北京市妫水河底泥微生物群落结构特征

微生物对外界环境变化较为敏感,常被作为指示生物用于监测和反映水质情况。为满足延庆世园会和冬奥会举办对妫水河水质的调控要求,探讨妫水河底泥微生物群落结构特征及环境因子对其分布的影响。基于妫水河12个不同断面的水样和底泥样品,进行了水质、底泥理化性质分析,并对底泥的微生物群落结构特征进行了研究。结果表明,妫水河中、下游水体水质COD、NH~+_4-N、TN超标,其中上覆水TN含量与底泥TN含量呈极显著正相关(P=0.914);MiSeq高通量测序发现,妫水河底泥微生物共检出70门228纲1168属,变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、绿弯菌门(Chloroflexi)、厚壁菌门(Firmicutes)、蓝细菌门(Cyanobacteria)、绿菌门(Chlorobi)、疣微菌门(Verrucomicrobia)和硝化螺旋菌门(Nitrospirae)是妫水河底泥微生物群落结构中的主要菌门,在各个样品中相对丰度之和均占84%以上,其中变形菌门为第一优势门,占比达到45.3%—69.1%,而不同断面样品的优势菌属有所不同。妫水河底泥微生物群落丰度总体较高,多样性也相对较高,其中世园段D7点Ace丰富度指数和Shannon多样性指数均较其他点位低,分别为2673和6.56。RDA(redundancy analysis)分析表明,底泥氨氮和温度是影响其微生物群落结构的主要因子(F=2.92,P=0.038;F=2.81,P=0.014),妫水河底泥的优势反硝化菌属为脱氮单孢菌属和硫杆状菌属,其丰度与NH~+_4-N、水温呈正相关,同时与DO呈负相关。研究结果对妫水河水生态环境保护和水质管理提供数据支撑及理论指导意义。     

应用DGGE研究微生物群落时的常见问题分析

变性梯度凝胶电泳(DGGE)是通过核酸片段对微生物群落进行研究,可以监测未培养细菌及其功能基因,被广泛地应用于微生物群落多样性和动态分析,并成为微生物分子生态学研究中的重要手段之一。文中论述了DGGE操作过程中遇到的常见问题,并提出了相应的解决方法。全面分析了样品预处理过程和PCR扩增效果对DGGE分析的影响,探讨了DGGE图谱的优化过程和图谱分析方法,并对DGGE的应用前景进行了综述。     

DGGE技术监测生物制氢反应器微生物群落结构和演替

为了研究生物制氢反应器微生物群落结构, 揭示混合菌群的生态学效能. 从连续流生物制氢反应器CSTR运行不同时期取活性污泥, 利用变性梯度凝胶电泳(DGGE)技术研究了产氢混合菌群的多样性和动态变化. 研究表明, 反应器从启动到乙醇型发酵稳定的运行, 经历了明显的微生物群落结构演替过程, 28天后反应器微生物群落结构基本恒定, 形成顶级群落. 16S rDNA 序列同源性分析表明, 优势种群为低G + C含量革兰氏阳性细菌分支的Clostridium sp.和Ethanologenbacterium sp., b变形菌亚纲的Acidovorax sp., g变形菌亚纲的Kluyvera sp.和一些未被培养的拟杆菌群的细菌和螺旋体. 21天后产氢细菌Ethanologenbacterium sp., Clostridium sp. (Clostridiaceae bacterium 80 Kb)和一些未被培养的螺旋体群细菌的数量明显增加, 形成乙醇型发酵群落, 产氢量大幅度提高. 群落经过演替微生物多样性增强后降低, 在群落演替过程中一直存在的Clostridium sp., sp., Kluyvera sp.和未被培养的拟杆菌群等是构成群落结构的基本种群, 混合菌群之间存在着共代谢作用, 共同决定产氢效能.     

