分子微生物生态学技术在中国油田开发中的应用

分子微生物生态学技术近年来在研究油藏环境中微生物群落和生态系统等方面得到了广泛的应用,已经成为指导微生物采油技术开发和应用的一个不可或缺的工具.本文较系统地总结了我国利用分子微生物生态学方法研究油藏微生物群落结构的进展,其中包括大庆油田和西北部油田的16SrRNA基因序列分析,胜利油田16SrDNA的荧光标记末端多形态限制性片断分析技术(T-RFLP),以及吉林油田应用的DNA基因跟踪检测技术,并指出了存在问题和研究方向.图1参18     

嗜酸微生物生态学与矿物生物浸出技术

综述了嗜酸微生物存在的环境、生态结构和微生物多样性,以及温度、氧对嗜酸微生物的影响.总结了嗜酸微生物群落间存在竞争、捕食、共生、合作等相互作用关系,这对理解矿物的生物浸出具有重要意义.目前对嗜酸微生物生态学的理解主要基于传统的纯菌培养分离技术,但是分子生物学技术的发展提供了更科学的研究手段,将纯菌培养分离技术和分子生物学技术相结合是研究嗜酸微生物生态的有效方法.认为理解嗜酸微生物生态学规律,将有利于开发新的微生物矿物加工技术,我国有必要加强浸矿微生物生态学的研究.表1参24     

废水生物强化处理技术研究进展

生物强化技术具有高效去除目标污染物、加速系统启动、提高系统抗水力及有机负荷能力以及优化系统菌群结构和增强功能稳定性等功能,在废水生物处理实际应用中潜力巨大.总结了国内外废水生物强化处理技术研究进展,在功能微生物选育方面,通过传统选育手段与基因工程手段并举来实现;在功能菌应用与生物强化处理工艺方面,主要通过所投加的功能菌直接作用或是利用基因水平转移(HGT)来实现生物强化;在分子检测技术方面,随着分子生物学的发展,一些技术如变性梯度凝胶电泳(DGGE)、核糖体间隔基因分析方法(RISA)及荧光原位杂交(FISH)等在与微生物生态学研究中得到了广泛应用.分析认为,应用分子生物学等先进技术手段,探讨废水生物强化处理工程应用过程中的微生物生态学机制,并以此为指导研发高性能菌剂,将是本领域的研究重点与方向之一.     

分子生物学方法在微生物多样性及微生物生态研究中的应用

首先介绍了分子生物学技术在微生物多样性及微生物生态研究中应用的理论基础，以及在此基础上引入的分子生物学技术如：PCR、DNA杂交技术在分子层面上来研究微生物遗传多样性，并结合已有工作积累展望了分子微生物生态研究的发展前景．图2参20     

菌剂对堆肥的作用及其应用

好氧高温堆肥是一种受微生物控制的有机物降解和转化的过程。在堆肥过程的不同阶段对有机物降解起关键作用的微生物种群不同。接种菌剂可以使堆肥物料快速达到高温、控制堆肥过程中臭气的产生，缩短堆肥腐熟进程；可以有效杀灭病原体和降解有机污染物，提高堆肥质量。堆肥产品含有生物活性的微生物，作物增产效果显著。文章总结了接种菌剂在堆肥过程中的作用和应用效果，提出接种菌剂的研究首先应利用传统微生物研究法和先进的分子生态学技术摸清堆肥过程中微生物活动规律，逐步筛选出所需功能性菌群，在堆肥应用时要确定菌剂的最佳接种时间和接种量。     

