Denaturing gradient gel electrophoresis can rapidly display the bacterial diversity contained in 16S rDNA clone libraries.

Microbial Ecology
M D BurrA K Camper

Abstract

Two different strategies for molecular analysis of bacterial diversity, 16S rDNA cloning and denaturing gradient gel electrophoresis (DGGE), were combined into a single protocol that took advantage of the best attributes of each: the ability of cloning to package DNA sequence information and the ability of DGGE to display a community profile. In this combined protocol, polymerase chain reaction products from environmental DNA were cloned, and then DGGE was used to screen the clone libraries. Both individual clones and pools of randomly selected clones were analyzed by DGGE, and these migration patterns were compared to the conventional DGGE profile produced directly from environmental DNA. For two simple bacterial communities (biofilm from a humics-fed laboratory reactor and planktonic bacteria filtered from an urban freshwater pond), pools of 35-50 clones produced DGGE profiles that contained most of the bands visible in the conventional DGGE profiles, indicating that the clone pools were adequate for identifying the dominant genotypes. However, DGGE profiles of two different pools of 50 clones from a lawn soil clone library were distinctly different from each other and from the conventional DGGE profile, indicating that this ...Continue Reading

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Citations

Mar 9, 2007·Microbial Ecology·Andreas NockerAnne K Camper
Jun 6, 2009·FEMS Microbiology Ecology·Nanna BuesingMark O Gessner
Feb 1, 2011·FEMS Microbiology Ecology·Christine M ForemanDiane M McKnight
Mar 23, 2011·PloS One·Scott CairnsDavid Wynne Williams
Dec 10, 2016·Environmental Science and Pollution Research International·Ehssan TorabiMasoud Ahmadzadeh
Apr 24, 2009·Archives of Environmental Contamination and Toxicology·Sergio Martínez-HernándezFlor de María Cuervo-López

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