厌氧消化污泥微生物组研究方法及应用

污泥厌氧消化是在消化污泥微生物组的协调下将剩余污泥中有机物转化为甲烷的微生物过程。与传统厌氧消化过程不同,污泥厌氧消化系统的进料底物为含有大量微生物细胞及胞外多聚物等复杂大分子有机物的剩余污泥。因此,厌氧消化污泥微生物组的种群组成、功能及种群间互作关系等异常复杂,使厌氧消化污泥微生物组分析成为难点问题。但近年来高通量测序技术及生物信息学分析方法的快速发展为消化污泥微生物组研究提供了契机,并迅速推动了该研究领域的发展。本文从4个方面梳理、总结厌氧消化污泥微生物组的研究及应用现状:剩余活性污泥结构、组成及其厌氧消化;基于16SrRNA基因序列测序的微生物组研究;基于宏基因组及宏转录组分析的微生物组研究;厌氧消化污泥微生物组研究案例分析。最后我们提出了厌氧消化污泥微生物组研究亟待解决的关键科学问题。     

中高温污泥厌氧消化系统中微生物群落比较

【目的】结合中温与高温消化两者优势的两相厌氧消化工艺可能是推进污泥厌氧消化发展的重要方向,因此,探究和比较中温和高温污泥厌氧消化系统中微生物群落组成的异同具有重要意义。【方法】利用高通量测序技术检测中温和高温厌氧消化系统中细菌与古菌的16S r RNA基因序列信息和真菌的内转录间隔(ITS)序列信息,利用基因芯片(Geo Chip 5.0)检测病毒和病原菌致病基因的信息,以对比中温和高温条件下微生物群落在物种组成和功能基因层面上的异同。【结果】中温和高温条件下细菌和古菌在群落物种组成上存在显著差异,病毒和病原菌毒性基因也显著不同,而两种系统中真菌群落的物种组成相似且丰度相对较低。中温条件下产甲烷古菌和未分类微生物相对丰度较高,而高温条件下产酸及嗜热菌相对丰度较高,且高温消化后病毒和病原菌毒性基因相对丰度下降。微生物群落结构与COD、TS和VS有着显著相关性。【结论】微生物群落组成和功能基因在中高温的污泥厌氧消化系统中显著不同,从而解释了两个系统功能的差异。微生物群落的形成与进水参数相关,说明微生物对进水条件敏感。     

环境微生物宏基因组学研究中的生物信息学方法

高通量测序技术的发展促进了组学技术在环境微生物研究中的广泛应用,而宏基因组学是目前最为关键和成熟的组学方法。生物信息学在微生物宏基因组学研究中具有至关重要的作用。它贯穿于宏基因组学的数据收集和存储、数据处理和分析等各个阶段,既是宏基因组学推广的最大瓶颈,也是目前宏基因组学研究发展的关键所在。本文主要介绍和归纳了目前在高通量宏基因组测序中常用的生物信息学分析平台及其重要的信息分析工具。未来几年之内,测序成本的下降和测序深度的增加将进一步增大宏基因组学研究在数据存储、数据处理和数据挖掘层面的难度,因此相应生物信息学技术与方法的研究和发展也势在必行。近期内我们应该首先加强基础性分析和存储平台的建设以方便普通环境微生物研究者使用,同时针对目前生物信息分析的瓶颈步骤和关键任务重点突破,逐步发展。     

