PCR-DGGE技术在内源细菌选择性激活过程中的应用

分子生态学技术的发展大大促进了人们对环境中微生物群落的认识,也为研究油藏微生物群落提供了一个新的工具.在模拟油藏条件下,应用PCRDGGE技术研究激活剂的注入对油藏微生物群落结构的影响,考察了激活过程中菌群结构的变化情况.分析了常压（1 MPa）和高压（10 MPa）下内源激活DGGE条带变化,进行了激活过程中的PCR序列分析,考察了激活不同阶段中的优势菌,将优势条带序列构建系统发育树,并对激活过程中主要内源菌所在类群分析.结果表明,高压条件下,优势菌群结构与常压下差异较大,常压激活和高压激活细菌类群数量变化差异显著;激活后,优势菌的种类有所增加,群落结构也发生了变化.激活前,优势菌是芽孢杆菌,而激活剂的加入使变形菌的在种类上得到增加.     

生活垃圾堆肥过程中细菌群落演替规律

应用PCR-DGGE技术研究生活垃圾堆肥过程中的细菌群落演替规律,对堆肥不同时期的宏基因组DNA进行提取,扩增16S rDNA的V3区,分析生活垃圾堆肥过程中细菌群落的变化. DGGE图谱表明,随着堆体温度的升高,DNA条带表现出了明显的动态变化,降温期出现了新的优势条带并趋于稳定,说明堆肥不同时期的细菌群落发生了更替. 对条带分布进行聚类分析,结果表明:以55 ℃为界,将14个堆肥样品划分为2个族,族间的相似性仅为13%,说明堆肥过程中常温期(<55 ℃)和高温期(>55 ℃)微生物群落结构差别较大. 对优势条带回收测序的结果表明:在升温期,堆肥堆体中检测到H. obtusa和人类排泄物中的细菌;但随着温度的升高,具有纤维素降解功能的嗜热微生物Clostridium thermocellum成为堆肥高温期的优势细菌;当堆体温度小于55 ℃时出现了大量的未培养微生物.      

生物转鼓过滤器反硝化去除NO过程中微生物群落结构多样性解析

采用PCR-DGGE技术分析了生物转鼓过滤器(RDB)反硝化去除NO过程中的微生物多样性.研究结果表明,RDB中存在16种优势菌,并且沿填料径向不同位置的DGGE图谱差异性不大,细菌群落结构具有较高相似性.通过DGGE图形比较和微生物群落生物多样性指数计算,发现在RDB内加入CuⅡ(EDTA)络合剂后,NO去除率上升,而微生物群落多样性先增加后又下降,但群落结构变化不显著.对DGGE图谱中8条主带进行回收、扩增、克隆和测序,结果显示RDB中微生物群落主要由Cytopahga-Flexibacteria-Bacteroides(CFB)group Bacteroides、β-Proteobacterium、γ-Proteobacterium和Clostridium sp.组成.反硝化功能与条带G-5(属于γ-Proteobacterium)和G-6、G-8(属于β-Proteobacterium)所代表的菌种相关,相似性≥98%.G-3序列与GenBank数据库中2个最相似序列的相似性只有93%和92%,表明这个条带所代表的微生物可能为新的未培养微生物.     

市政污泥接种焦化废水好氧降解能力及微生物群落演替的响应分析

焦化废水是毒性很大的典型工业废水,生物处理过程中需要微生物具备很强的适应能力.以探讨焦化废水对微生物的毒性抑制以及微生物对焦化废水的适应过程为目的,通过于焦化废水原水中接种市政污泥,在考察COD、苯酚、氨氮和硫氰化物等主要污染物指标降解的基础上,运用Illumina高通量测序平台分析降解过程微生物群落组成及多样性变化的响应关系.结果表明,接种了市政污泥的焦化废水培养16 h后COD开始下降,40 h时苯酚降解了97.14%,72 h时硫氰化物开始降解,96 h时硫氰化物浓度低于检测限,氨氮浓度随着硫氰化物的降解而升高.群落测序分析表明,不同培养阶段污泥中微生物表现出群落结构及丰度上的差异:在苯酚降解阶段,苯酚优势降解菌Acinetobacter、Pseudomonas的丰度增大,48 h总相对丰度为13.04%;在硫氰化物降解阶段,Sphingobacterium、Brevundimonas、Lysobacter、Chryseobacterium为主导菌属,96 h时其总相对丰度为16.13%;在144 h阶段,优势菌属则变为Fluviicola、Stenotrophomonas和Thiobacillus,总相对丰度为22.45%.由此认为,市政污泥克服了焦化废水中毒性成分的抑制作用之后能迅速适应环境,表现出微生物群落结构随着废水降解成分的变化而改变,环境因子和降解功能菌之间的竞争是群落结构演变的主要因素.     

