Extreme Measures

Geomicrobiologists look to harsh environments for organisms “disobeying” traditional chemistry teaching.
(This story was originally written and reported in October, 2008 at the University of Southern California).

Petri dishes might not be replacing AA batteries at Radio Shack any time soon, but a growing body of research shows it may soon be possible to create fuel cells made up of bacteria cultured to digest sewage or other substances.

Such wastewater remediation is but one application of the field of geomicrobiology, which has evolved rapidly since 1966. That year, Tom Brock first shook the field with the discovery of organisms thriving in the cauldron of Yellowstone National Park's geothermal geysers. Before then, general wisdom held nothing could survive in such high temperatures.

“There's nothing more fun than finding something that disobeyed what your chemistry teacher told you 35 years ago,” says Ken Nealson, a geobiologist at the University of Southern California and a teacher of Orianna Bretschger and Yuri Gorby, two microbiologists working at San Diego's J. Craig Venter Institute on projects connected to wastewater remediation and biological fuel cells. Nealson is a Venter Institute board member.

After Brock's discovery, organisms were found all over in environments scientists had insisted life couldn't exist. Life was being discovered in places with high temperatures (more than 60 degrees celsius) or very low ones (zero degrees celsius), extremely acidic or highly alkaline soil, and even in areas devoid of oxygen; all areas lacking nutrients scientists thought organisms needed to survive.

These findings had far-reaching implications. Astrobiologists realized that if life could exist in so many different environments here on Earth, they may have been too narrow-minded in their search for extraterrestrial life.

But it didn't just mean E.T. might not look how we expect. Many microbiologists just thought it was outright wacky to imagine life could exist in such forbidding environments.

One way to understand life's adaptability to different environments is to think about how life is powered.

Think of a NiCad battery. Electrons flow from a positively charged nickel cathode to a negatively charged cadmium anode. That movement creates electricity. Placed in a circuit and switched on, the electrons move from the cathode to the anode, creating electric energy.

In humans, sugars take nickel's place and oxygen replaces cadmium. Oxygen speeds up the process of metabolism in which the sugars are broken down and cells are powered. Every organism has a similar process, but the cathode doesn't have to be sugar, and the anode doesn't need to be oxygen. As long as there's an atom supplying electrons and another receiving them, the process can occur.

Nealson spends much of his time in a strange landscape north of the San Francisco Bay area characterized by deposits of soil with high pH levels. That means the soil is similar to lye, a substance that destroys many chemical bonds and keeps oxygen away. But Nealson found a lifeform thriving there using excess hydrogen in the soil as an energy source.

“You know, if someone would have told you ten years ago that they had a bug that grew at pH 12, you'd just laugh at them and say 'yeah, you're just crazy. You've got something wrong with your experiments.” Nealson says. “And yet, we see plenty of bugs growing in these samples and we've now got some in culture here [at USC].”

It turned out the organisms used iron to receive electrons from the hydrogen.

“This is my microbiologist fun,” Nealson says. “These bugs disobey all the rules.”

As more and more research about organisms which broke the rules emerged, resistance in the scientific community began to to fade. In the 1980s Japanese scientist Koki Horikoshi discovered how microorganisms could be used to speed up digestion used in industrial processes. Researchers working with Nealson built on that research to study how organisms in a California lake were metabolizing iron and manganese without oxygen. The Air Force took note.

“It's almost the first thing I've ever done that has any application,” Nealson says.

Nealson's team had isolated the genes of the organism responsible for electricity production in that metabolism, and the air force realized it could build on ongoing research into the reactions to design a fuel cell. This is where Bretschger's work at the Venter institute on wastewater remediation comes in.

Already, wastewater treatment facilities use microorganisms which don't need oxygen to digest organic materials in sewage. In these oxygen-free environments bacteria dine on feces and other waste. The bacteria produce methane as a byproduct. That methane is used to power the sewage plants, but the bacteria produce so much there is often excess to burn off. Bretschger says it may be possible to skip that last step.

Lifeforms, whether bacterial or not, digest their energy sources because they've evolved to survive on the resources available in their environment. Bretschger says while she can get the reaction she wants to occur in a cup of water in a lab, it's still too difficult to scale up to an industrially useful process. She and her colleagues need to understand how to make those reactions happen quickly, and they have to happen consistently. For that to occur, they also need to learn how different organisms might react, compete in and adapt to environments changing constantly in terms of what substances, nutrients, and conditions are present in waste streams.

The bacteria she is studying, called shewanella oneidensis, or MR-1, interacts electronically with solid surfaces. It contains a collection of proteins necessary for electrons to move to those surfaces. If a gene controlling that movement is removed the transfer could be stopped. J. Craig Venter, Bretschger's employer's namesake, was the first person to sequence the human genome. His institute is now working on the world's first synthetic organism. The genetic tools developed at the institute might make it possible to engineer a catalyst for a microbial fuel cell or to identify other organisms with similar electrochemical processes.

Bretschger sees other impacts beyond Air Force fuel cells if this process can be properly honed.

“If we can understand the biological reactions well enough to both accelerate the degradation of organic waste and engineer a system that can efficiently harvest the energy released from this degradation, we could provide clean water to areas of the globe that presently have no energy infrastructure to employ conventional water treatment,” she says.

Nealson, meanwhile, cautions against thinking microorganisms can do anything and live absolutely anywhere.

It's one thing to take an organism and imagine how it might be able to live in seemingly harsh environments. You don't violate any scientific laws if, say, you rearrange the basic building blocks of life to withstand extremes, much as one might build different models with the same set of Lego blocks. But those blocks and the bonds holding them together must still be able to withstand the physical forces which govern our universe.

Right now the only known building blocks are proteins formed by carbon-to-carbon bonds. Those bonds can't withstand forces such as extremely high temperatures or very strong kinetic forces (think earthquakes and other geological forces), while there's a possibility life could be based on other substances besides carbon, such as silica, those bonds couldn't be supported in any environment that could support life as we know it.

Still, that doesn't mean there isn't vast opportunity for life on this planet and elsewhere.

“Chemistry is chemistry and physics is physics and you can't violate those laws, but within that range of not violating those laws you can do a whole lot of stuff we didn't think was possible,” Nealson says.