Microbes are everywhere and play crucial roles in nearly every process that sustains this planet, yet scientists estimate that less than 1 percent of the microbes that exist in nature have ever been grown or studied in the lab. Spurred by these truths, a breed of scientist, the microbe hunter, travels the globe collecting samples from remote rice paddies, deep-sea sediments or the soggy soils in their own backyards in the hopes of isolating a unique and previously undescribed species of microscopic being. It's a good day for the scientist who characterizes an unknown microbe but if that bug shows properties that could make it a useful tool in industry, medicine or the mitigation of environmental problems—that is nirvana.

Susan Leschine, a microbiologist at the University of Massachusetts in Amherst, may be one of those scientist-hunters nearing nirvana. Leschine studies microbes that break down plant material because these organisms play a critical role in the cycling of carbon through the air, water and soil. "As we're facing a changing climate and humans are producing more carbon dioxide, to understand the whole carbon cycle we need to also understand what's going on in the natural world especially the bacteria that break down plant material naturally," Leschine says.

When she started her research about 30 years ago, very little was known about these kinds of bacteria in certain environments where oxygen is limited such a the wet soils and sediments of marshes and watersheds. Biomass is abundant in these realms but since it doesn't accumulate indefinitely, biomass-degrading microbes must also be present. Leschine has spent the better part of her professional career collecting soil samples from environments like these around the world, including Europe, Brazil and Hawaii. But it wasn't from samples collected in these exotic places that Leschine discovered her jackpot microbe. It was soil from the Quabbin Reservoir in central Massachusetts, about 10 miles from her lab, that held the prize: an anaerobic bacterium dubbed the Q (for Quabbin) microbe that makes a huge range of enzymes for the degradation of a host of biomass feedstocks and the subsequent fermentation of those sugars into ethanol.

Quabbin is a man-made water reservoir built in the 1930s to supply drinking water to the exploding population of Boston. It is still one of the largest unfiltered drinking water supplies in the world. The watershed, which collects, filters and drains water into the reservoir, covers about 186 square miles and its soggy forest soils serve as a refuge for the Q microbe. By studying the microbes that inhabit oxygen-free soils, "we can understand more about the diversity of these bacteria, which carry out a process that's important in the environment, and we can isolate bacteria that could do interesting things with plant material, which happens to be one of our most valuable resources," Leschine explains. "Bacteria that grow without oxygen typically carry out fermentation and make very interesting products."

Although the soil samples that Q was isolated from were collected by Leschine's research assistant, Tom Warnick in the early-1990s, it wasn't until the fall of 1998 that the team realized they had found something different. "It takes a long time between collecting the soil samples and learning how to grow and isolate specific microbes in the lab," Leschine explains. "We've isolated dozens and dozens of microbes and they tend to be fairly similar but when we find one that's clearly novel—that's a new species—we single it out and get all the information we need to really prove that it hasn't been described before."

This information includes what the cells look like under a microscope and what the colonies look like on solid growth media; the optimal temperature for growth of the bacterial cells; the types of sugars the bacterium ferments and the end-products of those fermentations; and the DNA sequence of certain genes used for comparison against other known species. Based on the team's characterization, Q was found to be a unique bacterium of the genus Clostridium, which includes species that cause tetanus, gangrene and botulism. Leschine named her plant fermenter, Clostridium phytofermentans.

A Promising Trait
In late-1998, Leschine and colleagues knew that they had found something new and different. However, it wasn't until recently that they realized how special Q is. "We were working with this microbe for other reasons when we discovered that it made much higher amounts of ethanol in unexpected situations," Leschine says. "That, coupled with our other observations that it can break down many different kinds of plant material led us to believe that this bacterium could be an incredibly useful microbe."

Currently, the model for the biological conversion of biomass-to-ethanol involves several steps. First, the biomass feedstock undergoes a thermochemical pretreatment that opens the lignocellulose, thereby exposing the tough portion of the biomass to saccharification by enzymes, which is the second step in the process. The five-carbon and six-carbon sugars released in these early steps are then converted into ethanol by a fermenting microbe. The final steps of distillation and dehydration separate and purify the fuel.

A major barrier to the cost-competitive production of cellulosic ethanol is the expense of the enzymes needed for saccharification. The Holy Grail of cellulosic ethanol production, Leschine says, is consolidated bioprocessing (CBP) or a microbe that can go directly from the plant material-to-ethanol, thereby eliminating the costly enzyme step. Realizing that Q could be that microbe, Leschine and Warnick filed a provisional patent application in January 2006 followed by the final application a year later.

Out of the Lab
After filing the patent and continuing to work with Q, Leschine and Warnick realized that the bacterium was really good at making ethanol from cellulose. They then started looking into how they could move the process from the lab into the marketplace. "After exploring a few different connections and trying to raise interest, it became clear that the way to do this was to form your own company," Leschine explains. Coincidentally, Leschine was introduced to five local business people who had teamed up to identify and work to commercialize clean technologies. "We realized this would be a good association," she says. "An academic like me with very little knowledge about business coming together with seasoned entrepreneurs who were hungry to do something that was good for the environment."

In mid-August, the new company, called SunEthanol Inc., announced that it had secured its first round of funding for the commercialization of its CBP technology. Although the amount of funding was not released by press time, investors included VeraSun Energy Corp., Battery Ventures, Long River Ventures and AST Capital. "It wasn't hard convincing the investors to invest," says Jef Sharp, CEO of SunEthanol. "They recognized that the industry has been searching for a microbe that could do this for sometime." Battery Ventures, for instance, identified cellulosic ethanol as a promising opportunity on the horizon and looked at about three dozen biomass-to-biofuel technologies before choosing to invest in the Q microbe process. "This technology was the most promising," explains Jason Matlof, a partner at Battery Ventures. "The Q microbe is the only biological process technology with native traits biased toward bioconsolidated processing. The natural form of the bug can do that and that is extremely unique," he says.

Before anything else though, the process needs to be scaled up, which will be funded by this initial round of financing. "If it can be optimized and if we can do the process engineering to scale-up the technology, it has tremendous potential to simplify the entire cellulose-to-ethanol process," Sharp says. "Our ultimate goal is to have the technology work on feedstocks found in multiple countries making carbon neutral ethanol to power the planet's transportation fleet." Leschine's team has demonstrated the process at bench scale and with feedstocks ranging from filter paper to starches and pectins. They've also started looking at more appropriate and significant feedstocks such as corn stover, sugarcane bagasse, some of the native grasses such as switchgrass and wood pulp waste. "Now we need to bring it up in scale and make sure conditions are appropriate for commercial-scale production," she explains.

The staff and scientists that have joined the team are currently working on optimizing the microbe for scale-up. Simultaneously, the company is working on the process engineering. "We want these things to be operating in parallel so that when the time is right we can put a plant in the ground," Sharp says. Although this likely won't happen in 2008, he says the technology might be ready for pilot-plant scale in 2009. "When the technology is right and the conditions are right economically then we shouldn't have any problem in finding interest in a demonstration plant and then a full-scale plant," he says.

For now, Leschine has a modest goal. "I'll be happy to get it performing properly at a 20-liter fermentor size because then it becomes an engineering problem and there are people who know how to deal with that," she says. "I'll leave it to them."

Jessica Ebert is an Ethanol Producer Magazine staff writer. Reach her at jebert@bbibiofuels.com or (701) 746-8385.