接种纤维素降解菌对牛粪堆肥微生物群落的影响

以牛粪和稻草为堆肥原料,利用传统培养法和PCR-DGGE技术相结合对接种纤维素降解菌后堆肥的微生物群落的动态变化进行了分析.结果表明,接种菌堆肥与自然堆肥相比,微生物数量的变化趋势快于自然堆肥,接种菌在堆肥初期能够激发微生物增殖,快速启动堆肥发酵,缩短堆肥进程.接种菌堆肥比自然堆肥的DGGE凝胶图谱条带的差异性大,接种...     

PCR-DGGE技术解析固体碳源表面生物膜的微生物群落结构

以聚乳酸/聚羟基丁酸戊酸共聚酯(PLA/PHBV)作为填充床反应器的碳源和生物膜载体,对受硝酸盐污染的水进行生物反硝化脱氮.采用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)技术分析了PLA/PHBV表面生物膜中微生物群落的结构和动态变化.结果表明,反应器运行初期,生物膜中微生物多样性下降.当反应器稳定运行时,DGGE图谱特征条带的香农威尔指数和辛普森指数均变化不大,微生物群落结构保持相对稳定.DGGE图谱特征条带的16S rDNA序列分析及扫描电镜分析的结果表明,生物膜中的主要微生物均为革兰氏阴性杆菌,包括Diaphorobacter、Acidovorax、Rubrivivax、Azospira、Thermomonas和Devosia,它们分别属于变形菌门(Proteobacteria)的α-,β-和γ-变形菌纲,其中Diaphorobacter为反应器稳定运行期生物膜中丰度最高的菌群.     

PCR-DGGE技术分析塔式蚯蚓生态滤池微生物群落结构

利用PCR-DGGE技术研究塔式蚯蚓生态滤池微生物群落结构变化,结果表明,微生物的变化与滤池体积大小、水力停留时间和污染物负荷有关,微生物群落结构在不同滤池层中变化较大.12个样品泳道中的总细菌的Shannon-Wiener多样性指数从0.25变化到1.27,一级滤池微生物多样性指数从0.29变化到1.05,二级滤池微生物多样性指数从0.75变化到0.97,三级滤池微生物多样性指数先从0.87减少到0.25,后由于葡萄糖的加入增加到1.27.二级滤池出水中葡萄糖的加入,加强了系统内微生物的活性,从而三级滤池砂石和青石层细菌条带变亮变多.经过克隆测序和系统发育树分析,塔式蚯蚓生态滤池内的微生物多为单细胞菌属、假单细胞菌属、革兰氏阴性菌属和不可培养杆菌属,不同细菌条带在不同级滤池内差异变化明显.     

土壤微生物群落对多环芳烃污染土壤生物修复过程的响应

采用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)方法,研究了土壤微生物群落多样性对生物表面活性剂强化的植物-微生物联合修复多环芳烃(PAHs)污染土壤的响应.结果表明,细菌群落的Shannon-Weaver指数修复前为3.17,修复后为3.24～3.45,多样性整体呈上升趋势,其中以植物-菌根真菌-降解菌处理最高,但各处理间无显著差异(P>0.05).聚类分析结果显示,植物、植物-鼠李糖脂、植物-菌根真菌和植物-菌根真菌-鼠李糖脂这4个处理的群落相似度在90%以上,植物-降解菌处理与这4个处理群落结构最近,此外,植物-降解菌-鼠李糖脂、植物-降解菌-菌根真菌-鼠李糖脂群落相似度在80%以上.通过测序比对,DGGE图谱上优势及特征性条带分别为Bacillus、Pseudomonas、Acidobacteria、Sphingmonas、Rhodopseudomonas、Firmicutes和Methylocytaceae等,可能是与PAHs降解密切相关的种属.生物表面活性剂强化的植物-微生物联合修复污染土壤过程中,在提高PAHs生物有效性基础上,改变了土壤微生物群落结构和丰度,从而可以有效提高PAHs的降解率.     

