Two-step denaturing gradient gel electrophoresis (2S-DGGE), a gel-based strategy to capture full-length 16S rRNA gene sequences

2012 ◽  
Vol 95 (5) ◽  
pp. 1305-1312 ◽  
Author(s):  
Shanquan Wang ◽  
Jianzhong He
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Full Length ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gradient Gel Electrophoresis

scholarly journals Sulfate-Reducing Bacteria in Tubes Constructed by the Marine Infaunal Polychaete Diopatra cuprea

2004 ◽  
Vol 70 (12) ◽  
pp. 7053-7065 ◽  
Author(s):  
George Y. Matsui ◽  
David B. Ringelberg ◽  
Charles R. Lovell
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phospholipid Fatty Acid ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Sulfate Reducing

ABSTRACT Marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. Biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. The microbial communities in tubes of the marine infaunal polychaete Diopatria cuprea collected from two different sediment habitats were examined. The bacterial communities in the tubes from a sandy sediment differed from those in the tubes from a muddy sediment. The difference in community structure also extended to the sulfate-reducing bacterial (SRB) assemblage, although it was not as pronounced for this functional group of species. PCR-amplified 16S rRNA gene sequences recovered from Diopatra tube SRB by clonal library construction and screening were all related to the family Desulfobacteriaceae. This finding was supported by phospholipid fatty acid analysis and by hybridization of 16S rRNA probes specific for members of the genera Desulfosarcina, Desulfobacter, Desulfobacterium, Desulfobotulus, Desulfococcus, and Desulfovibrio and some members of the genera Desulfomonas, Desulfuromonas, and Desulfomicrobium with 16S rRNA gene sequences resolved by denaturing gradient gel electrophoresis. Two of six SRB clones from the clone library were not detected in tubes from the sandy sediment. The habitat in which the D. cuprea tubes were constructed had a strong influence on the tube bacterial community as a whole, as well as on the SRB assemblage.

scholarly journals Combined Phospholipid Biomarker-16S rRNA Gene Denaturing Gradient Gel Electrophoresis Analysis of Bacterial Diversity and Physiological Status in an Intertidal Microbial Mat

2004 ◽  
Vol 70 (11) ◽  
pp. 6920-6926 ◽  
Author(s):  
Laura Villanueva ◽  
Antoni Navarrete ◽  
Jordi Urmeneta ◽  
David C. White ◽  
Ricardo Guerrero
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Mat ◽  
Physiological Status ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Lipid Biomarker ◽  
Gradient Gel Electrophoresis

ABSTRACT A combined lipid biomarker-16S rRNA gene denaturing gradient gel electrophoresis analysis was used to monitor changes in the physiological status, biomass, and microbial composition of a microbial mat. In the morning hours, an increase in the biomass of layers containing a high density of phototrophs and a decrease in the growth rate in the deep layers were observed. The combined approach also revealed differences in major groups of microorganisms, including green nonsulfur, gram-positive, and heterotrophic bacteria.

Denaturing Gradient Gel Electrophoresis Detects Bacterial and Cyaonbacterial Diversities in Biological Soil Crusts in a Semiarid Desert, China

2013 ◽  
Vol 726-731 ◽  
pp. 3680-3684
Author(s):  
Ying Zhang ◽  
Cheng You Cao ◽  
Peng Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Biological Soil Crusts ◽  
Rrna Gene ◽  
Sandy Land ◽  
Specific Primers ◽  
Soil Crusts ◽  
Gradient Gel Electrophoresis

The purpose of this study is to assess the application of denaturing gradient gel electrophoresis (DGGE) for analyzing the bacterial and cyanobacterial diversities of biological soil crusts (BSCs) in sandy land. Soil microbial DNA was extracted from BSCs under different plantations in Horqin Sandy Land of Northeast China. 16S rRNA gene fragments from bacteria and cyanobacteria were amplified by universal bacterial and cyanobacteria-specific primers. Fourteen and six prominent bands were detected in the bacterial and cyanobacterial DGGE profiles, respectively. These bands were excised, cloned and sequenced. Phylogenetic analysis classified the bacterial sequences into the following main groups:Escherichia,Bacillus,Paenibacillus,Shigella, andPseudomonas. The cyanobacterial sequences were classified asMicrocoleus,LeptolyngbyaandHaslea. Our study suggests that DGGE is a useful technique for detecting dominant species compositions of bacterial and cyanobacterial communities in biological soil crusts, and specific primers are recommended for PCR of 16S rRNA gene fragments.

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