rRNA-targeted寡核苷酸探针识别活性污泥微生物群落结构与功能研究进展

活性污泥中微生物群落内部关系非常复杂 ,及时对活性污泥中优势菌群和群落内部关系进行监测是污水处理中采取正确措施的关键。历史研究表明传统培养方法经常导致活性污泥优势菌群检测的失败 ,而r RNA- targeted寡核苷酸探针作为一种快速原位监测活性污泥微生物群落结构和功能的新工具被引入 ,使我们对参与污水净化的微生物群落结构和优势菌群能有较全面的了解。就该方法在识别除磷污泥、脱氮污泥、污泥泡沫和膨胀污泥中微生物群落结构和功能的典型应用进行综述 ,分析了该方法存在的优点和缺点 ,并对目前已建立且应用于活性污泥微生物检测的 r RNA- targeted寡核苷酸探针进行了详细总结     

羊水菌群的研究进展

传统观念认为胎儿在宫内发育的过程是无菌的。随着研究方法的快速发展,针对于微生物的研究方法从传统的培养到现代分子生物学检测的进步,研究者已经认识到胎盘、羊水中具有微生物的存在。目前的研究尚不能明确胎儿宫内胎盘、羊水的菌群来源及菌群转移的具体途径,但已有的研究提示羊水菌群最可能来源为母亲肠道、生殖道以及口腔。本文综述了研究者对羊水菌群认识的转变、羊水菌群的来源以及羊水菌群与早产的相关性。     

分子生态学方法在微生物多样性研究中的应用

现代的核酸技术正在给生物学的研究带来新的革命,它使人们对于生命现象的研究更为深人,成为揭示生物科学规律的有力手段。自１９８５年Ｐａｔｅ等以核酸测序技术研究微生物的生态和进化问题以对］,对微生物多样性的研究进入了一个新阶段．以往对微生物的认识基于对微生物的培养和纯种分离技术,而在自然环境中的微生物９９．５％～９９．９％的种类至今尚是不可培养的［‘］,成为正确认识微生物生态系的严重障碍。分子生态技术的应用克服了培养技术的限制,对样品进行客观的分析,更精确地揭示微生物种类和遗传的多样性。因此,该技术与…     

活性污泥微生物群落宏组学研究进展

活性污泥是全球最常用的废水生物处理人工生态系统,微生物是驱动其污染净化能力的关键。活性污泥微生物群落所有物种与基因(简称"微生物组")的研究先后经历了"显微镜观察和纯菌培养分离"(1915)、"PCR扩增-测序"(1994)和"高通量测序-宏组学分析"(2006)三个重要阶段的发展变迁。相应地,我们对活性污泥微生物组的认知经历了从最早对微型动物(如钟虫和轮虫)及其他微生物的形貌观察和纯种培养鉴定到今天对整个微生物组的全局多样性认识的飞跃。近13年来,基于高通量测序的宏组学方法被广泛应用于揭示活性污泥微生物群落组成结构和功能,我们现在充分意识到活性污泥微生物组蕴藏着大量不可培养新物种和基因多样性,驱动着各类污染物的降解与转化。目前,特异性分子标记基因的扩增子测序技术已经被广泛应用于揭示城市和工业废水处理活性污泥微生物组和典型功能种群(如硝化细菌和聚磷菌)的时空多样性和群落构建机制,进而为未来实现活性污泥微生物组功能的精准调控奠定理论基础。宏基因组学研究在群落、种群和个体基因组水平全面解析了活性污泥微生物组驱动的碳、氮、磷元素循环过程,以及有机微污染物的生物降解和转化机理。将来活性污泥微生物组学研究需要在"标准化的组学分析方法和绝对定量""高通量培养组学""高通量功能基因组学"和"多组学方法的结合及多种方法并用"4个方面取得实现精准生态基因组学所需的技术突破,以最大限度发掘活性污泥微生物组在污水处理与资源回收领域的生态学与工程学价值。     

