IBEA Researchers Publish Results From Environmental Shotgun Sequencing of Sargasso Sea In Science; Discover 1,800 New Species And 1.2 Million New Genes, Including Nearly 800 New Photoreceptor Genes
IBEA Announces Sorcerer II Expedition, Global Expedition To Sample World's Oceans And Land To Characterize And Understand Microbial Populations Using Environmental DNA Sequencing
Gordon and Betty Moore Foundation give IBEA $4.25 Million Grant for Genomic Sequencing of DNA Samples from Expedition Discovery Channel to Film Expedition for TV Documentary
Discovery Channel to Film Expedition for TV Documentary
March 4, 2004 [14:00 EST]
ROCKVILLE, MD — J. Craig Venter, Ph.D., president of the Institute for Biological Energy Alternatives (IBEA), announced today the publication of a scientific paper in the journal Science which details results from sequencing and analysis of samples taken from the Sargasso Sea off Bermuda. Using the whole genome shotgun sequencing and high performance computing developed to sequence the human genome, IBEA researchers discovered at least 1,800 new species and more than 1.2 million new genes from the Sargasso Sea. This work was funded by the U.S. Department of Energy's Office of Science, and the J. Craig Venter Science Foundation. The work was performed in collaboration with researchers at The Institute for Genomic Research (TIGR), the University of Southern California, and the Bermuda Biological Station for Research (BBSR).
Dr. Venter also announced the official launch of the Sorcerer II Expedition, a scientific expedition of discovery that will circumnavigate the globe under sail, surveying marine and terrestrial microbial populations. The Expedition has the potential to uncover tens of thousands of new microbial species and tens of millions of new genes. The voyage and sample collection are being funded by the J. Craig Venter Science Foundation and by the Discovery Channel Quest Program. The Sorcerer II Expedition is the subject of a Discovery Channel documentary film slated to air in 2005. In addition to the DOE Office of Science grant previously announced, the Expedition has received an important new grant from the Gordon and Betty Moore Foundation for $4.25 million which will be used to sequence the DNA collected along the coast of North America.
"The field of environmental genomics has the potential to revolutionize the way our oceans, soil, and whole ecosystems and environments are studied," said Dr. Venter. "By taking relatively small samples of water or soil and using the tools and techniques of shotgun sequence analysis, we are able to identify and characterize the vast legions of unseen organisms living in the environment. It is estimated that over 99% of species remain to be discovered. Our work in the Sargasso Sea, an area thought to have low diversity of species, has shown that there is much that we do not yet understand about the ocean and its inhabitants."
"What excites the Department and our Office of Science about this project is its range of potential benefits," Secretary of Energy Spencer Abraham said. "Scientists have used DOE funds to determine the genetic sequences of all the microorganisms occurring in a natural microbial community, which may lead to the development of new methods for carbon sequestration or alternative energy production. This will offer a direct and early test of one of the central tenets of DOE's Genomics: GTL program - that microbes can be used to develop innovative solutions to address national energy needs."
Environmental Genomics Shotgun Sequencing of the Sargasso Sea
In February and May 2003 IBEA and BBSR researchers took sea water samples from six marine research sites in the Sargasso Sea. Using a protocol in which the water was filtered through decreasing size filters, from a plankton net, through a 3.0 micron filter, a 0.8 micron filter, and a 0.1 micron filter in order to collect different sized single cell organisms. Finally, a 50,000 molecular weight filter was used to collect the viruses. The filtered samples were taken to the IBEA laboratories where the genomic DNA of the species in the water was extracted and DNA libraries were made. The DNA was sequenced at the J. Craig Venter Science Foundation Joint Technology Center in Rockville, MD. Using whole genome shotgun sequencing, the same strategy used to sequence the first genome in history and the human genome, 1.045 billion base pairs of DNA sequence were produced. Using precise mathematical algorithms previously used to assemble sequence results from single species, the researchers were able to assemble whole genomes and major sections of genomes from the diverse microbial community found in the ocean. The paper describes a minimum of 1,800 new species identified in the Sargasso Sea. As well, there were 1,214,207 new genes identified by the researchers, which is a significant increase over the number currently in public databases.
