Characterizing Microbial Population Structures through Massively Parallel Sequencing

Abstract

Rank abundance plots of microbial populations are long-tailed distributions in which a few highly abundant populations account for most of the organisms in a community, whereas lower-abundance taxa represent a large number of different phylotypes. New massively parallel DNA pyrosequencing techniques that routinely sample many hundreds of thousands of homologous genes permit the detection of lower abundance taxa even in the presence of overwhelming levels of dominant microbial populations. The technology provides estimates of both richness (diversity) and evenness (relative abundance of different kinds of microbes). When applied to studies of marine and soil microbial populations, the massively parallel sequencing of many thousands of rapidly evolving regions in ribosomal RNA genes reveals that microbial diversity is 1–2 orders greater than all previously published estimates from traditional capillary DNA sequencing methodologies. Most of the diversity is accounted for by low-abundance phylotypes that constitute the rare biosphere. These taxa might represent “seed” organisms that under shifts in ecological conditions can become more abundant, or they might be persistently rare over large temporal and spatial scales.