杉木人工林土壤质量演变过程中土壤微生物群落结构变化

以中国科学院会同森林生态站自然林、杉木连栽林和杉木阔叶树混交林地土壤为研究对象,采用PCR-DGGE、DNA-sequencing和主成分分析(PCA)等方法分析土壤微生物群落结构变化及其与土壤质量变化之间的关系.结果表明,该地区杉木人工林土壤中细菌优势种群为α-、β-、γ-proteobacteria和Cytophaga-Flexibacter-Bacterioides (CFB)类群;真菌优势种群为子囊菌(Ascomycetes)和担子菌(Basidiomycetes)亚门的种属.杉木人工林替代自然林后,土壤细菌多样性指数显著降低,且随连栽代数增加呈持续降低趋势;杉木人工林土壤中与Pedobacter cryoconitis亲缘关系密切的细菌种群消失,出现与Xanthomonas sp.和Rhodanobacter sp.亲缘关系密切的细菌种群.土壤真菌群落结构的变化与细菌相反,杉木人工林替代自然林后并不断连栽时,土壤真菌多样性指数呈现上升的趋势,自然林土壤中优势真菌种群在杉木三代林中消失.杉木与火力楠或桤木混交后土壤细菌和真菌种群结构与自然林类似.土壤细菌多样性指数与土壤总有机碳、全氮、可溶性有机碳、铵态氮、速效磷、速效钾含量以及土壤pH值呈显著正相关关系(P＜0.05).土壤真菌多样性指数仅与土壤碳氮比呈显著正相关关系,而与土壤pH值呈显著负相关关系.杉木林土壤质量变化对土壤细菌和真菌优势种群有较大影响,细菌Burkholderia sp.、Pedobactersp.、Xanthomonas sp.和真菌Sclerotinia sclerotiorum、Mycosphaerella cannabis可能是引起土壤质量变化的关键种群.     

油藏微生物群落结构解析

微生物采油(Microbial enhanced oil recovery,MEOR)以其费用低廉、无环境污染、施工简单、应用范围广等优点得到学者以及油田开发者的认同。油藏中的微生物类型多样且功能各异,可促进原油的开采,大幅度提高油气资源的利用率。因此分析油藏中微生物的类型和组成,了解土     

接种S.fredii WGF03及突变体对大豆土壤微生物群落结构的影响

为了研究接种S.fredii WGF03及其exo D基因突变体对大豆结瘤及土壤的微生物群落影响,进一步了解exo D基因的功能,在大豆盛花期摘取每株大豆的根瘤并计数,利用PCR-DGGE电泳结合测序技术分析土壤的微生物群落。结果表明,大豆接种S.fredii WGF03后,根瘤数比不接种组增加191.67%。而大豆接种驻exo D突变体的根瘤数最少,比不接种组减少了16.67%。与空白相比,种植大豆后土壤细菌的种类和数量明显增加;接种不同根瘤菌后,细菌种类及细菌多样性也有变化;测序结果显示,土壤中细菌以Proteobacteria为主,占45.5%,土壤中土著根瘤菌为Bradyrhizobium。总之,S.fredii WGF03能够促进大豆结瘤,种植作物比接种根瘤菌对土壤细菌群落的影响更大。     

大庆聚驱后油藏微生物群落结构分析

目的:进一步研究大庆聚驱后油藏微生物种类.方法:应用T-RFLP方法比较系统地分析比较了聚驱后油藏微生物多样性,分析了与采油功能相关的主要微生物组成,初步研究了聚驱后油藏微生物分布特点及规律.结果:利用聚驱后油藏细菌群落16S rDNA构建克隆文库,共挑取了49个阳性克隆,T-RFLP分型结果,共出现21个不同类型.所得的序列在Genbank中比对的结果表明细菌克隆可分为5个类群,分属于变形杆菌、拟杆菌、脱铁杆菌、厚壁菌以及未确定分类的类群;同时构建了聚驱后油藏古菌群落16S rDNA的克隆文库,共挑取了48个阳性克隆,根据T-RF分型结果共有5个类群,构建的古菌克隆文库的12个阳性克隆分属5个不同的类群,这些克隆和产甲烷菌亲缘关系很近.结论:该研究为大庆油田本源微生物采油技术的应用提供了可靠的理论依据.     

