An international team of scientists and researchers, including one from SF State, has recently sequenced the genome of a diatom—unraveling some of the mysteries of the tiny ocean dwelling plant, along with opening the door for many avenues of further study to help better understand them, and their place in the worlds ecosystems.

Diatoms are microscopic, single-celled algae that live in the ocean and are an important part of the oceanic food chain—where they are often the first link in the chain, providing food for small animals such as zooplankton, which are in turn eaten by larger consumers, establishing a web that leads all the way up to large fish and mammals.

Diatoms are also an important part of the global carbon cycle. Like most plants, diatoms absorb carbon dioxide during photosynthesis, a process where they use the gas to create food for themselves. And they do it in amounts comparable to the all of the world’s rain forests combined, thereby possibly playing an important role in guarding against global warming.

Frances Wilkerson, who is a lecturer in the biology department at SF State and does research at the university’s Romberg Tiburon Center, was among a group of 44 scientists from 25 different institutions that worked on the project, whose results were published in the October 1 issue of the journal Science.

“Diatoms are very important for carbon sequestration…because they photosynthesize, [and] the carbon is held in this sort of heavy little container,” said Wilkerson. “So it’s a way in which you could, maybe if you knew more about it, use it as a carbon sequestration tool.”

Carbon sequestration, according to the Department of Energy’s Office of Science, is a process that is being explored as a potential way to provide long-term storage of carbon in different locations around the globe, including the oceans, so that the buildup of carbon dioxide—the principal greenhouse gas—in the atmosphere will reduce or slow.

Wilkerson has worked with phytoplankton, the larger umbrella group of microscopic plants that includes diatoms, for many years, and was invited to join the group because of her expertise about nutrient acquisition and use by diatoms. At the Romberg Tiburon Center, a marine laboratory that was established in 1978 by SF State and conducts a wide range of research, Wilkerson helps run the Phytoplankton Ecology Laboratory.

The research team chose the diatom Thalassiosira pseudonana to study because it’s widely found, and is easy to grow in the lab.

Ginger Armbrust, an associate professor of oceanography at the University of Washington, was the lead scientist for the project. She invited a diverse group of researchers representing several different fields of study, including oceanographers, molecular biologists, evolutionary biologists and ecologists, to join the team.

“The most exciting thing to come out of this project for me, personally, is that we can use this information to better understand how these organisms make a living out there," Armbrust said. "I’m very interested in how they function in ecosystems, and how ecosystems in turn function as a whole.”

“The ocean is a very complicated system, and from my point of view, understanding one of the key members of an ecosystem gives us a little bit better handle on understanding how those ecosystems work, and hopefully understanding better about how to protect those ecosystems.”

The project was funded by the Department of Energy, and conducted in collaboration with the DOE’s Joint Genome Institute (JGI), which was created in 1997 to study genome mapping, DNA sequencing, technology development, and information sciences.

According to Wilkerson, the JGI did the work of chopping up the DNA, running it through machines and computer models, and working out what each strand was made up of in terms of its component bases. Then the team met at JGI’s facility in Walnut Creek, where the scientists looked over and studied the results of what had come from the process and discussed whether the findings made sense.

“A lot of the things we were finding we didn’t think the diatom would have—particularly [that] it had a lot of animal-like genes that we weren’t really expecting—but the homology—how close they were to the sequences that are [already] available—[was] very close, so in the end it was decided that these genes probably really were similar to the animal ones,” said Wilkerson.

Wilkerson thinks that this might possibly mean that diatoms and some present day animals may have had a common ancestor way back in time but that more research needs to be done to verify the findings.

“Just because they have the genes, those genes ultimately have to be expressed. This is going to be make it possible for scientists to do lots of work, because now it gives you a taster, it says well, we’ve seen that there are genes for high affinity iron uptake, but can diatoms actually carry out an uptake at very high rates? We don’t know for sure if they actually use those genes, they may just be sitting in the DNA. They may just be part of their chromosomal makeup and don’t get used. It’s just telling us the diatom has the potential for all of these things. Now we need to go and find out.”

Armbrust echoed Wilkerson’s sentiment and also sees a wide range of possible research for the future.

“The thing about a genome project is that it generates hypotheses—it is a hypothesis generating machine. Now we all need to go out and test those hypotheses, both in the field and in the laboratory.”

Some of the other possible research may revolve around how diatoms use silica to create their cell walls, which could have implications in microchip manufacturing and nanotechnology, an emerging science that hopes to manipulate material on an atomic or molecular level to build microscopic devices.

“Somehow these plants can direct where to lay down that silica in a very detailed fashion, it can do it over and over again, and it’s not a mess—it’s a very defined pattern. The idea is that if we can understand more about how this laying down of the silica works, if you wanted to lay down very specific patterns of silica to make chips, you could use that process,” said Wilkerson.

Many other research possibilities have come out of the information gathered during the sequencing project, such as looking at cell biology, evolution, and ecology.

“I think that’s what been exciting about this—we brought people together, with a wide range of expertise, to sort of unravel all these different aspects of the biology of these organisms,” said Armbrust. “They are incredibly important organisms for the health of our planet.”