Global Ocean Sampling (GOS) Expedition

Marine microorganisms contribute to key elementary budgets in the biogeochemical cycles of our planet. For example, marine microbes act as part of a biological conduit that sequesters carbon dioxide from the atmosphere and transports it from the surface to the deep oceanic realms. By removing carbon from the atmosphere and sequestering it, marine microorganisms (eukaryotes, prokaryotes, and viruses) significantly affect global climate. Yet, we know little about their biogeography, or the physiological processes and complex interactions that impact global carbon cycles and ocean productivity.

In spring 2003, the J. Craig Venter Institute applied a new and powerful technique, called "whole environment shotgun genomics", to marine microorganisms collected in seawater samples from the nutrient-poor Sargasso Sea near Bermuda. This study revealed a remarkable breadth and depth of microbial diversity - about 1,800 microbial species were discovered including 148 novel phylotypes, encoding more than 1.2 million genes. A highlight of the study was the expansion of a family of proteorhodopsin genes encoding light-driven proton pumps used for phototrophic energy production. This study expanded our knowledge of ocean photobiology, microbial diversity, and evolution. Results were reported in Science in 2004.

While the Sargasso Sea analysis focused on prokaryotes, it became apparent that broader communities including viruses needed to be considered to fully understand the biological communities and their roles in fundamental processes in nature. For example, virus-mediated lysis of prokaryotic host cells in marine ecosystems has important global implications for the cycling of carbon through microbe-based food webs in the marine environment.

The Sargasso Sea pilot study served as the springboard for the Global Ocean Sampling (GOS) expedition, a global circumnavigation aboard the sailing yacht, Sorcerer II, with the aim of providing a comprehensive genomic survey of microbial (bacterial, archaeal, and viral) life in the world's oceans. The expedition started in Halifax, Canada, in August of 2003 and proceeded south into the Gulf of Maine, then along the U.S. east coast sampling in the ecologically important Narragansett, Delaware, and Chesapeake bays. The vessel then passed Cape Hatteras and traveled around Florida into the Gulf of Mexico, through the Panama Canal and to Cocos Island, then onto the Galapagos Islands. Sorcerer II then sampled across the central and south Pacific through French Polynesia, the Cook Islands, Tonga, Fiji, Vanuatu, and New Caledonia to Australia where they spent a year. The vessel then transited the Indian Ocean to South Africa, across the Atlantic and back to the United States. The full circumnavigation was completed in Florida in January 2006.

Fig. 1: The Yacht Sorcerer II

Shotgun sequence of microbial samples from approximately 150 open-ocean and coastal sites, and deep sequencing of 16S and 18S rRNA genes were performed to investigate the distribution of organisms and genomic variation across ecosystems. An initial analysis of the microbial sequence data from the first leg of the trip - Halifax to the Galapagos Islands - is to be reported in PLoS Biology in March 2007 (2-4). About 41 surface water samples collected from the North Atlantic to the South Pacific Oceans yielded 7.7 million new sequence reads encoding 6.12 million genes, including many new genes of ecological importance. These data comprised nearly all known prokaryotic protein families as well as numerous GOS-specific (and novel) clusters. Indeed, new protein families were discovered at an almost linear rate with the addition of new sequences, implying that we are still far from attaining saturation of data. Besides nearly doubling the number of current proteins, the predicted GOS proteins added a great deal of diversity to known protein families allowing deep exploration of protein family evolution, revealing structural basis for the observed diversity, and helping to improve remote homology detection. Analysis of samples from the Pacific and Indian Oceans is currently underway.

The information from these and other studies helps assess the abundance and diversity of microbes in the world's oceans and has potentially far-reaching implications for biological energy production and bioremediation, and for creating solutions for management of greenhouse gas levels in our biosphere.

The complete set of data and bioinformatic analysis tools associated with the GOS expedition study is available through CAMERA(5).

Fig. 2: Sorcerer II Expedition circumnavigation route and analysis progress as of January 2007.

References

Venter, J.C., et. al. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 (5667):66-74. Rusch. et al. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific, PLoS Biology. doi:10.1371/journal.pbio.0050077. Yooseph et. al. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families, PLoS Biology. doi: 10.1371/journal.pbio.0050016. Kannan et. al. Structural and Functional Diversity of the Microbial Kinom, PLoS Biology. doi:10.1371/journal.pbio.0050017 Seshadri et. al. A Community Resource for Metagenomics, PLoS Biology. doi:10.1371/journal.pbio.0050075.