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

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Journal of Environmental Sciences 2008年第2期20卷 224-230页

作者： ZHAO Xingqing YANG Liuyan YU Zhenyang PENG Naiying XIAO Lin YIN Daqiang QIN Boqiang State Key Laboratory of Pollution Control and Resource Reuse School of the Environment Nanjing University Nanjing 210093 China Nanjing Institute of Geography and Limnology Chinese Academy of Sciences Nanjing 210008 China

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.

关键词： 16S rRNA denaturing gradient gel electrophoresis （dgge） Lake Taihu microbial diversity sediment vertical distribution

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Vertical diversity of sediment bacterial communities in two different trophic states of the eutrophic Lake Taihu, China

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Journal of Environmental Sciences 2013年第6期25卷 1186-1194页

作者： Keqiang Shao Guang Gao Yongping Wang Xiangming Tang Boqiang Qin State Key Laboratory of Lake Science and Environment Nanjing Institute of Geography and LimnologyChinese Academy of Sciences Nanjing Institute of Hydraulic Research

Vertical diversity of sediment bacterial communities in 2 different trophic states （macrophyte-dominated and algae-dominated） of the large shallow eutrophic Lake Taihu, China, were investigated using denaturing gradient gel electropfioresis （dgge） and 16S rRNA sequence analysis. Clustering analysis of dgge profiles showed that different clusters were recognized in different depths of sediment cores in the 2 lake trophic states. Analyses of the bacterial diversity, as estimated by the Shannon index （H＇）, showed that different sediment layers of the macrophyte-dominated state had higher diversity than the algae-dominated state. In addition, bacterial diversity of the sediment in the macrophyte-dominated state changed abruptly throughout the layers, but bacterial diversity of the algae-dominated state decreased gradually with sediment depth. Phylogenetic analysis showed that Proteobacteria was the most abundant phylum in the middle sediment of the 2 lake trophic states. In the macrophyte-dominated state, clone sequences related to Betaproteobacteria （50.0%） were the most abundant, followed by Epsilonproteobacteria （21.1%）, Acidobacteria （7.9%）, Deltaproteobacteria （7.9%）, Chloroflexi （7.9%）, and Bacteroidetes （5.3%）; whereas in the algae-dominated state, sequences affiliated with Betaproteobacteria （84.4%） were predominant, followed by Deltaproteobacteria （12.5%） and Acidobacteria （3.1%）. Canonical correspondence analysis showed that organic matter and pH play key roles in driving the vertical changes of bacterial community composition.

关键词： bacterial diversity canonical correspondence analysis （CCA） denaturing gradient gel electrophoresis （dgge） sedimentcore macrophyte- and algae-dominated states 16S rRNA

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Comparing results of cultured and uncultured biological methods used in biological phosphorus removal

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Journal of Environmental Sciences 2007年第11期19卷 1373-1379页

作者： LIU Ya-nan XUE Gang YU Shui-li School of Environmental Science and Engineering Dong Hua University Shanghai 201620 China School of Municipal and Environmental Engineering Harbin Institute of Technology Harbin 150090 China

Increasing attention has been paid to phosphate-accumulating organisms （PAOs） for their important role in biological phosphorus removal. In this study, microbial communities of PAOs cultivated under different carbon sources （sewage, glucose, and sodium acetate） were investigated and compared through culture-dependent and culture-independent methods, respectively. The results obtained using denaturing gradient gel electrophoresis （dgge） of polymerase chain reaction-amplified 16S rDNA fragments revealed that the diversity of bacteria in a sewage-fed reactor （1#） was much higher than in a glucose-fed one （2#） and a sodium acetate-fed one （3#）; there were common PAOs in three reactors fed by different carbon sources. Five strains were separated from three systems by using a phosphaterich medium; they were from common bacteria isolated and three isolates could not be found in dgge profile at all. Two isolates had good phosphorus removal ability. When the microbial diversity was studied, the molecular biological method was better than the culture-dependent one. When phosphorus removal characteristics were investigated, culture-dependent approach was more effective. Thus a combination of two methods is necessary to have a comprehensive view of PAOs.

