肇庆星湖湿地放线菌多样性

摘要:【目的】了解肇庆星湖湿地放线菌多样性及其与底泥理化性质的关系。【方法】应用聚合酶链式反应-变性梯度凝胶电泳(polymerase chain reaction-density gradient gel electrophoresis,PCR-DGGE)技术对星湖湿地10个样点放线菌群落进行研究,根据DGGE图谱及克隆测序结果对其物种多样性进行分析,并结合样点理 化性质对其空间分布特征进行分析。【结果】通过PCR-DGGE指纹图谱发现各样品放线菌物种丰富度(S)、多样性指数(H')和均匀度指数(J')均有所不同。对不同样点放线菌群落相似性进行比较,发现它们的相似性系数存在着一定的关系,相邻样点间相似性较高。对DGGE优势条带进行回收、克隆、测序,显示优势类群主要分布于类诺卡氏菌科( Nocardioidaceae)、链霉菌科(Streptomycetaceae)、小单孢菌科(Micromonosporaceae)、微球菌科(Micrococaceae)、纤维素单胞菌科(Cellulomonadaceae)和原小单胞菌科(Promicromonosporaceae)。典型对应分析结果表明,星湖湿地放线菌群落结构变化的主要影响因子为底泥水溶性碳(WSOC)和速效磷(A-P)。【结论】肇庆星湖湿地蕴含着大量的放线菌资源,具有较高的物种多样性,需要进一步挖掘这些新资源。     

象山港网箱养殖区沉积物的古菌空间分布

对象山港网箱养殖区及其周边沉积物中古菌群落的空间分布进行研究,应用基于16S rRNA基因的T-RFLP(末端限制性片段多态性分析)技术分析象山港网箱养殖区及其周边不同深度沉积物中古菌的群落结构和多样性,并构建克隆文库进行系统发育学分析。测定沉积物各项理化因子,通过PCA和RDA分析了古菌群落分布及其与环境因子之间的关系。结果表明,泉古菌是港口沉积物中的优势古菌群,占古菌群落的50%以上。网箱养殖区沉积物的古菌群落结构较非养殖区简单,多样性降低。非养殖区古菌群落随深度呈现有规律的变化。营养盐类和pH是造成养殖区域古菌群落结构区别于非养殖区域的主要环境因素。     

PCR-DGGE技术用于湖泊沉积物中微生物群落结构多样性研究

采用PCR-DGGE分子指纹图谱技术比较南京市玄武湖、奠愁湖和太湖不同位置的表层沉积物微生物群落结构,研究结果表明,三湖泊沉积物微生物的16SrDNA的PCR扩增结果约为626bp,为16S rDNA V3～V5区特异性片段。玄武湖和莫愁湖表层沉积物中大约有20种优势菌群,且同一湖泊不同采样点DGGE图谱的差异性不大,细菌群落结构具有较高的相似性,而太湖样品DGGE条带的数目和位置表现出明显差异,且不同采样点图谱的差异性较大。三湖泊除具有特征性的微生物种属外,还分布约5个相同的细菌种群,可能与沉积物的理化性质和水生植被的影响相关。对DGGE图谱中7条主带进行回收、扩增和测序,结果显示其优势菌群具有不同的序列组成,其中5个序列与Genebank中已登录的细菌种群的同源性≥99％,2个序列的同源性为96％和93％,其中2个相似的细菌类群目前尚未获得纯培养。     

