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CSI: Microbial version without PCR
Date:9/21/2011

nt taxa. On land or in water, from tropical forests to backyard compost heaps, these microbial communities are the primary drivers of numerous ecosystem processes via their ability to decompose organic matter or catalyze important chemical reactions.

"With such complexity at the heart of so many ecosystem processes, there is a great need to be able to reliably and affordably analyze microbial communities in samples from different environments," Andersen says.

Scientists identify the individual microbial taxa in a sample via the genetic signatures of ribosomal RNA (rRNA), which is the genetic component of the ribosome, the machinery within a biological cell that makes proteins. PCR technology has typically been used to amplify the DNA in a sample to obtain a sufficient amount of genetic material for analysis.

"PCR amplification of microbial DNA introduces well-known distortions," says Kristen DeAngelis, lead author of the AEM paper who is now with the University of Massachusetts but remains a collaborator with the Joint BioEnergy Institute (JBEI), a DOE Bioenergy Research Center, which is led by Berkeley Lab. "For example, DNA extracted from natural environments may include DNA from microbial populations that are dead, dormant, or otherwise not directly contributing to an ecosystem's function."

Andersen, DeAngelis and their colleagues on this project were able to eliminate the need for problematic PCR amplification by using the PhyloChip. Developed by AEM paper co-authors Andersen, DeSantis and Brodie, plus Yvette Piceno, all with Berkeley Lab's Earth Sciences Division, the PhyloChip is a square-shaped microarray chip the size of a quarter. The latest version is packed with more than a million individual probes and can be used to quickly, accurately and comprehensively detect the presence of up to 50,000 different species of bacteria and archaea in a single sample from any environmental source, without the need of culturing. '/>"/>

Contact: Lynn Yarris
lcyarris@lbl.gov
510-486-5375
DOE/Lawrence Berkeley National Laboratory
Source:Eurekalert  

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