利用DGGE-菌落原位杂交法分离土壤中精喹禾灵降解菌

从自然环境中分离到的可降解农药的土著微生物,因其对环境的友好性及原位修复的可行性,受到了高度关注.为从土壤中筛选精喹禾灵降解菌株,首先利用PCR-DGGE技术分析了除草剂精喹禾灵胁迫下土壤细菌群落结构及多样性的变化.结果表明,添加精喹禾灵后,土壤细菌群落结构发生了明显的改变.精喹禾灵使细菌多样性呈现出增加-减少-增加的变化趋势,其中第9 d变化最大,后期趋于稳定.根据DGGE图谱条带的测序结果推断,Pseudomonas、Massilia、Burkholderia等属中的细菌对精喹禾灵具有耐受性或降解潜力,这些微生物类群可作为减少农药残留的土著微生物资源进行分离筛选.根据条带的测序结果,合成了地高辛(Digoxigenin)标记的探针,并进行了菌落原位杂交,筛选到了3株具有降解潜力的菌株,其中L1可以利用精喹禾灵作为唯一碳源生长,经16S rRNA基因鉴定该菌株属于假单胞菌属(Pseudomonas sp.).利用高效液相色谱法测定了菌株L1在无机盐培养基中降解精喹禾灵的效果.结果表明,培养7 d后,精喹禾灵的含量减少了近50%,且随着精喹禾灵含量的降低,L1菌体数量增加,证实了菌株L1具有降解精喹禾灵的能力.这一结果为今后研究菌株L1降解精喹禾灵的机制、功能基因等奠定了基础.     

PCR—DGGE技术在废水生物处理中的应用研究

聚合酶链式反应一变形梯度凝胶电泳（PCR—DGGE）作为一种分子指纹图谱能够较准确地反应污水处理过程中微生物群落结构多样性及其动态变化而广泛应用于废水生物处理技术的研究中。PCR—DGGE技术不仅能对样品中微生物群落结构多样性及种群演替进行分析,还能用于污水处理中优势菌群的分离与鉴定,克服了传统方法费时费力、培养条件苛刻等局限性,进而运用该技术构建高效的污染物降解工程菌,提高难降解有机物的去除效率,调节实际工艺参数,提高污水处理效率。     

分离海洋不动杆菌及其对石油烃降解性能研究

石油降解菌在石油污染生物修复技术中起到非常重要的作用。本研究分别以渤海湾油污区采集的水样,油样,水油泥混合样为材料富集分离石油降解菌,对其进行生理生化及分子生物学鉴定,并采用GC-MS测定烷烃、环烃、芳香烃等石油烃组分的变化。其中3株菌具有较高石油烃降解能力,16SrRNA序列分析表明该3株菌均与不动杆菌属（Acinetobacter）有99%序列相似性,可初步鉴定为不动杆菌属（Acinetobacter）。3株菌的石油烃降解能力依次为Tust-DM21＞Tust-DC12＞Tust-DW04,对原油成分的降解效果依次为烷烃＞芳香烃＞环烃。其中菌株Tust-DM21为一株高效石油烃降解菌,28℃于富集培养基培养10 d后,对烷烃（C10~C30）的降解率可达98%,对芳香烃和环烃的降解率达88%。研究表明,Tust-DM21菌株对烷烃,环烃,芳香烃都有较强的降解能力,是一株具有较好开发前景的石油降解菌。     

PCR-DGGE技术在城市污水化学生物絮凝处理中的特点

通过PCR-DGGE等分子生物学技术可以不经过常规培养直接从活性污泥和生物膜样品中提取DNA,对16Sr DNA V3区进行PCR扩增,结合DGGE(变性梯度凝胶电泳),从而分析活性污泥与生物膜中微生物种群结构.研究证实,活性污泥培养前后微生物种群结构发生很大的改变.同时对2种污水处理工艺中微生物种群结构进行了对比研究,对同一反应器不同位置微生物分布以及不同工况下的微生物种群结构进行了初步探讨.测定了活性污泥中部分菌种的16S rDNA V3区片段序列,通过NCBI(美国国立生物技术信息中心)基因库比对,初步确定细菌的属.结果显示,PCR-DGGE结合测序技术是一种完全可行的快速进行环境学样品微生物研究的分析方法.     

Phylogenetic diversity and specificity of bacteria associated with Microcystis aeruginosa and other cyanobacteria

Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics; however, little information on these interactions has been reported. In this study, the bacterial communities associated with five strains of Microcystis aeruginosa, three species of other Microcystis spp., and four representative species of non-Microcystis cyanobacteria were compared. Bacterial 16S rDNA fragments were amplified and separated by denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis. The similarities among bacterial communities associated with these cyanobacteria were compared to the digitized DGGE profiles using the cluster analyses. The bacterial community structure of all cyanobacterial cultures di ered. Cluster analysis showed that the similarity values among M. aeruginosa cultures were higher than those of other cyanobacterial cultures. Sequence analysis of DGGE fragments indicated the presence of bacteria including, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria in the cyanobacterial cultures. Members of the Sphingomonadales were the prevalent group among the Microcystis-associated bacteria. The results provided further evidence for species-specific associations between cyanoabcteria and heterotrophic bacteria, which are useful for understanding interactions between Microcystis and their associated bacteria.     