黄河内蒙古段表层沉积物细菌多样性及群落结构类型

为掌握黄河内蒙古段表层沉积物微生物多样性、群落结构类型及其影响因素,采用高通量测序技术分析了6个采样点表层沉积物中的微生物多样性及群落结构。研究结果表明,黄河内蒙古段沉积物细菌丰度大小排序为乌拉特前旗(H3)老牛湾(H6)临河(H2)包头(H4)托县(H5)乌海(H1),微生物多样性排序为H6 H2 H5 H4 H3 H1,乌海沉积物中细菌丰度和微生物多样性都是最低的一个采样点。黄河内蒙古段表层沉积物中三大优势菌群分别为变形菌门(Proteobacteria,相对丰度32.39%)、绿弯菌门(Chloroflexi,13.25%)和拟杆菌门(Bacteroidetes,12.16%)。细菌群落丰度与环境因子之间的冗余分析结果显示,沉积物中总有机碳(TOC)、离子交换容量(CEC)和总磷(TP)、总氮(TN)等环境因子对黄河内蒙古段沉积物细菌群落分布影响较大,负相关系数分别为82.5%、80.1%、85.5%和85.2%;微生物多样性与环境理化因子相关性分析结果表明,黄河沉积物微生物多样性格局与对氮磷等营养物质的损耗有直接关系。     

大熊猫肠道放线菌的种群组成及多样性分析

【目的】探究不同年龄、不同性别大熊猫肠道放线菌的多样性及群落结构,为寻找潜在产生活性化合物的放线菌资源提供理论依据。【方法】采用PCR-DGGE技术对大熊猫肠道放线菌进行分析,对电泳结果进行UPGMA聚类分析、主成分分析、生物多样性等多重比较。【结果】变性梯度凝胶电泳(DGGE)图谱显示,不同大熊猫肠道中放线菌的多样性及群落结构存在明显差异。随着年龄的增长,雌性大熊猫肠道中放线菌的多样性指数(H')和丰富度(S)逐渐减少,而雄性大熊猫肠道内放线菌的多样性指数(H')和丰富度(S)逐渐增多。不同个体的大熊猫肠道放线菌的群落结构存在明显差异,但相同性别之间的相似性很高。DGGE条带回收测序结果表明,获得的28条序列归属于10个放线菌属,其中链霉菌属(Streptomyces)为优势菌属,占总数的46%;北里孢菌属(Kitasatospora)、红球菌属(Rhodococcus)、棒杆菌属(Corynebacterium)、迪茨氏菌属(Dietziaceae)、大理石雕菌属(Marmoricola)、布登堡菌属(Beutenbergia)、微杆菌属(Microbacterium)、链嗜酸菌属(Streptacidiphilus)和芽生球菌属(Blastococcus)等为非链霉菌属,占总数的54%。【结论】大熊猫肠道内蕴藏着丰富的放线菌资源,其肠道菌群的结构与组成受年龄和性别的影响。     

新疆巴里坤、七角井和台特玛盐湖沉积物中免培养放线菌群落组成与离子成分分析

【背景】新型病原微生物层出不穷,放线菌作为最重要的抗生素生产菌仍受制于纯培养困难和菌种资源不足,而对于盐湖沉积物中的丰富放线菌资源却鲜有报道。【目的】探索巴里坤、七角井和台特玛盐湖沉积物放线菌群落结构及其多样性,分析盐湖沉积物中化学离子成分对放线菌群落的影响。【方法】每个盐湖采集5份样品并混合,使用SDS-CTAB抽提法提取总DNA,使用放线菌特异性引物进行PCR扩增并构建16S r RNA基因文库,每个样品随机挑选220个克隆子,经过Hae III酶切筛选后对阳性克隆子进行测序分析;对每个样品的8种主要化学离子进行检测,并将沉积物化学离子成分与放线菌群落进行关联性分析。【结果】获得的381个克隆序列属于143个操作分类单元(Operational taxonomic Unit,OTU),聚类结果显示从3个盐湖中共探测到37个放线菌属(台特玛盐湖:24;巴里坤盐湖:16;七角井盐湖:14)。3个盐湖共有的放线菌属为Aciditerrimonas、Aquihabitans、Demequina、Dietzia、Ilumatobacter和Amycolatopsis。从放线菌群落结构上看,台特玛盐湖与其他两湖差异性很大,巴里坤盐湖与七角井盐湖群落相似性更高,巴里坤、七角井和台特玛盐湖未知放线菌的组成分别为47.59%、53.07%和51.53%。利用RDA(Redundancy analysis)分析盐湖沉积物化学离子与放线菌群落的关联性,结果显示与Na~+、Cl~-和K~+相比,Mg~(2+)、Ca~(2+)、SO_4~(2-)、HCO_3~-和CO_3~(2-)与盐湖放线菌类群的相关关系要更加紧密。【结论】3个盐湖中具有丰富的放线菌多样性,包含大量的未知放线菌。盐湖沉积物不同的化学离子成分影响着各自独特的放线菌群落,可为开发新的盐湖放线菌资源提供依据。     

