Friday, February 14, 2014

DOE Science Highlights: Feeding at the biofuel trough

Researchers are using “experimental evolution” to develop bacteria that are more efficient at decomposing biomass

The Science

Clostridium phytofermentans is a soil-dwelling bacterium that helps decompose leaf litter. Researchers grew successive generations of bacteria on different woody material that make up plant cell walls (cellulose, cellobiose and xylan) and found that the bacteria adapted and became more efficient over generations. Genetic analysis found that mutations were in regions of DNA that coded for or regulated genes that were involved with carbohydrate (simple sugars) use or transport.

The Impact

This is the first experiment to use an “experimental evolution” approach with a microbe that feeds on cellulose, following generations of bacteria as they adapt to different living environments. The findings suggest that it may be possible to find key genes and mutations that can be used in pinpointing genes that can be used to efficiently break down biomass feedstock, the raw material of biofuels.

The bacteria in this study, Clostridium phytofermentans, were isolated near the Quabbin Reservoir in Massachusetts. The bacteria live in the soil and help break down leaf litter on the forest floor. (Image by Philip Halling via Wikimedia Commons)


Breaking down cellulose and other woody plant materials is one of the biggest challenges of producing efficient and sustainable biofuels. Biofuel developers depend on fungi and bacteria that are adept at breaking down these materials. Researchers from the University of Massachusetts, Amherst grew one of these bacteria, C. phytofermentans, in the lab on several different woody plant materials (xylan, cellobiose and cellulose) and studied the genes of subsequent generations as they adapted to their new nutrient-rich environment. They published their results in a paper published January 22, 2014 in the journal, PLOS ONE.

Cellulose and other woody plant materials are constructed from long chains of glucose units that can have anywhere from hundreds to thousands of glucose units. They’re a kind of carbohydrate, though humans have a hard time digesting cellulose and similar materials.

C. phytofermentans has more than 100 glycoside hydrolases, compounds for breaking down complex sugars and woody substances and about 50 different molecular transport system dedicated to moving them across cell membranes. So it’s an ideal organism to study genetic and molecular adaptations for carbohydrate metabolism. C. phytofermentans’s genome was sequenced as part of a DOE JGI Community Sequencing Project, which also partially supported this study.

After letting bacteria grow for many generations, the research team sequenced entire populations of adapted bacteria, which gave them a more complete picture of genetic adaptations. All the mutations the researchers identified were in the regions that coded or regulated a specific kind of transporter called CUT1, which are involved in transporting oligosaccharides, relatively small carbohydrate molecules. One series of mutations seemed to help the bacteria move glycoside hydrolases out of the cell faster. The adapted bacteria had several diverse mutations, hinting that there are many ways to efficiently feed off of woody materials – and many molecular pathways that can be tweaked to break down woody materials more efficiently.

The researchers suggest that further study of the mutations they identified is a good next step and that eventually, some of these mutations might someday be useful for breaking down biomass into useable renewable energy sources.


Jeffrey Blanchard
University of Massachusetts, Amherst


Mukherjee S, Thompson LK, Godin S, Schackwitz W, Lipzen A, et al. (2014) Population Level Analysis of Evolved Mutations Underlying Improvements in Plant Hemicellulose and Cellulose Fermentation by Clostridium phytofermentans. PLoS ONE 9(1): e86731. doi:10.1371/journal.pone.0086731


Department of Energy, Office of Science
The Isenberg School of Management at the University of Massachusetts Amherst
The National Science Foundation
The Howard Hughes Medical Institute Award
Qteros Inc.

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