Analysis of bacterial community structures in two sewage treatment plants with different sludge properties and treatment performance by nested PCR-DGGE method

The bacterial community structures in two sewage treatment plants with different processes and performance were investigated by denaturing gradient gel electrophoresis （DGGE） of nested polymerase chain reaction （nested PCR） amplified 16S rRNA gene fragments with group-specific primers. Samples of raw sewage and treated effluents were amplified using the whole-cell PCR method, and the activated sludge samples were amplified using the extracted genomic DNA before the PCR products were loaded on the same DGGE gel for bacterial community analysis. Ammonia-oxidizing bacterial and actinomycetic community analysis were also carried out to investigate the relationship between specific population structures and system or sludge performance. The two plants demonstrated a similarity in bacterial community structures of raw sewage and activated sludge, but they had different effluent populations. Many dominant bacterial populations of raw sewage did not appear in the activated sludge samples, suggesting that the dominant bacterial populations in raw sewage might not play an important role during wastewater treatment. Although the two plants had different sludge properties in terms of settleability and foam forming ability, they demonstrated similar actinomycetic community structures. For activated sludge with bad settling performance, the treated water presented a similar DGGE pattern with that of activated sludge, indicating the nonselective washout of bacteria from the system. The plant with better ammonium removal efficiency showed higher ammonia-oxidizing bacteria species richness. Analysis of sequencing results showed that the major populations in raw sewage were uncultured bacterium, while in activated sludge the predominant populations were beta proteobacteria.     

南海高效石油降解菌的筛选及降解特性研究

以南海10个采样点采集到的样品为研究材料,以石油降解率为筛选依据,初筛获得52株石油降解菌,从中进一步筛选出6株对石油烃有降解能力的细菌,通过16S rRNA序列分析对筛选得到的6株菌进行初步鉴定,并使用GC-MS内标法测定降解产物,对降解菌的降解特性进行进一步研究.结果表明,采用重量法筛选出来的6株细菌对石油的降解率为20%～55%.与Genbank中的16S rRNA基因序列BLAST对比结果显示,所筛选出的6株菌株中,3株菌株属于芽孢杆菌属(Bacillus),2株菌株属于假交替单胞菌属(Pseudoalteromonas),1株属于交替单胞菌属(Alteromonas).降解特性分析表明,所筛选6株菌的烷烃降解率均在40%以上,多环芳烃降解率均在70%以上,其中,菌株B08500m-3对石油中总烷烃和总芳香烃的降解效果较好,降解率分别为75%和87%.     

Bacterial diversity in soils around a lead and zinc mine

Five samples of soil collected from a lead and zinc mine were used to assess the effect of combined contamination of heavy metals on soil bacterial communities using a polyphasic approach including characterization of isolates by culture method, community level catabolic profiling in BIOLOG GN microplates, and genetic community fingerprinting by denaturing gradient gel electrophoresis of 16S rDNA fragments amplified by PCR from community DNA （PCR-DGGE）. The structure of the bacterial community was affected to a certain extent by heavy metals. The PCR-DGGE analysis of 16S rRNA genes showed that there were significant differences in the structure of the microbial community among the soil samples, which were related to the contamination levels. The number of bacteria and the number of denaturing gradient gel electrophoresis （DGGE） bands in the soils increased with increasing distance from the lead and zinc mine tailing, whereas the concentration of lead （Pb） and cadmium （Cd） was decreased. Heavily polluted soils could be characterized by a community that differs from those of lightly polluted soils in richness and structure of dominating bacterial populations. The clustering analysis of the DGGE profiles showed that the bacteria in all the five samples of soil belonged to three clusters. The data from the BIOLOG analysis also showed the same result. This study showed that heavy metal contamination decreased both the biomass and diversity of the bacterial community in soil.     