餐厨垃圾厌氧消化处理主要过程的微生物群落结构分析

【背景】厌氧消化是我国餐厨垃圾处理的主要方法,微生物在其处理过程中起到关键作用,但是目前对其不同工艺单元微生物群落结构的研究较少。【目的】通过分析各工艺单元的微生物多样性与群落结构,为改进餐厨垃圾资源化处理技术、提高资源利用效率提供科学依据。【方法】采集某餐厨垃圾处理厂油水分离、厌氧发酵、沼渣脱水等3个工艺单元产生的废液样品,采用16S rRNA基因高通量测序技术,研究其菌群组成、丰度、优势菌群及其与环境因子的相关性。【结果】初始油水分离样品中的微生物群落种类相对较少,而经厌氧发酵和沼渣脱水处理后样品中的微生物群落种类较丰富。在门水平上,厚壁菌门(Firmicutes)在各单元样品中所占平均比例最高,为81.1%,其次为拟杆菌门(Bacteroidetes)和绿弯菌门(Chloroflexi),分别占15.81%和4.59%;在属水平上,相对丰度较高的菌属为乳酸菌属(Lactobacillus)、互营单胞菌属(Syntrophomonas)等。餐厨垃圾处理过程中的部分菌属可能具有资源-环境双重属性,例如在沼渣脱水单元相对丰度高达32.67%的假单胞菌属(Pseudomonas),该菌属中既存在少部分致病菌或条件致病菌,也具有生产聚羟基脂肪酸酯的功能菌。影响各组样品微生物群落组成结构最显著的因子是p H值,其次是总糖的含量。【结论】研究明确了典型餐厨垃圾厌氧消化处理工艺单元的微生物群落结构和多样性,并提出了优化处理工艺、强化资源利用效率的建议。     

微生物组学及其应用研究进展

随着高通量测序技术和生物信息学的发展,尤其是宏基因组在人类肠道微生物鉴定方面的应用,微生物组学应运而生。概述了微生物组的多样性及其在人体健康、农作物生长、畜牧业发展、环境治理、工业生物技术产品生产等方面的应用,并对微生物组学的研究方向和应用前景作了展望。     

微生物组学的技术和方法及其应用

微生物组是指一个特定环境或生态系统中全部微生物及其遗传信息的集合, 其蕴藏着极为丰富的微生物资源。全面系统地解析微生物组的结构和功能, 将为解决人类面临的能源、生态环境、工农业生产和人体健康等重大问题带来新思路。然而, 微生物组学研究在很大程度上取决于其技术与方法的发展。在高通量测序技术出现以前, 微生物研究主要基于分离培养和指纹图谱等技术, 然而, 由于这些技术存在的缺陷, 人们对于微生物的认识十分有限。自21世纪初以来, 尽管高通量测序和质谱技术的革命性突破极大地促进了人们对于微生物的认识, 微生物组学技术在微生物组研究中的应用仍面临着诸多挑战。此外, 目前微生物组的结构和多样性等描述性研究已臻成熟, 微生物组学研究正处于从数量到质量、从结构到功能的关键转变时期。因此, 该文首先介绍了微生物组学的基本概念及其发展简史, 其次简述了微生物组学研究的相关技术和方法及其发展历程, 并进一步阐述了微生物组学的技术和方法在生态学研究中的应用及存在的主要问题, 最后从技术、理论和应用层面阐述了未来微生物组学技术和方法发展的前沿方向, 并提出了今后微生物组学研究的优先发展领域。     

组学视角下养殖动物消化道微生物组结构与功能研究进展北大核心

养殖动物消化道中含有大量的微生物,不仅参与动物对营养物质的消化和吸收,还对宿主生长发育及免疫起重要调节作用。动物消化道微生物组研究是目前国内外的热点领域,取得了一系列重要研究进展。深入了解养殖动物消化道微生物组的结构与功能,将为今后调控和应用消化道微生物、提高动物生产性能、改善动物胃肠道健康和实现绿色健康养殖奠定理论基础。本文以4种代表性养殖动物(牛、羊、猪和鸡)为主体,对组学视角下其消化道微生物群落结构、功能等研究进展进行总结和分析;并对未来研究方向进行展望。     

环境微生物的宏基因组学研究新进展

宏基因组学以环境中微生物的基因组的总和为研究对象,从而规避了传统方法中绝大部分微生物不能培养的缺陷,因此近年来在环境微生物学研究中得到了广泛应用.本文重点介绍了宏基因组学技术中关键的两类技术:即以罗氏454及Illumina为代表的高通量测序技术和以基因芯片(GeoChip)为代表的基因芯片技术在微生物研究中的应用.测序技术可以发现新物种和新基因,但由于测序深度有限,定量性差,不易发现低丰度物种,且易受污染物干扰.芯片技术很好地克服了这些局限,但不易于发现新基因.本文介绍了这些技术近年来在气候变化、水处理工程系统、极端环境、人体肠道、石油污染修复、生物冶金等方面取得的部分代表性成果.在此基础上,对宏基因组技术在环境微生物研究方面的未来发展方向提出了预判和展望.我们认为由于两种技术各自的优缺点,今后将两类技术结合起来的综合研究会越来越多.另外,由于大量数据的处理方法已成为制约宏基因组学发展的瓶颈,相应的生物信息学技术开发将是未来科研的热点和难点.     

