PCR-DGGE Comparison of Bacterial Community Structure in Fresh and Archived Soils Sampled along a Chihuahuan Desert Elevational Gradient |
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Authors: | James H Campbell Jeb S Clark John C Zak |
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Institution: | (1) Department of Biological Sciences, Texas Tech University, P.O. Box 43131, Lubbock, TX 79409-3131, USA;(2) Present address: Clean Air Laboratories, LLC, 228 Midway Lane, Suite B, Oak Ridge, TN 37830-7916, USA;(3) Present address: Department of Pediatrics, Division of Pediatric Nephrology, University of Mississippi Medical Center, Research Wing, Room R127, 2500 North State Street, Jackson, MS 39216-4505, USA |
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Abstract: | The polymerase chain reaction coupled with denaturing gradient gel electrophoresis (PCR-DGGE) has been used widely to determine
species richness and structure of microbial communities in a variety of environments. Researchers commonly archive soil samples
after routine chemical or microbial analyses, and applying PCR-DGGE technology to these historical samples offers evaluation
of long-term patterns in bacterial species richness and community structure that was not available with previous technology.
However, use of PCR-DGGE to analyze microbial communities of archived soils has been largely unexplored. To evaluate the stability
of DGGE patterns in archived soils in comparison with fresh soils, fresh and archived soils from five sites along an elevational
gradient in the Chihuahuan Desert were compared using PCR-DGGE of 16S rDNA. DNA from all archived samples was extracted reliably, but DNA in archived soils collected from a closed-canopy oak
forest site could not be amplified. DNA extraction yields were lower for most archived soils, but minimal changes in bacterial
species richness and structure due to archiving were noted in bacterial community profiles from four sites. Use of archived
soils to determine long-term changes in bacterial community structure via PCR-DGGE appears to be a viable option for addressing
microbial community dynamics for particular ecosystems or landscapes. |
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