Measuring soil microbial community diversity using polar lipid fatty acid and denaturing gradient gel electrophoresis data

2000 ◽  
Vol 41 (3) ◽  
pp. 235-248 ◽  
Author(s):  
David B Hedrick ◽  
Aaron Peacock ◽  
John R Stephen ◽  
Sarah J Macnaughton ◽  
Julia Brüggemann ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Microbial Community ◽  
Polar Lipid ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Diversity ◽  
Microbial Community Diversity ◽  
Soil Microbial ◽  
Lipid Fatty Acid ◽  
Gradient Gel Electrophoresis

scholarly journals GC Fractionation Enhances Microbial Community Diversity Assessment and Detection of Minority Populations of Bacteria by Denaturing Gradient Gel Electrophoresis

2004 ◽  
Vol 70 (4) ◽  
pp. 2263-2270 ◽  
Author(s):  
William E. Holben ◽  
Kevin P. Feris ◽  
Anu Kettunen ◽  
Juha H. A. Apajalahti
Keyword(s):  
Microbial Community ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Initial Step ◽  
Community Diversity ◽  
Minority Populations ◽  
Cloning And Sequencing ◽  
Microbial Community Diversity ◽  
Diversity Assessment ◽  
Gradient Gel Electrophoresis

ABSTRACT Effectively and accurately assessing total microbial community diversity is one of the primary challenges in modern microbial ecology. This is particularly true with regard to the detection and characterization of unculturable populations and those present only in low abundance. We report a novel strategy, GC fractionation combined with denaturing gradient gel electrophoresis (GC-DGGE), which combines mechanistically different community analysis approaches to enhance assessment of microbial community diversity and detection of minority populations of microbes. This approach employs GC fractionation as an initial step to reduce the complexity of the community in each fraction. This reduced complexity facilitates subsequent detection of diversity in individual fractions. DGGE analysis of individual fractions revealed bands that were undetected or only poorly represented when total bacterial community DNA was analyzed. Also, directed cloning and sequencing of individual bands from DGGE lanes corresponding to individual G+C fractions allowed detection of numerous phylotypes that were not recovered using a traditional random cloning and sequencing approach.

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.

scholarly journals Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient

2017 ◽  
Vol 75 (1) ◽  
pp. 193-203 ◽  
Author(s):  
Vincent Scola ◽  
Jean-Baptiste Ramond ◽  
Aline Frossard ◽  
Olivier Zablocki ◽  
Evelien M. Adriaenssens ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Desert Soil ◽  
Community Diversity ◽  
Namib Desert ◽  
Microbial Community Diversity ◽  
Soil Microbial ◽  
And Function
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