厌氧颗粒污泥微生物群落结构与功能的研究进展

厌氧颗粒污泥(anaerobicgranularsludge,AnGS)是由多种功能微生物组成的自固定化聚集体,具有容积负荷高、工艺简单、剩余污泥产量低等优点,在废水处理领域中显示出巨大的技术和经济潜力,被认为是一种很有前景的低碳废水处理工艺。本文系统总结了近年来厌氧颗粒污泥微生物结构和功能的研究成果,从微生物学角度讨论了厌氧颗粒污泥形成及稳定的影响因素,并对今后厌氧颗粒污泥的研究进行了展望,以期为后续厌氧颗粒污泥技术的深入研究和实际工程应用提供参考。     

微生物组学研究的“淘金时代”

人体及动物肠道中生存着数量庞大的共生微生物;这些微生物无时无刻不参与着宿主的生命活动。揭示这些共生微生物在宿主体内的变化规律、与宿主之间的依存和博弈关系等,将使人类更加全面的认知高等生物体的生命本质。本专刊从肠道微生物与疾病、肠道微生物群落结构、肠道微生物与宿主互作、肠道微生物资源和肠道微生物研究方法 5个层面展示了我国科研工作者在肠道微生物研究领域的新进展及新观点。     

厌氧消化过程的非模型控制

对废水淤泥的厌氧消化处理过程进行了研究．提出了一种基于神经网络的非模型控制方法。多变量控制系统的操作变量为供热量和进水量．被控变量为消化温度和消化污泥排出浓度。证明了控制算法的收敛性。讨论了控制系统的稳定性。仿真结果证实了非模型控制方法的有效性。该方法无需对象的模型．为复杂生化过程的控制提供了一种新途径。     

Enhanced Methane Production from Anaerobic Digestion of Disintegrated and Deproteinized Excess Sludge

To improve biogas yield and methane content in anaerobic digestion of excess sludge from the wastewater treatment plant, the sludge was disintegrated by using various methods (sonication, alkaline and thermal treatments). Since disintegrated sludge contains a high concentration of soluble proteins, the resulting metabolite, ammonia, may inhibit methane generation. Therefore, the effects of protein removal from disintegrated sludge on methane production were also studied. As a result, an obvious enhancement of biogas generation was observed by digesting disintegrated sludge (biogas yield increased from 15 to 36 ml/g COD_added·day for the raw excess sludge and the sonicated sludge, respectively). The quality of biogas was also improved by removing proteins from the disintegrated sludge. About 50% (w/w) of soluble proteins were removed from the suspension of disintegrated sludge by salting out using 35 g MgCl₂·6H₂O/l and also by isoelectric point precipitation at pH 3.3. For deproteinized sludge, methane production increased by 19%, and its yield increased from 145 ml/g COD_removed to 325 ml/g COD_removed. Therefore, the yield and quality of biogas produced from digestion of excess sludge can be enhanced by disintegrating the sludge and subsequent protein removal. Revisions requested 14 November 2005; Revisions received 13 January 2006     