利用DGGE法研究不同种植体系中根际微生物群落结构

利用DGGE技术研究不同间作和轮作种植体系对作物根际细菌和真菌群落结构的影响.运用16SrDNA和18SrDNA特异引物对,将土壤中提取的总DNA进行PCR扩增后,通过DGGE技术对PCR产物进行分析,结果表明:玉米-蚕豆轮作对蚕豆根际细菌和真菌群落结构影响明显,二者都与单作蚕豆有较大差异;小麦/蚕豆间作明显改变两种作物根际细菌群落结构和蚕豆根际真菌群落结构;玉米/蚕豆间作明显改变玉米根际细菌、真菌群落结构和蚕豆根际真菌群落结构.     

德兴铜矿酸性矿坑水水样与底泥中微生物群落多样性及其群落结构变化

江西铜业集团德兴铜矿是中国最大的露天开采铜矿,已有1000多年的开采历史,因此它为极端环境下微生物群落结构研究提供了一个优良素材。应用16S rRNA基因的PER克隆技术检测了来源于该铜矿3个不同样地的水样与底泥中的微生物多样性。通过RFLP分析获得40个OTUs,测序和系统发育分析表明它们属于7个不同的系统发育分区,即Acidobacteria,Actinobacteria,Nitrospira,α-Proteobacteria和γ-Proteobacteria,Firmicutes,δ-Proteobacteria。这些克隆中的大部分属于γ-Proteobacteria,α-Proteobacteria和Nitrospira。进一步的分析结果表明在各样点水样中的嗜酸氧化亚铁硫杆菌（Acidithiobacillus ferrooxidans）所占比例大于其在底泥中的比例,而底泥的嗜酸菌属（Acidiphilium）所占比例明显高于水样,这可能与底泥的缺氧环境和Acidiphilium菌能够将三价铁还原成二价铁的特性有关。     

云冈石窟石质文物表面及周边岩石样品中微生物群落分析

【目的】通过对云冈石窟石质文物表面及云冈石窟周边岩石样品中微生物的研究,建立可用于快速检测石质文物中微生物的方法。【方法】选取云冈石窟石质样品和云冈石窟周边岩石样品作为研究对象,应用PCR-DGGE技术对样品中的微生物群落结构进行了分析研究。【结果】根据系统发育树聚类分析,可以得出云冈石窟中检测出的微生物主要分为四大类群:γ-变形菌纲、鞘脂杆菌门、α-变形菌纲和放线菌纲;根据GenBank数据库中的序列比对结果,可以知道云冈石窟周边类似岩石样品中的微生物主要属于γ-变形菌纲、厚壁菌门和α-变形菌纲等。【结论】本实验成功检测出云冈石窟石质样品表面及云冈石窟周边岩石样品中的微生物类群,为云冈石窟的保护工作提供了有力依据,同时也证明了DEEG和分子克隆技术相结合的方法是检测石质文物中微生物群落结构的一种可操作性强、快速、准确的检测手段。     

