Spatial distribution of bacterial communities in sediment of a eutrophic lake revealed by denaturing gradient gel electrophoresis and multivariate analysis

2008 ◽  
Vol 54 (12) ◽  
pp. 1053-1063 ◽  
Author(s):  
Jin Zeng ◽  
Liu-Yan Yang ◽  
Yi Liang ◽  
Jia-Yun Li ◽  
Lin Xiao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Eutrophic Lake ◽  
Freshwater Ecosystems ◽  
Scaling Analysis ◽  
Gradient Gel Electrophoresis ◽  
Lake Xuanwu

Bacterial community structure and the effects of several environmental factors on the microbial community distribution were investigated in the sediment of the eutrophic Lake Xuanwu. Profiles of bacterial communities were generated using denaturing gradient gel electrophoresis (DGGE), and the results were interpreted with multivariate statistical analysis. Five major variables in sediment were examined in a principal component analysis, which indicates notable differences of physicochemical parameters among different sites of the lake. To assess changes in the genetic diversity of bacterial communities of different sampling sites, DGGE band patterns were analyzed by multidimensional scaling analysis, which indicated that sampling sites having similar environmental characteristics also have the similar microbial communities. Canonical correspondence analysis demonstrated that pH and redox potential had significant effects on the bacterial community composition in the sediments. Analysis of DNA sequences revealed that the dominant bacterial groups in Lake Xuanwu belonged to Proteobacteria , Actinobacteria , Verrucomicrobia , and Nitrospirae , which are commonly isolated from freshwater ecosystems.

DNA extraction procedure affects organic-aggregate-attached bacterial community profiles from a shallow eutrophic lake

2009 ◽  
Vol 55 (6) ◽  
pp. 776-782 ◽  
Author(s):  
Xiangming Tang ◽  
Guang Gao ◽  
Liping Zhu ◽  
Jianying Chao ◽  
Boqiang Qin
Keyword(s):  
Bacterial Community ◽  
Dna Extraction ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Lake Taihu ◽  
Bacterial Community Composition ◽  
Extraction Procedure ◽  
Eutrophic Lake ◽  
Hexadecyltrimethylammonium Bromide ◽  
Shallow Eutrophic Lake

Organic aggregates (OA) in aquatic ecosystems harbour diverse microbial communities. The colonization and growth of OA-attached bacteria are important processes in the degradation and transformation of the particles. The development of efficient and comparative DNA extraction methods is one of the most critical steps in the study of the composition and diversity of OA-attached bacterial communities. To evaluate whether different DNA extraction procedures affect the measurement of bacterial community composition, we compared four in situ lysis procedures using OA from three locations in a shallow eutrophic lake (Lake Taihu, China). The extracted DNA was analyzed using denaturing gradient gel electrophoresis profiles. We found that the choice of DNA extraction protocol had a significant influence on the fingerprints of the OA-attached bacterial community. This was shown not only in the number of bands but also in their relative representation of certain DNA bands. Using the bead-beating DNA extraction method in the presence of hexadecyltrimethylammonium bromide, we found that crude microbial DNA could be extracted efficiently from different OA types. This protocol is reproducible and gives very pure DNA of relatively high molecular mass. More importantly, the protocol provided more representative and informative data on the diversity of OA-attached bacterial communities.

scholarly journals Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey : Bacterial communities in produced waters of south-eastern Turkey reported in detail for the first time

2020 ◽  
Vol 64 (4) ◽  
pp. 452-466
Author(s):  
Tuğçe Tüccar ◽  
Esra Ilhan-Sungur ◽  
Gerard Muyzer
Keyword(s):  
Bacterial Community ◽  
Water Samples ◽  
Bacterial Communities ◽  
Produced Water ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Oil Fields ◽  
Rrna Gene ◽  
Gradient Gel Electrophoresis ◽  
First Time

Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%) groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.

scholarly journals Impact of Intensive Land-Based Fish Culture in Qingdao, China, on the Bacterial Communities in Surrounding Marine Waters and Sediments

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Qiufen Li ◽  
Yan Zhang ◽  
David Juck ◽  
Nathalie Fortin ◽  
Charles W. Greer
Keyword(s):  
Bacterial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Fish Culture ◽  
Fish Ponds ◽  
Marine Area ◽  
Gradient Gel Electrophoresis ◽  
Reducing Bacteria ◽  
The Impact ◽  
Nitrate Reducing Bacteria

The impact of intensive land-based fish culture in Qingdao, China, on the bacterial communities in surrounding marine environment was analyzed. Culture-based studies showed that the highest counts of heterotrophic, ammonium-oxidizing, nitrifying, and nitrate-reducing bacteria were found in fish ponds and the effluent channel, with lower counts in the adjacent marine area and the lowest counts in the samples taken from 500 m off the effluent channel. Denaturing gradient gel electrophoresis (DGGE) analysis was used to assess total bacterial diversity. Fewer bands were observed from the samples taken from near the effluent channel compared with more distant sediment samples, suggesting that excess nutrients from the aquaculture facility may be reducing the diversity of bacterial communities in nearby sediments. Phylogenetic analysis of the sequenced DGGE bands indicated that the bacteria community of fish-culture-associated environments was mainly composed of Flavobacteriaceae, gamma- and deltaproteobacteria, including generaGelidibacter, Psychroserpen, Lacinutrix,andCroceimarina.

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