Evaluation of the denaturing gradient gel electrophoresis-apparatus as a parameter influencing soil microbial community fingerprinting

2010 ◽  
Vol 26 (9) ◽  
pp. 1721-1726 ◽  
Author(s):  
J. Ascher ◽  
M. T. Ceccherini ◽  
A. Chroňáková ◽  
J. Jirout ◽  
F. Borgogni ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microbial ◽  
Gradient Gel Electrophoresis ◽  
Community Fingerprinting

scholarly journals Microbial Community Fingerprinting by Differential Display-Denaturing Gradient Gel Electrophoresis

2010 ◽  
Vol 77 (1) ◽  
pp. 351-354 ◽  
Author(s):  
M. C. Portillo ◽  
D. Villahermosa ◽  
A. Corzo ◽  
J. M. Gonzalez
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Differential Display ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Primers ◽  
Gradient Gel Electrophoresis ◽  
Community Fingerprinting ◽  
Community Complexity ◽  
Partial Fingerprint

ABSTRACTComplex microbial communities exhibit a large diversity, hampering differentiation by DNA fingerprinting. Herein, differential display-denaturing gradient gel electrophoresis is proposed. By adding a nucleotide to the 3′ ends of PCR primers, 16 primer pairs and fingerprints were generated per community. Complexity reduction in each partial fingerprint facilitates sample comparison.

scholarly journals Microbial Community Changes in a Perturbed Agricultural Soil Investigated by Molecular and Physiological Approaches

1998 ◽  
Vol 64 (7) ◽  
pp. 2739-2742 ◽  
Author(s):  
Lise Øvreås ◽  
Sigmund Jensen ◽  
Frida Lise Daae ◽  
Vigdis Torsvik
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Gel Electrophoresis ◽  
Agricultural Soil ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microbial Activity ◽  
Soil Microbial ◽  
Rrna Sequencing ◽  
Gradient Gel Electrophoresis ◽  
Community Changes

ABSTRACT Changes in soil microbial activity and diversity after incubation either with nitrogen or with a mixture of methane and air were examined. The perturbation by methane and air were characterized in detail and led to reduced diversity and enrichment of methanotrophs which were identified by denaturing gradient gel electrophoresis and 16S rRNA sequencing.

scholarly journals Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities

2009 ◽  
Vol 55 (No. 10) ◽  
pp. 413-423 ◽  
Author(s):  
V. Valášková ◽  
P. Baldrian
Keyword(s):  
Microbial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Genes Encoding ◽  
Gradient Gel Electrophoresis ◽  
Temperature Gradient Gel Electrophoresis ◽  
Experimental Treatments ◽  
Multiple Samples

In soil microbial ecology, the effects of environmental factors and their gradients, temporal changes or the response to specific experimental treatments of microbial communities can only be effectively analyzed using methods that address the structural differences among whole communities. Fingerprinting methods are the most appropriate technique for this task when multiple samples must be analyzed. Among the methods currently used to compare microbial communities based on nucleic acid sequences, the techniques based on differences in the melting properties of double-stranded molecules, denaturing gradient gel electrophoresis (DGGE) or temperature gradient gel electrophoresis (TGGE), are the most widely used. Their main advantage is that they provide the possibility to further analyze whole sequences contained in fingerprints using molecular methods. In addition to the analysis of microbial communities based on DNA extracted from soils, DGGE/TGGE can also be used for the assessment of the active part of the community based on the analysis of RNA-derived sequences or for the analysis of sequences of functional genes encoding for proteins involved in important soil processes.

Study of microbial community of brewery-treating granular sludge by denaturing gradient gel electrophoresis of 16S rRNA gene

2001 ◽  
Vol 43 (1) ◽  
pp. 77-82 ◽  
Author(s):  
O.-C. Chan ◽  
W.-T. Liu ◽  
H. H. Fang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Granular Sludge ◽  
Upflow Anaerobic Sludge Blanket ◽  
Anaerobic Sludge ◽  
Rrna Gene ◽  
Related Sequence ◽  
Gradient Gel Electrophoresis

The microbial community structure of granular sludge from an upflow anaerobic sludge blanket (UASB) reactor treating brewery effluent was studied by denaturing gradient gel electrophoresis (DGGE). Twelve major bands were observed in the DGGE fingerprint for the Bacteria domain and four bands for the Archaea domain. Of the bacterial bands observed, six were successfully purified and sequenced. Among them, three were related to the gram-positive low G+C group, one to the Delta subclass of the Proteobacteria, one to the Gamma subclass, and one to the Cytophaga group with no close related sequence. The 16S rRNA sequences of the four archaeal bands were closely associated with Methanosaeta concilii and Methanobacterium formicum.

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