基于宏组学方法认识微生物群落及其功能

进入后基因组学时代,测序技术飞速发展,测序成本明显下降,形成了涵盖宏基因组学、宏转录组学和宏蛋白质组学的宏组学技术,推动了对微生物群落的多样性、结构及潜在基因功能方面的深入研究。最近随着整合的宏组学技术的提出及应用,全面系统分析微生物群落动态变化及其代谢功能已成为可能,这将成为微生物生态学研究的新趋势。本文综述了宏组学在研究海洋湖泊、深海热泉、人体肠道、牛瘤胃生境、森林土壤与堆肥生境等环境中微生物群落的结构和功能方面的最新进展与成功应用案例。     

肠道微生物功能宏基因组学与代谢组学关联分析方法研究进展

近年来基于高通量基因测序的微生物组学研究极大加深了人们对微生物与健康和疾病关系的认识。然而基因测序方法不能直接测定微生物的功能活性,难以鉴定微生物中的关键功能分子,单独使用无法回答肠道微生物何种成员通过何种方式影响宿主等关键科学问题。单一组学研究弊端尽显,多组学联用势在必行。肠道微生物代谢组学以微生物群落所有小分子代谢物为研究对象,可发现肠道微生物随宿主病理生理变化的关键代谢物,为微生物组-宿主互作机制研究提供线索,成为微生物组学研究的重要补充。肠道微生物功能基因组学与代谢组学关联分析在宿主生理、疾病病理、药物药理等方面取得众多进展,展现良好应用前景。然而目前肠道微生物功能基因组学与代谢组学关联分析存在方法滥用、相关性结论与生物学知识相悖等突出问题。为帮助正确应用肠道微生物功能宏基因组学与代谢组学关联分析,本文综述了各种多组学数据整合分析方法的原理、优缺点与适用范围,并给出了应用建议。     

宏转录组技术及其研究进展

宏转录组学是一门在整体水平上研究某一特定环境、特定时期群体生物全部基因组转录情况以及转录调控规律的学科.简要概述宏转录组学的产生、研究策略及其应用情况,并对其应用前景进行展望.     

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。     

宏蛋白质组学:研究微生物群落的一种新策略

宏蛋白质组学是一种运用蛋白质组技术对特定微生物群落所产生的全部蛋白质进行大规模研究与分析的新技术。简要概述宏蛋白组学的产生、研究策略及其应用情况,并对其应用前景进行展望。     

宏蛋白质组学——研究微生物群落基因表达的新技术

宏蛋白质组学是应用蛋白质组学技术对微生物群落进行研究的一项新技术,其定义为在特定的时间对微生物群落的所有蛋白质组成进行大规模鉴定。通过对宏蛋白质组学的研究策略、进展情况的综述、介绍,展望了宏蛋白组学在研究微生物群落基因表达中的应用前景。     

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。     

肠道微生物基因组学与代谢组学分析联合应用的研究进展

随着肠道微生物对人类健康与疾病的作用日渐受到关注,肠道微生物的代谢作用已成为近年研究的热门领域之一.已有研究表明,将肠道微生物组学与代谢组学应用于宿主生理、疾病病理、药物药理等方面的研究具有重要价值.本文就肠道微生物基因组学和代谢组学分析联合应用的研究进展进行综述.     

污水处理活性污泥微生物群落多样性研究

为研究污水处理活性污泥微生物多样性,提取了活性污泥宏基因组DNA,并采用细菌通用引物27F和1492R扩增了上海污泥厂活性污泥细菌16S rDNA片段,构建了细菌16S rDNA克隆文库,并对该文库中的微生物群落进行了分析。共获得200条高质量序列并建立系统发育树,结果显示活性污泥主要的细菌类群为变形菌门(Proteobacteria)(91.9%)、厚壁菌门(Firmicures)(4.6%)、拟杆菌门(Bacteroidetes)(2%)、绿弯菌门(Chloroflexi)(0.5%)、硝化螺菌门(Nitrospirae)(1%)。其中,明显的优势菌群为Alcaligenes feacalis(55%)、Pseudomonas aeruginosa(12.8%)和Stenotrophomonas(12.8%),优势菌的产酶能力在活性污泥中显示生态修复功能菌的作用。     

