Researchers prepare to get a fix on microbes that trap carbon from air

The sky isn’t exactly falling, but burning fossil fuel certainly has pumped enough greenhouse gases into the air to auger changes in global climate if concentrations climb higher.

For that reason, DOE is funding a suite of programs at the national laboratories, including one led from Sandia, that include an examination of the ways microbes remove carbon from the atmosphere. The Genomes-to-Life projects, announced recently (see July 26 Lab News), include this $1.1 million, three-year effort to gain a better fundamental understanding that can improve predictions of climate change.

Computations will be a key component of the effort, says principal investigator Grant Heffelfinger (1802), involving both computer modeling and analysis of experimental data.

The winning proposal examines the role of so-called "molecular machines" that remove carbon from the atmosphere over oceans. The carbon-fixing systems are found in marine cyanobacteria, a type of blue-green algae particularly common among plankton floating on the surface of nutrient-poor regions of the ocean, such as the Sargasso Sea or equatorial areas.

"It’s one of the most abundant organisms on the planet," says Tony Martino (8130), who is principal investigator on the project along with Brian Palenik, a professor at the University of California, San Diego who is affiliated with the Scripps Institution of Oceanography. Evolving some 4 billion years ago, this simple unicellular creature launched our oxygen atmosphere by being the first living thing to pull carbon from the air. With photosynthesis, it uses the energy of sunlight to build atmospheric carbon into sugar molecules, releasing oxygen (from atmospheric CO2) in the process.

Plankton and photosynthesis

In the ocean, cyanobacteria account for nearly half of the photosynthesis carried out by plankton. Since oceans are where 40 percent of photosynthesis occurs worldwide, Tony said, this lowly bacteria is "a major player in global climate change."

Unlike plants that carry out photosynthesis in chloroplasts (rodlike units whose sunlight-capturing pigment confers color to leaves in spring and summer), the bacteria contain simple protein shells full of enzyme. The enzymes in these "carboxysome" structures catalyze chemical reactions in which carbon atoms are joined into loops or chains of sugars or starches.

Although carboxysomes were first identified in the 1970s, much remains unclear about them — whether they house more than one enzyme, how they take in carbon, and when a particular synthetic approach is favored (since the known enzyme has dual activity).

"These organisms are not well understood at all," says Todd Lane (8130), a microbial expert on this and related projects. "To improve computer models of the global carbon cycle, we need to understand the biology of these organisms in the marine environment."

Previous models assumed there was a purely chemical process involved in the carbon cycle. But plankton that are energized by sunlight form a "biological pump" by "fixing" carbon from air into cell structures and then sinking to the ocean bottom upon death. Besides cyanobacteria, that process also occurs in marine diatoms. Slightly more complex than bacteria, these single-cell organisms have a lacey armature that makes them heavy enough upon death to very reliably sink to form an ocean-floor sediment. (Such sediments are where fossil fuels have been generated over eons from decayed organic matter.)

Iron is critical limiting factor

As a research assistant professor at Princeton University, Todd studied a marine diatom that demonstrated the first known biological use of a trace toxic metal, cadmium. Several trace metals act as nutrients to help the organism carry out photosynthesis. Zinc is one trace metal that influences the rate of photosynthesis. But iron, Todd says, is the critical limiting factor.

"It can kind of gasp along without zinc, but without iron, it’s going nowhere. If you dump a lot of iron overboard, you can see a blue-green phytoplankton bloom."

The DOE project funding the carbon-sequestration research focused on delineating the sequence of subunits spelling out the genetic code for a closely related diatom to the one Todd studied, Thalassioria pseudonana. Todd recently returned from helping the DOE’s Joint Genome Institute to annotate their draft sequence of roughly 9,000 genes.

The bacterium, by contrast, possesses just 3,500-odd genes and can be grown on solid agar medium so that colonies of clones (which appear as small dots on the surface of the nutrient gel) can be lifted out and grown for study.

Todd has a friend who lives near the beach in San Francisco collect seawater for growing these microorganisms in the lab. He adds nutrients and incubates them in a lighted cabinet warmed to a toasty 23 degrees C (about as warm as a warm spring day).

Molecular machines

The experimental group is focusing on three main "molecular machines" within the bacteria — the carboxysome, trans-membrane protein complexes that actively transport nutrients and carbon across the protective membrane (called "ABC transporters" for adenosine triphosphate binding cassettes), and machinery that relays signals from the external environment inside the cell, histidine-kinase response regulators.

The chief interest in the last two is the interaction of those molecular machines. (Their genes are near each other, so their production may be triggered together when the genes are switched on.) The physical relationship of molecular machines can be studied through new chemical analysis tools using mass spectrometry to reveal which proteins are present in complexes.

The scientists also plan to create entire arrays of tell-tale messenger RNA molecules that appear when genes are turned on, carrying instructions for making a unique protein based on the genetic code sequence.

Overall, Todd says, the three-year project will focus on applying "high-throughput" analysis to the molecular biology of these systems.

The team will be aided by a large computational effort aimed at acquiring, managing, and analyzing the vast array of genetic information to come forth.

In addition to Scripps, collaborating institutions include Oak Ridge National Laboratory and the National Institute for Genome Research in Santa Fe. Sandians teaming on the project include Diana Roe (8130), Dave Haaland (1812), Steve Plimpton (9212), Danny Rintoul (9212), and Jean-Loup Faulon (9212).