新疆于田盐池放线菌群落结构

应用免培养技术和基于16S rRNA基因序列的系统发育分析对新疆于田盐池土壤放线菌群落结构进行研究。结果表明, 41个克隆序列属于26个OTUs, 分别分布于放线菌门放线菌亚纲(Actinobacteridae)的7个亚目和酸微菌亚纲(Acidimicrobidae), 其中链孢囊菌亚目(Streptosporangi- neae)中放线菌组成丰富, 占到了全部挑选克隆的42.3%, 是于田盐池放线菌群落中的优势菌, 而链霉菌不是高盐环境放线菌的优势菌群。在这些克隆序列中有71.8% 的克隆序列同已知序列的相似性低于97%, 属于放线菌的新类群, 这些可能的新类群中有15.3%的克隆序列与已知菌株的相似性小于85%, 这些克隆序列的分类地位都在科一级的分类单元上, 有的可能分类地位更高。这些研究结果说明于田盐池中存在有较为丰富的放线菌系统发育多样性, 并且潜藏着新类型的放线菌资源。另外, 由于微生态效应的存在, 不同高盐环境之间放线菌群落也存在明显差异。     

出土竹简饱水期间放线菌群落结构与功能

【背景】出土竹简需经历一个较长时间的饱水保存后才进行脱水处理,在此期间微生物的滋生和蔓延威胁竹简的安全保存。【目的】研究分析成都老官山汉墓出土竹简浸泡液中的放线菌群落结构与功能,为科学有效保存竹简提供理论依据。【方法】采用PCR-DGGE(变性梯度凝胶电泳)技术与传统可培养方法相结合的方式对成都老官山汉墓出土竹简夏季浸泡液中的放线菌群落结构和功能进行了初探。【结果】DGGE图谱显示,各样品间放线菌多样性指数(H′)、优势度指数(C)、辛普森指数(D)和均匀度指数(J)均有所不同,主成分分析结果反映出竹简浸泡液中放线菌种群结构存在较大差异;DGGE条带回收测序显示15条序列归于10个属,其中检出率较高的有原小单孢菌属(Promicromonospora)、纤维微菌属(Cellulosimicrobium)、芽球菌属(Blastococcus)、链霉菌属(Streptomyces),而原小单胞属(Promicromonospora)在各个样品中均有检出;可培养方法获得12株放线菌,分属于链霉菌属(Streptomyces)和原小单胞属(Promicromonospora);通过刚果红实验对分离获得的菌株进行初步筛选,得到5株具有纤维素降解能力的菌株。【结论】竹简浸泡液中的放线菌不仅种群丰富,而且存在降解竹简的潜在可能。     