基于宏基因组学解析不同质量等级中温大曲微生物组的异质性

【目的】中温大曲是浓香型白酒酿造中的糖化发酵剂和生香剂,目前其质量评价主要依赖于感官和理化特征。已有研究采用扩增子测序初步探索了大曲质量等级与微生物群落组成之间的关联性,但是微生物群落功能对大曲质量的影响尚缺乏深入研究。【方法】本研究采用宏基因组学解析和对比了不同质量等级大曲的微生物群落组成和潜在功能的差异,结合理化性质,聚焦分析了酶活、乳酸和乙酸代谢相关的关键酶基因丰度。【结果】两种等级大曲的真菌群落组成差异显著。一级大曲含有更高相对丰度的丝状真菌,主要分布在曲霉属(Aspergillus, 21.6%)、罗萨氏菌属(Rasamsonia, 6.8%)、拟青霉属(Paecilomyces, 5.0%)和篮状菌属(Talaromyces, 4.4%)等。一级大曲中与环境信息处理和细胞过程相关途径的基因相对丰度普遍显著高于二级大曲。一级大曲中薄层菌属(Hymenobacter)和曲霉属等提供了更高基因丰度的α-淀粉酶,使其具有显著较高的液化力。二级大曲则含有更高相对丰度的横梗霉属(Lichtheimia, 11.8%)、根霉属(Rhizopus, 13.4%)和毕赤酵母属(Pichia, 7.2%)以及乳酸菌类微生物,如伴生乳杆菌属(Companilactobacillus)、魏斯氏菌属(Weissella)和黏液乳杆菌属(Limosilactobacillus)等。二级大曲中与代谢相关途径的基因相对丰度显著较高,如碳水化合物代谢、能量代谢和核苷酸代谢等。二级大曲中较多的乳酸菌类群有利于提高乙醇脱氢酶基因丰度,同时,糖多孢菌属(Saccharopolyspora)、葡萄球菌属(Staphylococcus)、曲霉属和高温放线菌属(Thermoactinomyces)等提供了更多的羧酸酯酶基因丰度,分别使其具有较高的发酵力和酯化力。此外,二级大曲中较多的乳酸菌还可能产生更多的乳酸脱氢酶,降解乳酸,且更高基因丰度的乙酸代谢相关酶类可促进乙酸分解代谢,使得二级大曲酸度显著低于一级大曲。【结论】本研究在基因水平上研究了不同质量等级大曲酶活和酸度差异的微生物基础,可为建立完善的大曲质量评价体系以及理性地调控群落功能提供理论支撑。     

碳源对活性污泥微生物细胞膜特性和群落结构影响

【目的】揭示碳源对活性污泥微生物细胞膜特性(磷脂脂肪酸组成和流动性)以及群落结构的影响规律。【方法】采用原子力显微镜、磷脂脂肪酸(PLFA)、荧光漂白恢复(FRAP)和Mi Seq分析技术,考察以葡萄糖、乙酸钠、蛋白胨、葡萄糖?蛋白胨(1?1)和乙酸钠?蛋白胨(1?1)为基质的序批式活性污泥(SBR)反应器中,活性污泥微生物表面粘附力、细胞膜PLFA组成和流动性及群落结构的差异。【结果】含有蛋白胨为碳源时相比于葡萄糖和乙酸钠为单一碳源,细胞膜磷脂流动性增加,且18?1ω9c、15?0iso和17?0iso的含量提高了53.1%-354.7%、135.6%-407.9%和88.1%-264.3%;同时其微生物表面粘附力和群落多样性均增大。优势菌群对碳源的响应呈现出不一致的规律:葡萄糖和乙酸钠为单一碳源时其优势菌门分别为放线菌门和变形菌门,Nakamurella和Flavobacterium分别为其优势菌属,群落多样性指数分别为3.65和4.25;蛋白胨为碳源时促进了Candidatus Saccharibacteria门的累积,群落多样性指数在4.96-5.09。【结论】主成分分析(PCA)表明,含有蛋白胨为碳源时微生物细胞膜PLFA组成具有相似性;冗余分析(RDA)表明,不同碳源驯化出不同的微生物群落,进而也对细胞膜磷脂组成产生了影响。     

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.     

短程硝化活性污泥微生物群落结构及羟胺代谢对短程硝化的影响

活性污泥法随着技术的成熟,已应用在高氨氮污水/废水处理中,通过不断发展衍生出的很多新型工艺也成为研究热点,短程硝化反应作为代表已逐渐体现出优越性。短程硝化能达到高效净化污水的目的,其反应中的代谢产物羟胺也和微生物类群及反应产物之间有着至关重要的影响。反应器中活性污泥的微生物群落结构和动态密切相关,探究微生物群落结构能帮助生物强化、优化参数,提高脱氮效率。本文主要总结了近年来有关短程硝化/半短程硝化活性污泥微生物群落组成与结构及其与反应器处理效率之间的关系,以及羟胺代谢对短程硝化的影响等方面的研究进展,这些研究加深了对微生物群落结构和污水处理工艺之间的认识,但充分发掘生物信息、提高工艺效能之路仍然充满挑战,还需利用氮平衡方法、Real-time PCR法等多种生物技术手段对短程硝化进行全方位研究,为实践提供坚实的理论基础。     

Electricity generation using chocolate industry wastewater and its treatment in activated sludge based microbial fuel cell and analysis of developed microbial community in the anode chamber