细菌群落结构对水体富营养化的响应

于2005年2月在太湖不同营养水平湖区采集水样,寞接提取水样的总DNA,以细菌16SrDNA通用引物进行V3区PCR扩增,产物经DGGE(变性凝胶梯度电泳)分离后,获得水体细菌群落的16SrDNA指纹图谱;并运用FDC(表面荧光直接计数)方法对细菌丰度进行了测定.结果表明,水体中细菌的群落结构随着水体富营养化程度的改变产生明显变化,细菌数量呈现随水体营养水平增加而上升的趋势,营养水平较低的湖心区细菌数量仅为2.87×106 cells·mL-1,超富营养化的五里湖区水体中.细菌数量高达5.92×106cells·mL-1;细菌群落多样性随水体营养水平增加呈现显著的下降趋势,在超富营养化的1#、2#采样位点,细菌DGGE主要条带数量仅为23条,在沉水植物丰富区(贡湖湾)细菌DGGE主要条带数量达33条.PCA(主成分分析)的聚类结果表明,太湖水体中不同营养水平下的细菌群落多样性可大致归为3种类型,超富营养化的五里湖区水体细菌群落结构与梅粱湾及汞湖湾存在明显不同,可以大体归为超富营养类型、藻型湖区及草型湖区类型3种.此结果反映了水体富营养化过程中,由于营养物质的增加,促进了某些类群微生物的大量繁殖,水体中微生物的生物量显著增加;生态环境条件的恶化,造成了微生物多样性的下降,这可能导致原本稳定的水生态系统脆弱化.     

Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments

The characterization of microbial communities of different depth sediment samples was examined by a culture-independent method and compared with physicochemical parameters, those are organic matter （OM）, total nitrogen （TN）, total phosphorus （TP）, pH and redox potential （Eh）. Total genomic DNA was extracted from samples derived from different depths. After they were amplified with the GC-341 f/907r primer sets of partial bacterial 16S rRNA genes, the products were separated by denaturing gradient gel electrophoresis （DGGE）. The profile of DGGE fingerprints of different depth sediment samples revealed that the community structure remained relatively stable along the entire 45 cm sediment core, however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. The principle coordinates analysis suggested that the bacterial communities along the sediment core could be separated into two groups, which were located 0-20 cm and 21-45 cm, respectively. The sequencing dominant bands demonstrated that the major phylogenetic groups identified by DGGE belonged to Bacillus, Bacterium, Brevibacillus, Exiguobacterium, γ-Proteobacterium, Acinetobacter sp. and some uncultured or unidentified bacteria. The results indicated the existence of highly diverse bacterial community in the lake sediment core.     

铜尾矿库重金属Cu、Zn对细菌群落结构的影响

以湖北某铜矿尾矿库为主要研究对象,采集库内尾矿样品11个、对照样某小型废弃尾矿库尾矿样品2个和附近耕地土壤样品1个,采用变性梯度凝胶电泳方法对上述样品中细菌的16S rRNA V3~V6可变区扩增片段进行分析,利用分析得到的图谱数据与所测得样品的理化性质及重金属Cu、Zn含量进行相关性及冗余度(RDA)分析.结果表明,尾矿库内Cu、Zn污染严重并波及周边,与尾矿样品的理化性质存在不同的相关性,其中Zn的污染程度与有机质存在极显著正相关[R=0.668(P<0.01)].DGGE图谱分析结果发现,样品细菌多样性较低,相似性较高(最低相似度53.1%),优势菌群相对稳定,PCA分析表明,Cu和Zn对细菌多样性具有抑制作用.RDA分析结果说明Cu和Zn的含量对细菌种群分布影响很大,Cu对大部分种群具有抑制作用,而Zn一方面能促进某些种属数量,另一方面又能抑制其他种群的结构变化,这种影响并不是实验室研究的简单线性关系.     

超声波促进好氧/缺氧污泥消化过程中细菌群落结构分析

应用基于16S rDNA的PCR-DGGE对超声波-好氧/缺氧污泥消化过程中微生物种群的多样性进行研究.通过SDS细胞裂解法提取不同时期污泥中的基因组DNA,采用通用引物进行V3区域PCR扩增,长约190 bp的PCR产物经DGGE分离后,获得污泥微生物群落的DNA特征指纹图谱,对条带进行切胶测序,使用序列数据进行同源性分析并建立系统发育树.DGGE图谱表明,在反应器运行的不同时期,微生物群落结构发生动态演替.5、10、15、20、25 d微生物相似性与0 d相比分别为61.2%、48.2%、46.4%、42.6%、41.7%,总细菌Shannon指数经历了一个从逐渐减少到趋于稳定的过程,这表明超声波改变污泥内部性质,导致微生物多样性的降低.UPGMA聚类分析将DGGE图谱区分为三大族群并对应于不同运行时期.测序结果表明,超声波-好氧/缺氧污泥消化中微生物群落主要为Firmicute、Genuscitrobacter、Bacilli、α-Proteobacteria、β-Proteobacteria.