乌梁素海湖滨湿地细菌群落结构多样性

【目的】了解乌梁素海湖滨湿地水陆过渡带细菌群落结构及多样性变化,探讨富营养化湖泊湿地基质条件对细菌群落结构的影响。【方法】应用变性梯度凝胶电泳(PCR-DGGE)技术,分析和比较了依陆向分布的4个水陆过渡带样点的湿地细菌群落结构多样性,采用典型对应分析(CCA)探讨了湿地基质因子对细菌多样性的影响。【结果】DGGE图谱显示依湖泊水体沉积物(S-1)→湖滨芦苇沼泽沉积物(S-2)→湖滨碱蓬盐化草甸土壤(S-3)→岸上白刺荒漠土壤(S-4),4个样点的条带数依次减少,对应菌群结构及多样性变化显著;多样性指数分析结果显示,Shannon-Wiener指数(H)、均匀度(E)、丰富度(S)以及Simpson指数(DS)均显示依陆向分布逐步下降的规律,即:S-1S-2S-3S-4。序列比对结果显示,沉积物及土壤细菌分属于变形菌门(78.6%)、酸杆菌门(7.1%)、拟杆菌门(14.3%)这3个细菌类群,优势菌门为变形菌门,而变形菌门又分为5个亚群,其中ε变形菌纲为优势亚群;CCA结果表明,图中各条带对应物种的分布受铵态氮、总氮、有机碳、水溶盐总量、氯离子以及钾离子影响最大。【结论】乌梁素海富营养化湖泊的水陆过渡带湿地细菌群落结构存在较大差异,富营养化相关基质因子对细菌多样性影响较大。这为研究富营养化湖泊湿地水陆过渡带的细菌结构多样性及空间异质性提供了科学依据。     

越冬和复苏时期太湖水体蓝藻群落结构的时空变化

为研究太湖蓝藻在越冬与复苏时期群落结构的时空变化规律,于2008年11月,2009年2月,2009年4月,在太湖富营养化较严重的湖区选取8个采样点 (梅梁湾、竺山湾、贡湖湾、大浦、西太湖、南太湖、湖心和湖湾交汇处),分3层采水样,过滤并提取样品DNA经PCR扩增蓝藻16S rDNA序列,采用T-RFLP(末端标记的限制性酶切片段长度多样性)技术分析蓝藻群落结构和多样性变化。共得到87个不同的T-RFs(末端限制性酶切片段),表明太湖蓝藻具有丰富的基因多样性。T-RF相对丰度和聚类分析结果表明,太湖蓝藻群落结构在垂直空间上相似性较高,相似度 > 50%;在水平空间,与Microcystis spp.对应的信号峰在8个采样点均为最强峰(相对丰度为17.7% 47.5%)。竺山湾蓝藻多样性最低,西太湖最高,但其余采样点间蓝藻群落和Shannon多样性指数没有显著差异(P>0.05)。Microcystis相对丰度与Shannon多样性指数呈显著负相关(皮尔逊相关系数为-0.958)。在时间尺度上,相似性分析(Analysis of similarity,ANOSIM)结果显示太湖蓝藻群落结构存在极显著差异( P<0.01) 。春季复苏时蓝藻多样性最高,秋季衰亡时最低。聚类分析表明样品聚成两大特征类群,秋季衰亡时样品独自聚为1支,而春季复苏期和冬季越冬期样品彼此混杂。     

Sediment Enzyme Activities and Microbial Community Diversity in an Oligotrophic Drinking Water Reservoir,Eastern China

Drinking water reservoir plays a vital role in the security of urban water supply, yet little is known about microbial community diversity harbored in the sediment of this oligotrophic freshwater environmental ecosystem. In the present study, integrating community level physiological profiles (CLPPs), nested polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and clone sequence technologies, we examined the sediment urease and protease activities, bacterial community functional diversity, genetic diversity of bacterial and fungal communities in sediments from six sampling sites of Zhou cun drinking water reservoir, eastern China. The results showed that sediment urease activity was markedly distinct along the sites, ranged from 2.48 to 11.81 mg NH₃-N/(g·24h). The highest average well color development (AWCD) was found in site C, indicating the highest metabolic activity of heterotrophic bacterial community. Principal component analysis (PCA) revealed tremendous differences in the functional (metabolic) diversity patterns of the sediment bacterial communities from different sites. Meanwhile, DGGE fingerprints also indicated spatial changes of genetic diversity of sediment bacterial and fungal communities. The sequence BLAST analysis of all the sediment samples found that Comamonas sp. was the dominant bacterial species harbored in site A. Alternaria alternate, Allomyces macrogynus and Rhizophydium sp. were most commonly detected fungal species in sediments of the Zhou cun drinking water reservoir. The results from this work provide new insights about the heterogeneity of sediment microbial community metabolic activity and genetic diversity in the oligotrophic drinking water reservoir.     

