Global Ocean Sampling Expedition (GOS)
In 2004, after a successful pilot project of shotgun metagenomics sequencing at the Bermuda Atlantic Time Series site, J. Craig Venter, PhD, and a Venter Institute team launched the Sorcerer II Global Ocean Sampling (GOS) Expedition. Inspired by 19th Century sea voyages like Darwin's on the H.M.S. Beagle and Captain George Nares on the H.M.S. Challenger, The Sorcerer II circumnavigated the globe for more than two years, covering a staggering 32,000 nautical miles, visiting 23 different countries and island groups on four continents.
Millions of new genes and nearly 1000 genomes for uncultivated lineages of microbes, as well as a more comprehensive understanding of marine microbiology through community datamining resulted from this historic project. Collaborative efforts and subsequent expeditions to the inland seas and lakes of Europe, Antarctica, and the Amazon River have greatly increased the known diversity of ecosystems and microbial diversity.
Global analyses of the results have provided insight into what environmental variables most dictate microbial diversity and function in a lineage-specific basis. Numerous new lineages of viruses for both bacteria and eukaryotes have been identified. The most recent expeditions, conducted in 2017, systematically examined the microbes that colonize plastic pollution in the marine environment. Collaborative analyses of both local and global aspects of the GOS expedition data are ongoing and open to new partners.
Sorcerer II Circumnavigation 2004-2006
In 2004, Dr. Venter and his team at JCVI launched the Sorcerer II Global Ocean Sampling (GOS) Expedition. Inspired by 19th Century sea voyages like Darwin's on the H.M.S. Beagle and Captain George Nares on the H.M.S. Challenger, The Sorcerer II circumnavigated the globe for more than two years, covering a staggering 32,000 nautical miles, visiting 23 different countries and island groups on four continents. Funding for this voyage of the Sorcerer II came from the J. Craig Venter Science Foundation (now JCVI), the U.S. Department of Energy, and the Gordon and Betty Moore Foundation
After a successful pilot project in the Sargasso Sea in 2003, Dr. Venter and his Expedition team set out to evaluate the microbial diversity in the world's oceans using the tools and techniques developed to sequence the human and other genomes. With a better understanding of marine microbial biodiversity, scientists will be able to understand how ecosystems function and to discover new genes of ecological and evolutionary importance. The Sorcerer II Expedition finished its circumnavigation in 2006 and Venter Institute scientists and collaborators published the results from the first phase of the Expedition in PLoS Biology in March 2007.
This publication ushered in a new era in genomics. The GOS data represent the largest metagenomic dataset ever put into the public domain with more than 7.7 million sequences or 6.3 billion base pairs of DNA. The sheer size and complexity of this dataset has necessitated new tools and infrastructure to allow researchers worldwide access and analysis capabilities. The Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) is an online database and high-speed computational resource developed with funding from the Gordon and Betty Moore Foundation in a collaborative effort between UCSD's Division of the California Institute for Telecommunications and Information Technology (Calit2) and JCVI. This first glimpse into the gene, protein and protein family world of microbes has shattered long held notions about evolution, function, and diversity.
When the first third of the Sorcerer II Global Ocean Sampling Expedition was published, Dr. Venter and his team realized (as stunning and extensive as these results were — six million new genes and thousands of new protein families) they had only scratched the surface of the microbial diversity in the oceans. The team decided to continue their journey but this time focusing on diverse and in some cases, extreme environments. From surface waters to deep sea thermal vents, high saline ponds and polar ice, JCVI scientists continued to add to the microbial "earth catalogue" in 2007 and 2008.
The Sorcerer II set sail in December 2006 from Virginia heading through the Chesapeake Bay, and then south along the East Coast of the United States. After a transit through the Panama Canal, the vessel headed north through Central American waters and on to Mexico sampling in the Sea of Cortez for an extensive time. The Expedition continued up the West Coast of the U.S. into Alaska. While in Alaska the Sorcerer II took samples in Glacier Bay National Park including water taken from melting glaciers there. After this Sorcerer headed south again to her home port of San Diego.