Using Contaminated Plants Involved in Phytoremediation for Anaerobic Digestion

This study investigated the anaerobic digestion capability of five plants and the effects of copper (Cu) and S,S’-ethylenediaminedisuccinic acid (EDDS, a chelator widely used in chelant-assisted phytoremediation) on biogas production to determine a feasible disposal method for plants used in remediation. The results showed that in addition to Phytolacca americana L., plants such as Zea mays L., Brassica napus L., Elsholtzia splendens Nakai ex F. Maekawa, and Oenothera biennis L. performed well in biogas production. Among these, O. biennis required the shortest period to finish anaerobic digestion. Compared to normal plants with low Cu content, the plants used in remediation with increased Cu levels (100 mg kg^?1) not only promoted anaerobic digestion and required a shorter anaerobic digestion time, but also increased the methane content in biogas. When the Cu content in plants increased to 500, 1000, and 5000 mg kg^?1, the cumulative biogas production decreased by 12.3%, 14.6%, and 41.2%, respectively. Studies also found that EDDS conspicuously restrained biogas production from anaerobic digestion. The results suggest that anaerobic digestion has great potential for the disposal of contaminated plants and may provide a solution for the resource utilization of plants used in remediation.     

Software Sensors to Monitor the Dynamics of Microbial Communities: Application to Anaerobic Digestion

A mass balance based model has been derived to represent the dynamical behavior of the ecosystem contained in an anaerobic digester. The model considers two bacterial populations: acidogenic and methanogenic bacteria. It forms the basis for the design of a software sensor considering both a model of the biological system and on-line gaseous measurements. The software sensor computes the concentration of inorganic carbon and volatile fatty acids (VFA) in the digester. Another software sensor is dedicated to the estimation of the bacterial biomasses. The predictions of the software sensors for a real experiment are very close to the actual off-line measurements. The software sensors monitor the accumulation of VFA and thus very early detect a destabilization of the digester due to overloading. The presented methodology demonstrates the usefulness of advanced monitoring techniques for an improved understanding of the internal working of a biological system.     

Adaption of microbial community during the start-up stage of a thermophilic anaerobic digester treating food waste

A successful start-up enables acceleration of anaerobic digestion (AD) into steady state. The microbial community influences the AD performance during the start-up. To investigate how microbial communities changed during the start-up, microbial dynamics was analyzed via high-throughput sequencing in this study. The results confirmed that the AD was started up within 25 d. Thermophilic methanogens and bacterial members functioning in hydrolysis, acidogenesis, and syntrophic oxidation became predominant during the start-up stage, reflecting a quick adaption of microorganisms to operating conditions. Such predominance also indicated the great contribution of these members to the fast start-up of AD. Redundancy analysis confirmed that the bacterial abundance significantly correlated with AD conditions. The stable ratio of hydrogenotrophic methanogens to aceticlastic methanogens is also important to maintain the stability of the AD process. This work will be helpful to understand the contribution of microbial community to the start-up of AD.     

Focus: Microbiome: The Hoops,Hopes, and Hypes of Human Microbiome Research

Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging. Here, I will review 1) the methodological and analytic hoops a good microbiome study has to jump through, including DNA extraction and choice of bioinformatics tools, 2) the hopes this field has generated for diseases such as autism and inflammatory bowel diseases, and 3) some of the hypes that it has created, e.g., by confusing correlation and causation, and the recent pseudoscientific commercialization of microbiome research.     

汉阳陵陶俑表面微生物群落结构与种群多样性分析

【背景】汉阳陵是我国截至目前发现的规模最大、陪葬级别最高的汉代陶俑群,出土了大量形神毕肖的裸体俑群,考古学家认为这种裸体陶俑原本“着衣、装木臂”,称为“着衣式陶俑”,为皇室独有,异常珍贵。然而这些推测尚无科学依据,而且陶俑表面附着微生物可能会腐蚀俑体。【目的】通过比较研究汉陶俑表面微生物的组成差异,为汉裸体陶俑着有衣物且装有断臂的推测提供一定的科学佐证,同时为汉陶俑微生物腐蚀的防控提供靶标。【方法】应用微生物高通量测序与纯培养相结合的方法,对着衣式陶俑不同部位微生物进行测定。【结果】高通量测序结果显示女俑头部微生物多样性较高;男俑上半身微生物多样性最高,腿部居中,头部较低。汉陶俑表面微生物组成按俑的类别及不同部位聚集在一起,其优势菌为放线菌门的克洛斯氏菌属、糖多孢菌属、假诺卡氏菌属及链霉菌科,其他各部位优势类群相对丰度存在差异,断臂处与碳循环相关功能微生物的相对丰度最高。纯培养结果显示女俑头部的可培养细菌数量高于男俑头部可培养的细菌数量;男俑上身与腿部可培养的微生物数量高于男俑头部,表明上半身与腿部可能有衣物覆盖,导致其营养差异。【结论】汉陶俑头部与身体表面部位微生物多样性与组成存在明...     