Vertical distribution of bacterial community structure in the sediments of two eutrophic lakes revealed by denaturing gradient gel electrophoresis (DGGE) and multivariate analysis techniques

Vertical distribution of bacterial community structure was investigated in the sediments of two eutrophic lakes of China, Lake Taihu and Lake Xuanwu. Profiles of bacterial communities were generated using a molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis, and the results were interpreted with multivariate statistical analysis. To assess changes in the genetic diversity of bacterial communities with changing depth, DGGE banding patterns were analysed by cluster analysis. Distinct clusters were recognized in different sampling stations of Lake Taihu. Canonical correspondence analysis (CCA) was carried out to infer the relationship between environmental variables and bacterial community structure. DGGE samples collected at the same sampling site clustered together in both lakes. Total phosphorus, organic matter and pH were considered to be the key factors driving the changes in bacterial community composition.     

Actinobacterial community and diversity in rhizosphere soils of Aquilaria crassna Pierre ex Lec assessed by RT-PCR and PCR-DGGE

The actinobacterial community in rhizospheres of eaglewood (Aquilaria crassna Pierre ex Lec) was analyzed using culture-independent methods of RT-PCR and PCR DGGE of 16S rRNA gene. We conducted the experiments to investigate the difference in diversity and community structure of actinobacteria with respect to sampling sites and seasons and to determine effect of plant species on selection of rhizosphere community from different sampling sites. Total genomic DNA and RNA were extracted from rhizosphere soils collected from two plantations in Phetchabun province and one plantation in each Nakhonnayok province, Rayong province and Chiang Mai province of Thailand during dry and rainy seasons. The UPGMA dendrogram generated from DGGE fingerprints showed that the actinobacterial community was separated corresponding to sampling sites, suggesting sampling sites effect. The shift in community and diversity between two seasons was detected in all sampling sites. RNA-based analyses showed that several actinobacterial groups appeared to be ubiquitous but different in metabolic activity in different environments. Species diversity (S) and simple indexes (I) indicate the increase in species diversity of actinobacteria from all sampling sites in rainy season. Cloning and sequencing of 16S rRNA gene fragments obtained from DGGE bands revealed that 14 of 40 dominant species of actinobacteria in the rhizospheres of this plant belonged to uncultured actinobacteria. Besides the uncultured actinobacteria, Nocardioides sp., Streptomyces sp., Mycobacterium sp., Rhodococcus sp. and Actinoplanes sp. were indentified and frequently found more than other genera.     

Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China

Bacterioplankton community compositions in the Dongjiang River were characterized using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library construction. Water samples in nine different sites were taken along the mainstem and three tributaries. In total, 24 bands from DGGE gels and 406 clones from the libraries were selected and sequenced, subsequently analyzed for the bacterial diversity and composition of those microbial communities. Bacterial 16S rRNA gene sequences from freshwater bacteria exhibited board phylogenetic diversity, including sequences representing the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteriodetes, Verrucomicrobia, and candidate division TM7. Members of Betaproteobacteria group were the most dominant in all sampling sites, followed by Gammaproteobacteria, Alphaproteobacteria, and Actinobacteria. DGGE profiles and the ∫-LIBSHUFF analysis revealed similar patterns of bacterial diversity among most sampling sites, while spatial distribution variances existed in all sites along the river basin. Statistical analysis showed that bacterial species distribution strongly correlated with environmental variables, such as nitrate and ammonia, suggesting that nitrogen nutrients may shape the microbial community structure and composition in the Dongjiang River. This study had important implications for the comparison with other rivers elsewhere and contributed to the growing data set on the factors that structure bacterial communities in freshwater ecosystems.     

