Our planet is home to more than 14 million species, only an estimated 12 percent of which have been discovered. The vast majority of the
remaining uncharacterized species are microorganisms, invisible to the naked eye. However, these tiny organisms play a vital role in shaping the earth's environment by regulating the cycle of oxygen and
nutrients and breaking down organic matter. The advent of genomic science, which is the study of the genome -- the complete set of genetic blueprints -- of an organism, has helped scientists to study
microorganisms with much greater detail than ever before. The significance of microorganisms to this new scientific field is found in the incredible diversity of genetic material present in microbial
communities.Now, BBSR is on the forefront of the newest revolution in genomic science: ocean genomics. The challenge for BBSR's new program in ocean genomics is to explore the deep ocean, the largest
ecosystem on earth, and uncover the mysteries of its microbial communities and other marine inhabitants. In 2001, BBSR Scientist Hank Trapido-Rosenthal, BBSR alumnus Craig Carlson of the University of
California at Santa Barbara and Stephen Giovannoni of Oregon State University helped advance BBSR's standing in this field by proposing the creation of a
Marine Genome Bank, a collection of the genomes found in Bermuda's marine environments. BBSR's ocean
genomics initiative produced new and exciting discoveries in 2003. With the completion of a state-of-the-art molecular biology and genomics laboratory later this year, the program promises to lead to more
groundbreaking research with profound future impacts on society. In 2002, BBSR joined forces with genomics expert J. Craig Venter, best known for his pioneering work in the human genome project, to
sequence and analyze the DNA of microorganisms in the open ocean off Bermuda. The resulting joint genomics initiative was launched last year as scientists from Dr. Venter's Institute for Biological Energy Alternatives
(IBEA), BBSR and the University of Southern California
teamed up to collect samples of the microbial universe of the Sargasso Sea. During the February and May research cruises, single-celled organisms were collected from four marine research sites using a protocol in which water is filtered through decreasing filter sizes, from a plankton net, through a 3.0-micron filter, a 0.8-micron filter and finally a 0.1-micron filter. Viruses were also sampled using a 50,000-molecular-weight filter.
"Whole genome shotgun sequencing," a strategy used by Dr. Venter to sequence the DNA of the first genome in history and the DNA of the human genome, was applied to the Sargasso Sea samples by researchers
at IBEA laboratories. This process allows scientists to bypass the labor-intensive method of mapping DNA by first breaking DNA strands into fragments and then reassembling them at random using precise
computer algorithms. The researchers were then able to assemble whole genomes and major sections of genomes for the microbial community from the Sargasso Sea samples. The discovery was astounding: at least
1,800 new species and more than 1.2 million new genes were identified. In an area of the ocean often referred to as a floating desert because of its very poor levels of nutrients, how could such a rich
diversity of species survive? One of the most important single discoveries of the first round of results -- 782 new photoreceptor genes -- could provide the answer. Photoreceptor genes are sensitive to
light and, in humans, are responsible for vision, suggesting that certain microbes may be converting light into other types of energy. This finding challenges fundamental ideas about ocean biology, and
suggests that sunlight plays a far more important role in ocean ecosystems than previously supposed. Further investigation of the mechanisms responsible for photosynthesis in these and other microbes is a
major project for the future of ocean genomics, and may one day lead to the discovery of a method to efficiently and economically produce hydrogen as an alternative source of fuel. The results and analysis
of the joint project's initial findings from the 2003 Sargasso Sea expeditions were published in 2004 in Science
, a leading international scientific magazine. The paper, "Environmental Genome Shotgun Sequencing of the Sargasso Sea," was co-authored by BBSR
Director Tony Knap, Associate Research
Scientist Michael Lomas
and Laboratory Manager Rachel Parsons
, together with Dr. Venter and 15 other researchers. The success and international recognition of the ocean genomics collaboration between BBSR and Dr. Venter has inspired the Sorcerer II Expedition, a
year-and-a-half-long cruise that will circumnavigate the globe on a mission to identify new microbial species as well as new genes of ecological importance. The research team of the unprecedented undertaking
will take water samples approximately every 200 miles using the techniques first employed aboard BBSR's research ship, the
Weatherbird II, during the sampling of the Sargasso Sea. Dr. Knap will represent BBSR on the
scientific advisory board, an international committee of scientists who will ensure the highest level of science is provided for this unique expedition.
