Biodiversity and conservation
Biodiversity and general ecology issues

Ken Novak's Weblog

daily link  Sunday, September 07, 2003

Wired 10.12: Supermicrobe Man: Brief interview with Venter: "At the beach, a milliliter of surface water will typically contain 1 million bacteria and 10 million viruses. Think about that next time you fall off your surfboard and take a big swallow of seawater. In different parts of the ocean it varies. We're going to start the experiment with the Sargasso Sea [in the North Atlantic]. The Sargasso is nutrient-poor, so the number of species there and the density of life is much lower. Later, we plan to test whether we can take all the DNA from one of Yellowstone's volcanic pools and work out what's in there.

It would have been inconceivable to [do this for] most scientists even five years ago; they would have said it's impossible in terms of the processing power. Now, we think the Sargasso Sea experiment of sequencing every organism in the ocean will take about a week.

We're building an extremely large, state-of-the-art sequencing center with a higher capacity than anything existing today. It will ultimately be capable of more than 100 million sequences a year. Keep in mind that 26 million gave us the human genome. We're going to be trying some new technologies that might allow us to get information on maybe 10,000 genomes an hour in the microbial world."

  10:22:39 PM  permalink  

Genome pioneer sets sights on Sargasso Sea: Craig Venter aims to sequence every bug in entire ecosystem.:  "The Institute for Biological Energy Alternatives (IBEA), which Venter heads, has already begun sequencing every microbe in the Sargasso Sea, a region of the Atlantic Ocean between the Azores and the West Indies that is bounded by ocean currents. ..

The microbes' genes will also reveal how they make their living - what chemicals they feed off and produce, for example. Other studies of ocean bacteria have found new ways to turn sunlight into energy. Such research might bring about new technologies.  .. One of the stated goals of the IBEA, a non-profit organization based in Rockville, Maryland, which was founded by Venter in April last year, is to develop sustainable energy sources, such as a microbe that produces hydrogen. The institute is also working on biological tools to mitigate global warming by removing carbon dioxide from the atmosphere.

The IBEA team has filtered seawater from different depths and sites, and sequenced the microbes collected en masse. The researchers are using the shotgun sequencing method - breaking the genome into small segments and assembling the fragments with computers.  The sequence shards will need to be parcelled out into many different organisms. It's like trying to assemble thousands of individual jigsaws from a single box containing millions of pieces. ..Venter believes that the technique could be applied anywhere from the air to the human gut. "Based on the data we already have, we're predicting that this will become the number-one way for characterizing the environment," he says."

  10:14:00 PM  permalink  

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