The Sargasso Sea was chosen as a pilot study for the environmental genome shotgun sequencing strategy because it was thought to have very low nutrients and thus low species diversity. The Sargasso Sea is one of the most studied regions anywhere in the ocean. A Bermuda-based time series, begun in 1954, is considered to be the longest, continuous, year-round, study of any one point in the open ocean. This Hydrostation "S" time series, located 15 miles offshore from Bermuda, has greatly advanced the understanding of global climate change. The Bermuda Atlantic Time-series Study (BATS), begun in 1988 at a site 50 nautical miles from Bermuda, measures variations in ocean physics, chemistry and biology. After 16 years of sampling in the Sargasso Sea and in-depth laboratory analysis of the results, the findings of the BATS program are dramatically changing the way scientists around the world look at the ocean's ecosystems and the relationship between the ocean and global climate change. The BBSR has funding from the National Science Foundation (NSF) for these time series studies.
One of the most important single discoveries from the Sargasso Sea environmental shotgun sequencing study is the 782 new rhodopsin-like photoreceptor genes. Only a few dozen photoreceptors have been characterized in microorganisms to date and less than 200 photoreceptors have been discovered from all species, including human where they are responsible for our vision. Therefore, this discovery represents a substantial increase in the total number of this family of proteins. One interpretation of this finding is that at least 50% of the new species discovered use some type of photobiology and could explain the diversity of species in such a low nutrient environment. Better understanding of these photoreceptor genes could be very important to IBEA researchers as they explore the mechanisms of photosynthesis as a means to efficiently and economically produce hydrogen as a fuel source.
The data described in the Sargasso Sea manuscript has been deposited in GenBank in a new environmental genomic section.
The Sorcerer II Expedition
Inspired in part by the voyages of H.M.S. Beagle and the Challenger Expedition, as well as the results from the Sargasso Sea sequencing pilot project, the Sorcerer II Expedition began in August 2003 in Canada in Halifax, Nova Scotia on a year and a half long global sailing voyage of discovery. As the Sorcerer II Expedition circumnavigates the globe, the scientific team will explore marine and terrestrial community microbial biodiversity using sampling and analysis methods developed during the Sargasso Sea pilot project. As the team samples the waters approximately every 200 miles, the goals are to discover new species; to better understand microbial biodiversity; to discover new genes of ecological importance; and to establish a freely shared, global environmental genomics database that can be used by scientists around the world.
To ensure the highest level of science for the Expedition, an external scientific advisory board has been formed. This committee includes:
- Penny Chisholm, Professor of Civil and Environmental Engineering and Biology, Massachusetts Institute of Technology
- Ed DeLong, Senior Scientist, Monterey Bay Aquarium Research Institute
- Gustavo Fonseca, Conservation International. Senior Vice President, CI, and Executive Director for Applied Biodiversity Science
- Robert Gagosian, President and Director, Woods Hole Oceanographic Institution
- Victor Ariel Gallardo, Director, The Center for Oceanographic Research in the Eastern South Pacific, University of Concepcion, Chile
- Jo Handelsmann, University of Wisconsin
- Dave Karl, Professor of Oceanography, University of Hawaii
- Charles Kennel, Director, Scripps Institute of Oceanography
- Tony Knap, Director, Bermuda Biological Station for Research
- Ken Nealson, Wrigly Professor of Geobiology, University of Southern California
- Edward O. Wilson, Pellegrino University Professor Emeritus, Harvard University
The Expedition team is also creating a network of collaborators from each of the major sampling regions. Collaborating with these local researchers, who understand the ecological context of the sampling sites and can help evaluate the results in relation to the biological and physical characteristics of each region, is key to the success of the Expedition. IBEA has signed memoranda of understanding (MOUs) with the University of Conception in Chile and Universidad Nacional Autonoma de Mexico and is in discussions with other country collaborators. In addition to outlining ways to collaborate, these MOU's stress that the data collected from the Sorcerer II Expedition will go into the public domain and that intellectual property will not be claimed by any party based on raw sequence data.
Since leaving Halifax, Nova Scotia in August 2003, the Sorcerer II has sailed south along the coast of the U.S. sampling in the Chesapeake Bay, Delaware Bay, the coast of North Carolina, and Florida. From there the vessel sailed into the Gulf of Mexico, through the Caribbean to Panama, the Panama Canal, and Cocos Island. The Sorcerer II and her scientists and crew are currently in the Galapagos Islands where they just finished an intensive five week sampling phase throughout the archipelago.