Anaerobic digestion and wastewater treatment systems

Upflow Anaerobic Sludge Bed (UASB) wastewater (pre-)treatment systems represent a proven sustainable technology for a wide range of very different industrial effluents, including those containing toxic/inhibitory compounds. The process is also feasible for treatment of domestic wastewater with temperatures as low as 14–16° C and likely even lower. Compared to conventional aerobic treatment systems the anaerobic treatment process merely offers advantages. This especially is true for the rate of start-up. The available insight in anaerobic sludge immobilization (i.e. granulation) and growth of granular anaerobic sludge in many respects suffices for practice. In anaerobic treatment the immobilization of balanced microbial communities is essential, because the concentration of intermediates then can be kept sufficiently low.So far ignored factors like the death and decay rate of organisms are of eminent importance for the quality of immobilized anaerobic sludge. Taking these factors into account, it can be shown that there does not exist any need for phase separation when treating non- or slightly acidified wastewaters. Phase separation even is detrimental in case the acidogenic organisms are not removed from the effluent of the acidogenic reactor, because they deteriorate the settleability of granular sludge and also negatively affect the formation and growth of granular sludge. The growing insight in the role of factors like nutrients and trace elements, the effect of metabolic intermediates and end products opens excellent prospects for process control, e.g. for the anaerobic treatment of wastewaters containing mainly methanol.Anaerobic wastewater treatment can also profitably be applied in the thermophilic and psychrophilic temperature range. Moreover, thermophilic anaerobic sludge can be used under mesophilic conditions.The Expanded Granular Sludge Bed (EGSB) system particularly offers big practical potentials, e.g. for very low strength wastewaters (COD 1 g/l) and at temperatures as low as 10° C. In EGSB-systems virtually all the retained sludge is employed, while compared to UASB-systems also a substantially bigger fraction of the immobilized organisms (inside the granules) participates in the process, because an extraordinary high substrate affinity prevails in these systems. It looks necessary to reconsider theories for mass transfer in immobilized anaerobic biomass.Instead of phasing the digestion process, staging of the anaerobic reactors should be applied. In this way mixing up of the sludge can be significantly reduced and a plug flow is promoted. A staged process will provide a higher treatment efficiency and a higher process stability. This especially applies for thermophilic systems.     

冰川生态系统固碳微生物研究进展

[目的] 海南海口含有丰富的温泉资源,对温泉微生物多样性进行研究,有助于进一步开发和利用海南温泉微生物资源。[方法] 本文采用Illumina HiSeq高通量测序技术对海口3个温泉[海甸岛荣域温泉（S1）、火山口开心农场温泉（S2）和西海岸海长流温泉（S3）] 水样中微生物ITS序列和16S rRNA基因V3-V4区进行测序及生物信息学分析,探究海口市3个不同区域的温泉真菌多样性与细菌多样性。[结果] （1）α多样性分析表明,真菌群落中,S3 > S1 > S2,而在细菌群落中,S2 > S1 > S3。β多样性分析表明,3个温泉真菌群落和细菌群落组成差异皆显著。（2）分类分析表明,温泉真菌群落优势菌门为子囊菌门（Ascomycota）和担子菌门（Basidiomycota）,细菌群落优势菌门为变形菌门（Proteobacteria）、拟杆菌门（Bacteroidetes）、Thermi、硝化螺旋菌门（Nitrospirae）、绿菌门（Chlorobi）、厚壁菌门（Firmicutes）、绿弯菌门（Chloroflexi）、放线菌门（Actinobacteria）。（3）CCA（Canonical correspondence analysis）分析表明,3个温泉的真菌群落主要影响因子是温度,细菌群落主要影响因子是总磷。[结论] 海南省海口市温泉中含有丰富的微生物资源,其微生物群落组成受多种环境因子影响,且影响真菌和细菌的主要环境因子不同。