Bacterial communities in sediments of the shallow Lake Dongping in China

Aims: The purpose of this study was to discuss how the environmental inputs and anthropogenic activities impact bacterial communities in the sediments of a shallow, eutrophic and temperate freshwater lake. Methods and Results: Sediment cores were collected from Lake Dongping, located in Taian, Shandong, China. All samples were processed within 4 h of collection. Total nitrogen, total phosphorus (TP), total organic carbon, ammonium nitrogen and nitrate nitrogen content of samples were measured by Kjeldahl determination, sulphuric acid–perchloric acid digestion and molybdenum blue colorimetry, potassium dichromate titration, Nessler’s reagent colorimetric and the phenol disulphonic acid colorimetric method, respectively. Seasonal and temporal diversity of sediment bacterial communities at six stations in Lake Dongping were investigated using molecular approaches (terminal restriction fragment length polymorphism and 16S rDNA clone libraries). Noticeable seasonal and temporal variations were observed in bacterial diversity and composition at all six stations. Sediment bacterial communities in Lake Dongping belonged to 16 phyla: Proteobacteria (including α‐Proteobacteria, β‐Proteobacteria, δ‐Proteobacteria, ε‐Proteobacteria, γ‐Proteobacteria), Acidobacteria, Planctomycetes, Bacteroidetes, Firmicutes, Verrucomicrobia, Nitrospira, Chloroflexi, Gemmatimonadetes, Chlorobi, Cyanobacteria, Deferribacteres, Actinobacteria, OP8, Spirochaetes and OP11. Members of β‐, δ‐ and γ‐Proteobacterial sequences were predominant in 11 of 12 clone libraries derived from sediment samples. Sediment samples collected at stations 1 and 4 in July had the greatest bacterial diversity while those collected at station 2 in October had the least diversity. TP concentration was significantly correlated with the distribution of bacterial communities. Conclusions: Our results suggested that different environmental nutrient inputs contribute to seasonal and temporal variations of chemical features and bacterial communities in sediments of Lake Dongping. TP concentration was significantly correlated with the distribution of bacterial communities. Significance and Impact of the Study: This study has an important implication for the optimization of integrated ecosystem assessment of shallow temperate freshwater lake and provides interesting information for the subsequent of the ecosystem.     

山西运城盐湖土壤沉积物细菌多样性及影响因素分析

地处山西省西南部的运城盐湖历史悠久,气候特征与地理环境独特,蕴藏着丰富的微生物资源,研究其土壤沉积物生态系统对了解盐碱地土壤细菌多样性及其功能具有重要意义。【目的】探究运城盐湖土壤与沉积物中细菌的多样性,分析其影响因素,为盐碱地土壤生态系统的可持续管理和纯培养物挖掘提供科学依据与参考。【方法】对运城盐湖6个采样点的18个样品进行土壤理化分析,结合16S rRNA基因的扩增子高通量测序,分析环境因素对细菌多样性的影响。【结果】假单胞菌门(Pseudomonadota)、拟杆菌门(Bacteroidota)和芽孢杆菌门(Bacillota)为运城盐湖土壤微生物的优势类群,多样性和群落组成分析显示不同采样点间的微生物存在明显差异。典型相关分析(canonical correlation analysis, CCA)表明,总溶解固体(total dissolved solids, TDS)、总氮(total nitrogen, TN)、总碳(total carbon, TC)和SO₄^2-对土壤微生物多样性的影响最大,其次为Na⁺、Ca²⁺、Cl^-、土壤有效磷(available phosphorous, A-P)和pH,HCO₃^-、硝态氮(nitrate nitrogen, NO₃^--N)、氨态氮(ammonia nitrogen, NH₄⁺-N)、K⁺和Mg²⁺的影响较小。【结论】运城盐湖土壤微生物拥有较高的多样性,与环境因子关系密切。本研究完善了运城盐湖土壤细菌资源的生物信息,为盐湖细菌资源的挖掘和研究提供了理论依据。     

东太湖表层沉积物放线菌群落结构多样性及其空间异质性

采用基于16SrRNA基因变性梯度凝胶电泳(DGGE)方法,考察东太湖表层沉积物放线菌群落结构多样性及其空间分布特征.结果显示:东太湖表层沉积物中放线菌群落结构多样性较高,DGGE指纹图谱样品的平均条带数为21.5±2个,群落结构多样性(如Shannon-Wiener指数)在空间尺度上差异不明显;聚类分析表明放线菌群落结构空间分布特征表现为相邻采样位点群落结构较为相似,这可能与相邻位点沉积物理化性质类似有关.典型对应分析结果表明,东太湖表层沉积物中放线菌群落结构变化的主要影响因子为沉积物pH.     