肠道上皮与肠道微生物相互作用的研究现状

肠道上皮是肠上皮细胞及其分泌物有机构成的黏膜界面。随着技术的进步和对肠道菌群作用的逐渐重视,研究者对肠道上皮与肠道微生物相互作用的认识也不断深入。研究表明,肠道上皮调节并维持肠道微生物的定殖与分布,肠道微生物也影响肠道上皮的多种屏障功能,二者通过一系列细胞分子机制紧密联系,共同维持肠道稳态。此外,其过程中产生的宿主-肠道菌群共代谢物被发现可以反映宿主的生理病理状态,作为指标被应用于临床疾病诊断、治疗效果评估和预后推测。本文基于近年的研究,综述了肠道上皮与肠道微生物的相互作用及其细胞分子机制,为进一步研究和临床应用总结了理论基础,并探讨了未来可能的研究方向。     

分子生物学在食品微生物检测中的应用

食品安全是百姓关注的大问题,目前食品安全监测技术正在蓬勃发展,随着现代分子生物学技术的发展,对微生物学的研究也进入到分子、基因水平。病原微生物的检测也逐渐进入分子时代,本文介绍了应用于病原微生物检测的PCR技术、DNA指纹图谱等技术。     

中国微生物物种多样性研究进展

微生物是分布最为广泛的生命形式,几乎分布到地球上的所有生境,具有丰富的物种多样性。我国地域辽阔,跨越热带至寒温带,气候条件多样,地理环境与生态系统类型复杂,是世界上生物多样性最丰富的国家之一。我国已开展了大量微生物多样性研究,并证实我国多样的生境蕴藏着丰富的微生物物种多样性。目前我国已报道真核微生物(菌物)约14,700种,其中包括真菌约14,060种、卵菌约300种、黏菌约340种,而真菌中有药用菌473种、食用菌966个分类单元。特别是近年来通过免培养的分子生物学技术发现我国存在丰富的原核微生物多样性。本文概述了传统方法和现代分子生物学技术在我国原核微生物(古菌、细菌)和真核微生物(真菌、卵菌、黏菌)物种多样性研究的最新进展。     

微生物生态系统代谢网络研究进展

微生物生态系统代谢网络是自然生态系统中微生物遗传分子发挥功能作用的主要形式。本文通过全面介绍微生物生态系统代谢网络的特点及其研究的重要意义,综述了基于共培养技术、免培养高通量技术和计算生物学模拟技术的微生物生态系统代谢网络研究进展和所取得的主要发现,以及近年来快速发展的微生物生态系统代谢网络研究技术和方法体系。在此基础上,提出目前微生物生态系统代谢网络研究中存在的主要问题和重点研究方向,并对其在环境污染治理和资源化利用方面的应用潜力进行了展望。     

现代分子生物学技术在食品、药品微生物检测中的应用

食品与药品中存在的病原微生物直接关系到食品、药品的质量和安全,因此对食品和药品进行微生物检测对保护人类的身体健康具有非常重要的意义。近年来,随着现代分子生物学技术的飞速发展,其在食品和药品的微生物检测中得到了非常广泛的应用。本文主要通过对现代分子生物学技术在食品、药品微生物检测中的应用及进展进行相应的探讨,旨在为新型微生物检测及分型方法的发展提供依据。     

污水处理过程中微塑料去除的现状及发展趋势北大核心CSCD

微塑料(microplastics,MPs)被发现广泛存在于海洋、陆地以及大气等生态系统中。城市污水中的大量微塑料被污水处理厂截留在活性污泥中,但仍有不计其数的微塑料颗粒“逃脱”污水处理厂,排放到自然环境中。与此同时,污水处理过程中绝大部分微塑料会转移到污泥中,伴随着活性污泥的利用过程进入土壤环境,形成微塑料的二次污染。文中基于对国内外文献的调研,对环境中微塑料的来源、分布及危害进行了概述,对活性污泥工艺过程中微塑料的处理情况以及活性污泥中残留微塑料的处理方式进行了梳理;展望了生物技术及合成生物学在活性污泥核心菌群遗传改造,赋予核心菌群微塑料降解能力方面的应用;以期为优化污水处理厂MP的降解提供参考。     

