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Published Online February 1, 2007
Science DOI: 10.1126/science.1133420

Reports

Submitted on August 3, 2006
Accepted on January 19, 2007

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

C. von Mering 1, P. Hugenholtz 2, J. Raes 3, S. G. Tringe 2, T. Doerks 3, L. J. Jensen 3, N. Ward 4, P. Bork 3*

1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.; Present address: University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
2 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
3 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
4 Institute for Genomic Research, Rockville, MD 20850, USA.

* To whom correspondence should be addressed.
P. Bork , E-mail: peer.bork{at}embl.de

The taxonomic composition of environmental communities is an important indicator of their ecology and function. Here, we use a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative and accurate picture of community composition than traditional rRNA-based approaches using polymerase chain reaction (PCR). By mapping marker genes from four diverse environmental data sets onto a reference species phylogeny, we show that certain communities evolve faster than others, determine preferred habitats for entire microbial clades, and provide evidence that such habitat preferences are often remarkably stable over time.


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