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Serial Analysis of rRNA Genes and the Unexpected Dominance of Rare Members of Microbial Communities

Taxon Biosciences, Inc., 3152 Paradise Drive, Tiburon, California 94920,¹ Department of Molecular and Cell Biology, University of California, 16 Barker Hall, Berkeley, California 94720-3202,² The Institute for Genomic Research, J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850,³ Howard University, Department of Biology, 415 College Avenue, NW, Washington, D.C. 20059⁴

Received 20 December 2006/ Accepted 20 May 2007

The accurate description of a microbial community is an important first step in understanding the roles of its components in ecosystem function. A method for surveying microbial communities termed serial analysis of rRNA genes (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 genes from microbial communities. These tags are ligated to form concatemers comprised of 20 to 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. A comparison of duplicate profiles from one soil genomic DNA preparation revealed that the method was highly reproducible. The large numbers of singleton tags, together with nonparametric richness estimates, indicated that 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 a numerical or diversity standpoint, taxa with low abundance 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 roles of these rare members of microbial communities in qualitative and quantitative terms.

Published ahead of print on 25 May 2007.

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