C-MORE plumbs the depths of the microbial ocean

January 3rd, 2011  |  by  |  Published in Features, Jan. 2011  |  1 Comment

sea glider on a boat with Diamond Head in the background

New technologies such as the autonomous underwater sea glider collect data on microbial activities.

The naked eye sees a scoop of seawater as translucent and vacant, unable to glimpse the lively and vast ecological complexity in each drop. Yet life abounds at the microscopic level. If you were to tally the weights of all visible marine life—anemone to zebra turkeyfish as well as whales and coral reefs—the total tonnage would be less than the total weight for all largely invisible marine microbes.

“We know now that microbes dominate the biomass of the ocean,” says David Karl, director of the Center for Microbial Oceanography: Research and Education (C-MORE), headquartered at the University of Hawaiʻi at Mānoa.

“Every other breath you take contains oxygen produced in the sea by microorganisms” along with that photosynthesized by terrestrial plants. And the food you eat? “Most of it derives from solar-energy capture—about half on this planet from microorganisms that live in the sea.”

C-MORE Building exterior

C-MORE building exterior

Microbes also clean up after our man-made mistakes. “It’s microorganisms that are titrating backwards the pollutants of our planet,” breaking down everything from fossil fuel pollutants to pesticides, thereby helping to sustain Earth’s balance of life, Karl says.

Established in 2006, C-MORE is one of 17 National Science Foundation–sponsored Science and Technology Centers and the first to focus on microbes. The intensely competitive federal program—C-MORE was one of five new sites selected from 255 proposals—supports integrative partnerships that require long-term and large scale funding to produce top-notch research and education offerings.

C-MORE will draw $4 million a year in NSF funding through 2016. UH provides $1.2 million a year in matching funds.

Private sector organizations are also pitching in—the Gordon and Betty Moore Foundation, dedicated to environmental conservation and scientific research, has contributed about $40 million so far, and the Agouron Institute, which issues grants for biology and chemistry related endeavors, is funding student education and outreach efforts. (C-MORE’s outreach includes involving K–12 educators in shipboard research and providing classroom kits that cover topics from plankton and the underwater food web to the biological impacts of marine debris.)

C-MORE’s interdisciplinary team—scientists, engineers and educators at six institutions spread across as many time zones—describes its primary mission as linking genomes to biomes.

“We are looking through the microscope at the book of life to see what organisms are capable of doing, and then we’re looking through the telescope at the habitat that they’re living in,” which is the world’s largest biome, the global ocean, Karl explains.

This month, he and colleagues move into C-MORE Hale, a new $22.5 million facility at the UH Mānoa campus.

Occupants won’t spend long stretches working alone behind the closed doors of individual offices and laboratories. “ C-MORE Hale is totally open, and people will, we hope, interact more,” Karl says. That should help advance the fledgling discipline of microbial oceanography, which combines oceanography, microbiology, molecular biology, ecology and recent advances in computer-related technology and computation.

Oceanographer David Karl


“I got into this field of microbial oceanography before it had a name,” says Karl, who earned a PhD in oceanography in 1978 at Scripps Institution of Oceanography. Oceanography became a science in the mid-1800s, but virtually ignored marine life invisible to the naked eye for the next century.

Technologies and methods used to investigate microorganisms have improved in recent decades, but studies lag far behind those on dry land. For example, some 600 ground-based weather stations continuously sample atmospheric conditions, but only two—UH’s Station Aloha, about 60 miles north of Oʻahu, and a site in Bermuda—take underwater measurements on a routine basis.

Seawater data have been key to some important discoveries, such as ocean acidification (chemical changes in seawater pH due to the ocean’s absorption of carbon dioxide), says Karl. He hopes monitoring stations pervade the deep sea 50–100 years from now, allowing scientists to “take the pulse of the planet in a much more reasonable and exact way.”

