Seas Yield Surprising Catch of Unknown Genes
Wednesday, March 14, 2007
It took some mighty fine nets, but scientists who spent two years trawling the world's oceans for bacteria and viruses have completed the most thorough census ever of marine microbial life, revealing an astonishingly diverse and bizarre microscopic menagerie.
Countering a long-held assumption that ocean waters are not rich with microbial life, the new report, released yesterday, reveals an otherworldly world of organismal ferment, including thousands of novel life forms that could help speed the development of new antibiotics and alternative energy sources and clarify the ocean's role in climate change.
The census -- which in a single stroke has doubled the number of known genes in Earth's biological kingdom -- comes from a 21st-century version of Charles Darwin's 19th-century voyage on the HMS Beagle. Led by a Rockville-based team that circumnavigated the globe on a specially equipped sailboat, the project focused not on the microbes themselves -- most of which are too finicky to be kept alive in culture dishes -- but on their DNA, easily obtained from cells and later decoded on shore.
Perhaps most exciting, said study leader J. Craig Venter, is that the rate of discovery of new genes and proteins -- the building blocks of life -- was as great at the end of the voyage as it was at the start, suggesting that humanity is nowhere close to closing the logbooks on global biodiversity.
"Instead of being at the end of discovery, it means we're in the earliest stages," said Venter, chairman of the J. Craig Venter Institute, a nonprofit gene research center. "That is a pretty stunning view."
Mitchell Sogin of the Marine Biological Laboratory in Woods Hole, Mass., praised the work as a "remarkable technological achievement." Microbes account for up to 90 percent of the biomass in the oceans, he said, and control all the major biological and geochemical cycles that keep Earth's ecosystems in balance. So it is valuable to learn what those organisms are and where and how they live, he said.
The new findings, described in the March issue of the journal PLoS Biology, build on results Venter obtained during a 2003 test voyage in the Sargasso Sea, which had been considered an especially lifeless body of water. That netted more than 1 million genes entirely new to science -- evidence that Earth's seas harbor microbes far more numerous and far stranger than scientists had imagined.
The latest voyage, on Venter's 95-foot sloop, Sorcerer II, started in Nova Scotia, passed through the Panama Canal, then tagged the Galapagos, Polynesia, the Horn of Africa, the Caribbean and the U.S. East Coast, collaborating with local biologists as they went.
Every 200 miles, the team pumped 200 liters of seawater through a layered filter system that separated viruses and various kinds of cells by size. Yesterday's analysis covers about one-quarter of the samples -- from Nova Scotia to the Galapagos -- and only the viruses and smallest cells.
Yet DNA analyses on even that limited sample, conducted on an immensely powerful supercomputer designed for the project by the California Institute for Telecommunications and Information Technology, tallied genetic coding for more than 6 million new proteins, doubling the number already tabulated in the world's genetic databases.
Among them are more than 2,000 "proteorhodopsins," each of which can convert certain wavelengths of sunlight into biological energy through means wholly independent of photosynthesis, the process used by green vegetation. That gives scientists a slew of new methods to mimic for getting energy from the sun, Venter said.
Some new genes seem designed to help organisms get energy from carbon dioxide in the air, a tantalizing alternative to the oil and coal that most human technologies rely on. Researchers hope those biological blueprints may show them how to scrub greenhouse gases from the atmosphere.
Venter predicted that other genes will be found to direct the production of novel antibiotics, since bacteria are prodigious makers of such compounds, which they use to fend off other microbes.
The new data are being shared freely on the Web -- an approach many researchers and governments appreciate but that raised alarms in some countries that had considered profiting from the genetic heritages in their territorial waters. Although the Sorcerer team obtained permits for all their collections, there were occasional misunderstandings, Venter conceded -- one of which led to a one-week standoff in French Polynesia during which his boat was threatened by the French navy.
Sogin said follow-up surveys at different depths and locations will surely expand the database greatly.
"As amazing as this inventory is," Sogin said, "it's only scratching the surface of what's really there."