数学模型在合成微生物群落构建中的应用

微生物在自然环境中分布广泛、多样性高,作为群落成员发挥着重要的生态系统功能.然而,自然微生物群落的组成和相互作用极其复杂,简单可控的合成微生物群落更易于研究微生物群落多样性与生态系统功能的关系及其相互作用机制等关键微生物生态学问题.将数学模型应用于合成微生物群落是目前合成微生物生态学研究的重要手段,有助于理解微生物群落的动态演替和生态学原理.本文综述构建合成微生物群落的数学模型,分别描述微生物个体、种群和基因组水平构建模型的基本原理和优缺点及其在合成微生物群落构建中的应用最新进展,并讨论集成微生物个体、种群与基因组水平的建模方法,指出通过"设计—构建—分析—学习"的循环能更好地实现数学模型在合成微生物群落构建中的应用,推动合成微生物生态学的研究.同时,介绍合成微生物群落在工业技术、环境修复、人类健康等方面的应用,展望数学模型在合成微生物群落构建中应用的发展方向与应用前景.未来应从完善实验数据和模型算法以及两者更好地结合等方面入手,提高数学模型在微生物群落构建中的预测性、适用性与通用性,并将这些模型应用于合成微生物生态学和微生物组工程,为相关生物技术提供理论指导,促进生物经济的发展.(图1表1参95)     

微生物研究在土壤质量评估中的应用

为了防止土壤退化,实现资源的持续利用,必须对土壤质量进行评估.传统的理化指标已难满足需要,寻找能够全面反映土壤质量动态变化和判别胁迫环境或人为干扰下土壤质量变化的灵敏指标,已成为土壤生态学的研究热点.土壤微生物是土壤生态系统的重要组分,在生物地球化学循环过程中有重要的作用,对土壤环境变化和胁迫的反应十分灵敏.但由于土壤微生物种类繁多且难以培养,限制了其在土壤质量评价中的应用.近年来围绕土壤微生物总量、活性和组成的测定发展出了很多新的技术,如微生物生物量测定、土壤酶活件测定、土壤诱导呼吸强度测定、Biolog微量分析、纯培养、磷脂脂肪酸谱图分析和分子生物学技术等,极大地促进了微生物指标在土壤质量评价中的应用.本文就这3个方面的土壤微生物研究技术及其在土壤质量评价中的应用进行评述.表1参70.     

油藏厌氧微生物研究进展

地下深层油藏是独特的缺氧环境,目前还没有直接的微生物学证据表明油藏中存在真正意义上的“本源微生物”,但经注水开发后的油藏中确实蕴藏着复杂的微生物区系.油藏性质决定了油藏厌氧微生物特殊的群落结构,而油藏微生物的作用也可以改变油藏的理化及地质学特性.油藏中厌氧微生物按生理类群主要可分为发酵细菌、硝酸盐还原菌、铁还原菌、硫酸盐还原菌和产甲烷古菌.本文综述了国内外近年来油藏微生物学的研究进展,简述了微生物分子生态学在油藏微生物学研究中的应用,并对当前的研究提出了一些思考.图1参37     

分子技术在湿地微生物群落解析中的应用

人工湿地的研究和应用近年来受到了广泛重视。微生物是人工湿地系统的重要组成部分,其群落结构对于湿地的净化功能的发挥具有重要影响。与传统的微生物分析技术相比,分子生物学技术在解析人工湿地微生物群落结构时无需纯培养,具有高效、快速、简便的特点,使其广泛应用于环境微生物的研究。文章综述了近年来在聚合酶链反应技术（Polymerase Chain Reaction,PCR）基础上发展起来的几种新的分子生物技术,包括PCR-DGGE、LH-PCR、T-RFLP、PCR-SSCP和ARDRA,以及其在人工湿地微生物研究中的应用现状。通过这些分子技术,可以分析湿地处理特定废水过程中微生物的数量、丰度、多样性及优势种;鉴定湿地中特定功能菌群（如氨氧化细菌、反硝化细菌、除硫菌等）的数量、活动分布、空间变更及与污染物去除的关系;判断各种系统条件（如不同基质、植物、水力负荷等）的设置对微生物多样性和稳定性的影响。最后,对分子技术在湿地领域的未来发展进行了展望。     

宏基因组技术及其在环境保护和污染修复中的应用

宏基因组学是分子生物学技术应用于微生物生态学研究而形成的一个新概念,以环境中末培养微生物为研究对象,通过直接从环境样品中提取全部微生物的DNA,构建宏基因组文库,利用基因组学策略研究环境样品所包含的全部微生物的遗传组成及其群落功能.从1998年提出至今,该项技术已经广泛应用于工业、农业、医学等研究领域.文章在对宏基因组学的概念、研究方法、存在问题的综述基础上提出了相应的解决方法,并指出该技术在环境保护和污染修复中存在潜在的应用价值.利用该技术可以深入了解特定环境中微生物空间分布和动态变化,为环境监测、预警和评价提供理论依据.     