Research at C-MORE is organized into four intertwined themes, says Research Coordinator Ed DeLong, a professor of biological engineering at Massachusetts Institute of Technology. The basic questions are—

  • Who’s out there? Using laboratory-based cultivation techniques and high tech cell sorting methods to pinpoint microbial diversity.
  • What are they doing? Using genome libraries and biogeochemistry expertise to examine microbial metabolism, looking at how the flow of carbon, nitrogen and phosphorus is fueled by microbial activities ranging from gene exchanges to symbiosis.
  • How do we study microbes? Engineering tools for remote and continuous sensing of microbes, such as an autonomous underwater vehicle called a sea glider that can swim, dive and surface untethered while collecting data at depths up to 1,000 meters.
  • How do we put it all together? Using computerized ecosystem models that predict how the ocean will change in the future.

Among C-MORE accomplishments to date is principal investigator Jonathan Zehr’s discovery of a whole new group of ocean-dwelling organisms capable of fixing nitrogen. That is, they convert gaseous nitrogen into nitrate and ammonia, which serves as food for other organisms.

Without them, the planet’s nitrogen supply would be lost. “These microorganisms that draw us back into the (ecological) balance point are vitally important,” says Karl. Two such bacterial groups were known. Zehr, from UC Santa Cruz, identified a third, which may not be a complete organism but may live as an obligate parasite with other organisms.

DeLong led a group that discovered a process by which sea cells absorb sunlight without releasing oxygen. Instead of chlorophyll, which other plants use for photosynthesis, they contain rhodopsin, a purplish-red light-sensitive pigment that’s also present in the retinas of humans and other animals.

“They’re taking energy from sunlight and making a more efficient metabolism for themselves so that they don’t have to use as much food,” Karl explains. He likens it to putting a solar panel on your house to absorb the sun’s energy so you don’t have to use so much fossil fuel based electricity.

“These are nature’s hybrids,” resulting from more than 4 billion years of evolution, he continues. “It looks like almost every organism that’s in a lighted zone of the ocean has this mechanism. And we still don’t know how important it is.”

C-MORE fieldwork includes a series of annual cruises devoted to probing environmental concerns—global climate change, ocean acidification and plastic patches such as the mass of floating trash in the North Pacific Gyre. Cruises typically span three weeks and include team members from Monterey Bay Aquarium Research Institute, Oregon State University and Woods Hole Oceanographic Institution in addition to UH, MIT and UC Santa Cruz.

The C-MORE team hopes to send out a ship for half the year in 2013, an ambitious endeavor preceded by a year of planning. The longer cruise would enable researchers to more extensively observe interactions in underwater habitats and development of life forms, as well as investigate related matters such as the subtle roles sunlight and cloud cover play in whether a marine community thrives.

“Nobody has ever been to sea for six months” to explore microbial communities, Karl says. “We want to be the first. The ocean can’t be sampled at our convenience. It has to be sampled on the scale that matters to the microorganisms.”

Because microbes were the first life form on Earth, most of the diversity on our planet is found within their realm. “Time allows things to diversify and specialize, and microbes are the kings and queens of that,” Karl says. Time, and the evolving lens of microbial oceanography, can teach us fundamental things about the planet, he adds—how it operates, sustains itself, how fragile it is when confronted by man-made environmental problems.

“We develop paradigms and models for the way we think the Earth works, and they may be wrong,” he concedes. Ultimately, the exciting aspect of C-MORE’s research and plans for the future is this: “ We may be able to correct or improve our general understanding of what might be called the ’ecology of the planet.’”

Tags: , , ,


  1. Norman Grim says:

    January 14th, 2011at 12:45 pm(#)

    I am a retired biology professor from NAU in Flagstaff, AZ. Each Fall, I give talks to various grades—public & private schools—on the “magical world of ciliated protozoa.” I would delight in adding some info about the bacterial and protistan biomass & contributions in the oceans. As you might see, if your google me, I have published quite a bit on the protists that live in marine fish intestines & did some of that work in Kaneoe (sp?) bay.

    Any chance that you, Karl or Jonathan, have written a review on this topic (above) that I can read?

    Thank you for your most important work!!


    J. Norman Grim