DNA稳定同位素探针技术在宏基因组学中的应用及前景

DNA稳定同位素探针 (DNA-SIP) 是一种新兴的技术,通过将同位素稳定结合到特定的底物来确定环境中微生物的作用。DNA-SIP与宏基因组学结合可以让某些微生物的特性与其特殊新陈代谢联系在一起,不仅可以从宏基因组库里检测到低含量的微生物,而且加速了对新的酶类和其他生物活性物质的发现。以下总结了SIP-宏基因组学技术的原理、应用及研究进展,并讨论了其在环境微生物学和生物技术的应用前景。     

稳定同位素技术在个体溯源中的应用

个体身份确认是自然灾害、空难、爆炸、火灾、交通事故等事（案）件处置中的一项重要工作。利用稳定同位素分布的地域差异性对个体进行溯源，可以为个体身份确认提供重要信息。本文简要介绍了稳定同位素技术原理，系统阐述了用于个体溯源的元素类型和不同人体组织中稳定同位素蕴含的特征信息，并对该技术在个体溯源中的应用现状、存在问题以及未来发展进行了分析和展望。     

稳定同位素技术在植物水分利用研究中的应用

近20a稳定同位素技术在植物生态学研究中的应用得到了长足发展,使得对植物与水分关系也有了更深一步的了解。介绍稳定同位素性碳、氢、氧同位素在研究植物水分关系中的应用及进展,以期能为国内植物水分利用研究提供参考。由于植物根系从土壤中吸收水分时并不发生同位素分馏,对木质部水分同位素分析有助于对植物利用水分来源,生态系统中植物对水分的竞争和利用策略的研究,更好地了解生态系统结构与功能。稳定碳同位素作为植物水分利用效率的一个间接指标,在不同水分梯度环境中,及植物不同代谢产物与水分关系中有着广泛的应用。同位素在土壤-植被-大气连续体水分中的应用,有助于了解生态系统的水分平衡。随着稳定同位素方法的使用,植物与水分关系的研究将取得更大的进展。     

稳定同位素技术在水域生态系统研究中的应用

稳定同位素作为一种天然的示踪物,应用十分广泛,其在水域生态学中的应用也日益受到重视。生物同位素组成总是与其食物同位素组成相一致,能随食物的改变而相应地发生改变,是生物生存状况的理想指示物,为水域生态系统食物网结构与功能、物质流与能量流的研究提供了有力的技术支撑。在综评稳定同位素技术原理与方法的基础上,较为详细地对其应用于水域生态研究的理论基础与进展进行了总结。该方法的应用以水域中生产者同位素组成差异为前提,主要涉及确定食物来源、食物的贡献比例、营养级的确定、食物网结构的构建及鱼类等水生生物的洄游及迁移路线等方面,这些研究对了解生态系统的动态变化与外界环境对其影响具有重要意义。并对我国此类研究的前景和存在问题进行了探讨。     

氮稳定同位素技术在陆地生态系统氮循环研究中的应用

在过去几十年中, 氮(N)稳定同位素技术的发展提高了人们对于陆地生态系统氮循环的认识。该文回顾了氮稳定同位素技术在研究生态系统氮循环中的历史, 综述了最近十多年来氮稳定同位素技术在陆地生态系统氮循环研究中的典型案例, 包括利用氮同位素自然丰度鉴定植物氮来源、指示生态系统氮状态和量化过程速率, 利用¹⁵N标记技术示踪氮的去向和再分布等。该文同时指出这些应用中存在的问题, 以及在陆地生态系统上氮稳定同位素技术今后研究的重点发展方向。     

稳定性同位素核酸探针技术DNA-SIP 原理与应用

稳定性同位素核酸探针技术DNA-SIP(Stable isotope probing),是将复杂环境中微生物物种组成及其生理功能耦合分析的有力工具.微生物的体积在μm尺度,因此,自然环境中微生物群落在μm尺度下生理过程的发生、发展,其新陈代谢物质在环境中累积与消减的动力学变化规律,形成了微生物生理生态过程,决定了不同尺度下生态系统物质和能量的良性循环.利用稳定性同位素示踪复杂环境中微生物基因组DNA,实现了单一微生物生理过程研究向微生物群落生理生态研究的转变,能在更高更复杂的整体水平上定向发掘重要微生物资源,推动微生物生理生态学和生物技术开发应用.本文重点探讨了DNA-SIP的技术原理、主要技术瓶颈及对策,初步展望了DNA-SIP为基础的环境微生物基因组学发展趋势.     