Current molecular biologic techniques for characterizing environmental microbial community

Microbes are vital to the earth because of their enormous numbers and instinct function maintaining the natural balance. Since the microbiology was applied in environmental science and engineering more than a century ago, researchers desire for more and more information concerning the microbial spatio-temporal variations in almost every fields from contaminated soil to wastewater treatment plant (WWTP). For the past 30 years, molecular biologic techniques explored for environmental microbial community (EMC) have spanned a broad range of approaches to facilitate the researches with the assistance of computer science: faster, more accurate and more sensitive. In this feature article, we outlined several current and emerging molecular biologic techniques applied in detection of EMC, and presented and assessed in detail the application of three promising tools.     

SIZE DOESN'T MATTER: MICROBIAL SELECTION EXPERIMENTS ADDRESS ECOLOGICAL PHENOMENA

Experimental evolution is relevant to ecology because it can connect physiology, and in particular metabolism, to questions in ecology. The investigation of the linkage between the environment and the evolution of metabolism is tractable because these experiments manipulate a very simple environment to produce predictable evolutionary outcomes. In doing so, microbial selection experiments can examine the causal elements of natural selection: how specific traits in varying environments will yield different fitnesses. Here, we review the methodology of microbial evolution experiments and address three issues that are relevant to ecologists: genotype-by-environment interactions, ecological diversification due to specialization, and negative frequency-dependent selection. First, we expect that genotype-by-environment interactions will be ubiquitous in biological systems. Second, while antagonistic pleiotropy is implicated in some cases of ecological specialization, other mechanisms also seem to be at work. Third, while negative frequency-dependent selection can maintain ecological diversity in laboratory systems, a mechanistic (biochemical) analysis of these systems suggests that negative frequency dependence may only apply within a narrow range of environments if resources are substitutable. Finally, we conclude that microbial experimental evolution needs to avail itself of molecular techniques that could enable a mechanistic understanding of ecological diversification in these simple systems.     

微生物苯丙氨酸解氨酶(PAL)/肉桂酸途径生物转化制L-苯丙氨酸酶源菌种选育

Ｌ苯丙氨酸（Ｌｐｈｅｎｙｌａｌａｎｉｎｅ,ＬＰｈｅ）是生化营养的必需氨基酸之一,作为临床医药用氨基酸输液、食品、饲料添加剂的必需成份和一些抗癌药物苯丙氨酸氮芥、甲酰溶肉瘤素等合成的中间体而得到广泛应用．自１９６５年天冬甜肽（Ａｓｐａｒｔａｍｅ,ＡＰＭ,阿斯巴甜）发现并开发生产以来,这一新型甜味剂日渐风行,导致对高光学纯度ＬＰｈｅ这一主要构成原料需求量激增,人们纷纷开展ＬＰｈｅ的研制生产．在众多生物合成途径中,肉桂酸酶法转化生产ＬＰｈｅ的研究开发因其原料易得价廉,倍受国内外的许多公司和…     

醌类图谱分析在环境微生物生态测定中的应用

近年来，随着人们对各种非培养微生物测定法的重视，醌类图谱分析作为微生物群体指标已在各种环境中得到了应用．首先是样品的分析测定技术得到了提高，如用硅胶柱代替薄层色谱．醌类图谱分析的特点是能够同时对应微生物生态评价的3个重要指标，即微生物群体结构、生物量及微生物多样性．在结合统计分析的基础上，在土壤、污泥及堆肥等不同环境样品及不同微生物反应过程中，已通过醌类图谱分析对这3个指标在微生物生态系中的变动进行了成功的评价．另外，对C-14同位素标记醌类图谱分析法及醌类图谱分析法在污染物降解中的应用等最新进展也进行了简介．图4表3参43     

