Scientists find bacteria that could streamline biofuel production

Source: Umair Irfan, E&E reporter • Posted: Tuesday, May 22, 2012

A rainforest-dwelling bacterium may hold the key to a simpler way to make biofuels.

Researchers at the Joint BioEnergy Institute (JBEI) in Emeryville, Calif., said the microbe, Enterobacter lignolyticus, can tolerate ionic liquids used to process plant matter before it is converted to fuels for cars and planes. This eliminates several cleaning steps and makes the procedure less complicated, reducing costs.

Ionic liquids are usually liquid salts that can be used to break down cell walls in plants. This liberates lignocellulose, a sugar complex that is one of the most abundant organic substances on the planet. Engineered microbes can convert lignocellulose into fuels, making it a promising energy feedstock, but ionic liquids are toxic to many organisms. Great pains must be taken to separate the fluids from lignocellulose before it can be fed to bacteria or yeast.

But on the floor of the Puerto Rican rainforest, researchers found the ticket to a better solution. “The discovery of this organism that can tolerate ionic liquids was completely by accident,” said Blake Simmons, vice president of the deconstruction division at JBEI. Simmons and his team were looking among decaying plants to find organisms that produced enzymes to rapidly digest leaves, stems and stalks. While screening the microbes, the team found E. lignolyticus and discovered it had a very high tolerance for ionic liquids.

The researchers then grew a strain of this bacterium called SCF1 — named for the Short Cloud Forest field site in the El Yunque National Forest — in the presence of an ionic liquid and looked at what made this bug so special. After sequencing its genome and analyzing its cell wall, the scientists compared their findings to SCF1’s entire library of metabolic activity

First step to a biorefinery

From there, researchers pieced together the source of its strength. “It’s a combination of mechanisms,” explained Michael Thelen, a staff scientist at Lawrence Livermore National Laboratory and JBEI. “This SCF1 bacterium begins to rapidly remodel its membrane by modifying some of the phospholipid fatty acids.” The phospholipids in the cell wall then form a stiffer layer and do a better job of keeping ionic liquids outside of the bacterium.

SCF1 also forms molecular pumps that push any ionic liquids that do make it inside back out before they can do much damage. At the same time, the cell reduces the number of pores in its surface used to transport nutrients in and out to reduce unwanted chemicals. In addition, it produces solutes to relieve osmotic pressure. “It seems to be a specific response to certain salts and not a general response,” Simmons said.

Using these findings, researchers expect to engineer these traits into fuel-producing bacteria and yeast. “The next step is really to engineer a biofuel producing strain and test that out in a real situation,” Thelen said. “The advantage here is we can use the ionic liquids in the pre-treatment phase. Otherwise, we need a new way to break apart the biomass.”

Simmons said he is also looking for valuable mechanisms in other organisms. “We’re expanding out screening to different microbes in different environments,” he said. Eventually, the researchers will build a pilot production system that processes biomass into fuel while recycling components like ionic liquids. “Once we’ve demonstrated that, hopefully we’ll work with industry to take these out to the marketplace because that’s where it really counts,” he said.

Simmons, Thelen and their collaborators published their findings last week in the Proceedings of the National Academy of Sciences.