含氟有机废水处理过程活性污泥微生物群落研究进展

随着有机氟化物在各领域的广泛应用,含氟有机废水处理面临巨大挑战。活性污泥作为有机废水处理的核心技术之一,微生物在其中发挥着极其重要的作用。本综述首先聚焦在活性污泥微生物群落多样性、组成、结构和功能及其与含氟废水类型、处理工艺和处理效率之间的关系,进而讨论了功能微生物降解/转化有机氟化物的途径和作用机制,最后展望了结合分离培养降解有机氟化物的关键微生物,以及微生物组学技术解析活性污泥微生物群落构建、互作、代谢等核心问题,以提高对含氟有机废水微生物降解机理的认识,优化含氟有机废水处理工艺。     

污水处理过程中微生物群落多样性及其对环境因子响应的研究进展

污水生物处理系统的性能和稳定性与微生物群落结构和动态密切相关。通过深入了解活性污泥中微生物群落结构及其影响因素,有助于提高污水厂污染物的去除效果。在不同污水活性污泥处理系统中细菌群落主要以变形菌、绿弯菌、放线菌、厚壁菌和拟杆菌为功能菌群;活性污泥中寄居的大多数真菌来自于子囊菌门,还有少量担子菌门;古菌以产甲烷菌为主;而病毒中分布最广的噬菌体和致病性病毒是最主要的关注点。本文通过对相关文献分析及总结,综述了进水组成、不同处理工艺、参数(理化参数和运行参数)、地理位置和气候条件等环境因子对活性污泥中细菌、真菌、古菌以及病毒群落组成的影响,尽可能全面地介绍污水厂微生物群落多样性及其对环境因子的响应。同时,对未来研究方向进行探讨,以期能够为活性污泥中功能微生物的应用及调控提供理论和应用基础。     

Analysis of microbial communities using culture-dependent and culture-independent approaches in an anaerobic/aerobic SBR reactor

Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63% (137 of 217) in the standard PCR method to about 34% (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: alpha, beta, gamma- Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivation-based method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.     

Microbial cultivation and the role of microbial resource centers in the omics era

Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world’s culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the “Budapest Treaty” for establishment of an International Depositary Authority.     

Diversity and assembly patterns of activated sludge microbial communities: A review

Understanding diversity and assembly patterns of microbial communities in activated sludge (AS) is pivotal for addressing fundamental ecological questions and wastewater treatment engineering. Recent applications of molecular methods especially high-throughput sequencing (HTS) have led to the explosion of information about AS community diversity, including the identification of uncultured taxa, and characterization of low-abundance but environmentally important populations such as antibiotic resistant bacteria and pathogens. Those progresses have facilitated the leverage of ecological theories in describing AS community assembly. The lognormal species abundance curve has been applied to estimate AS microbial richness. Taxa-area and taxa-time relationships (TAR and TTR) have been observed for AS microbial communities. Core AS microbial communities have been identified. Meanwhile, the roles of both deterministic and stochastic processes in shaping AS community structures have been examined. Nonetheless, it remains challenging to define tempo-spatial scales for reliable identification of community turnover, and find tight links between AS microbial structure and wastewater treatment plant (WWTP) functions. To solve those issues, we expect that future research will focus on identifying active functional populations in AS using omics- methods integrated with stable-isotope probing (SIP) with the development of bioinformatics tools. Developing mathematic models to understand AS community structures and utilize information on AS community to predict the performance of WWTPs will also be vital for advancing knowledge of AS microbial ecology and environmental engineering.     

