Advancements in Genomics Fosters Deep Sea Discoveries Led by Scripps

Scripps Institution of Oceanography / University of California, San Diego

At one time, scientists wondered whether life existed in the deep recesses of the world's oceans. What kinds of creatures, they wondered, could withstand the dark, cold and extreme pressure of such an environment?

Researchers at Scripps Institution of Oceanography at the University of California, San Diego, and their colleagues have used innovations in genomics research to begin to develop an accurate portrayal of deep sea life forms and how they survive in the harsh conditions of the marine abyss.

Scripps Institution Professor Douglas Bartlett discussed the new findings at the American Chemical Society's (ACS) national meeting in San Diego on Monday, March 14, 2005. Related research was published in a scientific paper in the March 4 issue of the journal Science.

In the paper and ACS presentation, Bartlett and colleagues at the University of Padova (Italy), presented the first genetic blueprint for bacterial life in a cold deep-sea environment.

They also presented a detailed analysis of how the bacteria's genetic makeup allows it to function in high-pressure environments. These findings may help lay the groundwork for a variety of research outside of the deep ocean, including the application of deep sea bacterial genes for improving human nutrition and degrading pollutants, and calculating possibilities for life in pressurized environments elsewhere in the solar system.

"These organisms live in a world that is physically very different from the skin of the planet in which we humans reside," said Bartlett, who is part of the Scripps Marine Biology Research Division. "They live in a world where temperature, for the most part, doesn't vary very much, but pressure as they move up and down the water column can. They sense that pressure."
The overwhelming majority of the volume of the planet where life exists, more than 75 percent, exists in the deep sea, while some 20 percent exists in the shallow water environment and a mere half of a percent is on land.

Extreme deep ocean conditions include near freezing temperatures and up to 15,000 pounds per square inch of "skull-crushing" pressure. Scientists say precious information lies in discovering how organisms have adapted and evolved to such conditions.

Bartlett and his colleagues probed the genetic makeup of Photobacterium profundum, a bacterium that copes with pressures of 4,000 pounds per square inch. The researchers grow the microbes in high-pressure cylinders kept cold and dark in Bartlett's laboratory at Scripps.

Bartlett's past genetic analyses revealed a creature that can sense changes in pressure using a natural barometer-like mechanism, which adjusts the flexibility of its membranes to cope with different levels of pressure.

"There's a protein within the membrane that gets squeezed when the cells experience higher pressure, and that triggers a signal transduction event that activates the expression of genes that help the cells to adapt to the increased pressure," said Bartlett.

The scientists found other tantalizing discoveries in Photobacterium profundum, including a novel fermentative process, adaptations to electron, proton and nutrient transport across membranes and a large number of previously unknown genes.

Scripps has been a pioneer in researching life in the deep ocean abyss for more than 50 years. Bartlett's studies follow the pioneering work in the 1950s of Claude ZoBell, who provided the first evidence of deep sea high-pressure microbes, and research begun in the 1960s by Art Yayanos, who was the first to isolate pure cultures of high-pressure-adapted microbes from their native environments.

This work was funded at Scripps Institution by the National Science Foundation.