discussion of the main obstacles, an exploitation of a cloud point system, which has already been applied in a separation field known as a cloud point extraction, as a novel two-phase partitioning system for biotransformation, is reviewed by analysis of some topical examples. At the end of the review, the process control and downstream processing in the application of the novel two-phase partitioning system for biotransformation are also briefly discussed.     

Hypothetical Outcome Plots Outperform Error Bars and Violin Plots for Inferences about Reliability of Variable Ordering

Many visual depictions of probability distributions, such as error bars, are difficult for users to accurately interpret. We present and study an alternative representation, Hypothetical Outcome Plots (HOPs), that animates a finite set of individual draws. In contrast to the statistical background required to interpret many static representations of distributions, HOPs require relatively little background knowledge to interpret. Instead, HOPs enables viewers to infer properties of the distribution using mental processes like counting and integration. We conducted an experiment comparing HOPs to error bars and violin plots. With HOPs, people made much more accurate judgments about plots of two and three quantities. Accuracy was similar with all three representations for most questions about distributions of a single quantity.     

Enzymatic production of enantiopure ketoprofen in a solvent-free two-phase system

Enzymatic hydrolysis conducted in a medium composed of solely substrate is considered to resolve racemic ketoprofen esters. In a system composed of two components, the pure liquid substrate (organic phase) and water (aqueous phase), hydrolysis products can be efficiently removed from the reaction mixtures. Accordingly, in this study we designed a solvent-free two-phase system for the enantioselective enzymatic hydrolysis of ketoprofen esters. In order to further optimize this system, the influences of various factors, such as the pH of the aqueous phase, temperature, enzyme content, and the alcohol chain length of esters, were examined on conversion and enantiomeric excess. 1N NaHCO₃ was identified as the most efficient aqueous phase for the extraction of ketoprofen. Changes in the amount of enzyme did not significantly affect the maximum conversion or the enantiomeric excess. On the other hand, ketoprofen esters with shorter alcohol chains displayed higher initial reaction rates and conversions in solventless media. In the case of ketoprofen propyl ester, for example, the productivity of the solvent-free two-phase system was about 10–100 times higher than that obtained to date for ketoprofen esterification with alcohols in organic solvents. The enantioselectivities obtained in solvent-free media were similar to those obtained for the enantioselective esterification of ketoprofen in organic solvents.     

Recombinant carbazole-degrading strains for enhanced petroleum processing

Biotechnological upgrading of fossil fuels is of increasing interest as remaining stocks of petroleum show increasing levels of contaminants such as heavy metals, sulfur and nitrogen-containing heteroaromatic compounds. Carbazole is of particular interest as a major petroleum component known to reduce refining yields through catalyst poisoning. In this study, the biotransformation of carbazole was successfully demonstrated in a liquid two-phase system, when solubilized in either 1-methylnaphthalene or in diesel fuel. The effects of solvent toxicity were investigated by expressing the carbazole-transformation genes from MB1332, a rifampicin-resistant derivative of Pseudomonas sp. LD2, in a solvent-resistant heterologous host, P. putida Idaho [1]. This solvent-resistant strain successfully degraded carbazole solubilized in 1-methylnaphthalene and in the presence of 10 vol% xylenes similar to the non-recombinant strain Pseudomonas sp. LD2. Identification of a suitable recombinant host, however, was essential for further investigations of partial pathway transformations. Recombinant P. putida Idaho expressing only the initial dioxygenase enzymes transformed carbazole to an intermediate well retained in the oil phase. Partial carbazole transformation converts carbazole to non-aromatic species; their effect is unknown on refinery catalyst poisoning, but would allow almost complete retention of carbon content and fuel value. Electronic Publication     

Efficient Repeated Use of Alcohol Dehydrogenase with NAD + Regeneration in an Aqueous-organic Two-phase System

Bioconversion of cinnamyl alcohol to cinnamaldehyde was carried out in an aqueous-organic two-phase reaction system by the repeated use of horse liver alcohol dehydrogenase (HLADH) and NAD + with coenzyme regeneration. Both HLADH and the coenzyme were efficiently entrapped in the aqueous phase, while the substrate was supplied successively from the organic phase and the product was accumulated in the organic phase. Optimum conditions for cinnamaldehyde production in the aqueous-organic two-phase system were also examined, including substrate concentration, pH, and organic solvent type. Under suitable conditions, both HLADH and NAD + in the aqueous-organic two-phase system could be reused, and NAD + cycling numbers of 3040 were obtained after repeated operation for 40 λh.     