关键词： phosphate-accumulating organisms （PAOs） denaturing gradient gel electrophoresis （dgge） biological phosphorus removal culture-dependent approach culture-independent approach

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Plankton community composition in the Three Gorges Reservoir Region revealed by PCR-dgge and its relationships with environmental factors

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Journal of Environmental Sciences 2008年第6期20卷 732-738页

作者： YAN Qingyun YU Yuhe FENG Weisong YU Zhigang CHEN Hongtao Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China Graduate School of the Chinese Academy of Sciences Beijing 100039 China Ocean University of China Qingdao 266003 China

To explore the relationships between community composition and the environment in a reservoir ecosystem, plankton communities from the Three Gorges Reservoir Region were studied by PCR-denaturing gradient gel electrophoresis fingerprinting. Bacterial and eukaryotic operational taxonomic units （OTUs）, generated by dgge analysis of the PCR-amplified 16S and 18S rRNA genes, were used as surrogates for the dominant ＂biodiversity units＂. OTU composition among the sites was heterogeneous; 46.7% of the total bacterial OTUs （45） and 64.1% of the eukaryotic OTUs （39） were identified in less than half of the sampling sites. Unweighted pair group method with arithmetic averages （UPGMA） clustering of the OTUs suggested that the plankton communities in the Xiangxi Rive sites were not always significantly different from those from the Yangtze River sites, despite clear differences in their environmental characterizations. Canonical correspondence analysis （CCA） was applied to further investigate the relationships between OTU composition and the environmental factors. The first two CCA ordination axes suggested that the bacterial community composition was primarily correlated with the variables of NO3^--N, dissolved oxygen （DO）, and SiO3^2--Si, whereas, the eukaryotic community was mainly correlated with the concentrations of DO, PO4^3--P, and SiO3^2--Si.

关键词： plankton community environmental factors denaturing gradient gel electrophoresis （dgge） spatial pattern Three Gorges Reservoir Region

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维普期刊数据库

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Application of PCR-dgge in Research of Bacterial Diversity in Drinking Water

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Biomedical and Environmental Sciences 2006年第5期19卷 371-374页

作者： QING WU XIN-HUA ZHAO SHENG-YUE ZHAO Department of Environmental Science and Engineering Tianjin University Tianjin 300072 China

Objective To analyze the structure of bacteria in drinking water by molecular biological techniques, Methods DNA of bacteria in drinking water was directly extracted without culture. 16S ribosomal DNA fragments, including V-6, -7, and -8 regions, were amplified with universal primers （EUBf933CJC and EUBr1387） and analyzed by dgge. Results dgge indicated that amplification products could be separated, The results showed that dgge could be used in the separation of different microbial 16SrRNA genes extracted from drinkng water. Though there were special bacteria in different water samples, the predominant bacteria were essentially the same. Three sequences of the reclaimed specific bands were obtained, and phylogenetic tree of these bands was made. Conclusion Bacterial diversity in drinking water is identified by molecular biological techniques.

关键词： Drinking water denaturing gradient gel electrophoresis （dgge） 16S ribosome RNA Microbial diversity

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Microbial Community Dynamics During Biogas Slurry and Cow Manure Compost

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Journal of Integrative Agriculture 2013年第6期12卷 1087-1097页

作者： ZHAO Hong-yan LI Jie LIU Jing-jing Lü Yu-cai WANG Xiao-fen CUI Zong-jun College of Agronomy and Biotechnology/Center of Biomass Engineering China Agricultural University Agronomy of Yanbian University Alan G. MacDiarmid Research Institute of Renewable Energy China Three Gorges University

This study evaluated the microbial community dynamics and maturation time of two compost systems： biogas slurry compost and cow manure compost, with the aim of evaluating the potential utility of a biogas slurry compost system. denaturing gradient gel electrophoresis （dgge）, gene clone library, temperature, C/N ratio, and the germination index were employed for the investigation, cow manure compost was used as the control. Results showed that the basic strip and dominant strips of the dgge bands for biogas slurry compost were similar to those of cow manure compost, but the brightness of the respective strips for each system were different. Shannon-Weaver indices of the two compost systems differed, possessing only 22% similarity in the primary and maturity stages of the compost process. Using bacterial 16S rRNA gene clone library analysis, 88 bacterial clones were detected. Further, 18 and 13 operational taxonomic units （OTUs） were present in biogas slurry and cow manure compost, respectively. The 18 OTUs of the biogas slurry compost belonged to nine bacterial genera, of which the dominant strains were Bacillus sp. and Carnobacterium sp.; the 13 OTUs of the cow manure compost belonged to eight bacterial genera, of which the dominant strains were Psychrobacter sp., Pseudomonas sp., and Clostridium sp. Results demonstrated that the duration of the thermophilic phase （more than 50°C） for biogas slurry compost was 8 d less than the according duration for cow manure compost, and the maturation times for biogas slurry and cow manure compost were 45 and 60 d, respectively. It is an effective biogas slurry assimilate technology by application of biogas slurry as nitrogen additives in the manufacture of organic fertilizer.