Microbial stress-response physiology and its implications for ecosystem function

Microorganisms have a variety of evolutionary adaptations and physiological acclimation mechanisms that allow them to survive and remain active in the face of environmental stress. Physiological responses to stress have costs at the organismal level that can result in altered ecosystem-level C, energy, and nutrient flows. These large-scale impacts result from direct effects on active microbes' physiology and by controlling the composition of the active microbial community. We first consider some general aspects of how microbes experience environmental stresses and how they respond to them. We then discuss the impacts of two important ecosystem-level stressors, drought and freezing, on microbial physiology and community composition. Even when microbial community response to stress is limited, the physiological costs imposed on soil microbes are large enough that they may cause large shifts in the allocation and fate of C and N. For example, for microbes to synthesize the osmolytes they need to survive a single drought episode they may consume up to 5% of total annual net primary production in grassland ecosystems, while acclimating to freezing conditions switches Arctic tundra soils from immobilizing N during the growing season to mineralizing it during the winter. We suggest that more effectively integrating microbial ecology into ecosystem ecology will require a more complete integration of microbial physiological ecology, population biology, and process ecology.     

Application of temperature gradient gel electrophoresis technique to monitor changes in the structure of the eukaryotic leaf-epiphytic community of <Emphasis Type="Italic">Posidonia oceanica</Emphasis>

Seagrass leaves have been recognized as a suitable substratum in shallow sedimentary environments for the establishment of epiphytic communities. Microscope-based identification of species has been traditionally used to monitor changes in the composition of the eukaryotic leaf-epiphytic community of the seagrass Posidonia oceanica (L.) Delile. Our main goal was to adapt the temperature gradient gel electrophoresis (TGGE) barcoding technique largely used in molecular microbial ecology studies to monitor changes in the composition of P. oceanica epiphytic community. This molecular technique has been successful for handling large amounts of samples in a fast and reproducible manner. To that end, we applied the TGGE technique to study the epiphytic community in two different seasons and compare the results with those provided by the classical microscope approach. The results obtained with both approaches were generally consistent. The complexity of the banding pattern produced by TGGE was mirrored by the taxa richness of the community described using the classical approach. The minimum number of P. oceanica shoots necessary to adequately represent the composition of the eukaryotic leaf-epiphytic community was of the same order of magnitude for both techniques. Partial gene sequences of some selected bands affiliated with sequences of zoo and phytoephytic taxa. Some of them were detected using microscopy. Our results showed that TGGE is an excellent approach for comparative macrobenthic community studies that need parallel treatment of many samples at a time. To the best of our knowledge, this is the first time in which molecular barcoding techniques have been applied to the comparison of eukaryotic epiphytic communities.     

Identifying human-induced influence on microbial community: A comparative study in the effluent-receiving areas in Hangzhou Bay

Microbial compositions showed high differences in two study areas. COD was the key anthropogenic indicator in the coastal wastewater disposal area. Distinctive microbes capable of degrading toxic pollutants were screened. Microbial communities in effluent-receiving areas followed “niche theory”. Microbial community structure is affected by both natural processes and human activities. In coastal area, anthropegenetic activity can usually lead to the discharge of the effluent from wastewater treatment plant (WWTP) to sea, and thus the water quality chronically turns worse and marine ecosystem becomes unhealthy. Microorganisms play key roles in pollutants degradation and ecological restoration; however, there are few studies about how the WWTP effluent disposal influences coastal microbial communities. In this study, sediment samples were collected from two WWTP effluent-receiving areas (abbreviated as JX and SY) in Hangzhou Bay. First, based on the high-throughput sequencing of 16S rRNA gene, microbial community structure was analyzed. Secondly, several statistical analyses were conducted to reveal the microbial community characteristics in response to the effluent disposal. Using PCoA, the significant difference of in microbial community structure was determined between JX and SY; using RDA, water COD and temperature, and sediment available phosphate and ammonia nitrogen were identified as the key environmental factors for the community difference; using LDA effect size analysis, the most distinctive microbes were found and their correlations with environmental factors were investigated; and according to detrended beta-nearest-taxon-index, the sediment microbial communities were found to follow “niche theory”. An interesting and important finding was that in SY that received more and toxic COD, many distinctive microbes were related to the groups that were capable of degrading toxic organic pollutants. This study provides a clear illustration of eco-environmental deterioration under the long-term human pressure from the view of microbial ecology.