硫稳定同位素技术在生态学研究中的应用

随着人为SO₂释放的增加, 硫稳定同位素的动态已成为生物地球化学循环过程中研究的热点。该文对天然硫稳定同位素在大气自然过程中的硫来源分析及其在森林生态系统、农田生态系统和水域生态系统中的硫动态研究, 人为添加的硫稳定同位素在生态环境中的应用及硫稳定同位素技术在我国酸雨研究中的潜在贡献等进行了综述, 并从硫稳定同位素技术应用研究的范围、分析手段及源解析模型方面介绍了可能的发展方向。     

稳定同位素技术在头足类摄食生态学研究中的应用

头足类在海洋食物网营养关系中占有重要地位,然而对其复杂的生活史过程,尤其是摄食生态学信息仍知之甚少.稳定同位素技术作为传统食物网科学研究方法的有力补充,可更深层次地分析头足类的摄食习性和栖息地等方面的重要信息.本文在比较分析国内外头足类摄食生态学研究方法的基础上,系统归纳总结了稳定同位素技术在头足类摄食生态学研究中的发展现状并介绍最新进展情况,着重分析稳定同位素技术在头足类生活史信息,尤其是在摄食生态学研究中的应用现状及发展前景,包括测定样品标准化、头足类生长发育过程中的食性转换和洄游分布等核心问题,以促进其在头足类生物学研究中的应用.     

污染土壤中多环芳烃生物降解的调控研究

选用温度、湿度、表面活性剂ＴＷ８０和ＣＮＰ比４个因素为调控因子,采用正交法进行周期为１５０天的实验研究．结果表明,３０天后,土壤中ＰＡＨｓ的降解率可达４４．５～７４．６％,６０天后,达７０．４～９３．７％,降解率的不同与调控条件显著相关．在此期间,降解最佳条件为４０℃,湿度２５％,ＣＮＰ比为１２０１０１,ＴＷ８０分别为２００～５００ｍｇ·ｋｇ－１．实验结束时,土壤中ＰＡＨｓ的降解率达９１．２～９９．８％．降解的最佳条件是４０℃,湿度１５％．经Ｒ值判别表明,不同时期各因子对ＰＡＨｓ降解影响有所不同．温度对ＰＡＨｓ降解影响较大,表面活性剂对土壤中ＰＡＨｓ的生物降解有调控作用．     

碳稳定同位素技术在植物水分胁迫研究中的应用

植物体的碳稳定同位素组成主要由植物本身的生物学特性决定 ,但环境胁迫对其影响也十分明显。综述了碳稳定同位素技术在研究植物水分利用效率、生物量高低及判断历史气候依据等研究领域的进展 ,阐明了植物体的 δ1 3C值对干旱、盐分及其它环境因素的变化所引起的水分胁迫的响应 ,并对碳稳定同位素对水分胁迫的响应机理进行了归纳和推断     

Identification of anthracene degraders in leachate-contaminated aquifer using stable isotope probing

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in landfill leachate-contaminated aquifer. It is necessary to identify the microorganisms truly responsible for PAH degradation if bioremediation can be applied as an effective technology. DNA-based stable isotope probing (SIP) in combination with terminal restriction fragment length polymorphism (TRFLP) was used to identify the active anthracene degraders in the contaminated aquifer sediment. One kind of degrader was classified as Variovorax species within class ??-proteobacteria, but another belonged to unclassified bacteria. These findings also suggest novel microorganisms involved in PAH-degrading processes.     

滩涂底栖动物有机污染生态学研究进展

底栖动物由于对有机污染物具有较强的吸收能力,再加上其移动能力较差、生活方式比较固定,而被广泛运用于滩涂有机污染的研究.目前这些研究主要集中在如下几个方面：（1）有机污染物在底栖动物体内的分布特征及在底栖食物链中的动力学研究;（2）底栖动物对有机污染物的生理响应研究;（3）污染物对底栖动物群落组成和结构影响研究;（4）底栖动物在滩涂有机污染检测中的应用研究.研究结果表明：滩涂底栖动物对有机污染物的累积具有选择性和季节波动性;有机污染物可以在底栖食物链中传递;底栖动物体内的有机污染物成分和含量可以有效地指示其生存环境的有机污染状况;底栖动物的混合功能氧化酶和抗氧化酶系统对体内有机污染物的累积产生积极的响应;有机污染物对底栖动物的免疫系统造成不利影响,并对遗传物质造成破坏;有机污染对底栖动物的群落组成和结构具有显著的影响.     

Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies

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DNA buoyant density shifts during 15N-DNA stable isotope probing

DNA-based stable isotope probing (SIP) is a novel technique for the identification of organisms actively assimilating isotopically labeled compounds. Herein, we define the limitations to using ¹⁵N-labeled substrates for SIP and propose modifications to compensate for these shortcomings. Changes in DNA buoyant density (BD) resulting from ¹⁵N incorporation were determined using cultures of disparate GC content (Escherichia coli and Micrococcus luteus). Incorporation of ¹⁵N into DNA increased BD by 0.015±0.002 g mL⁻¹ for E. coli and 0.013±0.002 g mL⁻¹ for M. luteus. The DNA BD shift was greatly increased (0.045 g mL⁻¹) when dual isotope (¹³C plus ¹⁵N) labeling was employed. Despite the limited DNA BD shift following ¹⁵N enrichment, we found the use of gradient fractionation, followed by a comparison of T-RFLP profiles from fractions of labeled and control treatments, facilitated detection of enrichment in DNA samples from either cultures or soil.     

Unraveling uncultivable pesticide degraders via stable isotope probing (SIP)

Uncultivable microorganisms account for over 99% of all species on earth, playing essential roles in ecological processes such as carbon/nitrogen cycle and chemical mineralization. Their functions remain unclear in ecosystems and natural habitats, requiring cutting-edge biotechnologies for a deeper understanding. Stable isotope probing (SIP) incorporates isotope-labeled elements, e.g. ^13?C, ^18?O or ^15?N, into the cellular components of active microorganisms, serving as a powerful tool to link phylogenetic identities to their ecological functions in situ. Pesticides raise increasing attention for their persistence in the environment, leading to severe damage and risks to the ecosystem and human health. Cultivation and metagenomics help to identify either cultivable pesticide degraders or potential pesticide metabolisms within microbial communities, from various environmental media including the soil, groundwater, activated sludge, plant rhizosphere, etc. However, the application of SIP in characterizing pesticide degraders is limited, leaving considerable space in understanding the natural pesticide mineralization process. In this review, we try to comprehensively summarize the fundamental principles, successful cases and technical protocols of SIP in unraveling functional-yet-uncultivable pesticide degraders, by raising its shining lights and shadows. Particularly, this study provides deeper insights into various feasible isotope-labeled substrates in SIP studies, including pesticides, pesticide metabolites, and similar compounds. Coupled with other techniques, such as next-generation sequencing, nanoscale secondary ion mass spectrometry (NanoSIMS), single cell genomics, magnetic-nanoparticle-mediated isolation (MMI) and compound-specific isotope analysis (CSIA), SIP will significantly broaden our understanding of pesticide biodegradation process in situ.     

Application of stable isotope ratio analysis for biodegradation monitoring in groundwater

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Highlights► Stable isotopes provide insights about in situ biodegradation mechanisms and rates. ► Isotopic approaches can be confounded by abiotic processes and heterogeneity effects. ► Isotopic applications are improving with new methods of analysis and modeling. ► Isotopic data are most useful when combined with other approaches for fate assessment.     

Enrichment and characterization of a sulfate-reducing toluene-degrading microbial consortium by combining in situ microcosms and stable isotope probing techniques

A toluene-degrading microbial consortium was enriched directly in a BTEX-contaminated aquifer under sulfate-reducing conditions using in situ microcosms consisting of toluene-loaded activated carbon pellets. Degradation of toluene and concomitant sulfide production by the consortium was subsequently demonstrated in laboratory microcosms. The consortium was physiologically and phylogenetically characterized by isotope tracer experiments using nonlabeled toluene, [¹³C]-α-toluene or [¹³C₇]-toluene as growth substrates. Cells incubated with [¹³C]-α-toluene or [¹³C₇]-toluene incorporated 8–15 at.%¹³C and 51–57 at.%¹³C into total lipid fatty acids, respectively, indicating a lower specific incorporation of ¹³C from [¹³C₇]-toluene. In order to identify the toluene-assimilating bacteria, the incorporation of carbon from both [¹³C]-α-toluene and [¹³C₇]-toluene into rRNA was analyzed by stable isotope probing. Time and buoyant density-resolved 16S rRNA gene-based terminal restriction fragment length polymorphism profiles, combined with cloning and sequencing, revealed that an uncultured bacterium (99% sequence similarity) related to the genus Desulfocapsa was the main toluene-degrading organism in the consortium. The ratio of the respective terminal restriction fragments changed over time, indicating trophic interactions within this consortium.