分子生物学技术在生物修复中的应用研究进展

随着分子生物学技术如分子杂交、PCR、电泳技术等的发展,微生物学研究领域发生了深刻的变革,灵敏的检测和精确的细菌鉴定成为可能.微生物分子生态学作为分子生物学与微生物生态学交叉而形成的学科,在生物修复方面得到广泛应用.从分子生物学实验技术角度综述了各种微生物分子生物学技术在生物修复中的应用研究情况.     

Microbial Biofilms: from Ecology to Molecular Genetics

Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development.     

Linking Molecular Microbial Ecology to Geochemistry in a Coastal Hypoxic Zone

Multiple environmental mechanisms have been proposed to control bottom water hypoxia (<2 mg O₂ L^?1) in the northern Gulf of Mexico Louisiana shelf. Near-bottom hypoxia has been attributed to a direct consumption of oxygen through benthic microbial respiration and a secondary chemical reaction between oxygen and reduced metabolites (i.e. ferrous iron and total sulfide) from these populations. No studies to date have examined the metabolically active microbial community structure in conjunction with the geochemical profile in these sediments. Temporal and spatial differences in dissolved and solid phase geochemistry were investigated in the upper 20 cm of the sediment column. Pyrosequencing of reverse transcribed small subunit (SSU) ribosomal ribonucleic acid (rRNA) was used to determine population distribution. Results indicated that populations shallower than 10 cm below surface were temporally variable yet uniform between sites, while below this depth, populations were more site-specific. This suggests a potential interaction between the water column and the benthic microbial population limited to a shallow depth. The presence of dissolved reduced iron in the upper sediment column was indicative of low oxygen concentration, yet sulfide was at or below detection limits. Putative sulfate and iron reducing and oxidizing populations were metabolically active at similar depths suggesting potential recycling of products. Results from this study indicate low carbon concentrations in the shallow sediments limit general metabolic activity, reducing the potential for microbial respiration. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

微生物分子生态学技术在湖泊微生物多样性研究中的应用

微生物是湖泊生物圈物质循环和能量流动的主要参与者,在湖泊的生态系统中起着重要的作用。但是,湖泊中存在着大量不可培养的细菌,利用传统的培养技术,无法对湖泊微生物的多样性进行深入而全面的研究,而不依赖培养的分子生物学技术的发展为此方面研究开辟了新的路径。微生物分子生态学作为分子生物学与微生物生态学交叉产生的学科,在研究湖泊微生物多样性方面已经得到了广泛的应用。主要综述了变性梯度凝胶电泳(PCR-DGGE)技术,末端限制性酶切片段长度多态性技术(T-RFLP),16SrDNA克隆文库技术等微生物分子生态学技术在研究湖泊微生物多样性方面的应用情况。     

How to Deal with Resource Productivity

Resource productivity enhancement stands at the center of tackling issues on environmental pollution and resource scarcity. Identifying influential socioeconomic factors should be the first step in establishing and improving resource management policy. This study compares and analyzes data from multiple countries to construct a resource productivity simulation model. The socioeconomic factors and their characteristic patterns are discussed in detail. The results demonstrate that the major factors influencing resource productivity include income level, population density, economic structure, energy structure, and raw material trade. Among these factors, the three most important are income level, population density, and economic structure. The influencing patterns can be summarized as follows: (1) Resource productivity increases with increasing income levels. (2) Countries with high population density are inclined to demonstrate high resource productivity. (3) The economic structure shows a biphase influence on resource productivity, that is, during industrialization, decreased agricultural activity and increased industrial activity lead to higher resource productivity. On the other hand, after industrialization, decreasing industrial activity and an expanding service sector become the major impetus of resource productivity enhancement. (4) Raw material export demonstrates a negative effect on resource productivity. Countries that depend heavily on raw material export show a unique resource productivity evolution pattern. For these countries, relatively high resource productivity in low income phases and relatively low resource productivity in high income phases show only small increases in resource efficiency and economic growth. Finally, insights from the study are transformed into suggestions for sustainable resource management and resource productivity enhancement.     

分子生物学方法及其在海洋微生物生态中的应用

微生物在生态系统中起着独一无二的生态作用.微生物生态学的发展和工农业、环境保护及社会科学有着紧密的联系.海洋作为地球上最大的生境,孕育着大量的生物资源,是研究微生物生态的主要来源.综述微生物生态研究相关的分子生物学方法及海洋微生物生态的应用进展.     

rRNA技术及其在分子微生物生态上的应用

传统的基于微生物培养与纯种分离的技术所具有的局限性,以及分子生物学及其有关技术的长足进展,使微生物生态学的研究进入了分子的阶段.其中rRNA技术的建立、发展及其成功应用,为分子微生物生态和微生物系统分类学的研究掀开了崭新的一页.对rRNA分子技术的研究进展、以之为基础的主要方法及其在环境微生物研究中的应用,以及应用过程中所存在的一些潜在问题及其解决办法等作了详细综述.     

油藏微生物多样性的分子生态学研究进展

油藏微生物是一类宝贵的资源,在油层生态系统的物质循环和能量流动中发着主导作用.传统上,主要依赖纯培养技术,使得大部分油藏微生物都没能得到充分认识.分子方法克服了纯培养方法中遇到的问题,能更好地了解环境微生物群落多样性.近年来,在油藏微生物群落多样性研究中的应用进展迅速,对油藏微生物学和生态学的发展产生了重要影响.文中评述了近年来国内外在油藏微生物分子生态方面的研究进展,并对进一步的研究提出了展望.     

