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Fine-scale phylogenetic architecture of a complex bacterial community

Abstract

Although molecular data have revealed the vast scope of microbial diversity1, 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 explored2. 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.

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Figure 1: Compositional pattern of the coastal bacterioplankton sample.
Figure 2: Phylogenetic distance relationships between the coastal bacterioplankton based on partial 16S rRNA sequencing.

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Acknowledgements

We thank S. Bertilsson (Uppsala University) for sample collection, D. Veneziano (MIT) for discussions on statistical extrapolation of sequence diversity, P. Chisholm (MIT) for numerous suggestions, and researchers and staff of the PIE-LTER (Plum Island Ecosystem-Long Term Ecological Research) for logistical support. This work was supported by grants from the National Science Foundation, the Department of Energy Genomes to Life program and a postdoctoral fellowship from the Spanish Ministry of Education to S.G.A.

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Correspondence to Martin F. Polz.

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The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Figure 1

Phylogenetic distance (neighbour-joining) tree of all unique 16S rRNA gene sequences (ribotypes) retrieved from the Plum Island bacterioplankton sample and representative reference sequences. (PDF 33 kb)

Supplementary Figure Legend

Key to cluster numbers from Figure 2a in main paper. (RTF 4 kb)

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Acinas, S., Klepac-Ceraj, V., Hunt, D. et al. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430, 551–554 (2004). https://doi.org/10.1038/nature02649

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