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IN RESEARCH: Scooping the ocean for its genome

By Dave Jones on March 16, 2007 in University

Boldly going where no one has gone before, a team of researchers led by the J. Craig Venter Institute has discovered a new universe of ocean microbes -- sequencing an "ocean genome" more than twice the size of the human genome. And that is just from scooping surface waters with a bucket.

Most of the microbes on the planet -- and therefore most, by far, of all the living things on Earth -- cannot be grown in a laboratory, said Jonathan Eisen, an author on two of the research papers and of one review paper published this week in the journal PLoS Biology. Professor Eisen is affiliated with the UC Davis Genome Center, the Department of Medical Microbiology and Immunology, and the Section of Evolution and Ecology.

In his review article, Eisen describes "environmental shotgun sequencing," one of the main methods used in the study. Instead of trying to sequence the genome of a single animal, plant or microbe in isolation, environmental shotgun sequencing scoops up all the DNA in one go, sequences it and produces a "metagenome" that includes the genomes of all the organisms present.

"This is the only way you can study these natural microbial communities," he said. It gives a view of the entire community, not just individuals.

The researchers extracted the DNA from water samples taken during a 10-month voyage from northeastern Canada to the South Pacific via the Caribbean, the Panama Canal and the Galapagos Islands. Then came the hard part: sequencing the microbe DNA in short chunks, then assembling the 6.5 million "reads" into a map that included the genomes of all the microbes in the water. Eisen compared the process to reconstructing an entire library from the scraps of pages torn from thousands of different books.

The study provides new insights into the extraordinary size and diversity of the microscopic life in the ocean. For example, the results almost double the number of proteins known to science. They also give insights into how microorganisms adapt to different conditions, for example light and salinity, in different parts of the ocean.

-- Andy Fell

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Dave Jones, Dateline, 530-752-6556,