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PMID: 15282603 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Fine-scale phylogenetic architecture of a complex bacterial community.

Nature ·Vol. 430 ·No. 6999 ·2004-07-29 ·Pages 551-4

Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, Distel DL, Polz MF

Abstract

Although molecular data have revealed the vast scope of microbial diversity, 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. 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.

MeSH Terms

Artifacts Bacteria/classification,genetics,isolation & purification Ecosystem Gene Library Genes, Bacterial/genetics Genetic Variation/genetics Genome, Bacterial Massachusetts Molecular Sequence Data Phylogeny Plankton/classification,genetics,isolation & purification,physiology RNA, Ribosomal, 16S/genetics Ribotyping Seawater/microbiology

Chemicals

RNA, Ribosomal, 16S

Authors & Affiliations

7 authors, click to expand affiliations / ORCID

Acinas Silvia G

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Klepac-Ceraj Vanja

Hunt Dana E

Pharino Chanathip

Ceraj Ivica

Distel Daniel L

Polz Martin F

Article Info

Journal

Nature

Abbr.

Nature

ISSN

1476-4687

DOI

10.1038/nature02649

Published

2004-07-29

Pages

551-4

Language

English

Region

England

NLM ID

0410462

Subset

Databases

GENBANK

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PMID: 15282590

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PubMed source DOI: 10.1038/nature02649 View journal details

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