关键词： biogas slurry fermentation compost denaturing gradient gel electrophoresis （dgge） gene clone library maturity

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Cultivation-Independent Analysis of the Development of the Lactobacillus spp.Community in the Intestinal Tract of Newborn Piglets

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Agricultural Sciences in China 2011年第3期10卷 438-447页

作者： YAO Wen ZHU Wei-yun Hauke Smidt Martin W A Verstegen College of Animal Science and Technology Nanjing Agricultural UniversityNanjing210095PR．China Laboratory of Microbiology Wageningen University Wageningen 6703 CT The Netherlands Department of Animal Sciences Wageningen University Wageningen 67004H The Netherlands

Molecular diversity and development of the Lactobacillus community in the intestinal tract, as influenced by age and intestinal compartment, were studied in one litter of 12 conventionally raised piglets. Piglets were euthanized at each week （3 animals per time）. Digesta and tissue samples from stomach, duodenum, jejunum, ileum, caecum, colon, and rectum were collected and analysed by using 16S ribosomal RNA-based methods. dgge （denaturing gradient gel electrophoresis） profiles revealed that the Lactobacillus communities throughout the GI tract from duodenum to rectum showed good stability at same age. This indicates that fecal Lactobacillus communities can effectively represent the intestinal community. Two dominant bands were found in tissue samples of the small intestine, suggesting that the lactobacilli can adhere to the small intestinal wall. The Lactobacillus communities in different GI tract compartments developed over time. A successional change of Lactobacillus communities was observed from birth, through creep feeding to one week after weaning, showing a trend from simple to complex and back to simple. Furthermore, a clone library of Lactobacillus spp. 16S rRNA gene sequences were generated from jejunal and colonic chymes. Six dominant dgge bands generated from jejunal chymes were matched with sequences that show 94-98% similarity to the bands derived from L. reuteri, L. delbrueckii, and L. crispatus. Seven dominant dgge bands generated from colon chymes were matched with sequences that show 88-99% similarity to those derived from L. reuteri, L. delbrueckii, L. amylovorus/L. sobrius, and L. acidophilus. Amplicons related to L. reuteri were found in all dgge fingerprints from jejunal digesta of age of weeks 1, 3, and 4. Amplicons related to L. amylovorus/L. sobrius were present in all dgge fingerprints from colonic digesta of age of week 1, 3, and 4. Amplicons related to L. delbrueckii were found before weaning, L. crispatus after creep feeding before weaning and L. acidophilus after weaning. This indica

关键词： molecular diversity 16S rRNA gene denaturing gradient gel electrophoresis （dgge） Lactobacillus community piglets

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维普期刊数据库

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The key procedures and advancement in microbial communities analysis of dgge

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Journal of Northeast Agricultural University(English Edition) 2007年第3期14卷 245-249页

作者： ZHANG Ying YANG Changfu WANG Aijie Resources and Environmental Sciences College Northeast Agricultural University Harbin 150030 China Department of Civil and Environmental Engineering University of California Berkeley CA94703 USA School of Municipal and Environmental Engineering Harbin Institute of Technology Harbin 150090 China

Recently, denaturing gradient gel electrophoresis （dgge） is well established molecular tool in microbial ecology that allows the study of diversity and dynamics of microbial communities. The technique has been gained the preference since reliable facilitative and inexpensive. In order to promote the dgge further development and make it become a general analysis technique earlier, the key procedures and the advances in microbial communities analysis of dgge were introduced in this paper.

关键词： denaturing gradient gel electrophoresis （dgge） microbial ecology PCR rRNA （rDNA）

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Effect of daidzein on lactobacillus community change in piglet digesta during in vitro fermentation as analyzed by dgge technique

Effect of daidzein on lactobacillus community change in pigl...

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2003北京国际养猪研讨会暨展览会

作者： Barbara A. Williams Seerp Tamminga Antoon D.L. Akkermans Wageningen Institute of Animal Sciences Wageningen University Wageningen Netherlands Wageningen Institute of Animal Sciences Wageningen University Wageningen Netherlands Laboratory of Microbiology Wageningen University Hesselink van Suchtelenweg 4 6703 CT Wageningen Netherlands

＜正＞ The effect of daidzein on Lactobacillus community change during in vitro fermentation ofpiglet digesta from different gastrointestinal （GI） compartment obtained at different ages was investigated.Every three conventionally raised healthy piglets from the same litter were slaughtered at age of 7, 14, 21and 28 days respectively. On each day of slaughtering, the digesta from the same GI compartment （jejunum,ileum, caecum and rectum） was pooled. The pooled digesta from each compartment was used as inocula inthree in vitro fermentation treatments: （a） VanSoest medium with 0.5g of glucose and 50ppm of daidzein;（b） VanSoest medium with 0.5g of glucose;（c） VanSoest medium only.After 48 hours fermentation,

关键词： denaturing gradient gel electrophoresis （dgge） lactobacillus daidzein dilution PCR digesta piglet

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