Document Detail


Denaturing gradient gel electrophoresis can rapidly display the bacterial diversity contained in 16S rDNA clone libraries.
MedLine Citation:
PMID:  16645925     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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 small number of clones poorly represented the bacterial diversity in soil. Individual clones with the same apparent DGGE mobility as prominent bands in the humics reactor community profiles were sequenced from the clone plasmid DNA rather than from bands excised from the gel. Because a longer fragment was cloned (approximately 1500 bp) than was actually analyzed in DGGE (approximately 350 bp), far more sequence information was available using this approach that could have been recovered from an excised gel band. This clone/DGGE protocol permitted rapid analysis of the microbial diversity in the two moderately complex systems, but was limited in its ability to represent the diversity in the soil microbial community. Nonetheless, clone/DGGE is a promising strategy for fractionating diverse microbial communities into manageable subsets consisting of small pools of clones.
Authors:
M D Burr; S J Clark; C R Spear; A K Camper
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Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2006-04-28
Journal Detail:
Title:  Microbial ecology     Volume:  51     ISSN:  0095-3628     ISO Abbreviation:  Microb. Ecol.     Publication Date:  2006 May 
Date Detail:
Created Date:  2006-06-23     Completed Date:  2006-08-30     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  7500663     Medline TA:  Microb Ecol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  479-86     Citation Subset:  IM    
Affiliation:
Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717-3980, USA. mark_b@erc.montana.edu
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MeSH Terms
Descriptor/Qualifier:
Bacteria / classification*,  genetics
Base Sequence
DNA Primers
DNA, Ribosomal / genetics*
Electrophoresis, Polyacrylamide Gel
RNA, Ribosomal, 16S / genetics*
Species Specificity
Chemical
Reg. No./Substance:
0/DNA Primers; 0/DNA, Ribosomal; 0/RNA, Ribosomal, 16S

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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