Anaerobic ammonium oxidation (Anammox) in immobilized activated sludge biofilms during the treatment of weak wastewater

This work studied the formation of molecular nitrogen by the microbial population of immobilized activated sludge of the domestic wastewater treatment plants (WWTP) that employ the technology developed by ZAO ECOS Company. The technology includes physicochemical water pretreatment and treated water recycling. A hard flexible fibrous brush carrier is used for the immobilization of microorganisms. The presence of both aerobic and anaerobic microorganisms and functioning of the methanogenic microbial community was shown in the biofilms developing on the carrier fibers and in suspended sludge. The high efficiency of nitrogen removal at a low C/N ratio was established to be due to the conjugated nitrification, denitrification, and anammox processes, whose functioning was demonstrated by laboratory cultivation methods and by studying the processes in batch and continuous reactors. Fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes (FISH) revealed bacteria belonging to the order Planctomycetales, particularly their anammox group. This work is the first evidence of the important role of the anammox process in the combined system of physicochemical and biological treatment of weak wastewater (BCDEAMOX).     

现代分子生物学技术在瘤胃微生态系统研究中的应用

瘤胃中栖息着大量的微生物,由于这些微生物组成复杂且有些细菌在体外无法培养,目前对这些微生物的了解仍然很少。现代分子生物学技术的发展为研究瘤胃微生物提供了有效的方法,利用核酸探针、基因序列分析、遗传指纹技术、全细胞杂交和实时定量PCR等技术可以对瘤胃微生物的分类及进化关系、区系结构图、重要酶的表达以及目的微生物的准确定量进行更为深入和透彻的研究。发展和利用这些技术不仅可以研究微生物之间的关系以及微生物与饲料颗粒之间时间与空间的关系,还能直接在细菌自然生长的环境中对其各种特征进行研究。     

Diversity and dynamics of Archaea in an activated sludge wastewater treatment plant

ABSTRACT: BACKGROUND: The activated sludge process is one of the most widely used methods for treatment of wastewater and the microbial community composition in the sludge is important for the process operation. While the bacterial communities have been characterized in various activated sludge systems little is known about archaeal communities in activated sludge. The diversity and dynamics of the Archaea community in a full-scale activated sludge wastewater treatment plant were investigated by fluorescence in situ hybridization, terminal restriction fragment length polymorphism analysis and cloning and sequencing of 16S rRNA genes. RESULTS: The Archaea community was specialized and dominated by Methanosaeta-like species. During a 15 month period major changes in the community composition were only observed twice despite seasonal variations in environmental and operating conditions. Water temperature appeared to be the process parameter that affected the community composition the most. Several terminal restriction fragments also showed strong correlations with sludge properties and effluent water properties. The Archaea were estimated to make up 1.6-% of total cell numbers in the activated sludge and were present both as single cells and colonies of varying sizes. CONCLUSIONS: The results presented here show that Archaea can constitute a constant and integral part of the activated sludge and that it can therefore be useful to include Archaea in future studies of microbial communities in activated sludge.     

Ecosystem processes and interactions in a morass of diversity

High diversity in natural communities is indicated by both traditional, cultivation-based methods and molecular techniques, but the latter have significantly increased richness estimates. The increased ease and reduced cost associated with molecular analysis of microbial communities have fuelled interest in the links between richness, community composition and ecosystem function, and raise questions about our ability to understand mechanisms controlling interactions in highly complex communities. High-throughput sequencing is increasing the depth of sequencing but the relevance of such studies to important ecological questions is often unclear. This article discusses, and challenges, some of the often implicit assumptions made in community studies. It suggests greater focus on ecological questions, more critical analysis of accepted concepts and consideration of the fundamental mechanisms controlling microbial processes and interactions in situ. These considerations indicate that many questions do not require deeper sequence analysis and increased phylogenetic resolution but, rather, require analysis at smaller spatial scale, determination of phenotypic diversity and temporal, rather than snapshot, studies. Increasing realisation of the high richness of microbial communities, and potentially high physiological diversity, also require new conceptual approaches.