Later this month the Sorcerer II sets sail again across the Pacific, through French Polynesia, New Caledonia, Papua, New Guinea, the Great Barrier Reef and around Australia, across the southern Atlantic around Madagascar and South Africa, then up to the mouth of the Amazon River. The voyage will end with a trip through the Caribbean and back to the coast of the U.S.
Public education about the Expedition, its goals, and environmental genomics is an important component of the Sorcerer II Expedition. An interactive website, is also being launched today so that teachers, students, kids and parents can follow the progress of the Sorcerer II Expedition. In addition to public lectures and outreach in the various countries, the Expedition is also being filmed as part of a Discovery Channel documentary. The Expedition has received support from Discovery through the Channel's Quest Program, a unique program intended to help fund scientific projects and capture on film the research activities of scientists.
IBEA -The Institute for Biological Energy Alternatives (IBEA) is a not-for-profit, 501 (c) (3), research-based institution associated with the J. Craig Venter Science Foundation, dedicated to employing the tools of genomics to develop cost-effective biological fuels and other biological approaches to greenhouse mitigation and exploring solutions for carbon sequestration using microbes, microbial pathways, and plants. For example, IBEA will develop and use microbial pathways and microbial metabolism to produce carbon-neutral fuels in an environmentally sound fashion. IBEA will undertake genome engineering to better understand the evolution of cellular life and how these cell components function together in a living system. More information about IBEA is available at www.bioenergyalts.org
BBSR - The Bermuda Biological Station for Research (BBSR) is an independent, U.S. 501(c)(3) non-profit marine science organization, founded in 1903 by scientists from Harvard and New York University to take advantage of Bermuda's ideal location for marine research and education. Since the first scientists arrived at BBSR a century ago, Bermuda's varied and near-pristine natural environments, and their susceptibility to human influences, have been a principal focus of BBSR's research programs. In 1998, BBSR established the International Center for Ocean and Human Health, considered the first of its kind to address both the health of the ocean, such as marine contamination, and health from the ocean, from nutrients and marine product-derived pharmaceuticals, on a global scale.
US Department of Energy Office of Science
DOE's Office of Science is the single largest supporter of basic research in the physical sciences in the nation, manages 10 world-class national laboratories, and builds and operates some of the nation's most advanced R&D user facilities. Its website address is www.science.doe.gov . DOE's Genomics: GTL program aims to use the department's unique computational capabilities and research facilities to understand the activities of single-cell organisms on three levels: the proteins and multi-molecular machines that perform most of the cell's work; the gene regulatory networks that control these processes; and microbial associations or communities in which groups of different microbes carry out fundamental functions in nature. Once researchers understand how life functions at the microbial level, they hope to use the capabilities of these organisms to help meet many of our national challenges in energy and the environment. The program will combine research in biology, engineering and computation with the development of novel facilities for high-throughput biology projects. More information on the department's genomics programs is on the Web at http://www.doegenomes.org.
Gordon and Betty Moore Foundation
The Gordon and Betty Moore Foundation was established in November 2000 by Intel co-founder Gordon Moore and his wife Betty to create positive outcomes for future generations. The Foundation funds outcome-based grants and initiatives to achieve significant and measurable results. Grantmaking supports the Foundation's principal areas of concern: environmental conservation, science, higher education, and the San Francisco Bay Area.
In April 2002, Discovery Channel launched Discovery Channel Quest, a new initiative designed to inspire and fund the next generation of scientific achievement. Over the past two decades, the Discovery Channel has provided the resources for research that resulted in groundbreaking finds. Discovery Channel Quest seeks to expand this legacy by funding projects spearheaded by scientists and explorers who are at the vanguard of their fields. Their research activities will be chronicled via online and televised dispatches from sites around the world, in lecture series, and in landmark television specials that capture the toil, genius, setbacks and exhilaration that are the lifeblood of the search for knowledge. Discovery Channel Quest is meant to capture moments of revelation so compelling that they promise to change science, confound historians and electrify viewers.
Discovery Channel is one of the United States' largest cable television networks, serving 89.1 million households across the nation with the finest in informative entertainment. Discovery Networks, U.S., a unit of Discovery Communications, Inc., operates and manages the Discovery Channel, TLC, Animal Planet, the Travel Channel, Discovery Health Channel, Discovery HD Theater, Discovery Kids Channel, Discovery Times Channel, The Science Channel, Discovery Home & Leisure Channel, Discovery Wings Channel, Discovery en EspaÃƒÂ±ol and FitTV. The unit also distributes BBC America.