Throughout 2008, the Sorcerer II conducted extensive sampling in the waters off San Diego and the coast of California, Oregon and Washington. This was done to ensure that both coasts of the US had adequate samples taken. Much of this sampling was done onboard Sorcerer II but several excursions were conducted by JCVI scientists onboard other collaborators' vessels including those done with Scripps Institution of Oceanography, University of Washington, Oregon Health and Science University, Monterey Bay Aquarium Research Institute, and the California Cooperative Oceanic Fisheries Investigations.
Several JCVI researchers also participated in deep sea sampling cruises as part of expeditions onboard the R/V Atlantis which carries the deep-sea submersible, Alvin. These expeditions were done in collaboration with scientists from Woods Hole Oceanographic Institution, University of Delaware, and other institutions The JCVI scientists were interested in sampling the underwater geysers in the Pacific Ocean and the Sea of Cortez to capture the viruses living in these extreme conditions.
JCVI scientists also conducted several sampling trips to Antarctica where they sampled via collaborator vessels along the route to Antarctica, and in several stratified lakes to understand the microbial diversity in these harsh polar conditions. These are the first metagenomic/metaproteomic studies conducted in such low temperature extremes.
The J. Robert Beyster and Life Technologies Foundation 2009-2010 Research Voyage of the Sorcerer II Expedition
Having successfully completed a global circumnavigation, conducted ongoing sampling in waters off California and the west coast of the United States, and carried out sampling with other collaborators in extreme conditions such as Antarctica and deep-sea ocean vents, the research vessel Sorcerer II and Dr. Venter embarked on the waters of Europe. This two-year leg of the Sorcerer II Expedition, funded by generous donations from the Beyster Family Foundation Fund of The San Diego Foundation and Life Technologies Foundation, explored the microbial life in the waters of the Baltic, Mediterranean, and Black Seas. These are scientifically important because they are among the world's largest seas isolated from the major oceans.
The Sorcerer II left her home port of San Diego, California on March 19, 2009 heading south along the coast of Mexico, taking a 200 to 400 liters water sample approximately every 200 miles, filtered it through progressively smaller filters to capture the various sized organisms, and then freeze the filters with the captured microorganisms for shipment back to the JCVI labs in Rockville, MD or San Diego, CA where the sequencing and analysis is done. The team visited the following countries: England, Sweden, Finland, Norway, Denmark, Estonia, and other Baltic countries, Spain, Italy, Germany, and Bulgaria.
Scientific results from the Sorcerer II expedition have the potential to substantially advance the world's understanding of microbial communities, including the vital role that microorganisms play in the healthy functioning of natural ecosystems. For this reason, genomic sequencing data from the expedition will be publicly available to the international research and educational communities.
The genomic analysis of microbial communities may be particularly useful to the countries in which samples are taken. For example, these data may enhance a country's ability to monitor and protect its biodiversity. After these data are published, researchers in a given country may wish to pursue further study of microbes of particular scientific interest or potential commercial value.
The Venter Institute is a not-for-profit basic science research institute. Results from the microbial sampling and genomic sequencing research will be published in the scientific literature in collaboration with in-country scientists involved in the program. The data will be deposited in the publicly available GenBank or through a new web-based database established specifically for environmental genomics data. They will be publicly available to any scientist worldwide.
Consistent with national laws and applicable international treaties, and under the guidance of the U.S. Department of State, the Venter Institute obtains permits for research and sampling from every country in which samples will be taken. Scientific collaboration, education and training are an important part of the Sorcerer II Expedition as the vessel travels around the globe. In many countries, the Venter Institute has also signed memoranda of understanding describing additional components of the collaboration.
The Venter Institute develops cooperative relationships with leading international researchers located in each sampling region. All required research permits are obtained before sampling begins. In addition, the Venter Institute offers to develop memoranda of understanding (MOUs) with all countries where sampling takes place.
These memoranda typically include five fundamental principles of the Sorcerer II expedition:
- The purpose of the Expedition is to advance scientific knowledge of microbial biodiversity and humankind's basic understanding of oceanic biology, yielding insights into the complex interplay between groups of microorganisms that may affect environmental processes.
- Genomic sequence data from the study will be publicly available to scientists worldwide.
- No intellectual property rights will be sought by the Venter Institute on these genomic sequence data.
- The Venter Institute and its research collaborators will coauthor one (or more) scientific journal articles that describe and evaluate these genomic sequence data.
- The Venter Institute will offer training opportunities to scientists and students in the countries where sampling is conducted.