Global ocean sampling expedition

Can we ever know the true measure of microbial diversity in the sea or of proteins in nature?

In three new metagenomic studies published online in the open-access journal PLoS Biology, Craig Venter and his team take advantage of the vast amount of microbial sequence data collected during their Sorcerer II Global Ocean Sampling (GOS) expedition to reveal an unprecedented level of genetic and protein diversity in marine microbes.

Venter's team combined the expedition's latest bounty, 6.5 million sequencing "reads," with data previously collected during a pilot study in the Sargasso Sea. The result is a geographically diverse environmental genomic dataset of 6.3 billion base pairs—twice the size of the human genome.

The first paper and accompanying poster by Douglas B. Rusch and colleagues describe the immense amount of microbial diversity in the seas, and discuss how—or if—that diversity is structured and what might be shaping that structure. The second paper by Shibu Yooseph and colleagues studies the 6.12 million proteins identified in the GOS sequences to see if we're close to discovering all the proteins in nature. In the third study, Natarajan Kannan, Susan S. Taylor, Gerard Manning, and colleagues present their classification of 45,000 kinases (including 16,000 from the GOS dataset) into 20 distinct families, revealing their structural and functional diversity and an unexpected role for kinases in prokaryotic signaling.

This collection also includes an accessible and nontechnical summary of the broad significance of this research by Liza Gross. Some unexpected intellectual property challenges have arisen from this project, and these are explored in a feature by Henry Nicholls. A "challenge series" essay by Jonathan Eisen provides insight into the issues surrounding the field of metagenomics today.

To host all the additional metadata that surround metagenomic studies, a new database, CAMERA, has been established, funded by the Gordon and Betty Moore Foundation. The GOS data are publicly available and ready for mining in CAMERA. You can read about the capabilities of CAMERA in a Community Page article by Rekha Seshadri and colleagues.

Citation: Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol 5(3): e77. doi:10.1371/journal.pbio.0050077.

PLEASE ADD THE LINK TO THE PUBLISHED ARTICLE IN ONLINE VERSIONS OF YOUR REPORT: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050077

Citation: Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol 5(3): e16. doi:10.1371/journal.pbio.0050016.

PLEASE ADD THE LINK TO THE PUBLISHED ARTICLE IN ONLINE VERSIONS OF YOUR REPORT: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050016

Citation: Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G (2007) Structural and functional diversity of the microbial kinome. PLoS Biol 5(3): e17. doi:10.1371/journal.pbio.0050017.

PLEASE ADD THE LINK TO THE PUBLISHED ARTICLE IN ONLINE VERSIONS OF YOUR REPORT: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050017

CONTACT:

Douglas Rusch
The J. Craig Venter Institute
9704 Medical Center Dr
Rockville, MD 20850
+1-240-268-2788
+1-240-731-8689 (Alternate Telephone)
DRusch@venterinstitute.org

Shibu Yooseph
The J. Craig Venter Institute
9704 Medical Center Drive
Rockville, MD 20850
+1-240-268-2791
+1-240-268-4000 (fax)
shibu.yooseph@venterinstitute.org

Gerard Manning
Salk Institute for Biological Studies
Razavi-Newman Center for Bioinformatics
10010 North Torrey Pines Road
La Jolla, CA 92037
+1-858-453-4100 x 1757
+1-858-457-4765 (fax)
manning@salk.edu

PLEASE MENTION THE OPEN-ACCESS JOURNAL PLoS BIOLOGY (www.plosbiology.org) AS THE SOURCE FOR THESE ARTICLES AND PROVIDE A LINK TO THE FREELY-AVAILABLE TEXT. THANK YOU.

All works published in PLoS Biology are open access. Everything is immediately available—to read, download, redistribute, include in databases, and otherwise use—without cost to anyone, anywhere, subject only to the condition that the original authorship and source are properly attributed. Copyright is retained by the authors. The Public Library of Science uses the Creative Commons Attribution License.

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