Bacterial community along a historic lake sediment core of Ardley Island, west Antarctica

The bacterial community in a historic lake sediment core of Ardley Island, Antarctica, spanning approximately 1,600 years, was investigated by molecular approaches targeting the 16S rRNA gene fragments. The cell number in each 1 cm layer of the sediment core was deduced through semi-quantification of the 16S rRNA gene copies by quantitative competitive PCR (QC-PCR). It was found that the total bacterial numbers remained relatively stable along the entire 59 cm sediment core. Denaturing Gradient Gel Electrophoresis (DGGE) analysis and sequencing of PCR-amplified 16S rRNA gene fragments were performed to analyze the bacterial diversity over the entire column. Principle coordinates analysis suggested that the bacterial communities along the sediment core could be separated into three groups. There were obvious bacterial community shift among groups of 1–20 cm, 21–46 cm and 46–59 cm. Diversity indices indicated that the bacterial community in the 21–46 cm depth showed the highest species diversity and uniformity. The main bacterial groups in the sediments fell into 4 major lineages of the gram-negative bacteria: the α, γ and δ subdivision of Proteobacteria, the Cytophaga-Flavobacteria-Bacteroides, and some unknown sequences. The gram-positive bacteria Gemmatimonadetes, Firmicutes and Actinobacteria were also detected. The results demonstrated the presence of highly diverse bacterial community population in the Antarctic lake sediment core. And the possible influence of climate and penguin population change on the bacterial community shift along the sediment core was discussed.Shengkang Li and Xiang Xiao contributed equally to this paper     

Bacterial Community of the Largest Oligosaline Lake,Namco on the Tibetan Plateau

Bacterial abundances and diversity in the surface water of Lake Namco, the largest oligosaline lake on the Tibetan Plateau, were examined using flow cytometry approach and constructing 16S rRNA gene clone libraries. Bacterial abundances were from 0.08 × 10⁶ to 1.6 × 10⁶ cells mL^?1, and were in the reported range of other lakes of the Tibetan Plateau and high mountain regions. Bacterial abundances were significantly correlated with the concentrations of chlorophyll a (chl a), but showed no significant relationship with the dissolved organic carbon (DOC), which suggested that the amount of DOC released by algae was the key factor determining the bacterial abundance rather than the total DOC. The total trace elements concentrations also obviously connected with bacterial abundances, and 9 of 20 elements showed significant relationship. Bacterial 16S rRNA gene clone sequences were affiliated to the α-, β-, γ-, δ-, and ?-Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Acidobacteria, Planctomycetes, Verrucomicrobia, Candidate division OD1, or unclassified, and among these the β-Proteobacteria dominated. Bacteria in Lake Namco were most closely related to those retrieved from freshwater habitats. Relatively few sequences were closely related to those recovered from saline habitats. Eleven of 34 typical freshwater bacterial clusters were detected in the oligosaline Lake Namco. Bacterial diversity within the lake varied and was connected with the concentrations of DOC and chl a.     

青海湖岸带土壤与沉积物的地化特征与细菌群落对水位上升的响应

【目的】探究青海湖岸带土壤与沉积物的地化特征与细菌群落对水位扩张的响应。【方法】从岸上至岸下沿垂直青海湖岸带方向,采集距离湖面不同高度土壤(土壤：S1、S2)、岸边不同水深表层沉积物(过渡区：E0、E6、E17)及湖心表层沉积物(沉积物：D1、D2)样品,土壤与沉积物水深(土壤水深表示为负数)从小到大的变化表征岸边土壤被淹水转变为沉积物的过程。采用地球化学分析和16SrRNA基因高通量测序技术,探究岸带土壤与沉积物样品中的地化特征与微生物群落构成。【结果】青海湖水位上升导致的生境转变对岸带土壤与沉积物的理化性质、营养水平、有机碳类型等地化特征产生显著影响。具体表现为,随着水位升高,岸带土壤与沉积物的pH、矿物结合态有机碳含量显著升高,而碳氮比值、可溶性有机碳(dissolved organic carbon,DOC)、颗粒态有机碳含量显著下降。随着水位上升,青海湖岸带被淹没土壤的细菌群落多样性下降,且群落结构发生明显变化。这种变化与环境因子变化密切相关,具体表现为,细菌群落物种丰富度指数和香农多样性指数随着水位上升呈下降趋势;活性金属结合态有机碳含量与细菌群落多样性的变化密切相关;理化...     

Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan

The spatial and temporal variability of bacterial communities were determined for the nearshore waters of Lake Michigan, an oligotrophic freshwater inland sea. A freshwater estuary and nearshore sites were compared six times during 2006 using denaturing gradient gel electrophoresis (DGGE). Bacterial composition clustered by individual site and date rather than by depth. Seven 16S rRNA gene clone libraries were constructed, yielding 2717 bacterial sequences. Spatial variability was detected among the DGGE banding patterns and supported by clone library composition. The clone libraries from deep waters and the estuary environment revealed highest overall bacterial diversity. Betaproteobacteria sequence types were the most dominant taxa, comprising 40.2–67.7% of the clone libraries. BAL 47 was the most abundant freshwater cluster of Betaproteobacteria , indicating widespread distribution of this cluster in the nearshore waters of Lake Michigan. Incertae sedis 5 and Oxalobacteraceae sequence types were prevalent in each clone library, displaying more diversity than previously described in other freshwater environments. Among the Oxalobacteraceae sequences, a globally distributed freshwater cluster was determined. The nearshore waters of Lake Michigan are a dynamic environment that experience forces similar to the coastal ocean environment and share common bacterial diversity with other freshwater habitats.     

鄱阳湖湖泊细菌群落组成及结构——以松门山为例

于2011年5月在鄱阳湖——松门山湖区采集底泥与表层水样,分别提取了表层水体浮游和底泥微生物基因组DNA,利用454高通量测序技术对细菌的16S rRNA基因进行了序列测定,分析了湖泊底泥细菌、水体浮游细菌群落结构特征。结果显示:底泥细菌OTUs(Operational Taxonomic Units)为1454,表层水体浮游细菌OTUs为269;底泥细菌群落比表层水体更加多样化,底泥细菌的物种数大大多于表层水体。同时,底泥细菌群落与表层浮游细菌群落结构存在显著差异。物种分类显示鄱阳湖底泥细菌种类隶属于20门,228属,其中优势种群为δ-变形菌纲(Deltaproteobacteria)、β-变形菌纲(Betaproteobacteria)和疣微菌门(Verrucomicrobia);表层水体浮游细菌隶属于13门116属,优势种群为β-变形菌纲、拟杆菌门(Bacteroidetes)和放线菌门(Actinobacteria)。结果进一步揭示,无论是浮游细菌群落还是沉积物细菌群落,优势细菌种群的基因型多样性更高。     

基于高通量测序的鄱阳湖典型湿地土壤细菌群落特征分析

采用高通量测序技术分析了鄱阳湖典型湿地土壤细菌群落特征。测序结果表明,不同植被土壤细菌群落丰度与多样性的排序相同:苔草带苔草-虉草带芦苇带泥滩带藜蒿带。沿湖面至坡地,空间位置相近的土壤细菌群落结构具有更大的相似性,苔草-虉草带、苔草带和芦苇带的细菌群落结构相近,泥滩带和藜蒿带的细菌群落结构差异较大。变形菌门(30.0%)是湿地土壤平均相对丰度最高的门,其次为酸杆菌门(16.7%)和绿弯菌门(16.5%);多数门分类细菌相对丰度沿湖面至坡地存在一定变化趋势。硝化螺菌属是第一大属分类水平细菌群落。在土壤化学指标中,与鄱阳湖湿地细菌群落相关性较大的是总磷、铵态氮和有机质含量。以上研究结果表明,鄱阳湖湿地不同植被土壤细菌群落具有结构性差异,但沿湖面至坡地存在规律性变化。