Analysis of diurnal and vertical microbial diversity of a hypersaline microbial mat

Microbial mats are prokaryotic communities that provide model systems to analyze microbial diversity and ecophysiological interactions. Community diversity of microbial mat samples was assessed at 8:00 a.m. and 3:00 p.m. in a combined analysis consisting of 16S rRNA-denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid (PLFA) profiles. The divergence index determined from PLFA and DGGE data showed that depth-related differences have a greater influence on diversity than temporal variations. Shannon and Simpson indices yielded similar values in all samples, which suggested the stable maintenance of a structurally diverse microbial community. The increased diversity observed at 3:00 p.m. between 2.5 and 4 mm can be explained mainly by diversification of anaerobic microorganisms, especially sulfate-reducing bacteria. In the afternoon sampling, the diversity index reflected a higher diversity between 4 and 5.5 mm depth, which suggested an increase in the diversity of strict anaerobes and fermenters. The results are consistent with the conclusion that hypersaline microbial mats are characterized by high degree of diversity that shifts in response to the photobiological adaptations and metabolic status of the microbial community. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Dedicated to the memory of David C. White.     

Spatial heterogeneity of bacterial community structure in the sediments of the Pearl River estuary

Denaturing gradient gel electrophoresis (DGGE) and multivariate statistical analytical methods were applied to investigate the spatial variation of bacterial community structure in the Pearl River estuary sediment and to address the relationship between microbial community composition and bottom water chemistry in ten different stations. Preliminary results of sequencing analysis of the excised DGGE bands suggested that α-Proteobacteria, γ-Proteobacteria, Acidobacteria and Actinobacteria were the dominant bacterial groups in the Pearl River estuary sediment. Results of multidimensional scaling analysis of these field data suggested that the composition of bacterial communities varied with sampling sites. Finally, canonical correspondence analysis of the data of environmental variables and bacterial community suggested that bacterial community structure was significantly influenced by the change of environmental variables (total phosphorus, nitrite, ammonium, dissolved oxygen, pH and salinity).     

Determining Microeukaryotic Plankton Community around Xiamen Island,Southeast China,Using Illumina MiSeq and PCR-DGGE Techniques

Microeukaryotic plankton are important components of aquatic environments and play key roles in marine microbial food webs; however, little is known about their genetic diversity in subtropical offshore areas. Here we examined the community composition and genetic diversity of the microeukaryotic plankton in Xiamen offshore water by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis), clone-based sequencing and Illumina based sequencing. The Illumina MiSeq sequencing revealed a much (approximately two orders of magnitude) higher species richness of the microeukaryotic community than DGGE, but there were no significant difference in species richness and diversity among the northern, eastern, southern or western stations based on both methods. In this study, Copepoda, Ciliophora, Chlorophyta, Dinophyceae, Cryptophyta and Bacillariophyta (diatoms) were the dominant groups even though diatoms were not detected by DGGE. Our Illumina based results indicated that two northern communities (sites N2 and N3) were significantly different from others in having more protozoa and fewer diatoms. Redundancy analysis (RDA) showed that both temperature and salinity were the significant environmental factors influencing dominant species communities, whereas the full microeukaryotic community appeared to be affected by a complex of environmental factors. Our results suggested that extensive sampling combined with more deep sequencing are needed to obtain the complete diversity of the microeukaryotic community, and different diversity patterns for both abundant and rare taxa may be important in evaluating the marine ecosystem health.     

