By Nancy Weil and Kevin Davies
June 10, 2005 | While sailing across the Atlantic Ocean a couple of years ago, genomics scientist J. Craig Venter and his crew were suddenly engulfed in a bizarre sand storm — 1,800 miles off the coast of Africa. His initial reaction? “We actually thought we were hallucinating, so we cut off drinking for the rest of the voyage,” he joked during his keynote address on the final day of the 2005 Bio•IT World Conference + Expo in Boston.
But if heavy sand particles can travel thousands of miles into the mid-Atlantic, Venter reasoned, what did that mean for the plethora of microbes and viruses that might be swirling around the globe’s atmosphere? Venter decided to expand his horizons beyond the ongoing Sorcerer II expedition, which is sampling microbial life in seas and soils around the world, to the atmosphere. The field of environmental genomics now has an air genome component to it as well.
The first atmospheric sampling is taking place at the J. Craig Venter Institute and an undisclosed location in New York. Filtering the air collects 1 billion bacteria per filter per day, Venter said.
Even as the Sorcerer II prepares to embark on the latest leg of its round-the-world voyage, from Australia across the Indian Ocean later this year, Venter and colleagues are virtually drowning in the data they have collected onboard the vessel on its journey around central America and to the Galapagos Islands.
Scientists on Sorcerer II collect sea samples every 200 miles, filtering the water to trap bacteria and viruses, before the samples are flown to the J. Craig Venter Institute for high-throughput genomic sequencing and bioinformatic analysis. Each milliliter of seawater contains 1 million bacteria and 10 million viruses. “The next time you’re swimming in the ocean and you swallow a mouthful of sea water, think of the number of genomes you’ve just ingested,” he said.
Since publishing his initial analysis of microbes from the “ocean desert” of the Sargasso Sea last year (see “Venter Makes Waves — Again,” April 2004 Bio•IT World, page 1), Venter is particularly struck by the almost unfathomable abundance and diversity of microbes in the planet’s oceans. Each new sea sample contains 85 percent unique organisms in samples from neighboring geographic sampling points. Venter’s team has analyzed 8.3 million DNA sequences (1.9 million came from Sargasso, and a further 6.4 million were funded by the George and Betty Moore Foundation and the U.S. Department of Energy), which took 20,000 CPU hours to assemble. So far, Venter’s team has detected 100,000 microbial organisms, with 3.8 million genes and another 2.7 million putative genes.
“The diversity of species is mind blowing,” Venter said. For example, more than 3,000 photoreceptor genes have been sequenced, dwarfing the previously known total. The number of protein families is currently about 40,000, with no signs of saturation as new data are added.
Venter’s environmental genomics program has wide-ranging applications, which is spurring interest in the related field of synthetic biology. His group has been approached about the possibility of using their work to re-create extinct species by creating and recombining gene “cassettes,” but Venter rejected the notion because he doesn’t believe that is a good way to support species diversity.
Instead, he hopes research will lead to dramatic changes in the petrochemical industry, as well as the creation of new food sources, and possibly energy sources as well. Scientists also are figuring out how microbes can be used to control carbon dioxide levels, which are a key factor in global warming.
In the nearer term, the Sorcerer II data will be used to “assess the true safety of off-shore drilling,” as well as to monitor drinking water and to track ballast water from tanker ships that drain water from other parts of the world into harbors. “We’re moving species around and we’re not thinking about that in a very intelligent fashion,” Venter said.
The research also will be used to monitor the health of the world’s ocean reefs and to track emerging viruses. J. Craig Venter Institute scientists are already in contact with scientists in Southeast Asia, from which many virus threats emerge.
“As we sail around the world, our goal is to leave a lot of exciting new data and knowledge in our wake,” he said. The public database GenBank has set up an environmental section to handle the surge of genome data Venter and others are depositing, even though he noted that the authorities in French Polynesia briefly detained his boat and crew last year because they thought he was trying to “steal French genetic heritage.”