Microbe eats formaldehyde

In a world where dangerous chemicals abound, Rhodobacter sphaeroides may have a big future.

“It’s an organism that, historically, has done great good for society,” says Timothy Donohue, a University of Wisconsin–Madison professor of bacteriology whose intimate knowledge of this bacterium informs his insight into its potential as a microbial workhorse for sensing and purging chemical pollutants from the environment.

“For decades we knew that it had a metabolic lifestyle very similar to green plants. By analyzing how this bacterium makes a living, it has and continues to provide key insights into the processes by which plants harvest light and use the energy from photosynthesis to acquire essential nutrients like carbon dioxide and nitrogen from its surroundings,” says Donohue.

However, R. sphaeroides, in addition to its use as a model for understanding photosynthesis, has another quality that intrigues biologists: It posesses a capacity to render harmless toxic chemicals like formaldehyde. Formaldehyde is a handy chemical widely used in thousands of products — for everything from solutions for cleaning eggs for market to curing wood products — but in some places it has become a serious environmental contaminant. It also occurs in nature as a byproduct of natural chemical reactions.

Natural or manufactured, formaldehyde’s down side is that it is toxic. A known mutagen that causes cancer in rodents and a suspected carcinogen in people, the chemical is used in thousands of products and, depending on the industry and how the chemical is used, it can contaminate ground water and make some work environments hazardous. Around poultry farms, for example, formaldehyde solutions used to sterilize egg surfaces can seep into ground water and become an expensive and difficult problem to fix. Formaldehyde is also used in the large curing sheds where wood is softened with the chemical so it can be formed into sheets of plywood or pressed wood.

The problem of formaldehyde use and disposal also occurs in research labs and hospitals and clinics where it is used for such pedestrian chores as fixing samples on microscope slides.

Enter R. sphaeroides, a well-studied microbe that converts formaldehyde to benign carbon.

“Organisms like this have the ability to remediate formaldehyde problems,” says Donohue, who’s studied R. sphaeroides for more than two decades. “The other thing this bacterium has is the ability to see formaldehyde in the environment,” raising the prospect for the microbe to become useful not only as an environmental cleansing agent, but as a biosensor for places like the sheds where formaldehyde is used in large quantities to condition wood products.

“Depending on the industry, the issues are very different,” explains Donohue. “In the medical industry, formaldehyde is commonly used as a tissue fixative in high concentrations and in high volumes. Much of that goes to the landfill and it is an expensive chemical to dispose of in that way. It would be nice if there were a kit available to neutralize formaldehyde in the lab so its breakdown products could simply be poured down the drain.”

Toward that end, Donohue and his colleagues, with support from the U.S. Department of Energy Office of Basic Energy Sciences, have identified R. sphaeroides proteins that are required to remove formaldehyde. They have also shown that these proteins will allow other microbes to oxidize formaldehyde when they are present in cells that would normally be killed by this toxic compound.

The R. sphaeroides proteins that are involved in formaldehyde removal, notes Donohue, exist in other organisms as well, including humans whose livers have the same ability to process formaldehyde. “The machinery in your liver is the same as it is in the bacterium. The genes encoding the enzymes that convert formaldehyde have been conserved in nature as they are present across biology — in plants, animals and microbes.”

The Wisconsin biologists’ analysis of R. sphaeroides has also found genes that perk up in the presence of formaldehyde. Once the cells sense the presence of formaldehyde, the organism deploys specialized enzymes that do the job of converting formaldehyde to harmless breakdown products.

“The presence of this formaldehyde warning system means that it is also possible to use bacteria like this to report about how much formaldehyde is present in a given environment,” Donohue says. “The response makes perfect sense from a biological standpoint. Once they sniff out the formaldehyde, they turn on genes to metabolize formaldehyde faster. It is exciting to see both how it works and think about the potential benefits this information has to society”

The discovery of the pathway that permits R. sphaeroides to sniff out and then digest a nasty chemical like formaldehyde was pure accident, Donohue says, made while researching the organism’s photosynthetic properties. Knowing the pathway means it may one day be possible to “create designer organisms to be more efficient at a desirable metabolic processes like this. Depending on how we grow it, the bacterium can make all of its carbon from formaldehyde.”

Revving up R. sphaeroides’ capacity to process formaldehyde in environments like groundwater where contamination is an issue is one potential use. Another, says Donohue, is deploying the bug as a biosensor in places like the wood-curing sheds where formaldehyde is used in large volumes.

“This is where we could get into the biosensing game,” Donohue explains. “All that wood has to sit in warehouses for months and months in order for the formaldehyde to dissipate. If you can figure out levels of formaldehyde in those environments where it is evaporating from treated wood, it would be possible to get that material on the market a lot faster.”

Donohue’s team, through the Wisconsin Alumni Research Foundation (WARF), has patented the use of R. sphaeroides to remove formaldehyde from the environment and as a biosensor for the chemical.

With the support of Biological and Environmental Research Program at DOE, the entire genome sequence of this organism was determined in late 2000 by the Joint Genome Institute

“This information can now be used to efficiently acquire a complete picture of how cells sniff out formaldehyde, the genes that respond to this toxic compound, and the proteins that are required for its removal. The genome sequence also allows us to see how R. sphaeroides could contribute to society in other ways. For example, we now have a better idea of how this organism can be engineered to generate biodegradable plastics or produce clean-burning energy sources like hydrogen gas, or microbial products that can reduce our dependence on compounds that cause ecological problems.”

To take advantage of these opportunities, the Wisconsin group is now part of a large DOE- funded Genomes to Life research team that is investigating the potential uses for the voracious appetite of R. sphaeroides in other settings, such as around plants where carbon dioxide, a major greenhouse gas, is an unwanted byproduct.

“If a way can be found to use the microbe to produce clean energy, biodegradable products or soak up excess carbon dioxide emissions, R. sphaeroides could have the distinction of reducing the amount of greenhouse gases released into the atmosphere and improving the future quality of life in many other ways,” says Donohue.