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Appl. Environ. Microbiol. doi:10.1128/AEM.02956-06
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Serial Analysis of Ribosomal DNA and the Unexpected Dominance of Rare Members of Microbial Communities

Taxon Biosciences, Inc. 3152 Paradise Drive, Tiburon, CA 94920, USA; Department of Molecular & Cell Biology, University of California, 16 Barker Hall, Berkeley, CA 94720-3202, USA.; The Institute for Genomic Research, a Division of the J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA; Howard University, Department of Biology, 415 College Avenue, NW, Washington, D.C., 20059

^* To whom correspondence should be addressed. Email: ashbym{at}taxon.com.

	Abstract

Accurate description of a microbial community is an important first step in understanding the role of its components in ecosystem function. A method for surveying microbial communities termed Serial Analysis of Ribosomal DNA (SARD) is described here. Through a series of molecular cloning steps, short DNA sequence tags are recovered from the fifth variable (V5) region of the prokaryotic 16S rRNA gene from microbial communities. These tags are ligated to form concatemers comprised of 20-40 tags which are cloned and identified by DNA sequencing. Four agricultural soil samples were profiled with SARD to assess the method's utility. A total of 37,008 SARD tags comprising 3,127 unique sequences were identified. Comparison of duplicate profiles from one soil genomic DNA preparation revealed the method was highly reproducible. The large numbers of singleton tags together with non-parametric richness estimates indicated a significant amount of sequence tag diversity remained undetected with this level of sampling. The abundance classes of the observed tags were scale-free and conformed to a power law distribution. Numerically, the majority of the total tags observed belonged to abundance classes that were each present at less than 1% of the community. Over 99% of the unique tags individually made up less than 1% of the community. Therefore, from either numerical or diversity standpoints, low abundant taxa comprised a significant proportion of the microbial communities examined and could potentially make a large contribution to ecosystem function. SARD may provide a means to explore the ecological role of these rare members of microbial communities in qualitative and quantitative terms.

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