油藏微生物多样性的分子生态学研究进展

油藏微生物是一类宝贵的资源, 在油层生态系统的物质循环和能量流动中发挥着主导作用。传统上, 主要依赖纯培养技术, 使得大部分油藏微生物都没能得到充分认识。分子方法克服了纯培养方法中遇到的问题, 能更好地了解环境微生物群落多样性。近年来, 在油藏微生物群落多样性研究中的应用进展迅速, 对油藏微生物学和生态学的发展产生了重要影响。文中评述了近年来国内外在油藏微生物分子生态方面的研究进展, 并对进一步的研究提出了展望。     

分子生物学方法在水体微生物生态研究中的应用

微生物是生态系统的重要组成部分,研究水体中微生物的多样性和群落结构对于开发微生物资源、进行水体生物修复具有重要意义。现代分子生物学的发展为研究水体微生物提供了行之有效的方法。综述了16S rDNA文库构建、变性梯度凝胶电泳、限制性片段长度多态性、末端标记限制性片段长度多态性等技术的原理以及在水体微生物研究中的主要应用。     

现代分子生物学技术在冰川微生物生态研究中的应用

研究冰川中微生物的多样性对于揭示环境气候变迁,研究生物进化,开发微生物资源具有重要意义,现代分子生物学的发展为研究冰川微生物的多样性提供了行之有效的方法.简要综述了16S rDNA文库构建、变性梯度凝胶电泳、限制性片段长度多态性和荧光原位杂交等技术的原理及在冰川微生物生态研究中的应用现状.     

微生物生态学中分子生物学方法及T-RFLP技术研究

根据微生物基因 (DNA)多态性来研究微生物的多样性 ,是建立在多聚酶链式反应 (PCR)基础之上分子生物学的新方法 ,克服了传统微生物培养方法的限制。从理论、实验及应用角度出发 ,介绍了几种在微生物生态学中应用较为广泛的分子生物学技术 ;详细阐述了微生物生态学中分子生物学的一种新研究方法---末端限制性片段长度多态性 (T -RFLP)技术 ,该技术作为一种研究微生物群落特征的理想方法已经越来越受到人们的重视。     

未培养微生物的研究与微生物分子生态学的发展*

近年来现代分子技术和基因组学逐渐渗透到有关生命科学的整个领域,也为微生物生态学提供了新的研究方法和机遇。16S rRNA基因序列分析、DNA-DNA杂交、核酸指纹图谱以及宏基因组学等分子技术检查自然环境中的微生物,可以克服传统纯培养技术的不足,是一条探知未培养微生物、寻找新基因及其产物的新途径,开启了我们认识微生物多样性和获得新资源的大门。     

变性梯度凝胶电泳技术在微生物分子生态学研究中的应用

变性梯度凝胶电泳在微生物分子生态学研究中的应用日益广泛,已成为研究微生物多样性和动态变化的有力工具.对变性梯度凝胶电泳技术中存在的问题,如基因片段的选择、共迁移、背景色和异源双链分子的形成等作了综述,以期为进一步更好地利用该技术进行微生态的研究奠定基础.     

微生物分子生态学研究方法的新进展

环境中微生物的群落结构及多样性和微生物的功能及代谢机理是微生物生态学的研究热点,长期以来,由于受到研究技术的限制,对微生物的群落结构和多样性的认识还不全面,微生物的功能及代谢机理方面了解也很少.随着高通量测序、基因芯片等新技术的不断更新,微生物分子生态学的研究方法和研究途径也在不断变化.高通量测序技术改变了微生物多样性、宏基因组学和宏转录组学的研究方法,GeoChip高密度覆盖海量已知功能的基因探针于单张芯片,能快速确定微生物和已知功能基因的存在与否.总结和比较了目前最新的研究手段,并归纳了这些方法的适用性和优缺点.     

DGGE/TGGE技术在土壤微生物分子生态学研究中的应用

传统的微生物生态学研究方法只限于环境样品中极少部分(0.1%￣1%)可培养的微生物类群,极大程度地限制了对土壤微生物群落结构的研究。综述了以16S rDNA为主要研究对象的DGGE/TGGE(Denaturing gradientgel electrophoresis,DGGE/Temperature gradient gel electrophoresis,TGGE)技术原理,以其为主要手段结合PCR扩增、克隆建库、序列测定以及种系分析对土壤微生物的群落结构和多样性研究的最新动态。DGGE/TGGE技术极大地推动了土壤微生物分子生态学的发展,同时也为实际问题的诊断、作物生长跟踪监测等提供了技术支撑,在土壤微生物分子生态学研究和生产实践中起着越来越重要的作用。     

用于分析微生物种类组成的微生物生态学研究方法

对环境中微生物群落进行分析对于理解该环境中各类微生物的功能具有重要意义,因此日益受到重视。用于环境中微生物群落分析的方法很多,将简要介绍基于PCR的研究方法,原位杂交技术,基因芯片技术,宏蛋白质组学技术等研究方法的原理、应用及其优缺点。     

DegePrime,a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies

The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571–1579, 2011, http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.