Bacterial diversity and bioaugmentation in floodwater of a paddy field in the presence of the herbicide molinate

This work aimed at studying variations on the diversity and composition of the bacterial community of a rice paddy field floodwater, subjected to conventional management, namely by using the herbicide molinate. The promotion of the herbicide biodegradation either by the autochthonous microbiota or by a bioaugmentation process was also assessed. This study comprehended four sampling campaigns at key dates of the farming procedures (seeding, immediately and 6 days after application of the herbicide molinate, and after synthetic fertilization) and the subsequent physic-chemical and microbiological characterization (pH, DOC and molinate contents, total cells, cultivable bacteria and DGGE profiling) of the samples. Multivariate analysis of the DGGE profiles showed temporal variations in the bacterial community structure and the Shannon’s index values indicated that the bacterial diversity reached its minimum at the molinate application day. The highest bacterial diversity coincided with the periods with undetectable concentrations of the herbicide, although microcosm assays suggested that other factors than molinate may have been responsible for the decrease of the bacterial diversity. The ability of autochthonous microorganisms to degrade molinate and the influence of the herbicide on the bacterial community composition were assessed in microcosm assays using floodwater collected at the same dates. Given molinate was not degraded by autochthonous microorganisms, and considering it represents an environmental contaminant, bioaugmentation microcosms were assayed aiming the assessment of the feasibility of a bioremediation process to clean contaminated floodwater. A molinate-mineralizing culture, previously isolated, promoted molinate removal, induced alterations in the autochthonous bacterial community structure and diversity, and was undetected after 7 days of incubation, suggesting the feasibility of the process.     

Characterization of Freshwater Diatom Communities: Comparing Taxonomic and Genetic‐Fingerprinting Approaches

Benthic diatom assemblages from five sampling sites located on two rivers were characterized simultaneously by means of traditional microscopic observations and PCR‐DGGE fingerprinting with primers specifically designed for Bacillariophyceae. Community structure, richness, and diversity assessed by both methods were compared. Diatom lists obtained from morphological identification were separated into subsets, depending on (i) the taxonomic level considered (genus, species, variety) and, for each of them, (ii) the relative abundance (RA) of each component (the whole data set, RA > 1%, RA > 2%). These data were then compared to genetic fingerprinting data. Clusters based on taxonomic composition and DGGE banding patterns were very similar, showing good correspondence of community structure between the two methods. Data were compared by linear regressions between indices (richness, diversity) and by Mantel tests on dissimilarity matrices generated for each community composition data set. Statistical analysis indicated that the most reliable correlations with fingerprinting were obtained for genera representing more than 1% RA or species representing more than 2% RA. The results reveal that the PCR‐DGGE protocol described here offers a satisfactory alternative for performing preliminary screening of coarse differences in diatom global community structure between samples. It can be regarded as a good complement to taxonomic analyses, which still remain necessary to detect precise changes in richness and diversity, especially when considering species with low abundance in natural assemblages.     

Spatiotemporal heterogeneity of plankton communities in Lake Donghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation to biotic and abiotic factors.

The 16S and 18S rRNA genes of planktonic organisms derived from five stations with nutrient gradients in Lake Donghu, China, were studied by PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting, and the relationships between the genetic diversity of the plankton community and biotic/abiotic factors are discussed. The concentrations of total nitrogen (TN), total phosphorus (TP), NH(4)-N and As were found to be significantly related (P<0.05) to morphological composition of the plankton community. Both chemical and morphological analyses suggested that temporal heterogeneity was comparatively higher than spatial heterogeneity in Lake Donghu. Although the morphological composition was not identical to the DGGE fingerprints in characterizing habitat similarity, the two strongest eutrophic stations (I and II) were always initially grouped into one cluster. Canonical correspondence analysis suggested that the factors strongly correlated with the first two ordination axes were seasonally different. The concentrations of TN and TP and the densities of rotifers and crustaceans were generally the main factors related to the DGGE patterns of the plankton communities. The study suggested that genetic diversity as depicted by metagenomic techniques (such as PCR-DGGE fingerprinting) is a promising tool for ecological study of plankton communities and that such techniques are likely to play an increasingly important role in assessing the environmental conditions of aquatic habitats.