Direct extraction of DNA from soils for studies in microbial ecology

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Authors
Schneegurt, Mark A.
Dore, Sophia Y.
Kulpa, Charles F.
Advisors
Issue Date
2003-01
Type
Article
Keywords
Research Support, Non-U.S. Gov't , Review
Research Projects
Organizational Units
Journal Issue
Citation
Current issues in molecular biology. 2003 Jan; 5(1): 1-8.
Abstract

Molecular analyses for the study of soil microbial communities often depend on the extraction of DNA directly from soils. These extractions are by no means trivial, being complicated by humic substances that are inhibitory to PCR and restriction enzymes or being too highly colored for blot hybridization protocols. Many different published protocols exist, but none have been found to be suitable enough to be generally accepted as a standard. Most direct extraction protocols start with relatively harsh cell breakage steps such as bead-beating and freeze-thaw cycles, followed by the addition of detergents and high salt buffers and/or enzymic digestion with lysozyme and proteases. After typical organic extraction and alcohol precipitation, further purification is usually needed to remove inhibitory substances from the extract. The purification steps include size-exclusion chromatography, ion-exchange chromatography, silica gel spin columns, and cesium chloride gradients, among others. A direct DNA extraction protocol is described that has been shown to be effective in a wide variety of soil types. This protocol is experimentally compared to several published protocols.

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Publisher
Horizon Scientific Press
Journal
Book Title
Series
Current issues in molecular biology
PubMed ID
DOI
ISSN
1467-3037
EISSN