两相分配法制备南极红酵母质膜

用葡聚糖T-500(Dextran T-500)和聚乙二醇(PEG-3350)两相体系制备南极红酵母(Rhodotorula sp.)菌株 NJ298的质膜。首先在2 mmol/L KCl浓度下, 选用5种不同的聚合物浓度(5.6%、5.8%、6.0%、6.2%、6.4 %, W/W), 研究了NJ298质膜在两相体系中的分配情况, 在此基础上进一步研究了KCl浓度(2 mmol/L、4 mmol/L、6 mmol/L、8 mmol/L、10 mmol/L)对NJ298质膜的纯度及得率的影响。结果表明, 选用6.0%聚合物浓度, 4 mmol/L KCl的两相分配体系, 分离3次可得到相对纯度在78.2%的南极红酵母质膜组分, 标志酶鉴定及磷钨酸染色电镜检测均表明获得了高纯度密实的正向型的质膜囊泡。这为进一步研究该菌株的南极极端环境适应机制奠定了基础。     

两相分配法制备南极红酵母质膜

用葡聚糖 T-500(Dextran T-500)和聚乙二醇(PEG-3350)两相体系制备南极红酵母(Rhodotorula sp.)菌株 NJ298 的质膜.首先在 2 mmol/L KCl 浓度下,选用5种不同的聚合物浓度(5.6%、5.8%、6.0%、6.2%、6.4%,W/W),研究了 NJ298 质膜在两相体系中的分配情况,在此基础上进一步研究了 KCl 浓度(2 mmol/L、4 mmol/L、6 mmol/L、8 mmol/L、10 mmol/L)对 NJ298 质膜的纯度及得率的影响.结果表明,选用6.0%聚合物浓度,4 mmol/LKCl 的两相分配体系,分离3次可得到相对纯度在 78.2%的南极红酵母质膜组分,标志酶鉴定及磷钨酸染色电镜检测均表明获得了高纯度密实的正向型的质膜囊泡.这为进一步研究该菌株的南极极端环境适应机制奠定了基础.     

Reaction Medium Selection for An Enzymatic Peptide Synthesis in An Aqueous-Organic Two-Phase System

Efficient development of enzymatic synthesis in two-phase systems is closely related with appropriate selection of the reaction medium (especially the solvent and phase ratio). A selection procedure based on the calculation of the theoretically allowable conversion and product concentration is presented and applied to a peptide synthesis using papain. For the synthesis of the dipeptide Boc-Gly-Phe-OMe, the operating conditions have been determined, and the two-phase system to be used has been successfully selected (with trichloroethylene being the best solvent).     

Two-phase systems: potential for in situ extraction of microalgal products

Algae are currently used for production of niche products and are becoming increasingly interesting for the production of bulk commodities, such as biodiesel. For the production of these goods to become economically feasible, production costs will have to be lowered by one order of magnitude. The application of two-phase systems could be used to lower production costs. These systems circumvent the costly step of cell harvesting, whilst the product is extracted and prepared for downstream processing. The mechanism of extraction is a fundamental aspect of the practical question whether two-phase systems can be applied for in situ extraction, viz, simultaneous growth, product formation and extraction, or as a separate downstream processing step. Three possible mechanisms are discussed; 1) product excretion 2) cell permeabilization, and 3) cell death. It was shown that in the case of product excretion, the application of two-phase systems for in situ extraction can be very valuable. With permeabilization and cell death, in situ extraction is not ideal, but the application of two-phase systems as downstream extraction steps can be part of a well-designed biorefinery process. In this way, processing costs can be decreased while the product is mildly and selectively extracted.Thus far none of the algal strains used in two-phase systems have been shown to excrete their product; the output has always been the result of cell death. Two-phase systems can be a good approach as a downstream processing step for these species. For future applications of two-phase in situ extraction in algal production processes, either new species that show product excretion should be discovered, or existing species should be modified to induce product excretion.     

Whole cell microbial transformation in cloud point system

Cloud point system, consisting of nonionic surfactant in an aqueous solution, has been developed as a novel medium for whole cell microbial transformation. The basic properties of cloud point system including phase separation and solubilization are introduced. The application of cloud point system for extractive microbial transformation is different from that of water-organic solvent two-phase partitioning system or aqueous two-phase system are discussed, which mainly focus on the biocompatibility of microorganism in a cloud point system and a downstream process of microbial transformation in cloud point system with oil-water-surfactant microemulsion liquid-liquid extraction for surfactant recovery and product separation. Finally, examples of whole cell microbial transformation in cloud point systems, especially in situ extraction of moderate polar substrate/product, are also presented.