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Broadening the 'SCOPE' of microbial oceanography

With an infusion of funds from the Simons Foundation, a collaboration between MIT researchers and colleagues will break new ground in the study of marine microbes.
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Marine diatoms, a common type of phytoplankton.
Marine diatoms, a common type of phytoplankton.
Courtesy of Gordon T. Taylor

The Simons Foundation, a New York-based philanthropic organization that supports a range of basic science research, has made its first venture into microbial oceanography with a $40 million award to fund the creation of the Simons Collaboration on Ocean Processes and Ecology (SCOPE), a five-year program centered at the University of Hawaii at Manoa to study the role of microscopic organisms in the ocean ecosystem.

Marine bacteria and phytoplankton, which inhabit every drop of seawater, essentially dominate the ocean ecosystem — so much so that some say that they are the ocean. Microbes manufacture oxygen from sunlight, regulate the cycling of nutrients, and produce and consume greenhouse gases, with enormous implications for the ocean, and the entire planet.

SCOPE gives the field’s top researchers new ability to apply advanced genomics and systems-biology approaches to go after the most elusive details in the ocean biome — such as how the trillions of microbes living at the base of the food web respond to their environment, and how they influence it.

“The idea is to connect the dots between the microscale activities of microbes and the role they play in larger-scale processes in climate and nutrient cycling, but it’s actually quite difficult to connect them,” says Mick Follows, an associate professor in MIT's Department of Earth, Atmospheric, and Planetary Science (EAPS). “This award enables us to explore these issues in a way we have always wanted to do but haven’t had the resources.”

Follows is one of the eight founding SCOPE investigators, along with others at MIT, Woods Hole Oceanographic Institution, the University of Hawaii at Manoa, the University of California at Santa Cruz, and the University of Washington.

Home base for SCOPE is Station ALOHA, an established ocean research field site in the subtropical Pacific Ocean north of the Hawaiian island of Oahu. Since 1988, researchers on various projects have taken continual measurements of the biology, chemistry, and variability in the physical structure of the water column, yielding comprehensive time-series records. Now SCOPE researchers will build on the knowledge of this well-characterized patch of ocean at levels of higher and higher resolution.

SCOPE researchers see the ocean as a sea of microbial genes — or, as SCOPE investigator Penny Chisholm, the Lee and Geraldine Martin Professor of Environmental Studies, calls it, “dissolved information.” Microbes switch their protein-coding genes on and off in response to fluctuations in temperature, light, and nutrient availability; thus, the genes expressed by communities of microbes in the actual ocean over time reveals what microbes are doing, in a metabolic sense, in their home environment.

Ed DeLong, a pioneer of technologies to study microbial gene transcription in the ocean, will co-direct SCOPE with David Karl, a professor of microbial oceanography at the University of Hawaii at Manoa. DeLong, who has been on the faculty of MIT's Department of Civil and Environmental Engineering for the past 10 years, recently joined the oceanography faculty at the University of Hawaii at Manoa.

Microbial genomic research is already in full swing at Station ALOHA: In work recently published in Science, DeLong and his MIT-led team deployed the free-drifting robotic Environmental Sample Processor, a device that floats along with a water mass, sampling from the same community of microbes every two hours. The team then used RNA-sequencing techniques, which take a snapshot of the genes turned on or off at any given moment in the microbial population.

They found that marine bacteria have predictable 24-hour cycles of genetic activity. Some species start eating, breathing, and growing early in the morning; others "wake up" later. Their analysis suggested that multiple different species of marine bacteria coordinate their patterns of behavior over the day, as if working in shifts.

To comprehend how this kind of small-scale biology impacts energy transformation across the northern Pacific, researchers need help from computer models of ocean dynamics. That’s where Follows comes in: He and his team in the Darwin Group in EAPS, who develop and explore models of marine microbial communities, have come up with ideas about how certain organisms function and interact, which they hope will guide research in the actual ocean. “We hope to help shape some of the measurements that are made in SCOPE,” Follows says, “so we can test some of these hypotheses.”

In turn, Follows’ team will use the detailed physiological characterizations that emerge from SCOPE to better constrain their model organisms, bringing their virtual ocean closer to reality. “Ultimately, in a few years' time,” he says, “we will be able to refresh our simulations with components that reflect new understandings about what’s happening in the microbial ecosystem.”

With this new infusion of private funds, observationalists and ecosystem modelers — who usually work separately on small, individual projects — can immediately begin collaborating. Linking the ocean’s genome to the biome isn’t something one field can do alone.

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