Salt marsh sediment diversity : a test of the variability of the rare biosphere among environmental replicates

Abstract

Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because within site variability of the rare taxa may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences among samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and local scale variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. The concern was that variation resulting from incomplete sequencing could mask subtle community shifts caused by environmental perturbations. Our data indicate that salt marsh sediments contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish site-specific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.