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Microbes’ Genomes Promise Insight into Oceans


The world’s smallest photosynthetic organisms, microbes that can turn sunlight and carbon dioxide into living biomass, will be in the limelight next week. Three international teams of scientists, two funded in part by the National Science Foundation (NSF), will announce the genetic blueprints for four closely related forms of these organisms, which dominate the phytoplankton, the tiny floating plants of the oceans.

The work will be reported in the August 13 online issues of Nature and the Proceedings of the National Academy of Sciences.

Much like the sequencing of the human genome, the sequencing of the genomes of three strains of Prochlorococcus and one of closely related Synechococcus should crack many mysteries about these organisms-and about phytoplankton in general.

A better understanding of phytoplankton, which play a critical role in the regulation of atmospheric carbon dioxide, will aid studies on global climate change. The metabolic machinery of these single-celled organisms could serve as a model for sustainable energy production, as they can turn sunlight into chemical energy, according to Gabrielle Rocap of the University of Washington, lead author of the Nature paper that reports the genomes of two strains of Prochlorococcus. "The four genomes that have been sequenced represent numerous strains that populate ocean waters and form the base of the food web," says Rocap. "A hundred of these organisms can fit end-to- end across the width of a human hair, but they grow in such abundance that, small as they are, at times they amount to more than 50 percent of the photosynthetic biomass of the oceans."

It behooves us "to understand exactly how, with roughly 2,000 genes, this tiny cell converts solar energy into living biomass-basic elements into life," said Sallie (Penny) Chisholm, a biological oceanographer at the Massachusetts Institute of Technology (MIT). "These cells are not just esoteric little creatures; they dominate the oceans. There are some 100 million Prochlorococcus cells per liter of seawater, and they are responsible for a significant fraction of global photosynthesis."

This research addresses in a concrete way major questions in biological oceanography at levels finer than the species level, says Phillip Taylor, director of NSF’s biological oceanography program, which co- funded the research. "The work shows there is a rich and fascinating diversity of physiological capacity and adaptation in the sea, and that this diversity is not always revealed just by looking in the microscope."

Adds Raymond Orbach, director of the office of science at the Department of Energy (DOE), which funded the research, "While many questions remain, it’s clear that Prochlorococcus and Synechococcus play a significant role in photosynthetic ocean carbon sequestration. Having the completed genome in hand gives us a first-albeit crude-’parts list’ to use in exploring the mechanisms for these and other critically important processes that could be directly relevant to this critical DOE mission."

In the same issue of Nature, a team led by Brian Palenik of the Scripps Institution of Oceanography, part of the University of California at San Diego, will report the sequence of Synechococcus, a co- inhabitant of ocean waters with Prochlorococcus, that has a unique form of motility.

The Prochlorococcus and Synechococcus teams collaborated closely. "We learned a tremendous amount working together," said Palenik. "By coming at it from different perspectives, we were able to see common themes in how these organisms adapted to the open ocean."

A separate report, by a team led by Frederick Partensky, at the Centre National de la Recherche Scientifique, Station Biologique de Roscoff, describes the genome of a third strain of Prochlorococcus and will be published online August 13 in the Proceedings of the National Academy of Sciences.

The work of all three teams "will allow us to better understand what differentiates the ecology of these closely related organisms through comparative genomics," said Chisholm.

Rocap and her colleagues present a kind of case study for how this might work. They report the genetic sequences for two different Prochlorococcus strains, then go on to compare them. The resulting analysis "reveals many of the genetic foundations for the observed differences in [the two strains’] physiologies and vertical niche partitioning," the authors report. The latter refers to each strain’s slightly different ecological niche-they thrive at different depths in the ocean’s surface waters.

Chisholm emphasizes that, "we still don’t know the functions of nearly half of these organisms’ genes. We’re excited about unveiling those functions-particularly for those genes that are unique to the different strains-because they’ll alert us to key factors important in regulating marine productivity [photosynthesis] and plankton diversity."

The idea, she says, "is to let the organisms tell us what dimensions of their environment are important in determining their distribution and abundance. This will become easier and easier as the genomes of additional strains are sequenced, and the functions of the genes are understood."

Concludes Rocap, "Right now, we don’t even know the range of diversity that exists. We’ve had just a glimpse of the different genome types that are out there."

This research was also sponsored by the Seaver Foundation, the Israel-US Binational Science Foundation, and FP5-Margenes.

Cheryl Dybas | NSF
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