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Deep Diversity: Novel Approach to Overcoming the PCR Bias Encountered During Environmental Analysis of Microbial Populations for Alpha-DiversityAlpha-diversity studies are of crucial importance to environmental microbiologists. The polymerase chain reaction (PCR) method has been paramount for studies interrogating microbial environmental samples for taxon richness. Phylogenetic studies using this technique are based on the amplification and comparison of the 16S rRNA coding regions. PCR, due disproportionate distribution of microbial species in the environment, increasingly favors the amplification of the most predominant phylotypes with every subsequent reaction cycle. The genetic and chemical complexity of environmental samples are intrinsic factors that exacerbate an inherit bias in PCR-based quantitative and qualitative studies of microbial communities. We report that treatment of a genetically complex total genomic environmental DNA extract with Propidium Monoazide (PMA), a DNA intercalating molecule capable of forming a covalent cross-linkage to organic moieties upon light exposure, disproportionally inactivates predominant phylotypes and results in the exponential amplification of previously shadowed microbial ?-diversity quantified as a 19.5% increase in OUTs reported via phylogenetic screening using PhyloChip.
Document ID
20150005873
Acquisition Source
Jet Propulsion Laboratory
Document Type
Other
External Source(s)
Authors
Ramirez, Gustavo A
Vaishampayan, Parag A.
(Jet Propulsion Lab., California Inst. of Tech. Pasadena, CA, United States)
Date Acquired
April 17, 2015
Publication Date
August 1, 2011
Subject Category
Exobiology
Distribution Limits
Public
Copyright
Other
Keywords
phylogenetic microarray technologies
Alpha-diversity
polymerase chain reaction (PCR)

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