Researchers identify dozens of new microbial enzymes in cow rumen that could contribute to breakdown of biomass for biofuel production
Researchers have used a metagenomic analysis to discover dozens of previously unknown microbial enzymes in the bovine rumen—the cow’s primary grass-digestion chamber—that contribute to the breakdown of switchgrass, a renewable biofuel energy source. The study, reported in the current issue of the journal Science, tackles a major barrier to the development of more affordable and environmentally sustainable biofuels.
The team sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, the researchers identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates.
They also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass, they noted.
These results suggest that the bovine rumen is one of the best microbial habitats to explore for sources of plant-degrading enzymes, the researchers reported.
The research team also included scientists from the DOE Joint Genome Institute, the University of California at Berkeley and Illumina Inc. The BP-sponsored Energy Biosciences Institute funded the research carried out at Illinois.
The problem with second-generation biofuels is the problem of unlocking the soluble fermentable sugars that are in the plant cell wall. The cow's been doing that for millions of years. And we want to examine the mechanisms that the cow uses to find enzymes for application in the biofuels industry.—University of Illinois professor Roderick Mackie
In previous studies beginning in 2008, Mackie and Washington State University professor Matthias Hess (then a postdoctoral researcher at the US Department of Energy Joint Genome Institute in California) used a decades-old technique for studying ruminant nutrition. They placed small, mesh bags containing either milled alfalfa or switchgrass through a cannula (a permanent, surgically installed portal) into the cow rumen and examined the microbes that adhered to each plant type after two or three days. Visual and chemical analyses showed that microbes in the rumen were efficiently breaking down both types of plant matter, with a different community of microbes attacking each plant type.
This and later experiments proved that the technique could help scientists find the microbes in the cow rumen that were most efficient at degrading a particular type of plant matter, said Mackie, who is a professor in the U. of I. Institute for Genomic Biology.
In the new study, the researchers focused on switchgrass, a promising biofuels crop. After incubating the switchgrass in the rumen for 72 hours, researchers conducted a genomic analysis of all of the microbes that adhered to switchgrass.
This metagenomic approach, led by Edward Rubin, of the DOE Joint Genome Institute and the Lawrence Berkeley National Laboratory, analyzed all the genes in all the microbes present in a sample, rather than one at a time. This gave a more accurate picture of the processes in the rumen that make plant degradation possible, Mackie said.
Bacteria are microbes. They don’t live alone. They live in consortia, and they all contribute to the functioning and the services provided.—Roderick Mackie
Matthias Hess, Alexander Sczyrba, Rob Egan, Tae-Wan Kim, Harshal Chokhawala, Gary Schroth, Shujun Luo, Douglas S. Clark, Feng Chen, Tao Zhang, Roderick I. Mackie, Len A. Pennacchio, Susannah G. Tringe, Axel Visel, Tanja Woyke, Zhong Wang, and Edward M. Rubin (2011) Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen. Science 331 (6016), 463-467. doi: 10.1126/science.1200387