The new genomics initiatives at BBSR will work alongside the successful ongoing
Oceanic Microbial Observatory, which is funded by the U.S.
National Science Foundation. This program, a collaborative effort between Dr. Carlson, Dr. Giovannoni and Ms. Parsons, combines the expertise of
oceanography, biogeochemistry and an understanding of large-scale microbial processes with molecular biology and environmental genomics. In what used to take researchers weeks to accomplish, the Microbial
Observatory uses an advanced video microscope to catalog bacteria, viruses and other microbes in a matter of seconds, and provides scientists with unique insight into the community structure of microbes.
Looking ahead, the new ocean genomics program will add to the resources of the Oceanic Microbial Observatory and the molecular marine biology program in cataloging libraries of environmental DNA for storage
in BBSR's Marine Genome Bank. The second floor of BBSR's new laboratory building will be devoted to ocean genomics and molecular biology initiatives, allowing these programs to expand significantly. The
laboratory will provide facilities for new technologies in genomic and genetic research for BBSR's ocean genomics and coral reef programs, and culture facilities on the first floor will allow for the
culturing and isolation of marine microbes. From the millions of species of microorganisms remaining to be studied in the vast depths of the oceans, might researchers discover genetic material that holds
the key to processing alternative fuel sources or that contains the cure for a life-threatening disease? These are just two of the questions that ocean genomics allows scientists to address as we continue to
uncover the unique potential of the life in our oceans. |
Finding Health in the Ocean's Genes BBSR's marine bioprospecting
program will also benefit greatly from the molecular biology, genomics and microbial culturing facilities in the new laboratory building. The program began in 1993, when molecular biologist
Hank Trapido-Rosenthal
joined the faculty. Bioprospecting uses the cutting-edge tools and techniques of genomics and genetic engineering to investigate whether chemicals produced by marine organisms could be of use in medicines or for other applications.
Advances in this field involve identifying particular processes that are promoted or inhibited in nature, which might then be developed for the benefit of human health. Continuing advances in
genomic science have introduced new technologies that make identifying these processes more economical and environmentally friendly than ever before. Yet the ocean's potential value as a source
of chemicals that could lead to lifesaving pharmaceuticals remains largely a mystery. The greatest marine resources for this application, and the focus of the bioprospecting program at BBSR,
are the vast communities of microorganisms found in the deep ocean, as well as in shallower inshore waters where they live in symbiosis with larger marine organisms. Microorganisms are so vital
to this research because they possess untapped and novel genomic diversity, within which the blueprints for sought-after chemicals may be found. A classic example of a valuable chemical derived
from a microorganism is penicillin, which revolutionized the treatment of bacterial infections. BBSR scientists use genomic and genetic engineering technologies to extract the DNA from a small
sample of a sponge and its associated microbes, for instance, and clone it into a domesticated strain of laboratory bacteria. The cloned DNA contains all of the necessary blueprints for the
biological synthesis of the chemicals the sponge and microbes were capable of producing. It then becomes possible to "train" the genetically engineered bacteria to create large quantities of the
drug or chemical of interest to scientists. This research into the genetic material of marine organisms will be significantly enhanced by the expanded facilities of the new
laboratory. Coupled with BBSR's ideal mid-Atlantic location, which allows for easy access to the microbial universe of the ocean, the bioprospecting program is well positioned to discover
numerous chemicals that may lead to exciting new benefits for human health. |
|