Feasibility of using chocolate industry wastewater as a substrate for electricity generation using activated sludge as a source of microorganisms was investigated in two-chambered microbial fuel cell. The maximum current generated with membrane and salt bridge MFCs was 3.02 and 2.3 A/m², respectively, at 100 Ω external resistance, whereas the maximum current generated in glucose powered MFC was 3.1 A/m². The use of chocolate industry wastewater in cathode chamber was promising with 4.1 mA current output. Significant reduction in COD, BOD, total solids and total dissolved solids of wastewater by 75%, 65%, 68%, 50%, respectively, indicated effective wastewater treatment in batch experiments. The 16S rDNA analysis of anode biofilm and suspended cells revealed predominance of β-Proteobacteria clones with 50.6% followed by unclassified bacteria (9.9%), α-Proteobacteria (9.1%), other Proteobacteria (9%), Planctomycetes (5.8%), Firmicutes (4.9%), Nitrospora (3.3%), Spirochaetes (3.3%), Bacteroides (2.4%) and γ-Proteobacteria (0.8%). Diverse bacterial groups represented as members of the anode chamber community.     

Impacts of single‐walled carbon nanotubes on microbial community structure in activated sludge

Aims: Single‐walled carbon nanotubes (SWNTs) are likely to become increasingly widespread and yet their environmental impact is not well understood. The purpose of the current study was to evaluate the impact of SWNTs on microbial communities in a ‘sentinel’ environmental system, activated sludge batch‐scale reactors. Methods and Results: Triplicate batch reactors were exposed to SWNTs and compared to control reactors exposed to impurities associated with SWNTs. Automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterial community structure in each reactor. SWNT exposure was found to impact microbial community structure, while SWNT‐associated impurities had no effect, compared to controls. 16S rRNA gene sequence analysis indicated that dominant phylotypes detected by ARISA included members of the families Sphingomonadaceae and Cytophagacaceae and the genus Zoogloea. ARISA results indicated an adverse impact of SWNTs on the sphingomonad relative to other community members. Changes in community structure also occurred in both SWNT‐exposed and control reactors over the experimental time period and with the date on which activated sludge was obtained from a wastewater treatment facility. Conclusions: These results indicate that SWNTs differentially impact members of the activated sludge reactor bacterial community. Significance and Impact of the Study: The finding that community structure was affected by SWNTs indicates that this emerging contaminant differentially impacted members of the activated sludge bacterial community and raises the concern that SWNTs may also affect the services it provides.     

Identification of the microbial community responsible for thiocyanate and thiosulfate degradation in an activated sludge process

An activated sludge reactor fed with thiocyanate and/or thiosulfate was operated to examine the characteristics of its microbial community. Terminal-restriction fragment length polymorphism analyses were conducted to detect shifts in the microbial community structure corresponding to influent conditions. Then, clone library analyses and RNA-based stable-isotope probing were conducted to identify sulfur-oxidizing bacteria (SOB) responsible for the degradation of each substrate. The results suggested that there were two types of SOB: thiocyanate-degrading bacteria (that can utilize both thocyanate and thiosulfate) and thiosulfate-specific bacteria (that cannot utilize thiocyanate). Thiocyanate-degrading SOB, however, were outcompeted by thiosulfate-specific SOB when the influent contained only thiosulfate. Of the sequenced clones, Marinicella-related (with 98.7% identity) and Methylobacter-related (with 91.3% identity) bacteria were identified as thiocyanate-degrading SOB, whereas Thiomicrospira thermophila-related (with 100% identity over 903 bp) bacteria were identified as thiosulfate-specific SOB.     

Characterization of microbial traits associated with glyphosate biodegradation in industrial activated sludge

Summary The microorganisms from two industrial (I1, I2) activated sludges that treat glyphosate (N-phosphonomethyl glycine) wastes and one domestic (D1) sludge were enumerated by microscopic examination and by the use of eight selective media. I1 and I2 had higher total counts but fewer pseudomonads and no yeasts. The enumerations correlated directly with traditional biological performance measurements. A total of 393 microbial strains were isolated from the sludges to correlate the occurrence and relationship of glyphosate-degrading activity (GDA) to 155 biochemical and morphological characteristics. Each activated sludge contained unique bacterial populations with the microbes treating industrial wastes, capable of utilizing a wide range of carbohydrates. Numerical taxonomy (arithmetic average linkage) using simple matching and Jaccard coefficients confirmed that there were five (D1), three (I1), and 12 (I2) clusters. GDA was found in only a small portion of the industrial clusters and did not correlate with any other characteristic tested, even though the GDA strains had a large phenotypic diversity. This suggests that GDA is not a universal trait and its expression requires enrichment through specific selective pressures.     

活性污泥中菌群多样性及其功能调控研究进展

活性污泥是污水处理厂生物处理工艺的功能主体,活性污泥中菌群的种类、数量及活性是提高污水处理能力与效果的重要基础。本文综述了活性污泥处理工艺中的主要功能细菌(絮凝菌、脱氮菌、除磷菌等)生物群落的多样性与生态特征,并对目前主流的菌群鉴定方式进行总结,最后从运行条件、定向驯化及生物强化3个方面对菌群调控进行论述,以期为活性污泥法污水处理工艺提供一些理论指导。