Yacht voyage turns up sample of genes

They have found genes that help microbes use the sun’s energy in new ways, genes that help them use nitrogen and genes that protect organisms from ultraviolet light, they reported.

Writing in the Public Library of Science Journal PLoS Biology, Venter’s team said they had identified more than 6 million new proteins.

They have not identified new organisms because in their unusual experiment, called the Global Ocean Sampling Expedition, they are looking only at the DNA of the tiny organisms they are sampling.

“We are starting to view the world in a gene-centered fashion,” said Venter, one of the researchers who mapped the human genome in a project that wrapped up in 2000.

“Our goal is actually to try and sort out evolution, working back to what organisms are there.” He calls his approach “metagenomics.”

Venter’s team took regular samples of seawater as they traveled aboard the Sorcerer II yacht, which had been transformed into a scientific vessel.

“The purpose ... other than having fun ourselves, is to inspire people that science can be fun at all levels,” said Venter, who founded Celera Genomics and now directs the non-profit Craig Venter Institute.

His team’s three reports are published online at http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050077. They carry data on one-quarter of all the floating organisms sampled — the very tiniest ones, smaller even than plankton.

Colleagues at the Venter Institute broke out the DNA of the organisms, mostly bacteria and similar microbes known as Archaea, blasted them apart and then sequenced the DNA.

Powerful computers at the University of California San Diego analyzed the information to figure out which gene sequences carried the codes for amino acids, which in turn make up proteins — which carry out the functions of a living organism.

EYE PROTEINS

One of the first things the expedition found was that these little floating organisms make proteorhodopsins — proteins that are also found in the human eye and detect colored light.

Why would bacteria have eye proteins? Venter believes they can use energy from the sun, as plants do, but without photosynthesis.

For instance, some seem particularly well adapted to the area where they were found, in a confluence of warm currents in the middle of the North Atlantic called the Sargasso Sea.

“The Sargasso Sea is deep indigo blue. The organisms that live there see primarily blue light,” Venter said.

While the findings are scientifically interesting on their own, Venter said studying tiny ocean microbes could have practical applications.

“They are largely responsible for the atmosphere we breathe,” Venter said. The ocean is also a huge carbon sink. This means it absorbs carbon from the carbon dioxide in the air — to the tune of 100 billion tons a year.

Tweaking this just might help make up for some of the carbon dioxide buildup that human activity is causing, Venter said — although he did not go so far as to say it might reverse global warming.

Bacteria also provide unexpected sources of new antibiotics, Venter said.

“Most microbes have developed defense mechanisms to try and kill other microbes,” he said. Scientists can study these often very complex mechanisms to design drugs, he said.

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