|How the Other Half Lives: Marine Microbes Capture the Limelight|
By Nancy Touchette
September 5, 2003
Lush tropical rainforests, green prairie pastures and other soil-bound vegetation have long flourished in the ecological limelight. But now the other half of the planet is about to enjoy its day in the sun. Half of the world’s oxygen supply is produced by tiny microbes that live in the sea. And researchers sequencing their genomes have turned up some surprising results.
For example, researchers have found a gene in one genome that codes for one of largest bacterial proteins ever discovered. The novel protein is thought to help the microbe swim.
“Photosynthetic organisms in the ocean are as important as photosynthetic organisms on earth,” says Frédéric Partensky, of the Biological Research Station in Roscoff, France, who coordinated the analysis of the genome of one of the marine microbes.
“The organisms in the ocean are much less impressive than trees in terms of size, but are extremely important to the biosphere. They produce a significant fraction of the oxygen we breathe, and, fortunately for us, are in less danger than the tropical forests,” he says.
Three international research teams sequenced the genomes of a total of four closely related marine organisms that use sunlight to fix carbon and make organic matter. The genomes are among the smallest ever found in photosynthetic organisms. The smallest genome in the group contains just 1,716 genes distributed among 1,660,000 base pairs of DNA.
“They are tiny,” says Partensky. “They are the smallest known photosynthetic organisms. That’s a major reason why they are so successful in the nutrient-poor areas of the ocean, which cover large expanses of our planet. Studying their genomes was important to understanding why they manage to be so small.”
One group of researchers led by Sallie Chisholm at the Massachusetts Institute of Technology in Cambridge, analyzed the genomes of two strains of the marine microbe Prochlorococcus marinus. One of the strains, called MED4, lives close to the surface and is exposed to high amounts of sunlight. The second strain, called MIT9313, lives at lower depths in low-light conditions.
A second group of researchers, led by Partensky, analyzed another form of Prochlorococcus, called SS120, which was isolated from the Sargasso Sea off Bermuda. The microbe normally lives between 120 and 200 meters, in extremely low-light conditions.
Thus, between the two studies, researchers were able to compare closely related genomes of the same species that have adapted to different ecological niches.
A third group of researchers, led by Brian Palenik at the Scripps Institution of Oceanography in La Jolla, California, sequenced a related species, called Synechococcus WH8102, which was isolated about 25 years ago. Synechococcus is slightly larger than Prochlorococcus and has a larger genome than MED4 or SS120.
Both Prochlorococcus and Synechococcus are much smaller than other marine microbes that carry out photosynthesis. Their small size increases the ratio of surface area of the cell to the internal volume of the cell. This allows the microbe to do a better job at capturing sunlight and taking up nutrients than larger bacteria.
“We think these organisms have adapted to an unchanging environment,” says Palenik. “In the middle of the ocean, the amount of sunlight, nutrients and temperature are all quite constant. So these organisms don’t need much in terms of regulatory machinery.”
The researchers also noticed that one form of Prochlorococcus is missing a key gene for a DNA repair enzyme. DNA repair enzymes correct damage to DNA but in the process can sometimes introduce mutations into the genome. According to Partensky, this process, which may help drive an organism’s evolution and adaptation to the environment, appears to be lacking in Prochlorococcus SS120.
The researchers believe the organisms exchange and rearrange their DNA with the help of phages--viruses that infect bacteria. The researchers noticed many sites within the bacterial genomes where phages insert or remove DNA.
The researchers also noticed several differences among the four different genomes. The Prochlorococcus strain that lives closest to the surface and is exposed to the most sunlight has only one gene that encodes a light-harvesting protein. The intermediate strain has two such genes, and the one that lives in extremely low-light conditions has eight genes for capturing sunlight.
One of the most striking differences between the Prochlorococcus and Synechococcus bacteria is their motility. Prochlorococcus cannot swim and don’t have any genes that code for proteins that produce motility.
Synechococcus, on the other hand, can swim, but no one knows how or exactly why. The microbe has no obvious flagella, or tail, and the genome did not reveal any genes that typically produce motility. But the researchers did find a new gene they call swmB that codes for a novel motility protein.
“I’m just in awe of it all,” says Palenik. “I had this mental picture of how these organisms live and behave, but the genome sequence has turned the picture upside down.”
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