Journal Article

Fine-scale phylogenetic architecture of a complex bacterial community

Acinas, Silvia G., Hunt, Dana E., Klepac-Ceraj, Vanja, Pharino, Chanathip, Ceraj, Ivica, Polz, Martin F., Distel, Daniel L.

2004

Overview

Although molecular data have revealed the vast scope of microbial diversity 1 , two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored 2 . Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community. We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition. At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population. More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence. This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community. We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.

• Publisher: Nature Publishing Group UK,Nature Publishing,Nature Publishing Group
• Subject: Animal, plant and microbial ecology / Bacteria / Bacteria - classification / Bacteria - genetics / Bacteria - isolation & purification / Biodiversity / Biogeography / Biological and medical sciences / Community composition / Ecosystem / Fundamental and applied biological sciences. Psychology / Gene Library / Genes, Bacterial - genetics / Genetic Variation - genetics / Genome, Bacterial / Humanities and Social Sciences / letter / Marine / Massachusetts / Microbial activity / Microbial ecology / Microbiology / Microorganisms / Molecular Sequence Data / multidisciplinary / Phylogeny / Plankton / Plankton - classification / Plankton - genetics / Plankton - isolation & purification / Plankton - physiology / Population biology / Ribonucleic acid / Ribotyping / RNA / RNA, Ribosomal, 16S - genetics / Science / Science (multidisciplinary) / Seawater - microbiology / Various environments (extraatmospheric space, air, water)